#ifdef _cplusplus extern "C" { #endif #include "genomewise9.h" # line 5 "genomewise9.c" /***************** C functions ****************/ /* Written using dynamite */ /* Tue Nov 6 09:31:59 2001 */ /* email birney@sanger.ac.uk */ /* http://www.sanger.ac.uk/Users/birney/dynamite */ /*************************************************/ /* Please report any problems or bugs to */ /* Ewan Birney, birney@sanger.ac.uk */ /* basic set of macros to map states to numbers */ #define UTR5 0 #define UTR5_INTRON 1 #define START_CODON 2 #define CDS 3 #define CDS_INTRON_0 4 #define CDS_INTRON_1 5 #define CDS_INTRON_2 6 #define STOP_CODON 7 #define UTR3 8 #define UTR3_INTRON 9 #define PREGENE_INTERGENIC 0 #define POSTGENE_INTERGENIC 1 #define INTERGENIC 2 #define SPECIAL_UTR5 3 #define SPECIAL_UTR3 4 #define SPECIAL_CDS 5 #define START 6 #define END 7 #define GenomeWise9_EXPL_MATRIX(this_matrix,i,j,STATE) this_matrix->basematrix->matrix[((j+10)*10)+STATE][i+0] #define GenomeWise9_EXPL_SPECIAL(matrix,i,j,STATE) matrix->basematrix->specmatrix[STATE][j+10] #define GenomeWise9_READ_OFF_ERROR -11 #define GenomeWise9_VSMALL_MATRIX(mat,i,j,STATE) mat->basematrix->matrix[(j+11)%11][((i+0)*10)+STATE] #define GenomeWise9_VSMALL_SPECIAL(mat,i,j,STATE) mat->basematrix->specmatrix[(j+11)%11][STATE] /* Function: search_GenomeWise9(dbsi,out,evi,targetdb,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function makes a database search of GenomeWise9 * It uses the dbsi structure to choose which implementation * to use of the database searching. This way at run time you * can switch between single threaded/multi-threaded or hardware * * * Arg: dbsi [UNKN ] Undocumented argument [DBSearchImpl *] * Arg: out [UNKN ] Undocumented argument [Hscore *] * Arg: evi [UNKN ] Undocumented argument [GenomeEvidenceSet*] * Arg: targetdb [UNKN ] Undocumented argument [GenomicDB*] * Arg: switchcost [UNKN ] Undocumented argument [int] * Arg: newgenecost [UNKN ] Undocumented argument [int] * Arg: non_start_codon [UNKN ] Undocumented argument [int] * Arg: non_stop_codon [UNKN ] Undocumented argument [int] * Arg: rndcodon [UNKN ] Undocumented argument [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ Search_Return_Type search_GenomeWise9(DBSearchImpl * dbsi,Hscore * out,GenomeEvidenceSet* evi,GenomicDB* targetdb ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { #ifdef PTHREAD int i; int thr_no; pthread_attr_t pat; struct thread_pool_holder_GenomeWise9 * holder; #endif if( out == NULL ) { warn("Passed in a null Hscore object into search_GenomeWise9. Can't process results!"); return SEARCH_ERROR; } if( dbsi == NULL ) { warn("Passed in a null DBSearchImpl object into search_GenomeWise9. Can't process results!"); return SEARCH_ERROR; } if( dbsi->trace_level > 5 ) warn("Asking for trace level of %d in database search for GenomeWise9, but it was compiled with a trace level of 416. Not all trace statements can be shown",dbsi->trace_level); switch(dbsi->type) { /*switch on implementation*/ case DBSearchImpl_Serial : return serial_search_GenomeWise9(out,evi, targetdb ,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon); case DBSearchImpl_Pthreads : #ifdef PTHREAD holder = (struct thread_pool_holder_GenomeWise9 *) ckalloc(sizeof(struct thread_pool_holder_GenomeWise9)); if( holder == NULL ) { warn("Unable to allocated thread pool datastructure..."); return SEARCH_ERROR; } holder->out = out; holder->dbsi = dbsi; holder->evi = evi; holder->targetdb = targetdb; holder->switchcost = switchcost; holder->newgenecost = newgenecost; holder->non_start_codon = non_start_codon; holder->non_stop_codon = non_stop_codon; holder->rndcodon = rndcodon; if( pthread_mutex_init(&(holder->input_lock),NULL) != 0 ) fatal("Unable to iniated input mutex lock"); if( pthread_mutex_init(&(holder->output_lock),NULL) != 0 ) fatal("Unable to iniated output mutex lock"); /* Let us rock! */ thr_no = number_of_threads_DBSearchImpl(dbsi); holder->pool = ckcalloc (thr_no,sizeof(pthread_t)); if( holder->pool == NULL ) { warn("Unable to allocated thread pools"); return SEARCH_ERROR; } /* Build a thread attribute to make sure we get the most out of SMP boxes */ pthread_attr_init(&pat); /* Give thread libraries a hint that threads should be kernel threads */ #ifndef __sgi /* SGI can't set system scope ... */ #ifdef HAS_PTHREAD_SETSCOPE pthread_attr_setscope(&pat, PTHREAD_SCOPE_SYSTEM); #endif /* set scope */ #endif /* sgi */ /* Give thread libraries a hint that there are num of threads to run */ #ifdef HAS_PTHREAD_SETCONCURRENCY pthread_setconcurrency(thr_no+1); #endif /* set concurrency */ for(i=0;ipool+i,&pat,thread_loop_GenomeWise9,(void *)holder) ) fatal("Unable to create a thread!"); } /* Now - wait for all the threads to exit */ for(i=0;ipool[i],NULL) != 0 ) fatal("Unable to join a thread!"); } /* Deallocate the thread structures */ ckfree(holder->pool); ckfree(holder); return SEARCH_OK; #else /* not compiled with threads */ warn("You did not specifiy the PTHREAD compile when compiled the C code for GenomeWise9"); #endif /* finished threads */ default : warn("database search implementation %s was not provided in the compiled dynamite file from GenomeWise9",impl_string_DBSearchImpl(dbsi)); return SEARCH_ERROR; } /* end of switch on implementation */ } /* Function: serial_search_GenomeWise9(out,evi,targetdb,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function makes a database search of GenomeWise9 * It is a single processor implementation * * * Arg: out [UNKN ] Undocumented argument [Hscore *] * Arg: evi [UNKN ] Undocumented argument [GenomeEvidenceSet*] * Arg: targetdb [UNKN ] Undocumented argument [GenomicDB*] * Arg: switchcost [UNKN ] Undocumented argument [int] * Arg: newgenecost [UNKN ] Undocumented argument [int] * Arg: non_start_codon [UNKN ] Undocumented argument [int] * Arg: non_stop_codon [UNKN ] Undocumented argument [int] * Arg: rndcodon [UNKN ] Undocumented argument [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ Search_Return_Type serial_search_GenomeWise9(Hscore * out,GenomeEvidenceSet* evi,GenomicDB* targetdb ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { ComplexSequence* gen; int db_status; int score; int query_pos = 0; int target_pos = 0; DataScore * ds; push_errormsg_stack("Before any actual search in db searching"); target_pos = 0; gen = init_GenomicDB(targetdb,&db_status); if( db_status == DB_RETURN_ERROR ) { warn("In searching GenomeWise9, got a database init error on the target [gen] database"); return SEARCH_ERROR; } for(;;) { /*For all target entries*/ /* No maximum length - allocated on-the-fly */ score = score_only_GenomeWise9(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon); if( should_store_Hscore(out,score) == TRUE ) { /*if storing datascore*/ ds = new_DataScore_from_storage(out); if( ds == NULL ) { warn("GenomeWise9 search had a memory error in allocating a new_DataScore (?a leak somewhere - DataScore is a very small datastructure"); return SEARCH_ERROR; } /* Now: add query/target information to the entry */ dataentry_add_GenomicDB(ds->target,gen,targetdb); ds->score = score; add_Hscore(out,ds); } /* end of if storing datascore */ pop_errormsg_stack(); push_errormsg_stack("DB searching: just finished [Query Pos: %d] [Target Pos: %d]",query_pos,target_pos); gen = reload_GenomicDB(gen,targetdb,&db_status); if( db_status == DB_RETURN_ERROR ) { warn("In searching GenomeWise9, Reload error on database gen, position %d,%d",query_pos,target_pos); return SEARCH_ERROR; } if( db_status == DB_RETURN_END ) break; /* Out of target loop */ target_pos++; } /* end of For all target entries */ close_GenomicDB(gen,targetdb); pop_errormsg_stack(); return SEARCH_OK; } /* Function: score_only_GenomeWise9(evi,gen,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function just calculates the score for the matrix * I am pretty sure we can do this better, but hey, for the moment... * It calls /allocate_GenomeWise9_only * * * Arg: evi [UNKN ] query data structure [GenomeEvidenceSet*] * Arg: gen [UNKN ] target data structure [ComplexSequence*] * Arg: switchcost [UNKN ] Resource [int] * Arg: newgenecost [UNKN ] Resource [int] * Arg: non_start_codon [UNKN ] Resource [int] * Arg: non_stop_codon [UNKN ] Resource [int] * Arg: rndcodon [UNKN ] Resource [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [int] * */ int score_only_GenomeWise9(GenomeEvidenceSet* evi,ComplexSequence* gen ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { int bestscore = NEGI; int i; int j; int k; GenomeWise9 * mat; mat = allocate_GenomeWise9_only(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon); if( mat == NULL ) { warn("Memory allocation error in the db search - unable to communicate to calling function. this spells DIASTER!"); return NEGI; } if((mat->basematrix = BaseMatrix_alloc_matrix_and_specials(11,(mat->leni + 0) * 10,11,8)) == NULL) { warn("Score only matrix for GenomeWise9 cannot be allocated, (asking for 10 by %d cells)",mat->leni*10); mat = free_GenomeWise9(mat); return 0; } mat->basematrix->type = BASEMATRIX_TYPE_VERYSMALL; /* Now, initiate matrix */ for(j=0;j<12;j++) { for(i=(-0);ileni;i++) { for(k=0;k<10;k++) GenomeWise9_VSMALL_MATRIX(mat,i,j,k) = NEGI; } GenomeWise9_VSMALL_SPECIAL(mat,i,j,PREGENE_INTERGENIC) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,INTERGENIC) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR5) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR3) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_CDS) = NEGI; GenomeWise9_VSMALL_SPECIAL(mat,i,j,START) = 0; GenomeWise9_VSMALL_SPECIAL(mat,i,j,END) = NEGI; } /* Ok, lets do-o-o-o-o it */ for(j=0;jlenj;j++) { /*for all target positions*/ auto int score; auto int temp; for(i=0;ileni;i++) { /*for all query positions*/ /* For state UTR5 */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_UTR5 to state UTR5 */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state START to state UTR5 */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,START) + GNE_UTR5_START(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state INTERGENIC to state UTR5 */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,INTERGENIC) + (GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)); if( temp > score ) { score = temp; } /* From state PREGENE_INTERGENIC to state UTR5 */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,PREGENE_INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,UTR5) = score; /* state UTR5 is a source for special SPECIAL_UTR5 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR5) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR5) = temp; } /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,UTR5_INTRON) = score; /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,START_CODON) = score; /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score ) { score = temp; } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score ) { score = temp; } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score ) { score = temp; } /* From state UTR5 to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score ) { score = temp; } /* From state START_CODON to state CDS */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_CDS to state CDS */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-3,SPECIAL_CDS) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state INTERGENIC to state CDS */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-3,INTERGENIC) + (GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,CDS) = score; /* state CDS is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,INTERGENIC) = temp; } /* state CDS is a source for special SPECIAL_CDS */ temp = score + ((mat->switchcost+mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)])) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_CDS) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_CDS) = temp; } /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,CDS_INTRON_0) = score; /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,CDS_INTRON_1) = score; /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,CDS_INTRON_2) = score; /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,STOP_CODON) = score; /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state CDS to state UTR3 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score ) { score = temp; } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Has restricted position */ if( (j-1) == 0 ) { /* From state INTERGENIC to state UTR3 */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,UTR3) = score; /* state UTR3 is a source for special POSTGENE_INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) = temp; } /* state UTR3 is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,INTERGENIC) = temp; } /* state UTR3 is a source for special SPECIAL_UTR3 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR3) ) { GenomeWise9_VSMALL_SPECIAL(mat,i,j,SPECIAL_UTR3) = temp; } /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_VSMALL_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_UTR3 to state UTR3_INTRON */ temp = GenomeWise9_VSMALL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_VSMALL_MATRIX(mat,i,j,UTR3_INTRON) = score; /* Finished calculating state UTR3_INTRON */ } /* end of for all query positions */ /* Special state PREGENE_INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_VSMALL_SPECIAL(mat,0,j,PREGENE_INTERGENIC); /* Source START is a special source for PREGENE_INTERGENIC */ temp = GenomeWise9_VSMALL_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) score = temp; /* Put back score... (now updated!) */ GenomeWise9_VSMALL_SPECIAL(mat,0,j,PREGENE_INTERGENIC) = score; /* Finished updating state PREGENE_INTERGENIC */ /* Special state POSTGENE_INTERGENIC has no special to special movements */ /* Special state INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_VSMALL_SPECIAL(mat,0,j,INTERGENIC); /* Source INTERGENIC is a special source for INTERGENIC */ temp = GenomeWise9_VSMALL_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) score = temp; /* Source CDS for state INTERGENIC is not special... already calculated */ /* Source UTR3 for state INTERGENIC is not special... already calculated */ /* Put back score... (now updated!) */ GenomeWise9_VSMALL_SPECIAL(mat,0,j,INTERGENIC) = score; /* Finished updating state INTERGENIC */ /* Special state SPECIAL_UTR5 has no special to special movements */ /* Special state SPECIAL_UTR3 has no special to special movements */ /* Special state SPECIAL_CDS has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_VSMALL_SPECIAL(mat,0,j,SPECIAL_CDS); /* Source CDS for state SPECIAL_CDS is not special... already calculated */ /* Source SPECIAL_CDS is a special source for SPECIAL_CDS */ temp = GenomeWise9_VSMALL_SPECIAL(mat,0,j - 3,SPECIAL_CDS) + (mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) + (0); if( temp > score ) score = temp; /* Put back score... (now updated!) */ GenomeWise9_VSMALL_SPECIAL(mat,0,j,SPECIAL_CDS) = score; /* Finished updating state SPECIAL_CDS */ /* Special state START has no special to special movements */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_VSMALL_SPECIAL(mat,0,j,END); /* Source INTERGENIC is a special source for END */ /* Has restricted position */ if( j == mat->lenj-1 ) { temp = GenomeWise9_VSMALL_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) score = temp; } /* Put back score... (now updated!) */ GenomeWise9_VSMALL_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ if( bestscore < GenomeWise9_VSMALL_SPECIAL(mat,0,j,END) ) bestscore = GenomeWise9_VSMALL_SPECIAL(mat,0,j,END); } /* end of for all target positions */ mat = free_GenomeWise9(mat); return bestscore; } /* Function: PackAln_bestmemory_GenomeWise9(evi,gen,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon,dpenv,dpri) * * Descrip: This function chooses the best memory set-up for the alignment * using calls to basematrix, and then implements either a large * or small memory model. * * It is the best function to use if you just want an alignment * * If you want a label alignment, you will need * /convert_PackAln_to_AlnBlock_GenomeWise9 * * * Arg: evi [UNKN ] query data structure [GenomeEvidenceSet*] * Arg: gen [UNKN ] target data structure [ComplexSequence*] * Arg: switchcost [UNKN ] Resource [int] * Arg: newgenecost [UNKN ] Resource [int] * Arg: non_start_codon [UNKN ] Resource [int] * Arg: non_stop_codon [UNKN ] Resource [int] * Arg: rndcodon [UNKN ] Resource [RandomCodonScore *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_bestmemory_GenomeWise9(GenomeEvidenceSet* evi,ComplexSequence* gen ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon,DPEnvelope * dpenv,DPRunImpl * dpri) { int total; GenomeWise9 * mat; PackAln * out; DebugMatrix * de; DPRunImplMemory strategy; assert(dpri); total = evi->len * gen->seq->len; if( dpri->memory == DPIM_Default ) { if( (total * 10 * sizeof(int)) > 1000*dpri->kbyte_size) { strategy = DPIM_Linear; } else { strategy = DPIM_Explicit; } } else { strategy = dpri->memory; } if( strategy == DPIM_Linear ) { /* use small implementation */ if( (mat=allocate_Small_GenomeWise9(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon)) == NULL ) { warn("Unable to allocate small GenomeWise9 version"); return NULL; } out = PackAln_calculate_Small_GenomeWise9(mat,dpenv); } else { /* use Large implementation */ if( (mat=allocate_Expl_GenomeWise9(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon)) == NULL ) { warn("Unable to allocate large GenomeWise9 version"); return NULL; } if( dpri->debug == TRUE) { fatal("Asked for dydebug, but dynamite file not compiled with -g. Need to recompile dynamite source"); } else calculate_GenomeWise9(mat); out = PackAln_read_Expl_GenomeWise9(mat); } mat = free_GenomeWise9(mat); return out; } /* Function: allocate_GenomeWise9_only(evi,gen,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function only allocates the GenomeWise9 structure * checks types where possible and determines leni and lenj * The basematrix area is delt with elsewhere * * * Arg: evi [UNKN ] query data structure [GenomeEvidenceSet*] * Arg: gen [UNKN ] target data structure [ComplexSequence*] * Arg: switchcost [UNKN ] Resource [int] * Arg: newgenecost [UNKN ] Resource [int] * Arg: non_start_codon [UNKN ] Resource [int] * Arg: non_stop_codon [UNKN ] Resource [int] * Arg: rndcodon [UNKN ] Resource [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [GenomeWise9 *] * */ GenomeWise9 * allocate_GenomeWise9_only(GenomeEvidenceSet* evi,ComplexSequence* gen ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { GenomeWise9 * out; if((out= GenomeWise9_alloc()) == NULL) { warn("Allocation of basic GenomeWise9 structure failed..."); return NULL; } out->evi = evi; out->gen = gen; out->switchcost = switchcost; out->newgenecost = newgenecost; out->non_start_codon = non_start_codon; out->non_stop_codon = non_stop_codon; out->rndcodon = rndcodon; out->leni = evi->len; out->lenj = gen->seq->len; return out; } /* Function: allocate_Expl_GenomeWise9(evi,gen,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function allocates the GenomeWise9 structure * and the basematrix area for explicit memory implementations * It calls /allocate_GenomeWise9_only * * * Arg: evi [UNKN ] query data structure [GenomeEvidenceSet*] * Arg: gen [UNKN ] target data structure [ComplexSequence*] * Arg: switchcost [UNKN ] Resource [int] * Arg: newgenecost [UNKN ] Resource [int] * Arg: non_start_codon [UNKN ] Resource [int] * Arg: non_stop_codon [UNKN ] Resource [int] * Arg: rndcodon [UNKN ] Resource [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [GenomeWise9 *] * */ GenomeWise9 * allocate_Expl_GenomeWise9(GenomeEvidenceSet* evi,ComplexSequence* gen ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { GenomeWise9 * out; out = allocate_GenomeWise9_only(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon); if( out == NULL ) return NULL; if( (out->basematrix = BaseMatrix_alloc_matrix_and_specials((out->lenj+10)*10,(out->leni+0),8,out->lenj+10)) == NULL) { warn("Explicit matrix GenomeWise9 cannot be allocated, (asking for %d by %d main cells)",out->leni,out->lenj); free_GenomeWise9(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_EXPLICIT; init_GenomeWise9(out); return out; } /* Function: init_GenomeWise9(mat) * * Descrip: This function initates GenomeWise9 matrix when in explicit mode * Called in /allocate_Expl_GenomeWise9 * * * Arg: mat [UNKN ] GenomeWise9 which contains explicit basematrix memory [GenomeWise9 *] * */ void init_GenomeWise9(GenomeWise9 * mat) { register int i; register int j; if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) { warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that"); return; } for(i= (-0);ievi->len;i++) { for(j= (-10);j<11;j++) { GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; } } for(j= (-10);jgen->seq->len;j++) { for(i= (-0);i<1;i++) { GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; } GenomeWise9_EXPL_SPECIAL(mat,i,j,PREGENE_INTERGENIC) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,INTERGENIC) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR5) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR3) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_CDS) = NEGI; GenomeWise9_EXPL_SPECIAL(mat,i,j,START) = 0; GenomeWise9_EXPL_SPECIAL(mat,i,j,END) = NEGI; } return; } /* Function: recalculate_PackAln_GenomeWise9(pal,mat) * * Descrip: This function recalculates the PackAln structure produced by GenomeWise9 * For example, in linear space methods this is used to score them * * * Arg: pal [UNKN ] Undocumented argument [PackAln *] * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * */ void recalculate_PackAln_GenomeWise9(PackAln * pal,GenomeWise9 * mat) { int i,j,k,offi,offj; PackAlnUnit * prev; PackAlnUnit * pau; for(k=1,prev=pal->pau[0];k < pal->len;k++,prev=pau) { pau = pal->pau[k]; i = pau->i; j = pau->j; offi = pau->i - prev->i; offj = pau->j - prev->j; switch(pau->state) { case UTR5 : if( offi == 0 && offj == 1 && prev->state == UTR5 ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == UTR5_INTRON ) { pau->score = GNE_UTR_3SS(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 1 && prev->state == (SPECIAL_UTR5+10) ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 1 && prev->state == (START+10) ) { pau->score = GNE_UTR5_START(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 1 && prev->state == (INTERGENIC+10) ) { pau->score = (GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)) + (0); continue; } if( offj == 1 && prev->state == (PREGENE_INTERGENIC+10) ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state UTR5, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case UTR5_INTRON : if( offi == 0 && offj == 1 && prev->state == UTR5_INTRON ) { pau->score = GNE_UTR_INTRON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == UTR5 ) { pau->score = GNE_UTR_5SS(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state UTR5_INTRON, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case START_CODON : if( offi == 0 && offj == 3 && prev->state == UTR5_INTRON ) { pau->score = GNE_START_CODON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == UTR5 ) { pau->score = GNE_START_CODON(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state START_CODON, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case CDS : if( offi == 0 && offj == 3 && prev->state == CDS ) { pau->score = GNE_CDS(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 6 && prev->state == CDS_INTRON_0 ) { pau->score = GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0) + (0); continue; } if( offi == 0 && offj == 5 && prev->state == CDS_INTRON_1 ) { pau->score = GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1) + (0); continue; } if( offi == 0 && offj == 4 && prev->state == CDS_INTRON_2 ) { pau->score = GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2) + (0); continue; } if( offi == 0 && offj == 2 && prev->state == CDS ) { pau->score = GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2) + (0); continue; } if( offi == 0 && offj == 4 && prev->state == CDS ) { pau->score = GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == UTR5 ) { pau->score = (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == START_CODON ) { pau->score = GNE_CDS(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 3 && prev->state == (SPECIAL_CDS+10) ) { pau->score = GNE_CDS(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 3 && prev->state == (INTERGENIC+10) ) { pau->score = (GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)) + (0); continue; } warn("In recaluclating PackAln with state CDS, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case CDS_INTRON_0 : if( offi == 0 && offj == 1 && prev->state == CDS_INTRON_0 ) { pau->score = GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 8 && prev->state == CDS ) { pau->score = GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0) + (0); continue; } warn("In recaluclating PackAln with state CDS_INTRON_0, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case CDS_INTRON_1 : if( offi == 0 && offj == 1 && prev->state == CDS_INTRON_1 ) { pau->score = GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 9 && prev->state == CDS ) { pau->score = GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1) + (0); continue; } warn("In recaluclating PackAln with state CDS_INTRON_1, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case CDS_INTRON_2 : if( offi == 0 && offj == 1 && prev->state == CDS_INTRON_2 ) { pau->score = GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 10 && prev->state == CDS ) { pau->score = GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2) + (0); continue; } warn("In recaluclating PackAln with state CDS_INTRON_2, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case STOP_CODON : if( offi == 0 && offj == 3 && prev->state == CDS ) { pau->score = GNE_STOP_CODON(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state STOP_CODON, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case UTR3 : if( offi == 0 && offj == 1 && prev->state == UTR3 ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == CDS ) { pau->score = (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == STOP_CODON ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == UTR3_INTRON ) { pau->score = GNE_UTR_3SS(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 1 && prev->state == (INTERGENIC+10) ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state UTR3, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case UTR3_INTRON : if( offi == 0 && offj == 1 && prev->state == UTR3_INTRON ) { pau->score = GNE_UTR_INTRON(mat->evi,i,mat->gen,j) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == UTR3 ) { pau->score = GNE_UTR_5SS(mat->evi,i,mat->gen,j) + (0); continue; } if( offj == 1 && prev->state == (SPECIAL_UTR3+10) ) { pau->score = GNE_UTR(mat->evi,i,mat->gen,j) + (0); continue; } warn("In recaluclating PackAln with state UTR3_INTRON, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case (PREGENE_INTERGENIC+10) : if( offj == 1 && prev->state == (START+10) ) { pau->score = 0 + (0); continue; } warn("In recaluclating PackAln with state PREGENE_INTERGENIC, got a bad source state. Error!"); break; case (POSTGENE_INTERGENIC+10) : if( offj == 0 && prev->state == UTR3 ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = (mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j)) + (0); continue; } warn("In recaluclating PackAln with state POSTGENE_INTERGENIC, got a bad source state. Error!"); break; case (INTERGENIC+10) : if( offj == 1 && prev->state == (INTERGENIC+10) ) { pau->score = 0 + (0); continue; } if( offj == 0 && prev->state == CDS ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = (mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j)) + (0); continue; } if( offj == 0 && prev->state == UTR3 ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = (mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j)) + (0); continue; } warn("In recaluclating PackAln with state INTERGENIC, got a bad source state. Error!"); break; case (SPECIAL_UTR5+10) : if( offj == 0 && prev->state == UTR5 ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->switchcost + (0); continue; } warn("In recaluclating PackAln with state SPECIAL_UTR5, got a bad source state. Error!"); break; case (SPECIAL_UTR3+10) : if( offj == 0 && prev->state == UTR3 ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->switchcost + (0); continue; } warn("In recaluclating PackAln with state SPECIAL_UTR3, got a bad source state. Error!"); break; case (SPECIAL_CDS+10) : if( offj == 0 && prev->state == CDS ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = (mat->switchcost+mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) + (0); continue; } if( offj == 3 && prev->state == (SPECIAL_CDS+10) ) { pau->score = mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)] + (0); continue; } warn("In recaluclating PackAln with state SPECIAL_CDS, got a bad source state. Error!"); break; case (START+10) : warn("In recaluclating PackAln with state START, got a bad source state. Error!"); break; case (END+10) : if( offj == 1 && prev->state == (INTERGENIC+10) ) { pau->score = 0 + (0); continue; } warn("In recaluclating PackAln with state END, got a bad source state. Error!"); break; default : warn("In recaluclating PackAln got a bad recipient state. Error!"); } prev = pau; } return; } /* divide and conquor macros are next */ #define GenomeWise9_HIDDEN_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[(j-hiddenj+10)][(i+0)*10+state]) #define GenomeWise9_DC_SHADOW_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[((j+11)*8) % 88][(i+0)*10+state]) #define GenomeWise9_HIDDEN_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state][(j+10)]) #define GenomeWise9_DC_SHADOW_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state*8][(j+10)]) #define GenomeWise9_DC_SHADOW_MATRIX_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->matrix[((((j+11)*8)+(shadow+1)) % 88)][(i+0)*10 + state]) /* Function: allocate_Small_GenomeWise9(evi,gen,switchcost,newgenecost,non_start_codon,non_stop_codon,rndcodon) * * Descrip: This function allocates the GenomeWise9 structure * and the basematrix area for a small memory implementations * It calls /allocate_GenomeWise9_only * * * Arg: evi [UNKN ] query data structure [GenomeEvidenceSet*] * Arg: gen [UNKN ] target data structure [ComplexSequence*] * Arg: switchcost [UNKN ] Resource [int] * Arg: newgenecost [UNKN ] Resource [int] * Arg: non_start_codon [UNKN ] Resource [int] * Arg: non_stop_codon [UNKN ] Resource [int] * Arg: rndcodon [UNKN ] Resource [RandomCodonScore *] * * Return [UNKN ] Undocumented return value [GenomeWise9 *] * */ #define GenomeWise9_DC_SHADOW_SPECIAL_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->specmatrix[state*8 +shadow+1][(j+10)]) GenomeWise9 * allocate_Small_GenomeWise9(GenomeEvidenceSet* evi,ComplexSequence* gen ,int switchcost,int newgenecost,int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon) { GenomeWise9 * out; out = allocate_GenomeWise9_only(evi, gen , switchcost, newgenecost, non_start_codon, non_stop_codon, rndcodon); if( out == NULL ) return NULL; out->basematrix = BaseMatrix_alloc_matrix_and_specials(88,(out->leni + 0) * 10,64,out->lenj+10); if(out == NULL) { warn("Small shadow matrix GenomeWise9 cannot be allocated, (asking for 11 by %d main cells)",out->leni+1); free_GenomeWise9(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_SHADOW; return out; } /* Function: PackAln_calculate_Small_GenomeWise9(mat,dpenv) * * Descrip: This function calculates an alignment for GenomeWise9 structure in linear space * If you want only the start/end points * use /AlnRangeSet_calculate_Small_GenomeWise9 * * The function basically * finds start/end points * foreach start/end point * calls /full_dc_GenomeWise9 * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_calculate_Small_GenomeWise9(GenomeWise9 * mat,DPEnvelope * dpenv) { int endj; int score; PackAln * out; PackAlnUnit * pau; int starti; int startj; int startstate; int stopi; int stopj; int stopstate; int temp; int donej; /* This is for reporting, will be passed as a & arg in */ int totalj; /* This also is for reporting, but as is not changed, can be passed by value */ if( mat->basematrix->type != BASEMATRIX_TYPE_SHADOW ) { warn("Could not calculate packaln small for GenomeWise9 due to wrong type of matrix"); return NULL; } out = PackAln_alloc_std(); start_reporting("Find start end points: "); dc_start_end_calculate_GenomeWise9(mat,dpenv); score = start_end_find_end_GenomeWise9(mat,&endj); out->score = score; stopstate = END; /* Special to specials: have to eat up in strip and then drop back to full_dc for intervening bits */ log_full_error(REPORT,0,"End at %d Score %d",endj,score); stop_reporting(); for(;;) { /*while there are more special bits to recover*/ start_reporting("Special cell aln end %d:",endj); if( read_special_strip_GenomeWise9(mat,0,endj,stopstate,&endj,&startstate,out) == FALSE ) { warn("Problem in reading off special state system... going to return partial alignment"); break; } if( startstate == START || endj <= 0) { log_full_error(REPORT,0,"Recovered complete alignment"); stop_reporting(); break; } log_full_error(REPORT,0,"Finished to %d",endj); stop_reporting(); /* Ok... have to eat up another piece of matrix */ temp = startstate; starti = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,0); startj = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,1); startstate = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,2); stopi = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,3); stopj = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,4); stopstate = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,5); /* Get out the score of this block. V. important! */ temp = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,6); totalj = stopj - startj; donej = 0; start_reporting("Main matrix aln [%d,%d]:",startj,stopj); if(full_dc_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,out,&donej,totalj,dpenv) == FALSE) { warn("In the alignment GenomeWise9 [%d,%d][%d,%d], got a problem. Please report bug ... giving you back a partial alignment",starti,startj,stopi,stopj); return out; } /* now have to figure out which special we came from... yikes */ max_matrix_to_special_GenomeWise9(mat,starti,startj,startstate,temp,&stopi,&stopj,&stopstate,&temp,NULL); if( stopi == GenomeWise9_READ_OFF_ERROR) { warn("In GenomeWise9 read off ending at %d ... got a bad matrix to special read off... returning partial alignment",startj); invert_PackAln(out); recalculate_PackAln_GenomeWise9(out,mat); return out; } /* if at start, break, otherwise, back to eat another strip */ if( stopstate == START) { log_full_error(REPORT,0,"Recovered complete alignment "); stop_reporting(); break; } log_full_error(REPORT,0,"Finished alignment to %d ",startj); stop_reporting(); endj = stopj; /* stopstate is correct as it is */ } /* end of while there are more special bits to recover */ invert_PackAln(out); recalculate_PackAln_GenomeWise9(out,mat); return out; } /* Function: AlnRangeSet_calculate_Small_GenomeWise9(mat) * * Descrip: This function calculates an alignment for GenomeWise9 structure in linear space * If you want the full alignment, use /PackAln_calculate_Small_GenomeWise9 * If you have already got the full alignment, but want the range set, use /AlnRangeSet_from_PackAln_GenomeWise9 * If you have got the small matrix but not the alignment, use /AlnRangeSet_from_GenomeWise9 * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_calculate_Small_GenomeWise9(GenomeWise9 * mat) { AlnRangeSet * out; start_reporting("Find start end points: "); dc_start_end_calculate_GenomeWise9(mat,NULL); log_full_error(REPORT,0,"Calculated"); out = AlnRangeSet_from_GenomeWise9(mat); return out; } /* Function: AlnRangeSet_from_GenomeWise9(mat) * * Descrip: This function reads off a start/end structure * for GenomeWise9 structure in linear space * If you want the full alignment use * /PackAln_calculate_Small_GenomeWise9 * If you have not calculated the matrix use * /AlnRange_calculate_Small_GenomeWise9 * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_from_GenomeWise9(GenomeWise9 * mat) { AlnRangeSet * out; AlnRange * temp; int jpos; int state; if( mat->basematrix->type != BASEMATRIX_TYPE_SHADOW) { warn("Bad error! - non shadow matrix type in AlnRangeSet_from_GenomeWise9"); return NULL; } out = AlnRangeSet_alloc_std(); /* Find the end position */ out->score = start_end_find_end_GenomeWise9(mat,&jpos); state = END; while( (temp = AlnRange_build_GenomeWise9(mat,jpos,state,&jpos,&state)) != NULL) add_AlnRangeSet(out,temp); return out; } /* Function: AlnRange_build_GenomeWise9(mat,stopj,stopspecstate,startj,startspecstate) * * Descrip: This function calculates a single start/end set in linear space * Really a sub-routine for /AlnRangeSet_from_PackAln_GenomeWise9 * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: stopspecstate [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int *] * Arg: startspecstate [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [AlnRange *] * */ AlnRange * AlnRange_build_GenomeWise9(GenomeWise9 * mat,int stopj,int stopspecstate,int * startj,int * startspecstate) { AlnRange * out; int jpos; int state; if( mat->basematrix->type != BASEMATRIX_TYPE_SHADOW) { warn("Bad error! - non shadow matrix type in AlnRangeSet_from_GenomeWise9"); return NULL; } /* Assumme that we have specials (we should!). Read back along the specials till we have the finish point */ if( read_special_strip_GenomeWise9(mat,0,stopj,stopspecstate,&jpos,&state,NULL) == FALSE) { warn("In AlnRanger_build_GenomeWise9 alignment ending at %d, unable to read back specials. Will (evenutally) return a partial range set... BEWARE!",stopj); return NULL; } if( state == START || jpos <= 0) return NULL; out = AlnRange_alloc(); out->starti = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,0); out->startj = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,1); out->startstate = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,2); out->stopi = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,3); out->stopj = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,4); out->stopstate = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,5); out->startscore = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,6); out->stopscore = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,jpos,state); /* Now, we have to figure out where this state came from in the specials */ max_matrix_to_special_GenomeWise9(mat,out->starti,out->startj,out->startstate,out->startscore,&jpos,startj,startspecstate,&state,NULL); if( jpos == GenomeWise9_READ_OFF_ERROR) { warn("In AlnRange_build_GenomeWise9 alignment ending at %d, with aln range between %d-%d in j, unable to find source special, returning this range, but this could get tricky!",stopj,out->startj,out->stopj); return out; } /* Put in the correct score for startstate, from the special */ out->startscore = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,*startj,*startspecstate); /* The correct j coords have been put into startj, startspecstate... so just return out */ return out; } /* Function: read_hidden_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: startstate [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: stopstate [UNKN ] Undocumented argument [int] * Arg: out [UNKN ] Undocumented argument [PackAln *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean read_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out) { int i; int j; int state; int cellscore; int isspecial; /* We don't need hiddenj here, 'cause matrix access handled by max funcs */ PackAlnUnit * pau; /* stop position is on the path */ i = stopi; j = stopj; state= stopstate; isspecial = FALSE; while( i >= starti && j >= startj) { /* Put away current i,j,state */ pau = PackAlnUnit_alloc();/* Should deal with memory overflow */ pau->i = i; pau->j = j; pau->state = state; add_PackAln(out,pau); max_hidden_GenomeWise9(mat,startj,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == GenomeWise9_READ_OFF_ERROR) { warn("In GenomeWise9 hidden read off, between %d:%d,%d:%d - at got bad read off. Problem!",starti,startj,stopi,stopj); return FALSE; } if( i == starti && j == startj && state == startstate) { /* Put away final state (start of this block) */ pau = PackAlnUnit_alloc(); /* Should deal with memory overflow */ pau->i = i; pau->j = j; pau->state = state; add_PackAln(out,pau); return TRUE; } if( i == starti && j == startj) { warn("In GenomeWise9 hidden read off, between %d:%d,%d:%d - hit start cell, but not in start state. Can't be good!.",starti,startj,stopi,stopj); return FALSE; } } warn("In GenomeWise9 hidden read off, between %d:%d,%d:%d - gone past start cell (now in %d,%d,%d), can't be good news!.",starti,startj,stopi,stopj,i,j,state); return FALSE; } /* Function: max_hidden_GenomeWise9(mat,hiddenj,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: hiddenj [UNKN ] Undocumented argument [int] * Arg: i [UNKN ] Undocumented argument [int] * Arg: j [UNKN ] Undocumented argument [int] * Arg: state [UNKN ] Undocumented argument [int] * Arg: isspecial [UNKN ] Undocumented argument [boolean] * Arg: reti [UNKN ] Undocumented argument [int *] * Arg: retj [UNKN ] Undocumented argument [int *] * Arg: retstate [UNKN ] Undocumented argument [int *] * Arg: retspecial [UNKN ] Undocumented argument [boolean *] * Arg: cellscore [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [int] * */ int max_hidden_GenomeWise9(GenomeWise9 * mat,int hiddenj,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { register int temp; register int cscore; *reti = (*retj) = (*retstate) = GenomeWise9_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->evi->len || j > mat->gen->seq->len) { warn("In GenomeWise9 matrix special read off - out of bounds on matrix [i,j is %d,%d state %d in standard matrix]",i,j,state); return -1; } /* Then you have to select the correct switch statement to figure out the readoff */ /* Somewhat odd - reverse the order of calculation and return as soon as it is correct */ cscore = GenomeWise9_HIDDEN_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case UTR5 : /* Not allowing special sources.. skipping PREGENE_INTERGENIC */ /* Not allowing special sources.. skipping INTERGENIC */ /* Not allowing special sources.. skipping START */ /* Not allowing special sources.. skipping SPECIAL_UTR5 */ temp = cscore - (GNE_UTR_3SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5_INTRON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5_INTRON); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR5_INTRON : temp = cscore - (GNE_UTR_5SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5); } temp = cscore - (GNE_UTR_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5_INTRON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR5_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case START_CODON : temp = cscore - (GNE_START_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5); } temp = cscore - (GNE_START_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5_INTRON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS : /* Not allowing special sources.. skipping INTERGENIC */ /* Not allowing special sources.. skipping SPECIAL_CDS */ temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,START_CODON) ) { *reti = i - 0; *retj = j - 3; *retstate = START_CODON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,START_CODON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,START_CODON); } temp = cscore - ((GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,UTR5); } temp = cscore - (GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 4,CDS) ) { *reti = i - 0; *retj = j - 4; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-4,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 4,CDS); } temp = cscore - (GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 2,CDS) ) { *reti = i - 0; *retj = j - 2; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-2,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 2,CDS); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 4,CDS_INTRON_2) ) { *reti = i - 0; *retj = j - 4; *retstate = CDS_INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-4,CDS_INTRON_2); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 4,CDS_INTRON_2); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 5,CDS_INTRON_1) ) { *reti = i - 0; *retj = j - 5; *retstate = CDS_INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-5,CDS_INTRON_1); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 5,CDS_INTRON_1); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 6,CDS_INTRON_0) ) { *reti = i - 0; *retj = j - 6; *retstate = CDS_INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-6,CDS_INTRON_0); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 6,CDS_INTRON_0); } temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,CDS); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_0 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 8,CDS) ) { *reti = i - 0; *retj = j - 8; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-8,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 8,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_0) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_0); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_0); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_1 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 9,CDS) ) { *reti = i - 0; *retj = j - 9; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-9,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 9,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_1) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_1); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_1); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_2 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 10,CDS) ) { *reti = i - 0; *retj = j - 10; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-10,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 10,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_2); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS_INTRON_2); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case STOP_CODON : temp = cscore - (GNE_STOP_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 3,CDS); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3 : /* Not allowing special sources.. skipping INTERGENIC */ temp = cscore - (GNE_UTR_3SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3_INTRON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3_INTRON); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,STOP_CODON) ) { *reti = i - 0; *retj = j - 1; *retstate = STOP_CODON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,STOP_CODON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,STOP_CODON); } temp = cscore - ((GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,CDS); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3_INTRON : /* Not allowing special sources.. skipping SPECIAL_UTR3 */ temp = cscore - (GNE_UTR_5SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3); } temp = cscore - (GNE_UTR_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3_INTRON); } return GenomeWise9_HIDDEN_MATRIX(mat,i - 0,j - 1,UTR3_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: read_special_strip_GenomeWise9(mat,stopi,stopj,stopstate,startj,startstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: stopstate [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int *] * Arg: startstate [UNKN ] Undocumented argument [int *] * Arg: out [UNKN ] Undocumented argument [PackAln *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean read_special_strip_GenomeWise9(GenomeWise9 * mat,int stopi,int stopj,int stopstate,int * startj,int * startstate,PackAln * out) { int i; int j; int state; int cellscore; int isspecial; PackAlnUnit * pau; /* stop position is on the path */ i = stopi; j = stopj; state= stopstate; isspecial = TRUE; /* Loop until state has the same j as its stop in shadow pointers */ /* This will be the state is came out from, OR it has hit !start */ /* We may not want to get the alignment, in which case out will be NULL */ while( j > GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,state,4) && state != START) { /*while more specials to eat up*/ /* Put away current state, if we should */ if(out != NULL) { pau = PackAlnUnit_alloc(); /* Should deal with memory overflow */ pau->i = i; pau->j = j; pau->state = state + 10; add_PackAln(out,pau); } max_special_strip_GenomeWise9(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == GenomeWise9_READ_OFF_ERROR) { warn("In special strip read GenomeWise9, got a bad read off error. Sorry!"); return FALSE; } } /* end of while more specials to eat up */ /* check to see we have not gone too far! */ if( state != START && j < GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,state,4)) { warn("In special strip read GenomeWise9, at special [%d] state [%d] overshot!",j,state); return FALSE; } /* Put away last state */ if(out != NULL) { pau = PackAlnUnit_alloc();/* Should deal with memory overflow */ pau->i = i; pau->j = j; pau->state = state + 10; add_PackAln(out,pau); } /* Put away where we are in startj and startstate */ *startj = j; *startstate = state; return TRUE; } /* Function: max_special_strip_GenomeWise9(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: A pretty intense internal function. Deals with read-off only in specials * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: i [UNKN ] Undocumented argument [int] * Arg: j [UNKN ] Undocumented argument [int] * Arg: state [UNKN ] Undocumented argument [int] * Arg: isspecial [UNKN ] Undocumented argument [boolean] * Arg: reti [UNKN ] Undocumented argument [int *] * Arg: retj [UNKN ] Undocumented argument [int *] * Arg: retstate [UNKN ] Undocumented argument [int *] * Arg: retspecial [UNKN ] Undocumented argument [boolean *] * Arg: cellscore [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [int] * */ int max_special_strip_GenomeWise9(GenomeWise9 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { int temp; int cscore; *reti = (*retj) = (*retstate) = GenomeWise9_READ_OFF_ERROR; if( isspecial == FALSE ) { warn("In special strip max function for GenomeWise9, got a non special start point. Problem! (bad!)"); return (-1); } if( j < 0 || j > mat->gen->seq->len) { warn("In GenomeWise9 matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case PREGENE_INTERGENIC : /* source START is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,START); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,START) ; } case POSTGENE_INTERGENIC : /* Source UTR3 is not a special */ case INTERGENIC : /* Source UTR3 is not a special */ /* Source CDS is not a special */ /* source INTERGENIC is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } case SPECIAL_UTR5 : /* Source UTR5 is not a special */ case SPECIAL_UTR3 : /* Source UTR3 is not a special */ case SPECIAL_CDS : /* source SPECIAL_CDS is a special */ temp = cscore - (mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 3,SPECIAL_CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = SPECIAL_CDS; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-3,SPECIAL_CDS); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 3,SPECIAL_CDS) ; } /* Source CDS is not a special */ case START : case END : /* source INTERGENIC is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } default: warn("Major problem (!) - in GenomeWise9 special strip read off, position %d,%d state %d no source found dropped into default on source switch!",i,j,state); return (-1); } /* end of switch on special states */ } /* Function: max_matrix_to_special_GenomeWise9(mat,i,j,state,cscore,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: i [UNKN ] Undocumented argument [int] * Arg: j [UNKN ] Undocumented argument [int] * Arg: state [UNKN ] Undocumented argument [int] * Arg: cscore [UNKN ] Undocumented argument [int] * Arg: reti [UNKN ] Undocumented argument [int *] * Arg: retj [UNKN ] Undocumented argument [int *] * Arg: retstate [UNKN ] Undocumented argument [int *] * Arg: retspecial [UNKN ] Undocumented argument [boolean *] * Arg: cellscore [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [int] * */ int max_matrix_to_special_GenomeWise9(GenomeWise9 * mat,int i,int j,int state,int cscore,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { int temp; *reti = (*retj) = (*retstate) = GenomeWise9_READ_OFF_ERROR; if( j < 0 || j > mat->lenj) { warn("In GenomeWise9 matrix to special read off - out of bounds on matrix [j is %d in special]",j); return -1; } switch(state) { /*Switch state */ case UTR5 : temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,PREGENE_INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = PREGENE_INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,PREGENE_INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,PREGENE_INTERGENIC) ; } temp = cscore - ((GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } temp = cscore - (GNE_UTR5_START(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,START); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,START) ; } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,SPECIAL_UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = SPECIAL_UTR5; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,SPECIAL_UTR5); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,SPECIAL_UTR5) ; } /* Source UTR5_INTRON is not a special, should not get here! */ /* Source UTR5 is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR5_INTRON : /* Source UTR5 is not a special, should not get here! */ /* Source UTR5_INTRON is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case START_CODON : /* Source UTR5 is not a special, should not get here! */ /* Source UTR5_INTRON is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS : temp = cscore - ((GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 3,INTERGENIC) ) { *reti = i - 0; *retj = j - 3; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-3,INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 3,INTERGENIC) ; } temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 3,SPECIAL_CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = SPECIAL_CDS; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-3,SPECIAL_CDS); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 3,SPECIAL_CDS) ; } /* Source START_CODON is not a special, should not get here! */ /* Source UTR5 is not a special, should not get here! */ /* Source CDS is not a special, should not get here! */ /* Source CDS is not a special, should not get here! */ /* Source CDS_INTRON_2 is not a special, should not get here! */ /* Source CDS_INTRON_1 is not a special, should not get here! */ /* Source CDS_INTRON_0 is not a special, should not get here! */ /* Source CDS is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_0 : /* Source CDS is not a special, should not get here! */ /* Source CDS_INTRON_0 is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_1 : /* Source CDS is not a special, should not get here! */ /* Source CDS_INTRON_1 is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_2 : /* Source CDS is not a special, should not get here! */ /* Source CDS_INTRON_2 is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case STOP_CODON : /* Source CDS is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3 : temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } /* Source UTR3_INTRON is not a special, should not get here! */ /* Source STOP_CODON is not a special, should not get here! */ /* Source CDS is not a special, should not get here! */ /* Source UTR3 is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3_INTRON : temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,SPECIAL_UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = SPECIAL_UTR3; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,SPECIAL_UTR3); } return GenomeWise9_DC_SHADOW_MATRIX(mat,i - 0,j - 1,SPECIAL_UTR3) ; } /* Source UTR3 is not a special, should not get here! */ /* Source UTR3_INTRON is not a special, should not get here! */ warn("Major problem (!) - in GenomeWise9 matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: calculate_hidden_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: startstate [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: stopstate [UNKN ] Undocumented argument [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * */ void calculate_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) { register int i; register int j; register int score; register int temp; register int hiddenj; hiddenj = startj; init_hidden_GenomeWise9(mat,starti,startj,stopi,stopj); GenomeWise9_HIDDEN_MATRIX(mat,starti,startj,startstate) = 0; for(j=startj;j<=stopj;j++) { for(i=starti;i<=stopi;i++) { /* Should *not* do very first cell as this is the one set to zero in one state! */ if( i == starti && j == startj ) continue; if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; continue; } /* end of Is not in envelope */ /* For state UTR5 */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5) = score; /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5_INTRON) = score; /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,START_CODON) = score; /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score ) { score = temp; } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score ) { score = temp; } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score ) { score = temp; } /* From state UTR5 to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score ) { score = temp; } /* From state START_CODON to state CDS */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS) = score; /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_0) = score; /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_1) = score; /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_2) = score; /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,STOP_CODON) = score; /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state CDS to state UTR3 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score ) { score = temp; } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3) = score; /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_HIDDEN_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3_INTRON) = score; /* Finished calculating state UTR3_INTRON */ } } return; } /* Function: init_hidden_GenomeWise9(mat,starti,startj,stopi,stopj) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * */ void init_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int stopi,int stopj) { register int i; register int j; register int hiddenj; hiddenj = startj; for(j=(startj-10);j<=stopj;j++) { for(i=(starti-0);i<=stopi;i++) { GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_HIDDEN_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; } } return; } /* Function: full_dc_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,out,donej,totalj,dpenv) * * Descrip: The main divide-and-conquor routine. Basically, call /PackAln_calculate_small_GenomeWise9 * Not this function, which is pretty hard core. * Function is given start/end points (in main matrix) for alignment * It does some checks, decides whether start/end in j is small enough for explicit calc * - if yes, calculates it, reads off into PackAln (out), adds the j distance to donej and returns TRUE * - if no, uses /do_dc_single_pass_GenomeWise9 to get mid-point * saves midpoint, and calls itself to do right portion then left portion * right then left ensures PackAln is added the 'right' way, ie, back-to-front * returns FALSE on any error, with a warning * * * Arg: mat [UNKN ] Matrix with small memory implementation [GenomeWise9 *] * Arg: starti [UNKN ] Start position in i [int] * Arg: startj [UNKN ] Start position in j [int] * Arg: startstate [UNKN ] Start position state number [int] * Arg: stopi [UNKN ] Stop position in i [int] * Arg: stopj [UNKN ] Stop position in j [int] * Arg: stopstate [UNKN ] Stop position state number [int] * Arg: out [UNKN ] PackAln structure to put alignment into [PackAln *] * Arg: donej [UNKN ] pointer to a number with the amount of alignment done [int *] * Arg: totalj [UNKN ] total amount of alignment to do (in j coordinates) [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean full_dc_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) { int lstarti; int lstartj; int lstate; if( mat->basematrix->type != BASEMATRIX_TYPE_SHADOW) { warn("*Very* bad error! - non shadow matrix type in full_dc_GenomeWise9"); return FALSE; } if( starti == -1 || startj == -1 || startstate == -1 || stopi == -1 || stopstate == -1) { warn("In full dc program, passed bad indices, indices passed were %d:%d[%d] to %d:%d[%d]\n",starti,startj,startstate,stopi,stopj,stopstate); return FALSE; } if( stopj - startj < 50) { log_full_error(REPORT,0,"[%d,%d][%d,%d] Explicit read off",starti,startj,stopi,stopj);/* Build hidden explicit matrix */ calculate_hidden_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv); *donej += (stopj - startj); /* Now read it off into out */ if( read_hidden_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,out) == FALSE) { warn("In full dc, at %d:%d,%d:%d got a bad hidden explicit read off... ",starti,startj,stopi,stopj); return FALSE; } return TRUE; } /* In actual divide and conquor */ if( do_dc_single_pass_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,(int)(*donej*100)/totalj) == FALSE) { warn("In divide and conquor for GenomeWise9, at bound %d:%d to %d:%d, unable to calculate midpoint. Problem!",starti,startj,stopi,stopj); return FALSE; } /* Ok... now we have to call on each side of the matrix */ /* We have to retrieve left hand side positions, as they will be vapped by the time we call LHS */ lstarti= GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,0); lstartj= GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,1); lstate = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,2); /* Call on right hand side: this lets us do the correct read off */ if( full_dc_GenomeWise9(mat,GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,3),GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,4),GenomeWise9_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,5),stopi,stopj,stopstate,out,donej,totalj,dpenv) == FALSE) { /* Warning already issued, simply chained back up to top */ return FALSE; } /* Call on left hand side */ if( full_dc_GenomeWise9(mat,starti,startj,startstate,lstarti,lstartj,lstate,out,donej,totalj,dpenv) == FALSE) { /* Warning already issued, simply chained back up to top */ return FALSE; } return TRUE; } /* Function: do_dc_single_pass_GenomeWise9(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: startstate [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: stopstate [UNKN ] Undocumented argument [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: perc_done [UNKN ] Undocumented argument [int] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean do_dc_single_pass_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_done) { int halfj; halfj = startj + ((stopj - startj)/2); init_dc_GenomeWise9(mat); GenomeWise9_DC_SHADOW_MATRIX(mat,starti,startj,startstate) = 0; run_up_dc_GenomeWise9(mat,starti,stopi,startj,halfj-1,dpenv,perc_done); push_dc_at_merge_GenomeWise9(mat,starti,stopi,halfj,&halfj,dpenv); follow_on_dc_GenomeWise9(mat,starti,stopi,halfj,stopj,dpenv,perc_done); return TRUE; } /* Function: push_dc_at_merge_GenomeWise9(mat,starti,stopi,startj,stopj,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * */ void push_dc_at_merge_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) { register int i; register int j; register int k; register int count; register int mergej;/* Sources below this j will be stamped by triples */ register int score; register int temp; mergej = startj -1; for(count=0,j=startj;count<10;count++,j++) { for(i=starti;i<=stopi;i++) { if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,1) = (-100); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,0) = (-100); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,1) = (-100); continue; } /* end of Is not in envelope */ /* For state UTR5, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,2) = UTR5; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,5) = UTR5; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,2) = UTR5_INTRON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,5) = UTR5; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = score; /* Finished with state UTR5 */ /* For state UTR5_INTRON, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,2) = UTR5_INTRON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,5) = UTR5_INTRON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,2) = UTR5; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,5) = UTR5_INTRON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = score; /* Finished with state UTR5_INTRON */ /* For state START_CODON, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,2) = UTR5_INTRON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,5) = START_CODON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5_INTRON,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,2) = UTR5; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,5) = START_CODON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = score; /* Finished with state START_CODON */ /* For state CDS, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score) { score = temp; if( j - 6 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-6; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS_INTRON_0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 6,CDS_INTRON_0,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score) { score = temp; if( j - 5 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-5; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS_INTRON_1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 5,CDS_INTRON_1,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score) { score = temp; if( j - 4 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-4; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS_INTRON_2; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS_INTRON_2,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score) { score = temp; if( j - 2 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-2; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,CDS,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score) { score = temp; if( j - 4 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-4; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score) { score = temp; if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = UTR5; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,2) = START_CODON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,5) = CDS; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,START_CODON,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = score; /* Finished with state CDS */ /* For state CDS_INTRON_0, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,2) = CDS_INTRON_0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,5) = CDS_INTRON_0; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_0,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score) { score = temp; if( j - 8 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,1) = j-8; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,5) = CDS_INTRON_0; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 8,CDS,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = score; /* Finished with state CDS_INTRON_0 */ /* For state CDS_INTRON_1, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,2) = CDS_INTRON_1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,5) = CDS_INTRON_1; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_1,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score) { score = temp; if( j - 9 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,1) = j-9; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,5) = CDS_INTRON_1; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 9,CDS,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = score; /* Finished with state CDS_INTRON_1 */ /* For state CDS_INTRON_2, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,2) = CDS_INTRON_2; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,5) = CDS_INTRON_2; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_2,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score) { score = temp; if( j - 10 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,1) = j-10; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,5) = CDS_INTRON_2; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 10,CDS,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = score; /* Finished with state CDS_INTRON_2 */ /* For state STOP_CODON, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); if( j - 3 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,1) = j-3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,5) = STOP_CODON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = score; /* Finished with state STOP_CODON */ /* For state UTR3, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,2) = UTR3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,5) = UTR3; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,2) = CDS; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,5) = UTR3; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,2) = STOP_CODON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,5) = UTR3; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,STOP_CODON,k); } } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,2) = UTR3_INTRON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,5) = UTR3; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = score; /* Finished with state UTR3 */ /* For state UTR3_INTRON, pushing when j - offj <= mergej */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,2) = UTR3_INTRON; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,5) = UTR3_INTRON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); } temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score) { score = temp; if( j - 1 <= mergej) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,0) = i-0; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,1) = j-1; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,2) = UTR3; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,3) = i; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,4) = j; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,5) = UTR3_INTRON; } else { for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); } } /* Add any movement independant score */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = score; /* Finished with state UTR3_INTRON */ } } /* Put back j into * stop j so that calling function gets it correct */ if( stopj == NULL) warn("Bad news... NULL stopj pointer in push dc function. This means that calling function does not know how many cells I have done!"); else *stopj = j; return; } /* Function: follow_on_dc_GenomeWise9(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: perc_done [UNKN ] Undocumented argument [int] * */ void follow_on_dc_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done) { int i; int j; int k; int score; int temp; int localshadow[7]; long int total; long int num; total = (stopi - starti+1) * (stopj - startj+1); num = 0; for(j=startj;j<=stopj;j++) { /*for each valid j column*/ for(i=starti;i<=stopi;i++) { /*this is strip*/ num++; if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; continue; } /* end of Is not in envelope */ if( num % 1000 == 0 ) log_full_error(REPORT,0,"[%d%%%% done]After mid-j %5d Cells done %d%%%%",perc_done,startj,(num*100)/total); /* For state UTR5 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5_INTRON,k); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 6,CDS_INTRON_0,k); } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 5,CDS_INTRON_1,k); } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS_INTRON_2,k); } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,CDS,k); } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS,k); } /* From state UTR5 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } /* From state START_CODON to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,START_CODON,k); } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_0,k); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 8,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_1,k); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 9,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_2,k); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 10,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); /* From state CDS to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS,k); } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,STOP_CODON,k); } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR3_INTRON */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: run_up_dc_GenomeWise9(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: perc_done [UNKN ] Undocumented argument [int] * */ } void run_up_dc_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done) { register int i; register int j; register int score; register int temp; long int total; long int num; total = (stopi - starti+1) * (stopj - startj+1); if( total <= 0 ) total = 1; num = 0; for(j=startj;j<=stopj;j++) { /*for each valid j column*/ for(i=starti;i<=stopi;i++) { /*this is strip*/ if( j == startj && i == starti) continue; num++; if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; continue; } /* end of Is not in envelope */ if( num % 1000 == 0 ) log_full_error(REPORT,0,"[%d%%%% done]Before mid-j %5d Cells done %d%%%%",perc_done,stopj,(num*100)/total); /* For state UTR5 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = score; /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = score; /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = score; /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score ) { score = temp; } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score ) { score = temp; } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score ) { score = temp; } /* From state UTR5 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score ) { score = temp; } /* From state START_CODON to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = score; /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = score; /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = score; /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = score; /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = score; /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state CDS to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score ) { score = temp; } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = score; /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = score; /* Finished calculating state UTR3_INTRON */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: init_dc_GenomeWise9(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * */ } void init_dc_GenomeWise9(GenomeWise9 * mat) { register int i; register int j; register int k; for(j=0;j<12;j++) { for(i=(-0);ievi->len;i++) { GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; for(k=0;k<7;k++) { GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = (-1); GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,k) = (-1); } } } return; } /* Function: dc_start_end_calculate_GenomeWise9(mat,dpenv) * * Descrip: Calculates special strip, leaving start/end/score points in the shadow matrix * One tricky thing is that we need to add score-independent calcs in the states * As we have to evaluate them then. This is not ideally implemented therefore * In fact it is *definitely* not ideal. Will have to do for now * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean dc_start_end_calculate_GenomeWise9(GenomeWise9 * mat,DPEnvelope * dpenv) { int i; int j; int k; int score; int temp; int leni; int lenj; int localshadow[7]; long int total; long int num=0; init_start_end_linear_GenomeWise9(mat); leni = mat->evi->len; lenj = mat->gen->seq->len; total = leni * lenj; for(j=0;jevi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); } /* From state SPECIAL_UTR5 to state UTR5 */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,SPECIAL_UTR5) + GNE_UTR(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [SPECIAL_UTR5] is a special for UTR5... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR5; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state START to state UTR5 */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,START) + GNE_UTR5_START(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [START] is a special for UTR5... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR5; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state INTERGENIC to state UTR5 */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC) + (GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)) + (0); if( temp > score ) { score = temp; /* This state [INTERGENIC] is a special for UTR5... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR5; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state PREGENE_INTERGENIC to state UTR5 */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,PREGENE_INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [PREGENE_INTERGENIC] is a special for UTR5... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR5; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state UTR5 is a source for special SPECIAL_UTR5 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_UTR5) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_UTR5) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR5,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR5,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR5,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR5,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR5,5) = UTR5; } /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5_INTRON,k); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR5,k); } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5_INTRON,k); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 6,CDS_INTRON_0,k); } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 5,CDS_INTRON_1,k); } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS_INTRON_2,k); } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,CDS,k); } /* From state CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 4,CDS,k); } /* From state UTR5 to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,UTR5,k); } /* From state START_CODON to state CDS */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,START_CODON,k); } /* From state SPECIAL_CDS to state CDS */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-3,SPECIAL_CDS) + GNE_CDS(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [SPECIAL_CDS] is a special for CDS... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= CDS; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state INTERGENIC to state CDS */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-3,INTERGENIC) + (GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)) + (0); if( temp > score ) { score = temp; /* This state [INTERGENIC] is a special for CDS... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= CDS; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state CDS is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,INTERGENIC) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,5) = CDS; } /* state CDS is a source for special SPECIAL_CDS */ temp = score + ((mat->switchcost+mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)])) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_CDS) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_CDS) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,5) = CDS; } /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_0,k); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 8,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_1,k); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 9,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS_INTRON_2,k); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 10,CDS,k); } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,CDS,k); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); /* From state CDS to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,CDS,k); } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,STOP_CODON,k); } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); } /* From state INTERGENIC to state UTR3 */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [INTERGENIC] is a special for UTR3... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR3; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state UTR3 is a source for special POSTGENE_INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,POSTGENE_INTERGENIC,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,POSTGENE_INTERGENIC,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,POSTGENE_INTERGENIC,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,POSTGENE_INTERGENIC,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,POSTGENE_INTERGENIC,5) = UTR3; } /* state UTR3 is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,INTERGENIC) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,5) = UTR3; } /* state UTR3 is a source for special SPECIAL_UTR3 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_UTR3) ) { GenomeWise9_DC_SHADOW_SPECIAL(mat,i,j,SPECIAL_UTR3) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR3,k) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,k); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR3,6) = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,6); GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR3,3) = i; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR3,4) = j; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_UTR3,5) = UTR3; } /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3_INTRON,k); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_DC_SHADOW_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,UTR3,k); } /* From state SPECIAL_UTR3 to state UTR3_INTRON */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,i-0,j-1,SPECIAL_UTR3) + GNE_UTR(mat->evi,i,mat->gen,j) + (0); if( temp > score ) { score = temp; /* This state [SPECIAL_UTR3] is a special for UTR3_INTRON... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= UTR3_INTRON; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = score; for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state UTR3_INTRON */ } /* end of for each i position in strip */ /* Special state PREGENE_INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,PREGENE_INTERGENIC); /* Source START is a special source for PREGENE_INTERGENIC */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,PREGENE_INTERGENIC,k) = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,START,k); } /* Put back score... (now updated!) */ GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,PREGENE_INTERGENIC) = score; /* Finished updating state PREGENE_INTERGENIC */ /* Special state POSTGENE_INTERGENIC has no special to special movements */ /* Special state INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,INTERGENIC); /* Source INTERGENIC is a special source for INTERGENIC */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,INTERGENIC,k) = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,INTERGENIC,k); } /* Source CDS for state INTERGENIC is not special... already calculated */ /* Source UTR3 for state INTERGENIC is not special... already calculated */ /* Put back score... (now updated!) */ GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,INTERGENIC) = score; /* Finished updating state INTERGENIC */ /* Special state SPECIAL_UTR5 has no special to special movements */ /* Special state SPECIAL_UTR3 has no special to special movements */ /* Special state SPECIAL_CDS has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,SPECIAL_CDS); /* Source CDS for state SPECIAL_CDS is not special... already calculated */ /* Source SPECIAL_CDS is a special source for SPECIAL_CDS */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j - 3,SPECIAL_CDS) + (mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,SPECIAL_CDS,k) = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 3,SPECIAL_CDS,k); } /* Put back score... (now updated!) */ GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,SPECIAL_CDS) = score; /* Finished updating state SPECIAL_CDS */ /* Special state START has no special to special movements */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,END); /* Source INTERGENIC is a special source for END */ temp = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i,j,END,k) = GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,INTERGENIC,k); } /* Put back score... (now updated!) */ GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ } /* end of for each j strip */ return TRUE; } /* Function: start_end_find_end_GenomeWise9(mat,endj) * * Descrip: First function used to find end of the best path in the special state !end * * * Arg: mat [UNKN ] Matrix in small mode [GenomeWise9 *] * Arg: endj [WRITE] position of end in j (meaningless in i) [int *] * * Return [UNKN ] Undocumented return value [int] * */ int start_end_find_end_GenomeWise9(GenomeWise9 * mat,int * endj) { register int j; register int max; register int maxj; max = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,mat->gen->seq->len-1,END); maxj = mat->gen->seq->len-1; for(j= mat->gen->seq->len-2 ;j >= 0 ;j--) { if( GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,END) > max ) { max = GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,END); maxj = j; } } if( endj != NULL) *endj = maxj; return max; } /* Function: init_start_end_linear_GenomeWise9(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * */ void init_start_end_linear_GenomeWise9(GenomeWise9 * mat) { register int i; register int j; for(j=0;j<12;j++) { for(i=(-0);ievi->len;i++) { GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR5_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR5_INTRON,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,START_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,START_CODON,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_0) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_0,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_1) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_1,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,CDS_INTRON_2) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,CDS_INTRON_2,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,STOP_CODON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,STOP_CODON,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3,0) = (-1); GenomeWise9_DC_SHADOW_MATRIX(mat,i,j,UTR3_INTRON) = NEGI; GenomeWise9_DC_SHADOW_MATRIX_SP(mat,i,j,UTR3_INTRON,0) = (-1); } } for(j=(-10);jgen->seq->len;j++) { GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,PREGENE_INTERGENIC) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,PREGENE_INTERGENIC,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,POSTGENE_INTERGENIC) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,POSTGENE_INTERGENIC,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,INTERGENIC) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,INTERGENIC,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,SPECIAL_UTR5) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,SPECIAL_UTR5,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,SPECIAL_UTR3) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,SPECIAL_UTR3,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,SPECIAL_CDS) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,SPECIAL_CDS,0) = (-1); GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,START) = 0; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,START,0) = j; GenomeWise9_DC_SHADOW_SPECIAL(mat,0,j,END) = NEGI; GenomeWise9_DC_SHADOW_SPECIAL_SP(mat,0,j,END,0) = (-1); } return; } /* Function: convert_PackAln_to_AlnBlock_GenomeWise9(pal) * * Descrip: Converts a path alignment to a label alignment * The label alignment is probably much more useful than the path * * * Arg: pal [UNKN ] Undocumented argument [PackAln *] * * Return [UNKN ] Undocumented return value [AlnBlock *] * */ AlnBlock * convert_PackAln_to_AlnBlock_GenomeWise9(PackAln * pal) { AlnConvertSet * acs; AlnBlock * alb; acs = AlnConvertSet_GenomeWise9(); alb = AlnBlock_from_PackAln(acs,pal); free_AlnConvertSet(acs); return alb; } static char * query_label[] = { "UTR5","START_CODON","CDS","CDS_INTRON","STOP_CODON","UTR3","INTERGENIC","SPECIAL","END" }; /* Function: AlnConvertSet_GenomeWise9(void) * * Descrip: No Description * * * Return [UNKN ] Undocumented return value [AlnConvertSet *] * */ static char * target_label[] = { "UTR5","UTR5_INTRON","CODON","3SS_PHASE_0","3SS_PHASE_1","3SS_PHASE_2","SEQUENCE_DELETION","CDS_INTRON","5SS_PHASE_0","5SS_PHASE_1","5SS_PHASE_2","STOP_CODON","UTR3","UTR3_INTRON","RANDOM_DNA","END" }; AlnConvertSet * AlnConvertSet_GenomeWise9(void) { AlnConvertUnit * acu; AlnConvertSet * out; out = AlnConvertSet_alloc_std(); acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5; acu->state2 = UTR5; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5_INTRON; acu->state2 = UTR5; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SPECIAL_UTR5 + 10; acu->is_from_special = TRUE; acu->state2 = UTR5; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 10; acu->is_from_special = TRUE; acu->state2 = UTR5; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTERGENIC + 10; acu->is_from_special = TRUE; acu->state2 = UTR5; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = PREGENE_INTERGENIC + 10; acu->is_from_special = TRUE; acu->state2 = UTR5; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5_INTRON; acu->state2 = UTR5_INTRON; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[1]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5; acu->state2 = UTR5_INTRON; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[1]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5_INTRON; acu->state2 = START_CODON; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5; acu->state2 = START_CODON; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_0; acu->state2 = CDS; acu->offi = 0; acu->offj = 6; acu->label1 = query_label[2]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_1; acu->state2 = CDS; acu->offi = 0; acu->offj = 5; acu->label1 = query_label[2]; acu->label2 = target_label[4]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_2; acu->state2 = CDS; acu->offi = 0; acu->offj = 4; acu->label1 = query_label[2]; acu->label2 = target_label[5]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS; acu->offi = 0; acu->offj = 2; acu->label1 = query_label[2]; acu->label2 = target_label[6]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS; acu->offi = 0; acu->offj = 4; acu->label1 = query_label[2]; acu->label2 = target_label[6]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5; acu->state2 = CDS; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START_CODON; acu->state2 = CDS; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SPECIAL_CDS + 10; acu->is_from_special = TRUE; acu->state2 = CDS; acu->offi = (-1); acu->offj = 3; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTERGENIC + 10; acu->is_from_special = TRUE; acu->state2 = CDS; acu->offi = (-1); acu->offj = 3; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_0; acu->state2 = CDS_INTRON_0; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[7]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS_INTRON_0; acu->offi = 0; acu->offj = 8; acu->label1 = query_label[3]; acu->label2 = target_label[8]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_1; acu->state2 = CDS_INTRON_1; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[7]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS_INTRON_1; acu->offi = 0; acu->offj = 9; acu->label1 = query_label[3]; acu->label2 = target_label[9]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS_INTRON_2; acu->state2 = CDS_INTRON_2; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[7]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = CDS_INTRON_2; acu->offi = 0; acu->offj = 10; acu->label1 = query_label[3]; acu->label2 = target_label[10]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = STOP_CODON; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[4]; acu->label2 = target_label[11]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3; acu->state2 = UTR3; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = UTR3; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = STOP_CODON; acu->state2 = UTR3; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3_INTRON; acu->state2 = UTR3; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTERGENIC + 10; acu->is_from_special = TRUE; acu->state2 = UTR3; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3_INTRON; acu->state2 = UTR3_INTRON; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[13]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3; acu->state2 = UTR3_INTRON; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[13]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SPECIAL_UTR3 + 10; acu->is_from_special = TRUE; acu->state2 = UTR3_INTRON; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[13]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 10; acu->state2 = PREGENE_INTERGENIC + 10; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[6]; acu->label2 = target_label[14]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3; acu->state2 = POSTGENE_INTERGENIC + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[6]; acu->label2 = target_label[14]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTERGENIC + 10; acu->state2 = INTERGENIC + 10; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[6]; acu->label2 = target_label[14]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = INTERGENIC + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[6]; acu->label2 = target_label[14]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3; acu->state2 = INTERGENIC + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[6]; acu->label2 = target_label[14]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR5; acu->state2 = SPECIAL_UTR5 + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[7]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = UTR3; acu->state2 = SPECIAL_UTR3 + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[7]; acu->label2 = target_label[12]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = CDS; acu->state2 = SPECIAL_CDS + 10; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[7]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SPECIAL_CDS + 10; acu->state2 = SPECIAL_CDS + 10; acu->offi = (-1); acu->offj = 3; acu->label1 = query_label[7]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTERGENIC + 10; acu->state2 = END + 10; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[8]; acu->label2 = target_label[15]; add_collapse_label_AlnConvertSet(out,"UTR5","UTR5"); add_collapse_label_AlnConvertSet(out,"UTR3","UTR3"); add_collapse_label_AlnConvertSet(out,"UTR5","UTR5_INTRON"); add_collapse_label_AlnConvertSet(out,"UTR3","UTR3_INTRON"); add_collapse_label_AlnConvertSet(out,"INTERGENIC","RANDOM_DNA"); add_collapse_label_AlnConvertSet(out,"CDS_INTRON","CDS_INTRON"); return out; } /* Function: PackAln_read_Expl_GenomeWise9(mat) * * Descrip: Reads off PackAln from explicit matrix structure * * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_read_Expl_GenomeWise9(GenomeWise9 * mat) { register PackAln * out; int i; int j; int state; int cellscore = (-1); boolean isspecial; PackAlnUnit * pau = NULL; PackAlnUnit * prev = NULL; if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) { warn("In GenomeWise9_basic_read You have asked for an alignment from a non-explicit matrix: c'est impossible [current type is %d - %s]", mat->basematrix->type,basematrix_type_to_string(mat->basematrix->type)); return NULL; } out = PackAln_alloc_std(); if( out == NULL ) return NULL; out->score = find_end_GenomeWise9(mat,&i,&j,&state,&isspecial); /* Add final end transition (at the moment we have not got the score! */ if( (pau= PackAlnUnit_alloc()) == NULL || add_PackAln(out,pau) == FALSE ) { warn("Failed the first PackAlnUnit alloc, %d length of Alignment in GenomeWise9_basic_read, returning a mess.(Sorry!)",out->len); return out; } /* Put in positions for end trans. Remember that coordinates in C style */ pau->i = i; pau->j = j; if( isspecial != TRUE) pau->state = state; else pau->state = state + 10; prev=pau; while( state != START || isspecial != TRUE) { /*while state != START*/ if( isspecial == TRUE ) max_calc_special_GenomeWise9(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); else max_calc_GenomeWise9(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if(i == GenomeWise9_READ_OFF_ERROR || j == GenomeWise9_READ_OFF_ERROR || state == GenomeWise9_READ_OFF_ERROR ) { warn("Problem - hit bad read off system, exiting now"); break; } if( (pau= PackAlnUnit_alloc()) == NULL || add_PackAln(out,pau) == FALSE ) { warn("Failed a PackAlnUnit alloc, %d length of Alignment in GenomeWise9_basic_read, returning partial alignment",out->len); break; } /* Put in positions for block. Remember that coordinates in C style */ pau->i = i; pau->j = j; if( isspecial != TRUE) pau->state = state; else pau->state = state + 10; prev->score = cellscore; prev = pau; } /* end of while state != START */ invert_PackAln(out); return out; } /* Function: find_end_GenomeWise9(mat,ri,rj,state,isspecial) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: ri [UNKN ] Undocumented argument [int *] * Arg: rj [UNKN ] Undocumented argument [int *] * Arg: state [UNKN ] Undocumented argument [int *] * Arg: isspecial [UNKN ] Undocumented argument [boolean *] * * Return [UNKN ] Undocumented return value [int] * */ int find_end_GenomeWise9(GenomeWise9 * mat,int * ri,int * rj,int * state,boolean * isspecial) { register int j; register int max; register int maxj; max = GenomeWise9_EXPL_SPECIAL(mat,0,mat->gen->seq->len-1,END); maxj = mat->gen->seq->len-1; for(j= mat->gen->seq->len-2 ;j >= 0 ;j--) { if( GenomeWise9_EXPL_SPECIAL(mat,0,j,END) > max ) { max = GenomeWise9_EXPL_SPECIAL(mat,0,j,END); maxj = j; } } if( ri != NULL) *ri = 0; if( rj != NULL) *rj = maxj; if( state != NULL) *state = END; if( isspecial != NULL) *isspecial = TRUE; return max; } /* Function: GenomeWise9_debug_show_matrix(mat,starti,stopi,startj,stopj,ofp) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: starti [UNKN ] Undocumented argument [int] * Arg: stopi [UNKN ] Undocumented argument [int] * Arg: startj [UNKN ] Undocumented argument [int] * Arg: stopj [UNKN ] Undocumented argument [int] * Arg: ofp [UNKN ] Undocumented argument [FILE *] * */ void GenomeWise9_debug_show_matrix(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,FILE * ofp) { register int i; register int j; for(i=starti;ievi->len;i++) { for(j=startj;jgen->seq->len;j++) { fprintf(ofp,"Cell [%d - %d]\n",i,j); fprintf(ofp,"State UTR5 %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5)); fprintf(ofp,"State UTR5_INTRON %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5_INTRON)); fprintf(ofp,"State START_CODON %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,START_CODON)); fprintf(ofp,"State CDS %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,CDS)); fprintf(ofp,"State CDS_INTRON_0 %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_0)); fprintf(ofp,"State CDS_INTRON_1 %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_1)); fprintf(ofp,"State CDS_INTRON_2 %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_2)); fprintf(ofp,"State STOP_CODON %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,STOP_CODON)); fprintf(ofp,"State UTR3 %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3)); fprintf(ofp,"State UTR3_INTRON %d\n",GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3_INTRON)); fprintf(ofp,"\n\n"); } } } /* Function: max_calc_GenomeWise9(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: i [UNKN ] Undocumented argument [int] * Arg: j [UNKN ] Undocumented argument [int] * Arg: state [UNKN ] Undocumented argument [int] * Arg: isspecial [UNKN ] Undocumented argument [boolean] * Arg: reti [UNKN ] Undocumented argument [int *] * Arg: retj [UNKN ] Undocumented argument [int *] * Arg: retstate [UNKN ] Undocumented argument [int *] * Arg: retspecial [UNKN ] Undocumented argument [boolean *] * Arg: cellscore [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [int] * */ int max_calc_GenomeWise9(GenomeWise9 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { register int temp; register int cscore; *reti = (*retj) = (*retstate) = GenomeWise9_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->evi->len || j > mat->gen->seq->len) { warn("In GenomeWise9 matrix special read off - out of bounds on matrix [i,j is %d,%d state %d in standard matrix]",i,j,state); return -1; } /* Then you have to select the correct switch statement to figure out the readoff */ /* Somewhat odd - reverse the order of calculation and return as soon as it is correct */ cscore = GenomeWise9_EXPL_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case UTR5 : temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,PREGENE_INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = PREGENE_INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,PREGENE_INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,PREGENE_INTERGENIC); } temp = cscore - ((GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,INTERGENIC); } temp = cscore - (GNE_UTR5_START(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,START); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,START); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,SPECIAL_UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = SPECIAL_UTR5; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,SPECIAL_UTR5); } temp = cscore - (GNE_UTR_3SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5_INTRON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5_INTRON); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR5_INTRON : temp = cscore - (GNE_UTR_5SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5); } temp = cscore - (GNE_UTR_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5_INTRON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR5_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case START_CODON : temp = cscore - (GNE_START_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5); } temp = cscore - (GNE_START_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5_INTRON) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5_INTRON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS : temp = cscore - ((GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 3,INTERGENIC) ) { *reti = i - 0; *retj = j - 3; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-3,INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,INTERGENIC); } temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 3,SPECIAL_CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = SPECIAL_CDS; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-3,SPECIAL_CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,SPECIAL_CDS); } temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,START_CODON) ) { *reti = i - 0; *retj = j - 3; *retstate = START_CODON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,START_CODON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,START_CODON); } temp = cscore - ((GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5) ) { *reti = i - 0; *retj = j - 3; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,UTR5); } temp = cscore - (GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 4,CDS) ) { *reti = i - 0; *retj = j - 4; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-4,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 4,CDS); } temp = cscore - (GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 2,CDS) ) { *reti = i - 0; *retj = j - 2; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-2,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 2,CDS); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 4,CDS_INTRON_2) ) { *reti = i - 0; *retj = j - 4; *retstate = CDS_INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-4,CDS_INTRON_2); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 4,CDS_INTRON_2); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 5,CDS_INTRON_1) ) { *reti = i - 0; *retj = j - 5; *retstate = CDS_INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-5,CDS_INTRON_1); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 5,CDS_INTRON_1); } temp = cscore - (GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 6,CDS_INTRON_0) ) { *reti = i - 0; *retj = j - 6; *retstate = CDS_INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-6,CDS_INTRON_0); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 6,CDS_INTRON_0); } temp = cscore - (GNE_CDS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,CDS); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_0 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 8,CDS) ) { *reti = i - 0; *retj = j - 8; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-8,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 8,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_0) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_0); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_0); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_1 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 9,CDS) ) { *reti = i - 0; *retj = j - 9; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-9,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 9,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_1) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_1); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_1); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case CDS_INTRON_2 : temp = cscore - (GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 10,CDS) ) { *reti = i - 0; *retj = j - 10; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-10,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 10,CDS); } temp = cscore - (GNE_CDS_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS_INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_2); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS_INTRON_2); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case STOP_CODON : temp = cscore - (GNE_STOP_CODON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,CDS); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3 : /* Has restricted position */ if( (j-1) == 0 ) { temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,INTERGENIC); } } temp = cscore - (GNE_UTR_3SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3_INTRON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3_INTRON); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,STOP_CODON) ) { *reti = i - 0; *retj = j - 1; *retstate = STOP_CODON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,STOP_CODON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,STOP_CODON); } temp = cscore - ((GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS) ) { *reti = i - 0; *retj = j - 1; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,CDS); } temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); case UTR3_INTRON : temp = cscore - (GNE_UTR(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,SPECIAL_UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = SPECIAL_UTR3; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,SPECIAL_UTR3); } temp = cscore - (GNE_UTR_5SS(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3); } temp = cscore - (GNE_UTR_INTRON(mat->evi,i,mat->gen,j)) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3_INTRON) ) { *reti = i - 0; *retj = j - 1; *retstate = UTR3_INTRON; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3_INTRON); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,UTR3_INTRON); } warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: max_calc_special_GenomeWise9(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GenomeWise9 *] * Arg: i [UNKN ] Undocumented argument [int] * Arg: j [UNKN ] Undocumented argument [int] * Arg: state [UNKN ] Undocumented argument [int] * Arg: isspecial [UNKN ] Undocumented argument [boolean] * Arg: reti [UNKN ] Undocumented argument [int *] * Arg: retj [UNKN ] Undocumented argument [int *] * Arg: retstate [UNKN ] Undocumented argument [int *] * Arg: retspecial [UNKN ] Undocumented argument [boolean *] * Arg: cellscore [UNKN ] Undocumented argument [int *] * * Return [UNKN ] Undocumented return value [int] * */ int max_calc_special_GenomeWise9(GenomeWise9 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { register int temp; register int cscore; *reti = (*retj) = (*retstate) = GenomeWise9_READ_OFF_ERROR; if( j < 0 || j > mat->gen->seq->len) { warn("In GenomeWise9 matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = GenomeWise9_EXPL_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case PREGENE_INTERGENIC : /* source START is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,START); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,START) ; } case POSTGENE_INTERGENIC : /* source UTR3 is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ) { *reti = i - 0; *retj = j - 0; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ; } } /* end of for i >= 0 */ case INTERGENIC : /* source UTR3 is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ) { *reti = i - 0; *retj = j - 0; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ; } } /* end of for i >= 0 */ /* source CDS is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,CDS) ) { *reti = i - 0; *retj = j - 0; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,CDS) ; } } /* end of for i >= 0 */ /* source INTERGENIC is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } case SPECIAL_UTR5 : /* source UTR5 is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->switchcost) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR5) ) { *reti = i - 0; *retj = j - 0; *retstate = UTR5; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,UTR5); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR5) ; } } /* end of for i >= 0 */ case SPECIAL_UTR3 : /* source UTR3 is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->switchcost) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ) { *reti = i - 0; *retj = j - 0; *retstate = UTR3; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,UTR3); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,UTR3) ; } } /* end of for i >= 0 */ case SPECIAL_CDS : /* source SPECIAL_CDS is a special */ temp = cscore - (mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 3,SPECIAL_CDS) ) { *reti = i - 0; *retj = j - 3; *retstate = SPECIAL_CDS; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-3,SPECIAL_CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 3,SPECIAL_CDS) ; } /* source CDS is from main matrix */ for(i= mat->evi->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - ((mat->switchcost+mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)])) - (0); if( temp == GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,CDS) ) { *reti = i - 0; *retj = j - 0; *retstate = CDS; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_MATRIX(mat,i-0,j-0,CDS); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 0,CDS) ; } } /* end of for i >= 0 */ case START : case END : /* source INTERGENIC is a special */ temp = cscore - (0) - (0); if( temp == GenomeWise9_EXPL_SPECIAL(mat,i - 0,j - 1,INTERGENIC) ) { *reti = i - 0; *retj = j - 1; *retstate = INTERGENIC; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC); } return GenomeWise9_EXPL_MATRIX(mat,i - 0,j - 1,INTERGENIC) ; } default: warn("Major problem (!) - in GenomeWise9 read off, position %d,%d state %d no source found dropped into default on source switch!",i,j,state); return (-1); } /* end of switch on special states */ } /* Function: calculate_GenomeWise9(mat) * * Descrip: This function calculates the GenomeWise9 matrix when in explicit mode * To allocate the matrix use /allocate_Expl_GenomeWise9 * * * Arg: mat [UNKN ] GenomeWise9 which contains explicit basematrix memory [GenomeWise9 *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean calculate_GenomeWise9(GenomeWise9 * mat) { int i; int j; int leni; int lenj; int tot; int num; if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT ) { warn("in calculate_GenomeWise9, passed a non Explicit matrix type, cannot calculate!"); return FALSE; } leni = mat->leni; lenj = mat->lenj; tot = leni * lenj; num = 0; start_reporting("GenomeWise9 Matrix calculation: "); for(j=0;jevi,i,mat->gen,j); /* From state UTR5_INTRON to state UTR5 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_UTR5 to state UTR5 */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR5) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state START to state UTR5 */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,START) + GNE_UTR5_START(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state INTERGENIC to state UTR5 */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC) + (GNE_UTR(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)); if( temp > score ) { score = temp; } /* From state PREGENE_INTERGENIC to state UTR5 */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,PREGENE_INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5 */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5) = score; /* state UTR5 is a source for special SPECIAL_UTR5 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR5) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR5) = temp; } /* Finished calculating state UTR5 */ /* For state UTR5_INTRON */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR5 to state UTR5_INTRON */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR5) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR5_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,UTR5_INTRON) = score; /* Finished calculating state UTR5_INTRON */ /* For state START_CODON */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5_INTRON) + GNE_START_CODON(mat->evi,i,mat->gen,j); /* From state UTR5 to state START_CODON */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5) + GNE_START_CODON(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for START_CODON */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,START_CODON) = score; /* Finished calculating state START_CODON */ /* For state CDS */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,CDS) + GNE_CDS(mat->evi,i,mat->gen,j); /* From state CDS_INTRON_0 to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-6,CDS_INTRON_0) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-3),0); if( temp > score ) { score = temp; } /* From state CDS_INTRON_1 to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-5,CDS_INTRON_1) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-2),1); if( temp > score ) { score = temp; } /* From state CDS_INTRON_2 to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-4,CDS_INTRON_2) + GNE_CDS_3SS(mat->evi,i,mat->gen,(j-1),2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-2,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,2); if( temp > score ) { score = temp; } /* From state CDS to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-4,CDS) + GNE_CDS_FRAMESHIFT(mat->evi,i,mat->gen,j,4); if( temp > score ) { score = temp; } /* From state UTR5 to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,UTR5) + (GNE_CDS(mat->evi,i,mat->gen,j)+mat->non_start_codon); if( temp > score ) { score = temp; } /* From state START_CODON to state CDS */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,START_CODON) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_CDS to state CDS */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-3,SPECIAL_CDS) + GNE_CDS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state INTERGENIC to state CDS */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-3,INTERGENIC) + (GNE_CDS(mat->evi,i,mat->gen,j)+GNE_UTR5_START(mat->evi,i,mat->gen,j)); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,CDS) = score; /* state CDS is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,INTERGENIC) = temp; } /* state CDS is a source for special SPECIAL_CDS */ temp = score + ((mat->switchcost+mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)])) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_CDS) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_CDS) = temp; } /* Finished calculating state CDS */ /* For state CDS_INTRON_0 */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_0) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_0 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-8,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),0); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_0 */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_0) = score; /* Finished calculating state CDS_INTRON_0 */ /* For state CDS_INTRON_1 */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_1) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_1 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-9,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),1); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_1 */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_1) = score; /* Finished calculating state CDS_INTRON_1 */ /* For state CDS_INTRON_2 */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS_INTRON_2) + GNE_CDS_INTRON(mat->evi,i,mat->gen,j); /* From state CDS to state CDS_INTRON_2 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-10,CDS) + GNE_CDS_5SS(mat->evi,i,mat->gen,(j-7),2); if( temp > score ) { score = temp; } /* Ok - finished max calculation for CDS_INTRON_2 */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,CDS_INTRON_2) = score; /* Finished calculating state CDS_INTRON_2 */ /* For state STOP_CODON */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-3,CDS) + GNE_STOP_CODON(mat->evi,i,mat->gen,j); /* Ok - finished max calculation for STOP_CODON */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,STOP_CODON) = score; /* Finished calculating state STOP_CODON */ /* For state UTR3 */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); /* From state CDS to state UTR3 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,CDS) + (GNE_UTR(mat->evi,i,mat->gen,j)+mat->non_stop_codon); if( temp > score ) { score = temp; } /* From state STOP_CODON to state UTR3 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,STOP_CODON) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state UTR3_INTRON to state UTR3 */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_3SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Has restricted position */ if( (j-1) == 0 ) { /* From state INTERGENIC to state UTR3 */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,INTERGENIC) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } } /* Ok - finished max calculation for UTR3 */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3) = score; /* state UTR3 is a source for special POSTGENE_INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,POSTGENE_INTERGENIC) = temp; } /* state UTR3 is a source for special INTERGENIC */ temp = score + ((mat->newgenecost+GNE_UTR3_END(mat->evi,i,mat->gen,j))) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,INTERGENIC) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,INTERGENIC) = temp; } /* state UTR3 is a source for special SPECIAL_UTR3 */ temp = score + (mat->switchcost) + (0) ; if( temp > GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR3) ) { GenomeWise9_EXPL_SPECIAL(mat,i,j,SPECIAL_UTR3) = temp; } /* Finished calculating state UTR3 */ /* For state UTR3_INTRON */ /* setting first movement to score */ score = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3_INTRON) + GNE_UTR_INTRON(mat->evi,i,mat->gen,j); /* From state UTR3 to state UTR3_INTRON */ temp = GenomeWise9_EXPL_MATRIX(mat,i-0,j-1,UTR3) + GNE_UTR_5SS(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* From state SPECIAL_UTR3 to state UTR3_INTRON */ temp = GenomeWise9_EXPL_SPECIAL(mat,i-0,j-1,SPECIAL_UTR3) + GNE_UTR(mat->evi,i,mat->gen,j); if( temp > score ) { score = temp; } /* Ok - finished max calculation for UTR3_INTRON */ /* Add any movement independant score and put away */ GenomeWise9_EXPL_MATRIX(mat,i,j,UTR3_INTRON) = score; /* Finished calculating state UTR3_INTRON */ } /* Special state PREGENE_INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_EXPL_SPECIAL(mat,0,j,PREGENE_INTERGENIC); /* Source START is a special source for PREGENE_INTERGENIC */ temp = GenomeWise9_EXPL_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) score = temp; /* Put back score... (now updated!) */ GenomeWise9_EXPL_SPECIAL(mat,0,j,PREGENE_INTERGENIC) = score; /* Finished updating state PREGENE_INTERGENIC */ /* Special state POSTGENE_INTERGENIC has no special to special movements */ /* Special state INTERGENIC has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_EXPL_SPECIAL(mat,0,j,INTERGENIC); /* Source INTERGENIC is a special source for INTERGENIC */ temp = GenomeWise9_EXPL_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) score = temp; /* Source CDS for state INTERGENIC is not special... already calculated */ /* Source UTR3 for state INTERGENIC is not special... already calculated */ /* Put back score... (now updated!) */ GenomeWise9_EXPL_SPECIAL(mat,0,j,INTERGENIC) = score; /* Finished updating state INTERGENIC */ /* Special state SPECIAL_UTR5 has no special to special movements */ /* Special state SPECIAL_UTR3 has no special to special movements */ /* Special state SPECIAL_CDS has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_EXPL_SPECIAL(mat,0,j,SPECIAL_CDS); /* Source CDS for state SPECIAL_CDS is not special... already calculated */ /* Source SPECIAL_CDS is a special source for SPECIAL_CDS */ temp = GenomeWise9_EXPL_SPECIAL(mat,0,j - 3,SPECIAL_CDS) + (mat->rndcodon->codon[CSEQ_GENOMIC_CODON(mat->gen,j)]) + (0); if( temp > score ) score = temp; /* Put back score... (now updated!) */ GenomeWise9_EXPL_SPECIAL(mat,0,j,SPECIAL_CDS) = score; /* Finished updating state SPECIAL_CDS */ /* Special state START has no special to special movements */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = GenomeWise9_EXPL_SPECIAL(mat,0,j,END); /* Source INTERGENIC is a special source for END */ /* Has restricted position */ if( j == mat->lenj-1 ) { temp = GenomeWise9_EXPL_SPECIAL(mat,0,j - 1,INTERGENIC) + (0) + (0); if( temp > score ) score = temp; } /* Put back score... (now updated!) */ GenomeWise9_EXPL_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ } stop_reporting(); return TRUE; } /* Function: GenomeWise9_alloc(void) * * Descrip: Allocates structure: assigns defaults if given * * * * Return [UNKN ] Undocumented return value [GenomeWise9 *] * */ GenomeWise9 * GenomeWise9_alloc(void) { GenomeWise9 * out; /* out is exported at end of function */ /* call ckalloc and see if NULL */ if((out=(GenomeWise9 *) ckalloc (sizeof(GenomeWise9))) == NULL) { warn("GenomeWise9_alloc failed "); return NULL; /* calling function should respond! */ } out->dynamite_hard_link = 1; out->basematrix = NULL; out->leni = 0; out->lenj = 0; return out; } /* Function: free_GenomeWise9(obj) * * Descrip: Free Function: removes the memory held by obj * Will chain up to owned members and clear all lists * * * Arg: obj [UNKN ] Object that is free'd [GenomeWise9 *] * * Return [UNKN ] Undocumented return value [GenomeWise9 *] * */ GenomeWise9 * free_GenomeWise9(GenomeWise9 * obj) { if( obj == NULL) { warn("Attempting to free a NULL pointer to a GenomeWise9 obj. Should be trappable"); return NULL; } if( obj->dynamite_hard_link > 1) { obj->dynamite_hard_link--; return NULL; } if( obj->basematrix != NULL) free_BaseMatrix(obj->basematrix); /* obj->evi is linked in */ /* obj->gen is linked in */ /* obj->switchcost is linked in */ /* obj->newgenecost is linked in */ /* obj->non_start_codon is linked in */ /* obj->non_stop_codon is linked in */ /* obj->rndcodon is linked in */ ckfree(obj); return NULL; } #ifdef _cplusplus } #endif