#ifdef _cplusplus extern "C" { #endif #include "gwlite.h" # line 5 "gwlite.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 MATCH 0 #define INSERT 1 #define DELETE 2 #define INTRON_0 3 #define INTRON_1 4 #define INTRON_2 5 #define START 0 #define END 1 #define GeneLiteModel_EXPL_MATRIX(this_matrix,i,j,STATE) this_matrix->basematrix->matrix[((j+3)*6)+STATE][i+1] #define GeneLiteModel_EXPL_SPECIAL(matrix,i,j,STATE) matrix->basematrix->specmatrix[STATE][j+3] #define GeneLiteModel_READ_OFF_ERROR -5 #define GeneLiteModel_VSMALL_MATRIX(mat,i,j,STATE) mat->basematrix->matrix[(j+4)%4][((i+1)*6)+STATE] #define GeneLiteModel_VSMALL_SPECIAL(mat,i,j,STATE) mat->basematrix->specmatrix[(j+4)%4][STATE] /* Function: search_GeneLiteModel(dbsi,out,querydb,targetdb,gp) * * Descrip: This function makes a database search of GeneLiteModel * 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: querydb [UNKN ] Undocumented argument [GeneWiseDB*] * Arg: targetdb [UNKN ] Undocumented argument [GenomicDB*] * Arg: gp [UNKN ] Undocumented argument [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ Search_Return_Type search_GeneLiteModel(DBSearchImpl * dbsi,Hscore * out,GeneWiseDB* querydb,GenomicDB* targetdb ,GeneParser4Score * gp) { #ifdef PTHREAD int i; int thr_no; pthread_attr_t pat; struct thread_pool_holder_GeneLiteModel * holder; #endif if( out == NULL ) { warn("Passed in a null Hscore object into search_GeneLiteModel. Can't process results!"); return SEARCH_ERROR; } if( dbsi == NULL ) { warn("Passed in a null DBSearchImpl object into search_GeneLiteModel. Can't process results!"); return SEARCH_ERROR; } if( dbsi->trace_level > 5 ) warn("Asking for trace level of %d in database search for GeneLiteModel, 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_GeneLiteModel(out,querydb, targetdb ,gp); case DBSearchImpl_Pthreads : #ifdef PTHREAD holder = (struct thread_pool_holder_GeneLiteModel *) ckalloc(sizeof(struct thread_pool_holder_GeneLiteModel)); if( holder == NULL ) { warn("Unable to allocated thread pool datastructure..."); return SEARCH_ERROR; } holder->out = out; holder->dbsi = dbsi; holder->querydb = querydb; holder->targetdb = targetdb; holder->gp = gp; 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_GeneLiteModel,(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 GeneLiteModel"); #endif /* finished threads */ default : warn("database search implementation %s was not provided in the compiled dynamite file from GeneLiteModel",impl_string_DBSearchImpl(dbsi)); return SEARCH_ERROR; } /* end of switch on implementation */ } /* Function: thread_loop_GeneLiteModel(ptr) * * Descrip: Infinite loop code foreach thread for GeneLiteModel * * * Arg: ptr [UNKN ] Undocumented argument [void *] * * Return [UNKN ] Undocumented return value [void *] * */ #ifdef PTHREAD void * thread_loop_GeneLiteModel(void * ptr) { struct thread_pool_holder_GeneLiteModel * holder; int db_status; int score; DataScore * ds; GwLiteScore* query; ComplexSequence* target; holder = (struct thread_pool_holder_GeneLiteModel *) ptr; if ( holder->dbsi->trace_level >= 1 ) fprintf(holder->dbsi->trace_file,"Entering infinite loop for thread...\n"); while(1) { /*Infinite loop over all models*/ /* Get input lock */ if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"About to get input lock for main reload\n"); if( pthread_mutex_lock(&(holder->input_lock))!= 0 ) fatal("Error on getting input lock for GeneLiteModel"); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Got input lock for main reload\n"); if( holder->search_has_ended == TRUE ) { if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Database search finished for me!...\n"); if( pthread_mutex_unlock(&(holder->input_lock))!= 0 ) fatal("Error in releasing input lock for GeneLiteModel"); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Released lock and broken out of loop\n"); break; } /* Get storage space now, as we have to read in the info for the db now */ if ( holder->dbsi->trace_level >= 3 ) fprintf(holder->dbsi->trace_file,"Getting new DataScore from storage...\n"); ds = new_DataScore(); /* We need to get our query object */ if ( holder->dbsi->trace_level >= 3 ) fprintf(holder->dbsi->trace_file,"Starting query database...\n"); if( holder->query_init == FALSE) { holder->query = init_GwLite_GeneWiseDB(holder->querydb,&db_status); holder->query_init = TRUE; if( db_status == DB_RETURN_ERROR ) fatal("Unable to initalise query database in GeneLiteModel search"); } query = hard_link_GwLiteScore(holder->query); /* get query information into datascore */ dataentry_add_GwLite_GeneWiseDB(ds->query,query,holder->querydb); if( holder->target_init == FALSE ) { /*if the db has not been init'd*/ if ( holder->dbsi->trace_level >= 3 ) fprintf(holder->dbsi->trace_file,"Starting target database...\n"); target = init_GenomicDB(holder->targetdb,&db_status); holder->target_init = TRUE; } /* end of if the db has not been init'd */ else { /*Normal reload*/ target = reload_GenomicDB(NULL,holder->targetdb,&db_status); } /* end of Normal reload */ /* Check to see what the reload is like */ if( db_status == DB_RETURN_ERROR ) { fatal("In searching GeneLiteModel, Reload error on database target, in threads"); } if( db_status == DB_RETURN_END) { /*End of target database*/ /* close target database and schedule it for initalisation by next thread */ close_GenomicDB(NULL,holder->targetdb); holder->target_init = FALSE; if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Target Database to be reloaded...\n"); /* free'ing the query object */ free_GwLiteScore(holder->query); /* get the next query object for the next thread */ holder->query = reload_GwLite_GeneWiseDB(NULL,holder->querydb,&db_status); if( db_status == DB_RETURN_ERROR ) fatal("In searching GeneLiteModel, reload error on database query, in threads"); if( db_status == DB_RETURN_END ) { /*last load!*/ /* End of target and query database - finished search! */ close_GwLite_GeneWiseDB(NULL,holder->querydb); holder->search_has_ended = TRUE; } /* end of last load! */ /* release input mutex */ if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Releasing input lock after end of target\n"); if( pthread_mutex_unlock(&(holder->input_lock))!= 0 ) fatal("Error in releasing input lock for GeneLiteModel"); continue; } /* end of End of target database */ else { /*Normal reload*/ if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Releasing input lock for normal reload\n"); if( pthread_mutex_unlock(&(holder->input_lock))!= 0 ) fatal("Error in releasing input lock for GeneLiteModel"); } /* end of Normal reload */ /* get target information into datascore */ dataentry_add_GenomicDB(ds->target,target,holder->targetdb); /* Now there is a new query/target pair ready for comparison */ if ( holder->dbsi->trace_level >= 1 ) fprintf(holder->dbsi->trace_file,"A new pair to be compared...\n"); score = score_only_GeneLiteModel(query, target ,holder->gp); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Getting output lock\n"); /* Getting lock on output */ if( pthread_mutex_lock(&(holder->output_lock))!= 0 ) fatal("Error on getting output lock for GeneLiteModel"); /* If the score is less than cutoff, schedule the datascore for reuse */ if( should_store_Hscore(holder->out,score) != TRUE) { free_DataScore(ds); } else { /*storing score*/ ds->score = score; add_Hscore(holder->out,ds); } /* end of storing score */ if( pthread_mutex_unlock(&(holder->output_lock))!= 0 ) fatal("Error on releasing output lock for GeneLiteModel"); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Released output lock\n"); /* Now free database objects */ if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"About to get input lock for free func\n"); if( pthread_mutex_lock(&(holder->input_lock))!= 0 ) fatal("Error on getting input lock for GeneLiteModel"); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Got input lock for free func\n"); free_GwLiteScore(query); free_ComplexSequence(target); if ( holder->dbsi->trace_level >= 2 ) fprintf(holder->dbsi->trace_file,"Releasing input lock after free'ing\n"); if( pthread_mutex_unlock(&(holder->input_lock))!= 0 ) fatal("Error in releasing input lock for GeneLiteModel"); } /* end of Infinite loop over all models */ if ( holder->dbsi->trace_level >= 1 ) fprintf(holder->dbsi->trace_file,"Exiting forever loop\n"); return NULL; } /* Function: serial_search_GeneLiteModel(out,querydb,targetdb,gp) * * Descrip: This function makes a database search of GeneLiteModel * It is a single processor implementation * * * Arg: out [UNKN ] Undocumented argument [Hscore *] * Arg: querydb [UNKN ] Undocumented argument [GeneWiseDB*] * Arg: targetdb [UNKN ] Undocumented argument [GenomicDB*] * Arg: gp [UNKN ] Undocumented argument [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ #endif /* PTHREAD */ Search_Return_Type serial_search_GeneLiteModel(Hscore * out,GeneWiseDB* querydb,GenomicDB* targetdb ,GeneParser4Score * gp) { GwLiteScore* query; ComplexSequence* target; 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"); query = init_GwLite_GeneWiseDB(querydb,&db_status); if( db_status == DB_RETURN_ERROR ) { warn("In searching GeneLiteModel, got a database reload error on the query [query] database"); return SEARCH_ERROR; } for(;;) { /*For all query entries*/ target_pos = 0; target = init_GenomicDB(targetdb,&db_status); if( db_status == DB_RETURN_ERROR ) { warn("In searching GeneLiteModel, got a database init error on the target [target] database"); return SEARCH_ERROR; } for(;;) { /*For all target entries*/ /* No maximum length - allocated on-the-fly */ score = score_only_GeneLiteModel(query, target , gp); if( should_store_Hscore(out,score) == TRUE ) { /*if storing datascore*/ ds = new_DataScore_from_storage(out); if( ds == NULL ) { warn("GeneLiteModel 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_GwLite_GeneWiseDB(ds->query,query,querydb); dataentry_add_GenomicDB(ds->target,target,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); target = reload_GenomicDB(target,targetdb,&db_status); if( db_status == DB_RETURN_ERROR ) { warn("In searching GeneLiteModel, Reload error on database target, 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(target,targetdb); query = reload_GwLite_GeneWiseDB(query,querydb,&db_status); if( db_status == DB_RETURN_ERROR) { warn("In searching GeneLiteModel, Reload error on database query, position %d,%d",query_pos,target_pos); return SEARCH_ERROR; } if( db_status == DB_RETURN_END) break; /* Out of query loop */ query_pos++; } /* end of For all query entries */ close_GwLite_GeneWiseDB(query,querydb); pop_errormsg_stack(); return SEARCH_OK; } /* Function: score_only_GeneLiteModel(query,target,gp) * * 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_GeneLiteModel_only * * * Arg: query [UNKN ] query data structure [GwLiteScore*] * Arg: target [UNKN ] target data structure [ComplexSequence*] * Arg: gp [UNKN ] Resource [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [int] * */ int score_only_GeneLiteModel(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp) { int bestscore = NEGI; int i; int j; int k; GeneLiteModel * mat; mat = allocate_GeneLiteModel_only(query, target , gp); 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(4,(mat->leni + 1) * 6,4,2)) == NULL) { warn("Score only matrix for GeneLiteModel cannot be allocated, (asking for 3 by %d cells)",mat->leni*6); mat = free_GeneLiteModel(mat); return 0; } mat->basematrix->type = BASEMATRIX_TYPE_VERYSMALL; /* Now, initiate matrix */ for(j=0;j<5;j++) { for(i=(-1);ileni;i++) { for(k=0;k<6;k++) GeneLiteModel_VSMALL_MATRIX(mat,i,j,k) = NEGI; } GeneLiteModel_VSMALL_SPECIAL(mat,i,j,START) = 0; GeneLiteModel_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 MATCH */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state DELETE to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state START to state MATCH */ temp = GeneLiteModel_VSMALL_SPECIAL(mat,i-1,j-3,START) + (mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,MATCH) = score; /* state MATCH is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_MATCH2END]) + (0) ; if( temp > GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state START to state INSERT */ temp = GeneLiteModel_VSMALL_SPECIAL(mat,i-0,j-3,START) + (mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,INSERT) = score; /* state INSERT is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_INSERT2END]) + (0) ; if( temp > GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; /* From state DELETE to state DELETE */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score ) { score = temp; } /* From state START to state DELETE */ temp = GeneLiteModel_VSMALL_SPECIAL(mat,i-1,j-0,START) + mat->query->seg[i]->transition[GW_START2DELETE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,DELETE) = score; /* state DELETE is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_DELETE2END]) + (0) ; if( temp > GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_VSMALL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,INTRON_0) = score; /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,INTRON_1) = score; /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_VSMALL_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ GeneLiteModel_VSMALL_MATRIX(mat,i,j,INTRON_2) = score; /* Finished calculating state INTRON_2 */ } /* end of for all query positions */ /* Special state START has no special to special movements */ /* Special state END has no special to special movements */ if( bestscore < GeneLiteModel_VSMALL_SPECIAL(mat,0,j,END) ) bestscore = GeneLiteModel_VSMALL_SPECIAL(mat,0,j,END); } /* end of for all target positions */ mat = free_GeneLiteModel(mat); return bestscore; } /* Function: PackAln_bestmemory_GeneLiteModel(query,target,gp,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_GeneLiteModel * * * Arg: query [UNKN ] query data structure [GwLiteScore*] * Arg: target [UNKN ] target data structure [ComplexSequence*] * Arg: gp [UNKN ] Resource [GeneParser4Score *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_bestmemory_GeneLiteModel(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp,DPEnvelope * dpenv,DPRunImpl * dpri) { int total; GeneLiteModel * mat; PackAln * out; DebugMatrix * de; DPRunImplMemory strategy; assert(dpri); total = query->len * target->seq->len; if( dpri->memory == DPIM_Default ) { if( (total * 6 * 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_GeneLiteModel(query, target , gp)) == NULL ) { warn("Unable to allocate small GeneLiteModel version"); return NULL; } out = PackAln_calculate_Small_GeneLiteModel(mat,dpenv); } else { /* use Large implementation */ if( (mat=allocate_Expl_GeneLiteModel(query, target , gp)) == NULL ) { warn("Unable to allocate large GeneLiteModel 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_GeneLiteModel(mat); out = PackAln_read_Expl_GeneLiteModel(mat); } mat = free_GeneLiteModel(mat); return out; } /* Function: allocate_GeneLiteModel_only(query,target,gp) * * Descrip: This function only allocates the GeneLiteModel structure * checks types where possible and determines leni and lenj * The basematrix area is delt with elsewhere * * * Arg: query [UNKN ] query data structure [GwLiteScore*] * Arg: target [UNKN ] target data structure [ComplexSequence*] * Arg: gp [UNKN ] Resource [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [GeneLiteModel *] * */ GeneLiteModel * allocate_GeneLiteModel_only(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp) { GeneLiteModel * out; if((out= GeneLiteModel_alloc()) == NULL) { warn("Allocation of basic GeneLiteModel structure failed..."); return NULL; } out->query = query; out->target = target; out->gp = gp; out->leni = query->len; out->lenj = target->seq->len; return out; } /* Function: allocate_Expl_GeneLiteModel(query,target,gp) * * Descrip: This function allocates the GeneLiteModel structure * and the basematrix area for explicit memory implementations * It calls /allocate_GeneLiteModel_only * * * Arg: query [UNKN ] query data structure [GwLiteScore*] * Arg: target [UNKN ] target data structure [ComplexSequence*] * Arg: gp [UNKN ] Resource [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [GeneLiteModel *] * */ GeneLiteModel * allocate_Expl_GeneLiteModel(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp) { GeneLiteModel * out; out = allocate_GeneLiteModel_only(query, target , gp); if( out == NULL ) return NULL; if( (out->basematrix = BaseMatrix_alloc_matrix_and_specials((out->lenj+3)*6,(out->leni+1),2,out->lenj+3)) == NULL) { warn("Explicit matrix GeneLiteModel cannot be allocated, (asking for %d by %d main cells)",out->leni,out->lenj); free_GeneLiteModel(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_EXPLICIT; init_GeneLiteModel(out); return out; } /* Function: init_GeneLiteModel(mat) * * Descrip: This function initates GeneLiteModel matrix when in explicit mode * Called in /allocate_Expl_GeneLiteModel * * * Arg: mat [UNKN ] GeneLiteModel which contains explicit basematrix memory [GeneLiteModel *] * */ void init_GeneLiteModel(GeneLiteModel * 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= (-1);iquery->len;i++) { for(j= (-3);j<4;j++) { GeneLiteModel_EXPL_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_2) = NEGI; } } for(j= (-3);jtarget->seq->len;j++) { for(i= (-1);i<2;i++) { GeneLiteModel_EXPL_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_2) = NEGI; } GeneLiteModel_EXPL_SPECIAL(mat,i,j,START) = 0; GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) = NEGI; } return; } /* Function: recalculate_PackAln_GeneLiteModel(pal,mat) * * Descrip: This function recalculates the PackAln structure produced by GeneLiteModel * For example, in linear space methods this is used to score them * * * Arg: pal [UNKN ] Undocumented argument [PackAln *] * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * */ void recalculate_PackAln_GeneLiteModel(PackAln * pal,GeneLiteModel * 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 MATCH : if( offi == 1 && offj == 3 && prev->state == MATCH ) { pau->score = (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offi == 1 && offj == 3 && prev->state == INSERT ) { pau->score = (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offi == 1 && offj == 3 && prev->state == DELETE ) { pau->score = (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offj == 3 && prev->state == (START+6) ) { pau->score = (mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offi == 1 && offj == 3 && prev->state == INTRON_0 ) { pau->score = ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))) + (0); continue; } if( offi == 1 && offj == 2 && prev->state == INTRON_1 ) { pau->score = ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))) + (0); continue; } if( offi == 1 && offj == 1 && prev->state == INTRON_2 ) { pau->score = ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))) + (0); continue; } if( offi == 1 && offj == 2 && prev->state == MATCH ) { pau->score = mat->gp->transition[GP4_DELETE_1_BASE] + (0); continue; } if( offi == 1 && offj == 1 && prev->state == MATCH ) { pau->score = mat->gp->transition[GP4_DELETE_1_BASE] + (0); continue; } warn("In recaluclating PackAln with state MATCH, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case INSERT : if( offi == 0 && offj == 3 && prev->state == MATCH ) { pau->score = (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == INSERT ) { pau->score = (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offj == 3 && prev->state == (START+6) ) { pau->score = (mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == INTRON_0 ) { pau->score = (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))) + (0); continue; } if( offi == 0 && offj == 2 && prev->state == INTRON_1 ) { pau->score = ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INTRON_2 ) { pau->score = ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))) + (0); continue; } if( offi == 0 && offj == 2 && prev->state == INSERT ) { pau->score = mat->gp->transition[GP4_DELETE_1_BASE] + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INSERT ) { pau->score = mat->gp->transition[GP4_DELETE_1_BASE] + (0); continue; } warn("In recaluclating PackAln with state INSERT, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case DELETE : if( offi == 1 && offj == 0 && prev->state == MATCH ) { pau->score = mat->query->seg[i]->transition[GW_MATCH2DELETE] + (0); continue; } if( offi == 1 && offj == 0 && prev->state == DELETE ) { pau->score = mat->query->seg[i]->transition[GW_DELETE2DELETE] + (0); continue; } if( offj == 0 && prev->state == (START+6) ) { pau->score = mat->query->seg[i]->transition[GW_START2DELETE] + (0); continue; } warn("In recaluclating PackAln with state DELETE, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case INTRON_0 : if( offi == 0 && offj == 1 && prev->state == MATCH ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INSERT ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INTRON_0 ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) + (0); continue; } warn("In recaluclating PackAln with state INTRON_0, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case INTRON_1 : if( offi == 0 && offj == 2 && prev->state == MATCH ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 2 && prev->state == INSERT ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INTRON_1 ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) + (0); continue; } warn("In recaluclating PackAln with state INTRON_1, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case INTRON_2 : if( offi == 0 && offj == 3 && prev->state == MATCH ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 3 && prev->state == INSERT ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); continue; } if( offi == 0 && offj == 1 && prev->state == INTRON_2 ) { pau->score = (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) + (0); continue; } warn("In recaluclating PackAln with state INTRON_2, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case (START+6) : warn("In recaluclating PackAln with state START, got a bad source state. Error!"); break; case (END+6) : if( offj == 0 && prev->state == MATCH ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->query->seg[i]->transition[GW_MATCH2END] + (0); continue; } if( offj == 0 && prev->state == INSERT ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->query->seg[i]->transition[GW_INSERT2END] + (0); continue; } if( offj == 0 && prev->state == DELETE ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->query->seg[i]->transition[GW_DELETE2END] + (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 GeneLiteModel_HIDDEN_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[(j-hiddenj+3)][(i+1)*6+state]) #define GeneLiteModel_DC_SHADOW_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[((j+4)*8) % 32][(i+1)*6+state]) #define GeneLiteModel_HIDDEN_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state][(j+3)]) #define GeneLiteModel_DC_SHADOW_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state*8][(j+3)]) #define GeneLiteModel_DC_SHADOW_MATRIX_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->matrix[((((j+4)*8)+(shadow+1)) % 32)][(i+1)*6 + state]) /* Function: allocate_Small_GeneLiteModel(query,target,gp) * * Descrip: This function allocates the GeneLiteModel structure * and the basematrix area for a small memory implementations * It calls /allocate_GeneLiteModel_only * * * Arg: query [UNKN ] query data structure [GwLiteScore*] * Arg: target [UNKN ] target data structure [ComplexSequence*] * Arg: gp [UNKN ] Resource [GeneParser4Score *] * * Return [UNKN ] Undocumented return value [GeneLiteModel *] * */ #define GeneLiteModel_DC_SHADOW_SPECIAL_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->specmatrix[state*8 +shadow+1][(j+3)]) GeneLiteModel * allocate_Small_GeneLiteModel(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp) { GeneLiteModel * out; out = allocate_GeneLiteModel_only(query, target , gp); if( out == NULL ) return NULL; out->basematrix = BaseMatrix_alloc_matrix_and_specials(32,(out->leni + 1) * 6,16,out->lenj+3); if(out == NULL) { warn("Small shadow matrix GeneLiteModel cannot be allocated, (asking for 4 by %d main cells)",out->leni+2); free_GeneLiteModel(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_SHADOW; return out; } /* Function: PackAln_calculate_Small_GeneLiteModel(mat,dpenv) * * Descrip: This function calculates an alignment for GeneLiteModel structure in linear space * If you want only the start/end points * use /AlnRangeSet_calculate_Small_GeneLiteModel * * The function basically * finds start/end points * foreach start/end point * calls /full_dc_GeneLiteModel * * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_calculate_Small_GeneLiteModel(GeneLiteModel * 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 GeneLiteModel due to wrong type of matrix"); return NULL; } out = PackAln_alloc_std(); start_reporting("Find start end points: "); dc_start_end_calculate_GeneLiteModel(mat,dpenv); score = start_end_find_end_GeneLiteModel(mat,&endj); out->score = score; stopstate = END; /* No special to specials: one matrix alignment: simply remove and get */ starti = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,0); startj = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,1); startstate = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,2); stopi = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,3); stopj = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,4); stopstate = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,5); temp = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,endj,END,6); log_full_error(REPORT,0,"[%d,%d][%d,%d] Score %d",starti,startj,stopi,stopj,score); stop_reporting(); start_reporting("Recovering alignment: "); /* Figuring how much j we have to align for reporting purposes */ donej = 0; totalj = stopj - startj; full_dc_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,out,&donej,totalj,dpenv); /* Although we have no specials, need to get start. Better to check than assume */ max_matrix_to_special_GeneLiteModel(mat,starti,startj,startstate,temp,&stopi,&stopj,&stopstate,&temp,NULL); if( stopi == GeneLiteModel_READ_OFF_ERROR || stopstate != START ) { warn("Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode"); invert_PackAln(out); recalculate_PackAln_GeneLiteModel(out,mat); return out; } /* Ok. Put away start start... */ pau = PackAlnUnit_alloc(); pau->i = stopi; pau->j = stopj; pau->state = stopstate + 6; add_PackAln(out,pau); log_full_error(REPORT,0,"Alignment recovered"); stop_reporting(); invert_PackAln(out); recalculate_PackAln_GeneLiteModel(out,mat); return out; } /* Function: AlnRangeSet_calculate_Small_GeneLiteModel(mat) * * Descrip: This function calculates an alignment for GeneLiteModel structure in linear space * If you want the full alignment, use /PackAln_calculate_Small_GeneLiteModel * If you have already got the full alignment, but want the range set, use /AlnRangeSet_from_PackAln_GeneLiteModel * If you have got the small matrix but not the alignment, use /AlnRangeSet_from_GeneLiteModel * * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_calculate_Small_GeneLiteModel(GeneLiteModel * mat) { AlnRangeSet * out; start_reporting("Find start end points: "); dc_start_end_calculate_GeneLiteModel(mat,NULL); log_full_error(REPORT,0,"Calculated"); out = AlnRangeSet_from_GeneLiteModel(mat); return out; } /* Function: AlnRangeSet_from_GeneLiteModel(mat) * * Descrip: This function reads off a start/end structure * for GeneLiteModel structure in linear space * If you want the full alignment use * /PackAln_calculate_Small_GeneLiteModel * If you have not calculated the matrix use * /AlnRange_calculate_Small_GeneLiteModel * * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_from_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel"); return NULL; } out = AlnRangeSet_alloc_std(); /* Find the end position */ out->score = start_end_find_end_GeneLiteModel(mat,&jpos); state = END; while( (temp = AlnRange_build_GeneLiteModel(mat,jpos,state,&jpos,&state)) != NULL) add_AlnRangeSet(out,temp); return out; } /* Function: AlnRange_build_GeneLiteModel(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_GeneLiteModel * * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel"); return NULL; } /* Assumme that we have specials (we should!). Read back along the specials till we have the finish point */ if( read_special_strip_GeneLiteModel(mat,0,stopj,stopspecstate,&jpos,&state,NULL) == FALSE) { warn("In AlnRanger_build_GeneLiteModel 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 = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,0); out->startj = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,1); out->startstate = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,2); out->stopi = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,3); out->stopj = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,4); out->stopstate = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,5); out->startscore = GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,6); out->stopscore = GeneLiteModel_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_GeneLiteModel(mat,out->starti,out->startj,out->startstate,out->startscore,&jpos,startj,startspecstate,&state,NULL); if( jpos == GeneLiteModel_READ_OFF_ERROR) { warn("In AlnRange_build_GeneLiteModel 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 = GeneLiteModel_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_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel(mat,startj,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == GeneLiteModel_READ_OFF_ERROR) { warn("In GeneLiteModel 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 GeneLiteModel 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 GeneLiteModel 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_GeneLiteModel(mat,hiddenj,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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) = GeneLiteModel_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->query->len || j > mat->target->seq->len) { warn("In GeneLiteModel 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 = GeneLiteModel_HIDDEN_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case MATCH : temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 1,MATCH) ) { *reti = i - 1; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-1,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 1,MATCH); } temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 2,MATCH) ) { *reti = i - 1; *retj = j - 2; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-2,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 2,MATCH); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 1,INTRON_2) ) { *reti = i - 1; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-1,INTRON_2); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 1,INTRON_2); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 2,INTRON_1) ) { *reti = i - 1; *retj = j - 2; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-2,INTRON_1); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 2,INTRON_1); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,INTRON_0) ) { *reti = i - 1; *retj = j - 3; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,INTRON_0); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,INTRON_0); } /* Not allowing special sources.. skipping START */ temp = cscore - ((mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,DELETE) ) { *reti = i - 1; *retj = j - 3; *retstate = DELETE; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,DELETE); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,DELETE); } temp = cscore - ((mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,INSERT) ) { *reti = i - 1; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,INSERT); } temp = cscore - ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,MATCH) ) { *reti = i - 1; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INSERT : temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INSERT) ) { *reti = i - 0; *retj = j - 1; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INSERT); } temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INSERT) ) { *reti = i - 0; *retj = j - 2; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INSERT); } temp = cscore - (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_2); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_2); } temp = cscore - (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INTRON_1) ) { *reti = i - 0; *retj = j - 2; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INTRON_1); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INTRON_1); } temp = cscore - ((((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3)))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INTRON_0) ) { *reti = i - 0; *retj = j - 3; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INTRON_0); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INTRON_0); } /* Not allowing special sources.. skipping START */ temp = cscore - ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INSERT) ) { *reti = i - 0; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INSERT); } temp = cscore - ((mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,MATCH) ) { *reti = i - 0; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case DELETE : /* Not allowing special sources.. skipping START */ temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 0,DELETE) ) { *reti = i - 1; *retj = j - 0; *retstate = DELETE; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-0,DELETE); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 0,DELETE); } temp = cscore - (mat->query->seg[i]->transition[GW_MATCH2DELETE]) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-0,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_0 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_0) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_0); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_0); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INSERT) ) { *reti = i - 0; *retj = j - 1; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_1 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_1) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_1); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_1); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INSERT) ) { *reti = i - 0; *retj = j - 2; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,MATCH) ) { *reti = i - 0; *retj = j - 2; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 2,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_2 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_2); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 1,INTRON_2); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INSERT) ) { *reti = i - 0; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INSERT); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,MATCH) ) { *reti = i - 0; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,MATCH); } return GeneLiteModel_HIDDEN_MATRIX(mat,i - 0,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: read_special_strip_GeneLiteModel(mat,stopi,stopj,stopstate,startj,startstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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 > GeneLiteModel_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 + 6; add_PackAln(out,pau); } max_special_strip_GeneLiteModel(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == GeneLiteModel_READ_OFF_ERROR) { warn("In special strip read GeneLiteModel, 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 < GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,state,4)) { warn("In special strip read GeneLiteModel, 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 + 6; add_PackAln(out,pau); } /* Put away where we are in startj and startstate */ *startj = j; *startstate = state; return TRUE; } /* Function: max_special_strip_GeneLiteModel(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 [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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) = GeneLiteModel_READ_OFF_ERROR; if( isspecial == FALSE ) { warn("In special strip max function for GeneLiteModel, got a non special start point. Problem! (bad!)"); return (-1); } if( j < 0 || j > mat->target->seq->len) { warn("In GeneLiteModel matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case START : case END : /* Source DELETE is not a special */ /* Source INSERT is not a special */ /* Source MATCH is not a special */ default: warn("Major problem (!) - in GeneLiteModel 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_GeneLiteModel(mat,i,j,state,cscore,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * mat,int i,int j,int state,int cscore,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { int temp; *reti = (*retj) = (*retstate) = GeneLiteModel_READ_OFF_ERROR; if( j < 0 || j > mat->lenj) { warn("In GeneLiteModel matrix to special read off - out of bounds on matrix [j is %d in special]",j); return -1; } switch(state) { /*Switch state */ case MATCH : /* Source MATCH is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ /* Source INTRON_2 is not a special, should not get here! */ /* Source INTRON_1 is not a special, should not get here! */ /* Source INTRON_0 is not a special, should not get here! */ temp = cscore - ((mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_DC_SHADOW_SPECIAL(mat,i - 1,j - 3,START) ) { *reti = i - 1; *retj = j - 3; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-1,j-3,START); } return GeneLiteModel_DC_SHADOW_MATRIX(mat,i - 1,j - 3,START) ; } /* Source DELETE is not a special, should not get here! */ /* Source INSERT is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INSERT : /* Source INSERT is not a special, should not get here! */ /* Source INSERT is not a special, should not get here! */ /* Source INTRON_2 is not a special, should not get here! */ /* Source INTRON_1 is not a special, should not get here! */ /* Source INTRON_0 is not a special, should not get here! */ temp = cscore - ((mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_DC_SHADOW_SPECIAL(mat,i - 0,j - 3,START) ) { *reti = i - 0; *retj = j - 3; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-0,j-3,START); } return GeneLiteModel_DC_SHADOW_MATRIX(mat,i - 0,j - 3,START) ; } /* Source INSERT is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case DELETE : temp = cscore - (mat->query->seg[i]->transition[GW_START2DELETE]) - (0); if( temp == GeneLiteModel_DC_SHADOW_SPECIAL(mat,i - 1,j - 0,START) ) { *reti = i - 1; *retj = j - 0; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-1,j-0,START); } return GeneLiteModel_DC_SHADOW_MATRIX(mat,i - 1,j - 0,START) ; } /* Source DELETE is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_0 : /* Source INTRON_0 is not a special, should not get here! */ /* Source INSERT is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_1 : /* Source INTRON_1 is not a special, should not get here! */ /* Source INSERT is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_2 : /* Source INTRON_2 is not a special, should not get here! */ /* Source INSERT is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in GeneLiteModel matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: calculate_hidden_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel(mat,starti,startj,stopi,stopj); GeneLiteModel_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*/ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_2) = NEGI; continue; } /* end of Is not in envelope */ /* For state MATCH */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state DELETE to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,MATCH) = score; /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INSERT) = score; /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; /* From state DELETE to state DELETE */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,DELETE) = score; /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_0) = score; /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_1) = score; /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_HIDDEN_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_2) = score; /* Finished calculating state INTRON_2 */ } } return; } /* Function: init_hidden_GeneLiteModel(mat,starti,startj,stopi,stopj) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int stopi,int stopj) { register int i; register int j; register int hiddenj; hiddenj = startj; for(j=(startj-3);j<=stopj;j++) { for(i=(starti-1);i<=stopi;i++) { GeneLiteModel_HIDDEN_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_HIDDEN_MATRIX(mat,i,j,INTRON_2) = NEGI; } } return; } /* Function: full_dc_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,out,donej,totalj,dpenv) * * Descrip: The main divide-and-conquor routine. Basically, call /PackAln_calculate_small_GeneLiteModel * 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_GeneLiteModel 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 [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel"); 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 < 15) { log_full_error(REPORT,0,"[%d,%d][%d,%d] Explicit read off",starti,startj,stopi,stopj);/* Build hidden explicit matrix */ calculate_hidden_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv); *donej += (stopj - startj); /* Now read it off into out */ if( read_hidden_GeneLiteModel(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_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,(int)(*donej*100)/totalj) == FALSE) { warn("In divide and conquor for GeneLiteModel, 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= GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,0); lstartj= GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,1); lstate = GeneLiteModel_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_GeneLiteModel(mat,GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,3),GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,4),GeneLiteModel_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_GeneLiteModel(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_GeneLiteModel(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel(mat); GeneLiteModel_DC_SHADOW_MATRIX(mat,starti,startj,startstate) = 0; run_up_dc_GeneLiteModel(mat,starti,stopi,startj,halfj-1,dpenv,perc_done); push_dc_at_merge_GeneLiteModel(mat,starti,stopi,halfj,&halfj,dpenv); follow_on_dc_GeneLiteModel(mat,starti,stopi,halfj,stopj,dpenv,perc_done); return TRUE; } /* Function: push_dc_at_merge_GeneLiteModel(mat,starti,stopi,startj,stopj,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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<3;count++,j++) { for(i=starti;i<=stopi;i++) { if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = (-100); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = (-100); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,1) = (-100); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,1) = (-100); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,1) = (-100); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,0) = (-100); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,1) = (-100); continue; } /* end of Is not in envelope */ /* For state MATCH, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = DELETE; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,DELETE,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = INTRON_0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INTRON_0,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score) { score = temp; if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = INTRON_1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,INTRON_1,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = INTRON_2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,INTRON_2,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score) { score = temp; if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,MATCH,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; /* Finished with state MATCH */ /* For state INSERT, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INTRON_0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INTRON_0,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score) { score = temp; if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INTRON_1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INTRON_1,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INTRON_2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score) { score = temp; if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,5) = INSERT; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = score; /* Finished with state INSERT */ /* For state DELETE, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; if( j - 0 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,1) = j-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,5) = DELETE; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score) { score = temp; if( j - 0 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,0) = i-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,1) = j-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,2) = DELETE; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,5) = DELETE; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,DELETE,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = score; /* Finished with state DELETE */ /* For state INTRON_0, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,5) = INTRON_0; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,5) = INTRON_0; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,2) = INTRON_0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,5) = INTRON_0; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_0,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = score; /* Finished with state INTRON_0 */ /* For state INTRON_1, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,5) = INTRON_1; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score) { score = temp; if( j - 2 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,1) = j-2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,5) = INTRON_1; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,2) = INTRON_1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,5) = INTRON_1; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_1,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = score; /* Finished with state INTRON_1 */ /* For state INTRON_2, pushing when j - offj <= mergej */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,2) = MATCH; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,5) = INTRON_2; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score) { score = temp; if( j - 3 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,1) = j-3; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,2) = INSERT; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,5) = INTRON_2; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } } temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score) { score = temp; if( j - 1 <= mergej) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,0) = i-0; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,1) = j-1; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,2) = INTRON_2; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,3) = i; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,4) = j; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,5) = INTRON_2; } else { for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } } /* Add any movement independant score */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = score; /* Finished with state INTRON_2 */ } } /* 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_GeneLiteModel(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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*/ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = 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 MATCH */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,MATCH,k); /* From state INSERT to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INSERT,k); } /* From state DELETE to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,DELETE,k); } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INTRON_0,k); } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,INTRON_1,k); } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,INTRON_2,k); } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,MATCH,k); } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INTRON_0,k); } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INTRON_1,k); } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); /* From state DELETE to state DELETE */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,DELETE,k); } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_0,k); } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,MATCH,k); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_1,k); } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_2 */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: run_up_dc_GeneLiteModel(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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*/ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = 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 MATCH */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state DELETE to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = score; /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; /* From state DELETE to state DELETE */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = score; /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = score; /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = score; /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = score; /* Finished calculating state INTRON_2 */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: init_dc_GeneLiteModel(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * */ } void init_dc_GeneLiteModel(GeneLiteModel * mat) { register int i; register int j; register int k; for(j=0;j<5;j++) { for(i=(-1);iquery->len;i++) { GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = NEGI; for(k=0;k<7;k++) { GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = (-1); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = (-1); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k) = (-1); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = (-1); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = (-1); GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = (-1); } } } return; } /* Function: dc_start_end_calculate_GeneLiteModel(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 [GeneLiteModel *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean dc_start_end_calculate_GeneLiteModel(GeneLiteModel * 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_GeneLiteModel(mat); leni = mat->query->len; lenj = mat->target->seq->len; total = leni * lenj; for(j=0;jquery->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,MATCH,k); /* From state INSERT to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INSERT,k); } /* From state DELETE to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,DELETE,k); } /* From state START to state MATCH */ temp = GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-1,j-3,START) + (mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); if( temp > score ) { score = temp; /* This state [START] is a special for MATCH... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= MATCH; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 3,INTRON_0,k); } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,INTRON_1,k); } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,INTRON_2,k); } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE] +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 2,MATCH,k); } /* From state MATCH to state MATCH */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE] +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state MATCH is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_MATCH2END]) + (0) ; if( temp > GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) ) { GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,6) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,6); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,3) = i; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,4) = j; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,5) = MATCH; } /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } /* From state START to state INSERT */ temp = GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-0,j-3,START) + (mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]) + (0); if( temp > score ) { score = temp; /* This state [START] is a special for INSERT... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= INSERT; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INTRON_0,k); } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INTRON_1,k); } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE] +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } /* From state INSERT to state INSERT */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE] +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state INSERT is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_INSERT2END]) + (0) ; if( temp > GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) ) { GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,k); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,6) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,6); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,3) = i; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,4) = j; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,5) = INSERT; } /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE] + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); /* From state DELETE to state DELETE */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE] +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,DELETE,k); } /* From state START to state DELETE */ temp = GeneLiteModel_DC_SHADOW_SPECIAL(mat,i-1,j-0,START) + mat->query->seg[i]->transition[GW_START2DELETE] + (0); if( temp > score ) { score = temp; /* This state [START] is a special for DELETE... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= DELETE; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state DELETE is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_DELETE2END]) + (0) ; if( temp > GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) ) { GeneLiteModel_DC_SHADOW_SPECIAL(mat,i,j,END) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,k) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,k); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,6) = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,6); GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,3) = i; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,4) = j; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,i,j,END,5) = DELETE; } /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INSERT,k); } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_0,k); } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,MATCH,k); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 2,INSERT,k); } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_1,k); } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) + (0); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,MATCH,k); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 3,INSERT,k); } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_DC_SHADOW_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]) +(0); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,INTRON_2,k); } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = score; for(k=0;k<7;k++) GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state INTRON_2 */ } /* end of for each i position in strip */ } /* end of for each j strip */ return TRUE; } /* Function: start_end_find_end_GeneLiteModel(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 [GeneLiteModel *] * Arg: endj [WRITE] position of end in j (meaningless in i) [int *] * * Return [UNKN ] Undocumented return value [int] * */ int start_end_find_end_GeneLiteModel(GeneLiteModel * mat,int * endj) { register int j; register int max; register int maxj; max = GeneLiteModel_DC_SHADOW_SPECIAL(mat,0,mat->target->seq->len-1,END); maxj = mat->target->seq->len-1; for(j= mat->target->seq->len-2 ;j >= 0 ;j--) { if( GeneLiteModel_DC_SHADOW_SPECIAL(mat,0,j,END) > max ) { max = GeneLiteModel_DC_SHADOW_SPECIAL(mat,0,j,END); maxj = j; } } if( endj != NULL) *endj = maxj; return max; } /* Function: init_start_end_linear_GeneLiteModel(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * */ void init_start_end_linear_GeneLiteModel(GeneLiteModel * mat) { register int i; register int j; for(j=0;j<5;j++) { for(i=(-1);iquery->len;i++) { GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = (-1); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INSERT) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INSERT,0) = (-1); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,DELETE) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,DELETE,0) = (-1); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_0) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_0,0) = (-1); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_1) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_1,0) = (-1); GeneLiteModel_DC_SHADOW_MATRIX(mat,i,j,INTRON_2) = NEGI; GeneLiteModel_DC_SHADOW_MATRIX_SP(mat,i,j,INTRON_2,0) = (-1); } } for(j=(-3);jtarget->seq->len;j++) { GeneLiteModel_DC_SHADOW_SPECIAL(mat,0,j,START) = 0; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,j,START,0) = j; GeneLiteModel_DC_SHADOW_SPECIAL(mat,0,j,END) = NEGI; GeneLiteModel_DC_SHADOW_SPECIAL_SP(mat,0,j,END,0) = (-1); } return; } /* Function: convert_PackAln_to_AlnBlock_GeneLiteModel(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_GeneLiteModel(PackAln * pal) { AlnConvertSet * acs; AlnBlock * alb; acs = AlnConvertSet_GeneLiteModel(); alb = AlnBlock_from_PackAln(acs,pal); free_AlnConvertSet(acs); return alb; } static char * query_label[] = { "MATCH_STATE","INSERT_STATE","DELETE_STATE","INTRON_STATE","END" }; /* Function: AlnConvertSet_GeneLiteModel(void) * * Descrip: No Description * * * Return [UNKN ] Undocumented return value [AlnConvertSet *] * */ static char * target_label[] = { "CODON","3SS_PHASE_0","3SS_PHASE_1","3SS_PHASE_2","SEQUENCE_DELETION","INSERT","5SS_PHASE_0","CENTRAL_INTRON","5SS_PHASE_1","5SS_PHASE_2","END" }; AlnConvertSet * AlnConvertSet_GeneLiteModel(void) { AlnConvertUnit * acu; AlnConvertSet * out; out = AlnConvertSet_alloc_std(); acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = MATCH; acu->offi = 1; acu->offj = 3; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = MATCH; acu->offi = 1; acu->offj = 3; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = DELETE; acu->state2 = MATCH; acu->offi = 1; acu->offj = 3; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 6; acu->is_from_special = TRUE; acu->state2 = MATCH; acu->offi = (-1); acu->offj = 3; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_0; acu->state2 = MATCH; acu->offi = 1; acu->offj = 3; acu->label1 = query_label[0]; acu->label2 = target_label[1]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_1; acu->state2 = MATCH; acu->offi = 1; acu->offj = 2; acu->label1 = query_label[0]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_2; acu->state2 = MATCH; acu->offi = 1; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = MATCH; acu->offi = 1; acu->offj = 2; acu->label1 = query_label[0]; acu->label2 = target_label[4]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = MATCH; acu->offi = 1; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[4]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = INSERT; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INSERT; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 6; acu->is_from_special = TRUE; acu->state2 = INSERT; acu->offi = (-1); acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_0; acu->state2 = INSERT; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[1]; acu->label2 = target_label[1]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_1; acu->state2 = INSERT; acu->offi = 0; acu->offj = 2; acu->label1 = query_label[1]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_2; acu->state2 = INSERT; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[1]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INSERT; acu->offi = 0; acu->offj = 2; acu->label1 = query_label[1]; acu->label2 = target_label[4]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INSERT; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[1]; acu->label2 = target_label[4]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = DELETE; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[5]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = DELETE; acu->state2 = DELETE; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[5]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 6; acu->is_from_special = TRUE; acu->state2 = DELETE; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[5]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = INTRON_0; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[6]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INTRON_0; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[6]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_0; acu->state2 = 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 = MATCH; acu->state2 = INTRON_1; acu->offi = 0; acu->offj = 2; acu->label1 = query_label[3]; acu->label2 = target_label[8]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INTRON_1; acu->offi = 0; acu->offj = 2; acu->label1 = query_label[3]; acu->label2 = target_label[8]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_1; acu->state2 = 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 = MATCH; acu->state2 = INTRON_2; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[3]; acu->label2 = target_label[9]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = INTRON_2; acu->offi = 0; acu->offj = 3; acu->label1 = query_label[3]; acu->label2 = target_label[9]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INTRON_2; acu->state2 = 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 = MATCH; acu->state2 = END + 6; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[10]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = INSERT; acu->state2 = END + 6; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[10]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = DELETE; acu->state2 = END + 6; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[10]; add_collapse_label_AlnConvertSet(out,"INTRON_STATE","CENTRAL_INTRON"); return out; } /* Function: PackAln_read_Expl_GeneLiteModel(mat) * * Descrip: Reads off PackAln from explicit matrix structure * * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_read_Expl_GeneLiteModel(GeneLiteModel * 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 GeneLiteModel_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_GeneLiteModel(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 GeneLiteModel_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 + 6; prev=pau; while( state != START || isspecial != TRUE) { /*while state != START*/ if( isspecial == TRUE ) max_calc_special_GeneLiteModel(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); else max_calc_GeneLiteModel(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if(i == GeneLiteModel_READ_OFF_ERROR || j == GeneLiteModel_READ_OFF_ERROR || state == GeneLiteModel_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 GeneLiteModel_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 + 6; prev->score = cellscore; prev = pau; } /* end of while state != START */ invert_PackAln(out); return out; } /* Function: find_end_GeneLiteModel(mat,ri,rj,state,isspecial) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * mat,int * ri,int * rj,int * state,boolean * isspecial) { register int j; register int max; register int maxj; max = GeneLiteModel_EXPL_SPECIAL(mat,0,mat->target->seq->len-1,END); maxj = mat->target->seq->len-1; for(j= mat->target->seq->len-2 ;j >= 0 ;j--) { if( GeneLiteModel_EXPL_SPECIAL(mat,0,j,END) > max ) { max = GeneLiteModel_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: GeneLiteModel_debug_show_matrix(mat,starti,stopi,startj,stopj,ofp) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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 GeneLiteModel_debug_show_matrix(GeneLiteModel * mat,int starti,int stopi,int startj,int stopj,FILE * ofp) { register int i; register int j; for(i=starti;iquery->len;i++) { for(j=startj;jtarget->seq->len;j++) { fprintf(ofp,"Cell [%d - %d]\n",i,j); fprintf(ofp,"State MATCH %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,MATCH)); fprintf(ofp,"State INSERT %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,INSERT)); fprintf(ofp,"State DELETE %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,DELETE)); fprintf(ofp,"State INTRON_0 %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_0)); fprintf(ofp,"State INTRON_1 %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_1)); fprintf(ofp,"State INTRON_2 %d\n",GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_2)); fprintf(ofp,"\n\n"); } } } /* Function: max_calc_GeneLiteModel(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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) = GeneLiteModel_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->query->len || j > mat->target->seq->len) { warn("In GeneLiteModel 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 = GeneLiteModel_EXPL_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case MATCH : temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 1,MATCH) ) { *reti = i - 1; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-1,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 1,MATCH); } temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 2,MATCH) ) { *reti = i - 1; *retj = j - 2; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-2,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 2,MATCH); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 1,INTRON_2) ) { *reti = i - 1; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-1,INTRON_2); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 1,INTRON_2); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 2,INTRON_1) ) { *reti = i - 1; *retj = j - 2; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-2,INTRON_1); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 2,INTRON_1); } temp = cscore - (((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,INTRON_0) ) { *reti = i - 1; *retj = j - 3; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,INTRON_0); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,INTRON_0); } temp = cscore - ((mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_SPECIAL(mat,i - 1,j - 3,START) ) { *reti = i - 1; *retj = j - 3; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_SPECIAL(mat,i-1,j-3,START); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,START); } temp = cscore - ((mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,DELETE) ) { *reti = i - 1; *retj = j - 3; *retstate = DELETE; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,DELETE); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,DELETE); } temp = cscore - ((mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,INSERT) ) { *reti = i - 1; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,INSERT); } temp = cscore - ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,MATCH) ) { *reti = i - 1; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INSERT : temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INSERT) ) { *reti = i - 0; *retj = j - 1; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INSERT); } temp = cscore - (mat->gp->transition[GP4_DELETE_1_BASE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INSERT) ) { *reti = i - 0; *retj = j - 2; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INSERT); } temp = cscore - (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_2); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_2); } temp = cscore - (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INTRON_1) ) { *reti = i - 0; *retj = j - 2; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INTRON_1); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INTRON_1); } temp = cscore - ((((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3)))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INTRON_0) ) { *reti = i - 0; *retj = j - 3; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INTRON_0); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INTRON_0); } temp = cscore - ((mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_SPECIAL(mat,i - 0,j - 3,START) ) { *reti = i - 0; *retj = j - 3; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_SPECIAL(mat,i-0,j-3,START); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,START); } temp = cscore - ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INSERT) ) { *reti = i - 0; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INSERT); } temp = cscore - ((mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,MATCH) ) { *reti = i - 0; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case DELETE : temp = cscore - (mat->query->seg[i]->transition[GW_START2DELETE]) - (0); if( temp == GeneLiteModel_EXPL_SPECIAL(mat,i - 1,j - 0,START) ) { *reti = i - 1; *retj = j - 0; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_SPECIAL(mat,i-1,j-0,START); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 0,START); } temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 0,DELETE) ) { *reti = i - 1; *retj = j - 0; *retstate = DELETE; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-0,DELETE); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 0,DELETE); } temp = cscore - (mat->query->seg[i]->transition[GW_MATCH2DELETE]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-1,j-0,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 1,j - 0,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_0 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_0) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_0; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_0); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_0); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INSERT) ) { *reti = i - 0; *retj = j - 1; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_1 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_1) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_1; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_1); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_1); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INSERT) ) { *reti = i - 0; *retj = j - 2; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,MATCH) ) { *reti = i - 0; *retj = j - 2; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 2,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); case INTRON_2 : temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON])) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_2) ) { *reti = i - 0; *retj = j - 1; *retstate = INTRON_2; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_2); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 1,INTRON_2); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INSERT) ) { *reti = i - 0; *retj = j - 3; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,INSERT); } temp = cscore - ((mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j))) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,MATCH) ) { *reti = i - 0; *retj = j - 3; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 3,MATCH); } warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in GeneLiteModel read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: max_calc_special_GeneLiteModel(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [GeneLiteModel *] * 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_GeneLiteModel(GeneLiteModel * 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) = GeneLiteModel_READ_OFF_ERROR; if( j < 0 || j > mat->target->seq->len) { warn("In GeneLiteModel matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = GeneLiteModel_EXPL_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case START : case END : /* source DELETE is from main matrix */ for(i= mat->query->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2END]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,DELETE) ) { *reti = i - 0; *retj = j - 0; *retstate = DELETE; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-0,DELETE); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,DELETE) ; } } /* end of for i >= 0 */ /* source INSERT is from main matrix */ for(i= mat->query->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2END]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,INSERT) ) { *reti = i - 0; *retj = j - 0; *retstate = INSERT; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-0,INSERT); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,INSERT) ; } } /* end of for i >= 0 */ /* source MATCH is from main matrix */ for(i= mat->query->len-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->query->seg[i]->transition[GW_MATCH2END]) - (0); if( temp == GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,MATCH) ) { *reti = i - 0; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - GeneLiteModel_EXPL_MATRIX(mat,i-0,j-0,MATCH); } return GeneLiteModel_EXPL_MATRIX(mat,i - 0,j - 0,MATCH) ; } } /* end of for i >= 0 */ default: warn("Major problem (!) - in GeneLiteModel 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_GeneLiteModel(mat) * * Descrip: This function calculates the GeneLiteModel matrix when in explicit mode * To allocate the matrix use /allocate_Expl_GeneLiteModel * * * Arg: mat [UNKN ] GeneLiteModel which contains explicit basematrix memory [GeneLiteModel *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean calculate_GeneLiteModel(GeneLiteModel * mat) { int i; int j; int leni; int lenj; int tot; int num; if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT ) { warn("in calculate_GeneLiteModel, passed a non Explicit matrix type, cannot calculate!"); return FALSE; } leni = mat->leni; lenj = mat->lenj; tot = leni * lenj; num = 0; start_reporting("GeneLiteModel Matrix calculation: "); for(j=0;jquery->seg[i]->transition[GW_MATCH2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state DELETE to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,DELETE) + (mat->query->seg[i]->transition[GW_DELETE2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state START to state MATCH */ temp = GeneLiteModel_EXPL_SPECIAL(mat,i-1,j-3,START) + (mat->query->seg[i]->transition[GW_START2MATCH]+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-3,INTRON_0) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_MATCH2MATCH]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-2,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-1,MATCH) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,MATCH) = score; /* state MATCH is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_MATCH2END]) + (0) ; if( temp > GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state MATCH */ /* For state INSERT */ /* setting first movement to score */ score = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,MATCH) + (mat->query->seg[i]->transition[GW_MATCH2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); /* From state INSERT to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INSERT) + (mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state START to state INSERT */ temp = GeneLiteModel_EXPL_SPECIAL(mat,i-0,j-3,START) + (mat->query->seg[i]->transition[GW_START2INSERT]+mat->query->seg[i]->insert[CSEQ_GENOMIC_CODON(mat->target,j)]); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INTRON_0) + (((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+mat->query->seg[i]->match[CSEQ_GENOMIC_CODON(mat->target,j)])+CSEQ_GENOMIC_3SS(mat->target,(j-3))); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INTRON_1) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-2))); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_2) + ((mat->query->seg[i]->transition[GW_INSERT2INSERT]+mat->gp->transition[GP4_INTRON2CDS])+CSEQ_GENOMIC_3SS(mat->target,(j-1))); if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* From state INSERT to state INSERT */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INSERT) + mat->gp->transition[GP4_DELETE_1_BASE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for INSERT */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,INSERT) = score; /* state INSERT is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_INSERT2END]) + (0) ; if( temp > GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state INSERT */ /* For state DELETE */ /* setting first movement to score */ score = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-0,MATCH) + mat->query->seg[i]->transition[GW_MATCH2DELETE]; /* From state DELETE to state DELETE */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; if( temp > score ) { score = temp; } /* From state START to state DELETE */ temp = GeneLiteModel_EXPL_SPECIAL(mat,i-1,j-0,START) + mat->query->seg[i]->transition[GW_START2DELETE]; if( temp > score ) { score = temp; } /* Ok - finished max calculation for DELETE */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,DELETE) = score; /* state DELETE is a source for special END */ temp = score + (mat->query->seg[i]->transition[GW_DELETE2END]) + (0) ; if( temp > GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) ) { GeneLiteModel_EXPL_SPECIAL(mat,i,j,END) = temp; } /* Finished calculating state DELETE */ /* For state INTRON_0 */ /* setting first movement to score */ score = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_0 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_0 to state INTRON_0 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_0) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_0 */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_0) = score; /* Finished calculating state INTRON_0 */ /* For state INTRON_1 */ /* setting first movement to score */ score = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_1 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-2,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_1 to state INTRON_1 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_1) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_1 */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_1) = score; /* Finished calculating state INTRON_1 */ /* For state INTRON_2 */ /* setting first movement to score */ score = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,MATCH) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); /* From state INSERT to state INTRON_2 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-3,INSERT) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+CSEQ_GENOMIC_5SS(mat->target,j)); if( temp > score ) { score = temp; } /* From state INTRON_2 to state INTRON_2 */ temp = GeneLiteModel_EXPL_MATRIX(mat,i-0,j-1,INTRON_2) + (mat->gp->intron[CSEQ_GENOMIC_BASE(mat->target,j)]+mat->gp->transition[GP4_INTRON2INTRON]); if( temp > score ) { score = temp; } /* Ok - finished max calculation for INTRON_2 */ /* Add any movement independant score and put away */ GeneLiteModel_EXPL_MATRIX(mat,i,j,INTRON_2) = score; /* Finished calculating state INTRON_2 */ } /* Special state START has no special to special movements */ /* Special state END has no special to special movements */ } stop_reporting(); return TRUE; } /* Function: GeneLiteModel_alloc(void) * * Descrip: Allocates structure: assigns defaults if given * * * * Return [UNKN ] Undocumented return value [GeneLiteModel *] * */ GeneLiteModel * GeneLiteModel_alloc(void) { GeneLiteModel * out;/* out is exported at end of function */ /* call ckalloc and see if NULL */ if((out=(GeneLiteModel *) ckalloc (sizeof(GeneLiteModel))) == NULL) { warn("GeneLiteModel_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_GeneLiteModel(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 [GeneLiteModel *] * * Return [UNKN ] Undocumented return value [GeneLiteModel *] * */ GeneLiteModel * free_GeneLiteModel(GeneLiteModel * obj) { if( obj == NULL) { warn("Attempting to free a NULL pointer to a GeneLiteModel 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->query is linked in */ /* obj->target is linked in */ /* obj->gp is linked in */ ckfree(obj); return NULL; } #ifdef _cplusplus } #endif