#ifdef _cplusplus extern "C" { #endif #include "clonewisedp.h" # line 5 "clonewisedp.c" /***************** C functions ****************/ /* Written using dynamite */ /* Tue Nov 6 09:31:58 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 SKIP_QUERY 1 #define SKIP_TARGET 2 #define START 0 #define TRUSTED_SPECIAL 1 #define END 2 #define CloneWise_EXPL_MATRIX(this_matrix,i,j,STATE) this_matrix->basematrix->matrix[((j+1)*3)+STATE][i+1] #define CloneWise_EXPL_SPECIAL(matrix,i,j,STATE) matrix->basematrix->specmatrix[STATE][j+1] #define CloneWise_READ_OFF_ERROR -3 #define CloneWise_VSMALL_MATRIX(mat,i,j,STATE) mat->basematrix->matrix[(j+2)%2][((i+1)*3)+STATE] #define CloneWise_VSMALL_SPECIAL(mat,i,j,STATE) mat->basematrix->specmatrix[(j+2)%2][STATE] /* Function: search_CloneWise(dbsi,out,q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * Descrip: This function makes a database search of CloneWise * 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: q [UNKN ] Undocumented argument [MappedCloneSet *] * Arg: t [UNKN ] Undocumented argument [MappedCloneSet *] * Arg: match [UNKN ] Undocumented argument [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Undocumented argument [Score] * Arg: target_skip [UNKN ] Undocumented argument [Score] * Arg: query_skip_start [UNKN ] Undocumented argument [Score] * Arg: query_skip [UNKN ] Undocumented argument [Score] * Arg: spread [UNKN ] Undocumented argument [int] * Arg: target_special_s [UNKN ] Undocumented argument [int] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ Search_Return_Type search_CloneWise(DBSearchImpl * dbsi,Hscore * out,MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { #ifdef PTHREAD int i; int thr_no; pthread_attr_t pat; struct thread_pool_holder_CloneWise * holder; #endif if( out == NULL ) { warn("Passed in a null Hscore object into search_CloneWise. Can't process results!"); return SEARCH_ERROR; } if( dbsi == NULL ) { warn("Passed in a null DBSearchImpl object into search_CloneWise. Can't process results!"); return SEARCH_ERROR; } if( dbsi->trace_level > 5 ) warn("Asking for trace level of %d in database search for CloneWise, 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_CloneWise(out,q,t ,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s); case DBSearchImpl_Pthreads : #ifdef PTHREAD holder = (struct thread_pool_holder_CloneWise *) ckalloc(sizeof(struct thread_pool_holder_CloneWise)); if( holder == NULL ) { warn("Unable to allocated thread pool datastructure..."); return SEARCH_ERROR; } holder->out = out; holder->dbsi = dbsi; holder->q = q; holder->t = t; holder->match = match; holder->target_skip_start = target_skip_start; holder->target_skip = target_skip; holder->query_skip_start = query_skip_start; holder->query_skip = query_skip; holder->spread = spread; holder->target_special_s = target_special_s; 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_CloneWise,(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 CloneWise"); #endif /* finished threads */ default : warn("database search implementation %s was not provided in the compiled dynamite file from CloneWise",impl_string_DBSearchImpl(dbsi)); return SEARCH_ERROR; } /* end of switch on implementation */ } /* Function: serial_search_CloneWise(out,q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * Descrip: This function makes a database search of CloneWise * It is a single processor implementation * * * Arg: out [UNKN ] Undocumented argument [Hscore *] * Arg: q [UNKN ] Undocumented argument [MappedCloneSet *] * Arg: t [UNKN ] Undocumented argument [MappedCloneSet *] * Arg: match [UNKN ] Undocumented argument [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Undocumented argument [Score] * Arg: target_skip [UNKN ] Undocumented argument [Score] * Arg: query_skip_start [UNKN ] Undocumented argument [Score] * Arg: query_skip [UNKN ] Undocumented argument [Score] * Arg: spread [UNKN ] Undocumented argument [int] * Arg: target_special_s [UNKN ] Undocumented argument [int] * * Return [UNKN ] Undocumented return value [Search_Return_Type] * */ Search_Return_Type serial_search_CloneWise(Hscore * out,MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { int db_status; int score; int query_pos = 0; int target_pos = 0; DataScore * ds; push_errormsg_stack("Before any actual search in db searching"); target_pos = 0; /* No maximum length - allocated on-the-fly */ score = score_only_CloneWise(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s); if( should_store_Hscore(out,score) == TRUE ) { /*if storing datascore*/ ds = new_DataScore_from_storage(out); if( ds == NULL ) { warn("CloneWise 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 */ 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); pop_errormsg_stack(); return SEARCH_OK; } /* Function: score_only_CloneWise(q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * 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_CloneWise_only * * * Arg: q [UNKN ] query data structure [MappedCloneSet *] * Arg: t [UNKN ] target data structure [MappedCloneSet *] * Arg: match [UNKN ] Resource [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Resource [Score] * Arg: target_skip [UNKN ] Resource [Score] * Arg: query_skip_start [UNKN ] Resource [Score] * Arg: query_skip [UNKN ] Resource [Score] * Arg: spread [UNKN ] Resource [int] * Arg: target_special_s [UNKN ] Resource [int] * * Return [UNKN ] Undocumented return value [int] * */ int score_only_CloneWise(MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { int bestscore = NEGI; int i; int j; int k; CloneWise * mat; mat = allocate_CloneWise_only(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s); 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(2,(mat->leni + 1) * 3,2,3)) == NULL) { warn("Score only matrix for CloneWise cannot be allocated, (asking for 1 by %d cells)",mat->leni*3); mat = free_CloneWise(mat); return 0; } mat->basematrix->type = BASEMATRIX_TYPE_VERYSMALL; /* Now, initiate matrix */ for(j=0;j<3;j++) { for(i=(-1);ileni;i++) { for(k=0;k<3;k++) CloneWise_VSMALL_MATRIX(mat,i,j,k) = NEGI; } CloneWise_VSMALL_SPECIAL(mat,i,j,START) = 0; CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = NEGI; CloneWise_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 = CloneWise_VSMALL_MATRIX(mat,i-1,j-1,MATCH) + (mat->match->matrix[i][j]+1); /* From state MATCH to state MATCH */ temp = CloneWise_VSMALL_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = CloneWise_VSMALL_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_VSMALL_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_VSMALL_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-1) == 0 && (j-1) == 0 ) { /* From state START to state MATCH */ temp = CloneWise_VSMALL_SPECIAL(mat,i-1,j-1,START) + 0; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ score += mat->match->matrix[i][j]; CloneWise_VSMALL_MATRIX(mat,i,j,MATCH) = score; /* state MATCH is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state MATCH */ /* For state SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_VSMALL_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_VSMALL_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_VSMALL_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-1) == 0 && (j-0) == 0 ) { /* From state START to state SKIP_QUERY */ temp = CloneWise_VSMALL_SPECIAL(mat,i-1,j-0,START) + mat->query_skip_start; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ score += mat->match->skip_iset[i]; CloneWise_VSMALL_MATRIX(mat,i,j,SKIP_QUERY) = score; /* state SKIP_QUERY is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_VSMALL_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_VSMALL_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_VSMALL_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-0) == 0 && (j-1) == 0 ) { /* From state START to state SKIP_TARGET */ temp = CloneWise_VSMALL_SPECIAL(mat,i-0,j-1,START) + mat->target_skip_start; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ score += mat->match->skip_jset[j]; CloneWise_VSMALL_MATRIX(mat,i,j,SKIP_TARGET) = score; /* state SKIP_TARGET is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_VSMALL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state SKIP_TARGET */ } /* end of for all query positions */ /* Special state START has no special to special movements */ /* Special state TRUSTED_SPECIAL has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_VSMALL_SPECIAL(mat,0,j,TRUSTED_SPECIAL); /* Source START is a special source for TRUSTED_SPECIAL */ /* Has restricted position */ if( (j-1) == 0 ) { temp = CloneWise_VSMALL_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) score = temp; } /* Source TRUSTED_SPECIAL is a special source for TRUSTED_SPECIAL */ temp = CloneWise_VSMALL_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + ((mat->match->skip_jset[j]-1)) + (0); if( temp > score ) score = temp; /* Source MATCH for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_QUERY for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_TARGET for state TRUSTED_SPECIAL is not special... already calculated */ /* Put back score... (now updated!) */ CloneWise_VSMALL_SPECIAL(mat,0,j,TRUSTED_SPECIAL) = score; /* Finished updating state TRUSTED_SPECIAL */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_VSMALL_SPECIAL(mat,0,j,END); /* Source TRUSTED_SPECIAL is a special source for END */ /* Has restricted position */ if( j == mat->lenj-1 ) { temp = CloneWise_VSMALL_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + (0) + (0); if( temp > score ) score = temp; } /* Put back score... (now updated!) */ CloneWise_VSMALL_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ if( bestscore < CloneWise_VSMALL_SPECIAL(mat,0,j,END) ) bestscore = CloneWise_VSMALL_SPECIAL(mat,0,j,END); } /* end of for all target positions */ mat = free_CloneWise(mat); return bestscore; } /* Function: PackAln_bestmemory_CloneWise(q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s,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_CloneWise * * * Arg: q [UNKN ] query data structure [MappedCloneSet *] * Arg: t [UNKN ] target data structure [MappedCloneSet *] * Arg: match [UNKN ] Resource [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Resource [Score] * Arg: target_skip [UNKN ] Resource [Score] * Arg: query_skip_start [UNKN ] Resource [Score] * Arg: query_skip [UNKN ] Resource [Score] * Arg: spread [UNKN ] Resource [int] * Arg: target_special_s [UNKN ] Resource [int] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_bestmemory_CloneWise(MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s,DPEnvelope * dpenv,DPRunImpl * dpri) { int total; CloneWise * mat; PackAln * out; DebugMatrix * de; DPRunImplMemory strategy; assert(dpri); total = q->length * t->length; if( dpri->memory == DPIM_Default ) { if( (total * 3 * 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_CloneWise(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s)) == NULL ) { warn("Unable to allocate small CloneWise version"); return NULL; } out = PackAln_calculate_Small_CloneWise(mat,dpenv); } else { /* use Large implementation */ if( (mat=allocate_Expl_CloneWise(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s)) == NULL ) { warn("Unable to allocate large CloneWise 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_CloneWise(mat); out = PackAln_read_Expl_CloneWise(mat); } mat = free_CloneWise(mat); return out; } /* Function: allocate_CloneWise_only(q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * Descrip: This function only allocates the CloneWise structure * checks types where possible and determines leni and lenj * The basematrix area is delt with elsewhere * * * Arg: q [UNKN ] query data structure [MappedCloneSet *] * Arg: t [UNKN ] target data structure [MappedCloneSet *] * Arg: match [UNKN ] Resource [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Resource [Score] * Arg: target_skip [UNKN ] Resource [Score] * Arg: query_skip_start [UNKN ] Resource [Score] * Arg: query_skip [UNKN ] Resource [Score] * Arg: spread [UNKN ] Resource [int] * Arg: target_special_s [UNKN ] Resource [int] * * Return [UNKN ] Undocumented return value [CloneWise *] * */ CloneWise * allocate_CloneWise_only(MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { CloneWise * out; if((out= CloneWise_alloc()) == NULL) { warn("Allocation of basic CloneWise structure failed..."); return NULL; } out->q = q; out->t = t; out->match = match; out->target_skip_start = target_skip_start; out->target_skip = target_skip; out->query_skip_start = query_skip_start; out->query_skip = query_skip; out->spread = spread; out->target_special_s = target_special_s; out->leni = q->length; out->lenj = t->length; return out; } /* Function: allocate_Expl_CloneWise(q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * Descrip: This function allocates the CloneWise structure * and the basematrix area for explicit memory implementations * It calls /allocate_CloneWise_only * * * Arg: q [UNKN ] query data structure [MappedCloneSet *] * Arg: t [UNKN ] target data structure [MappedCloneSet *] * Arg: match [UNKN ] Resource [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Resource [Score] * Arg: target_skip [UNKN ] Resource [Score] * Arg: query_skip_start [UNKN ] Resource [Score] * Arg: query_skip [UNKN ] Resource [Score] * Arg: spread [UNKN ] Resource [int] * Arg: target_special_s [UNKN ] Resource [int] * * Return [UNKN ] Undocumented return value [CloneWise *] * */ CloneWise * allocate_Expl_CloneWise(MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { CloneWise * out; out = allocate_CloneWise_only(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s); if( out == NULL ) return NULL; if( (out->basematrix = BaseMatrix_alloc_matrix_and_specials((out->lenj+1)*3,(out->leni+1),3,out->lenj+1)) == NULL) { warn("Explicit matrix CloneWise cannot be allocated, (asking for %d by %d main cells)",out->leni,out->lenj); free_CloneWise(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_EXPLICIT; init_CloneWise(out); return out; } /* Function: init_CloneWise(mat) * * Descrip: This function initates CloneWise matrix when in explicit mode * Called in /allocate_Expl_CloneWise * * * Arg: mat [UNKN ] CloneWise which contains explicit basematrix memory [CloneWise *] * */ void init_CloneWise(CloneWise * 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);iq->length;i++) { for(j= (-1);j<2;j++) { CloneWise_EXPL_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; } } for(j= (-1);jt->length;j++) { for(i= (-1);i<2;i++) { CloneWise_EXPL_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; } CloneWise_EXPL_SPECIAL(mat,i,j,START) = 0; CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = NEGI; CloneWise_EXPL_SPECIAL(mat,i,j,END) = NEGI; } return; } /* Function: recalculate_PackAln_CloneWise(pal,mat) * * Descrip: This function recalculates the PackAln structure produced by CloneWise * For example, in linear space methods this is used to score them * * * Arg: pal [UNKN ] Undocumented argument [PackAln *] * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * */ void recalculate_PackAln_CloneWise(PackAln * pal,CloneWise * 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 == 1 && prev->state == MATCH ) { pau->score = (mat->match->matrix[i][j]+1) + (mat->match->matrix[i][j]); continue; } if( offi == 0 && offj == 1 && prev->state == MATCH ) { pau->score = 0 + (mat->match->matrix[i][j]); continue; } if( offi == 1 && offj == 0 && prev->state == MATCH ) { pau->score = 0 + (mat->match->matrix[i][j]); continue; } if( offi == 1 && offj == 1 && prev->state == SKIP_QUERY ) { pau->score = 0 + (mat->match->matrix[i][j]); continue; } if( offi == 1 && offj == 1 && prev->state == SKIP_TARGET ) { pau->score = 0 + (mat->match->matrix[i][j]); continue; } if( offj == 1 && prev->state == (START+3) ) { pau->score = 0 + (mat->match->matrix[i][j]); continue; } warn("In recaluclating PackAln with state MATCH, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case SKIP_QUERY : if( offi == 1 && offj == 0 && prev->state == MATCH ) { pau->score = mat->query_skip_start + (mat->match->skip_iset[i]); continue; } if( offi == 1 && offj == 0 && prev->state == SKIP_TARGET ) { pau->score = mat->query_skip_start + (mat->match->skip_iset[i]); continue; } if( offi == 1 && offj == 0 && prev->state == SKIP_QUERY ) { pau->score = 0 + (mat->match->skip_iset[i]); continue; } if( offj == 0 && prev->state == (START+3) ) { pau->score = mat->query_skip_start + (mat->match->skip_iset[i]); continue; } warn("In recaluclating PackAln with state SKIP_QUERY, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case SKIP_TARGET : if( offi == 0 && offj == 1 && prev->state == MATCH ) { pau->score = mat->target_skip_start + (mat->match->skip_jset[j]); continue; } if( offi == 0 && offj == 1 && prev->state == SKIP_QUERY ) { pau->score = mat->target_skip_start + (mat->match->skip_jset[j]); continue; } if( offi == 0 && offj == 1 && prev->state == SKIP_TARGET ) { pau->score = 0 + (mat->match->skip_jset[j]); continue; } if( offj == 1 && prev->state == (START+3) ) { pau->score = mat->target_skip_start + (mat->match->skip_jset[j]); continue; } warn("In recaluclating PackAln with state SKIP_TARGET, from [%d,%d,%d], got a bad source state. Error!",offi,offj,prev->state); break; case (START+3) : warn("In recaluclating PackAln with state START, got a bad source state. Error!"); break; case (TRUSTED_SPECIAL+3) : if( offj == 1 && prev->state == (START+3) ) { pau->score = 0 + (0); continue; } if( offj == 1 && prev->state == (TRUSTED_SPECIAL+3) ) { pau->score = (mat->match->skip_jset[j]-1) + (0); continue; } if( offj == 0 && prev->state == MATCH ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->target_special_s + (0); continue; } if( offj == 0 && prev->state == SKIP_QUERY ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->target_special_s + (0); continue; } if( offj == 0 && prev->state == SKIP_TARGET ) { /* i here comes from the previous state ;) - not the real one */ i = prev->i; pau->score = mat->target_special_s + (0); continue; } warn("In recaluclating PackAln with state TRUSTED_SPECIAL, got a bad source state. Error!"); break; case (END+3) : if( offj == 1 && prev->state == (TRUSTED_SPECIAL+3) ) { pau->score = 0 + (0); continue; } warn("In recaluclating PackAln with state END, got a bad source state. Error!"); break; default : warn("In recaluclating PackAln got a bad recipient state. Error!"); } prev = pau; } return; } /* divide and conquor macros are next */ #define CloneWise_HIDDEN_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[(j-hiddenj+1)][(i+1)*3+state]) #define CloneWise_DC_SHADOW_MATRIX(thismatrix,i,j,state) (thismatrix->basematrix->matrix[((j+2)*8) % 16][(i+1)*3+state]) #define CloneWise_HIDDEN_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state][(j+1)]) #define CloneWise_DC_SHADOW_SPECIAL(thismatrix,i,j,state) (thismatrix->basematrix->specmatrix[state*8][(j+1)]) #define CloneWise_DC_SHADOW_MATRIX_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->matrix[((((j+2)*8)+(shadow+1)) % 16)][(i+1)*3 + state]) /* Function: allocate_Small_CloneWise(q,t,match,target_skip_start,target_skip,query_skip_start,query_skip,spread,target_special_s) * * Descrip: This function allocates the CloneWise structure * and the basematrix area for a small memory implementations * It calls /allocate_CloneWise_only * * * Arg: q [UNKN ] query data structure [MappedCloneSet *] * Arg: t [UNKN ] target data structure [MappedCloneSet *] * Arg: match [UNKN ] Resource [MappedCloneMatch*] * Arg: target_skip_start [UNKN ] Resource [Score] * Arg: target_skip [UNKN ] Resource [Score] * Arg: query_skip_start [UNKN ] Resource [Score] * Arg: query_skip [UNKN ] Resource [Score] * Arg: spread [UNKN ] Resource [int] * Arg: target_special_s [UNKN ] Resource [int] * * Return [UNKN ] Undocumented return value [CloneWise *] * */ #define CloneWise_DC_SHADOW_SPECIAL_SP(thismatrix,i,j,state,shadow) (thismatrix->basematrix->specmatrix[state*8 +shadow+1][(j+1)]) CloneWise * allocate_Small_CloneWise(MappedCloneSet * q,MappedCloneSet * t ,MappedCloneMatch* match,Score target_skip_start,Score target_skip,Score query_skip_start,Score query_skip,int spread,int target_special_s) { CloneWise * out; out = allocate_CloneWise_only(q, t , match, target_skip_start, target_skip, query_skip_start, query_skip, spread, target_special_s); if( out == NULL ) return NULL; out->basematrix = BaseMatrix_alloc_matrix_and_specials(16,(out->leni + 1) * 3,24,out->lenj+1); if(out == NULL) { warn("Small shadow matrix CloneWise cannot be allocated, (asking for 2 by %d main cells)",out->leni+2); free_CloneWise(out); return NULL; } out->basematrix->type = BASEMATRIX_TYPE_SHADOW; return out; } /* Function: PackAln_calculate_Small_CloneWise(mat,dpenv) * * Descrip: This function calculates an alignment for CloneWise structure in linear space * If you want only the start/end points * use /AlnRangeSet_calculate_Small_CloneWise * * The function basically * finds start/end points * foreach start/end point * calls /full_dc_CloneWise * * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_calculate_Small_CloneWise(CloneWise * 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 CloneWise due to wrong type of matrix"); return NULL; } out = PackAln_alloc_std(); start_reporting("Find start end points: "); dc_start_end_calculate_CloneWise(mat,dpenv); score = start_end_find_end_CloneWise(mat,&endj); out->score = score; stopstate = END; /* Special to specials: have to eat up in strip and then drop back to full_dc for intervening bits */ log_full_error(REPORT,0,"End at %d Score %d",endj,score); stop_reporting(); for(;;) { /*while there are more special bits to recover*/ start_reporting("Special cell aln end %d:",endj); if( read_special_strip_CloneWise(mat,0,endj,stopstate,&endj,&startstate,out) == FALSE ) { warn("Problem in reading off special state system... going to return partial alignment"); break; } if( startstate == START || endj <= 0) { log_full_error(REPORT,0,"Recovered complete alignment"); stop_reporting(); break; } log_full_error(REPORT,0,"Finished to %d",endj); stop_reporting(); /* Ok... have to eat up another piece of matrix */ temp = startstate; starti = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,0); startj = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,1); startstate = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,2); stopi = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,3); stopj = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,4); stopstate = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,5); /* Get out the score of this block. V. important! */ temp = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,endj,temp,6); totalj = stopj - startj; donej = 0; start_reporting("Main matrix aln [%d,%d]:",startj,stopj); if(full_dc_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,out,&donej,totalj,dpenv) == FALSE) { warn("In the alignment CloneWise [%d,%d][%d,%d], got a problem. Please report bug ... giving you back a partial alignment",starti,startj,stopi,stopj); return out; } /* now have to figure out which special we came from... yikes */ max_matrix_to_special_CloneWise(mat,starti,startj,startstate,temp,&stopi,&stopj,&stopstate,&temp,NULL); if( stopi == CloneWise_READ_OFF_ERROR) { warn("In CloneWise read off ending at %d ... got a bad matrix to special read off... returning partial alignment",startj); invert_PackAln(out); recalculate_PackAln_CloneWise(out,mat); return out; } /* if at start, break, otherwise, back to eat another strip */ if( stopstate == START) { log_full_error(REPORT,0,"Recovered complete alignment "); stop_reporting(); break; } log_full_error(REPORT,0,"Finished alignment to %d ",startj); stop_reporting(); endj = stopj; /* stopstate is correct as it is */ } /* end of while there are more special bits to recover */ invert_PackAln(out); recalculate_PackAln_CloneWise(out,mat); return out; } /* Function: AlnRangeSet_calculate_Small_CloneWise(mat) * * Descrip: This function calculates an alignment for CloneWise structure in linear space * If you want the full alignment, use /PackAln_calculate_Small_CloneWise * If you have already got the full alignment, but want the range set, use /AlnRangeSet_from_PackAln_CloneWise * If you have got the small matrix but not the alignment, use /AlnRangeSet_from_CloneWise * * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_calculate_Small_CloneWise(CloneWise * mat) { AlnRangeSet * out; start_reporting("Find start end points: "); dc_start_end_calculate_CloneWise(mat,NULL); log_full_error(REPORT,0,"Calculated"); out = AlnRangeSet_from_CloneWise(mat); return out; } /* Function: AlnRangeSet_from_CloneWise(mat) * * Descrip: This function reads off a start/end structure * for CloneWise structure in linear space * If you want the full alignment use * /PackAln_calculate_Small_CloneWise * If you have not calculated the matrix use * /AlnRange_calculate_Small_CloneWise * * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * * Return [UNKN ] Undocumented return value [AlnRangeSet *] * */ AlnRangeSet * AlnRangeSet_from_CloneWise(CloneWise * 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_CloneWise"); return NULL; } out = AlnRangeSet_alloc_std(); /* Find the end position */ out->score = start_end_find_end_CloneWise(mat,&jpos); state = END; while( (temp = AlnRange_build_CloneWise(mat,jpos,state,&jpos,&state)) != NULL) add_AlnRangeSet(out,temp); return out; } /* Function: AlnRange_build_CloneWise(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_CloneWise * * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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_CloneWise"); return NULL; } /* Assumme that we have specials (we should!). Read back along the specials till we have the finish point */ if( read_special_strip_CloneWise(mat,0,stopj,stopspecstate,&jpos,&state,NULL) == FALSE) { warn("In AlnRanger_build_CloneWise 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 = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,0); out->startj = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,1); out->startstate = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,2); out->stopi = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,3); out->stopj = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,4); out->stopstate = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,5); out->startscore = CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,jpos,state,6); out->stopscore = CloneWise_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_CloneWise(mat,out->starti,out->startj,out->startstate,out->startscore,&jpos,startj,startspecstate,&state,NULL); if( jpos == CloneWise_READ_OFF_ERROR) { warn("In AlnRange_build_CloneWise 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 = CloneWise_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_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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_CloneWise(mat,startj,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == CloneWise_READ_OFF_ERROR) { warn("In CloneWise 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 CloneWise 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 CloneWise 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_CloneWise(mat,hiddenj,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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) = CloneWise_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->q->length || j > mat->t->length) { warn("In CloneWise 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 = CloneWise_HIDDEN_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case MATCH : /* Not allowing special sources.. skipping START */ temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,SKIP_TARGET) ) { *reti = i - 1; *retj = j - 1; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,SKIP_TARGET); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,SKIP_TARGET); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,SKIP_QUERY) ) { *reti = i - 1; *retj = j - 1; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,SKIP_QUERY); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,SKIP_QUERY); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,MATCH); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,MATCH); } return CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH); } temp = cscore - ((mat->match->matrix[i][j]+1)) - (mat->match->matrix[i][j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,MATCH) ) { *reti = i - 1; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,MATCH); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 1,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_QUERY : /* Not allowing special sources.. skipping START */ temp = cscore - (0) - (mat->match->skip_iset[i]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,SKIP_QUERY) ) { *reti = i - 1; *retj = j - 0; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,SKIP_QUERY); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,SKIP_QUERY); } temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,SKIP_TARGET) ) { *reti = i - 1; *retj = j - 0; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,SKIP_TARGET); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,SKIP_TARGET); } temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,MATCH); } return CloneWise_HIDDEN_MATRIX(mat,i - 1,j - 0,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_TARGET : /* Not allowing special sources.. skipping START */ temp = cscore - (0) - (mat->match->skip_jset[j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,SKIP_TARGET) ) { *reti = i - 0; *retj = j - 1; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,SKIP_TARGET); } return CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,SKIP_TARGET); } temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,SKIP_QUERY) ) { *reti = i - 0; *retj = j - 1; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,SKIP_QUERY); } return CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,SKIP_QUERY); } temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,MATCH); } return CloneWise_HIDDEN_MATRIX(mat,i - 0,j - 1,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: read_special_strip_CloneWise(mat,stopi,stopj,stopstate,startj,startstate,out) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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 > CloneWise_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 + 3; add_PackAln(out,pau); } max_special_strip_CloneWise(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if( i == CloneWise_READ_OFF_ERROR) { warn("In special strip read CloneWise, 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 < CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,state,4)) { warn("In special strip read CloneWise, 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 + 3; add_PackAln(out,pau); } /* Put away where we are in startj and startstate */ *startj = j; *startstate = state; return TRUE; } /* Function: max_special_strip_CloneWise(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 [CloneWise *] * 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_CloneWise(CloneWise * 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) = CloneWise_READ_OFF_ERROR; if( isspecial == FALSE ) { warn("In special strip max function for CloneWise, got a non special start point. Problem! (bad!)"); return (-1); } if( j < 0 || j > mat->t->length) { warn("In CloneWise matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = CloneWise_DC_SHADOW_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case START : case TRUSTED_SPECIAL : /* Source SKIP_TARGET is not a special */ /* Source SKIP_QUERY is not a special */ /* Source MATCH is not a special */ /* source TRUSTED_SPECIAL is a special */ temp = cscore - ((mat->match->skip_jset[j]-1)) - (0); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,TRUSTED_SPECIAL) ) { *reti = i - 0; *retj = j - 1; *retstate = TRUSTED_SPECIAL; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-0,j-1,TRUSTED_SPECIAL); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 0,j - 1,TRUSTED_SPECIAL) ; } /* source START is a special */ temp = cscore - (0) - (0); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-0,j-1,START); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 0,j - 1,START) ; } case END : /* source TRUSTED_SPECIAL is a special */ temp = cscore - (0) - (0); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,TRUSTED_SPECIAL) ) { *reti = i - 0; *retj = j - 1; *retstate = TRUSTED_SPECIAL; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-0,j-1,TRUSTED_SPECIAL); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 0,j - 1,TRUSTED_SPECIAL) ; } default: warn("Major problem (!) - in CloneWise 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_CloneWise(mat,i,j,state,cscore,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * mat,int i,int j,int state,int cscore,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) { int temp; *reti = (*retj) = (*retstate) = CloneWise_READ_OFF_ERROR; if( j < 0 || j > mat->lenj) { warn("In CloneWise matrix to special read off - out of bounds on matrix [j is %d in special]",j); return -1; } switch(state) { /*Switch state */ case MATCH : temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 1,j - 1,START) ) { *reti = i - 1; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-1,j-1,START); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 1,j - 1,START) ; } /* Source SKIP_TARGET is not a special, should not get here! */ /* Source SKIP_QUERY is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in CloneWise matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_QUERY : temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 1,j - 0,START) ) { *reti = i - 1; *retj = j - 0; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-1,j-0,START); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 1,j - 0,START) ; } /* Source SKIP_QUERY is not a special, should not get here! */ /* Source SKIP_TARGET is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in CloneWise matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_TARGET : temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_DC_SHADOW_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_DC_SHADOW_SPECIAL(mat,i-0,j-1,START); } return CloneWise_DC_SHADOW_MATRIX(mat,i - 0,j - 1,START) ; } /* Source SKIP_TARGET is not a special, should not get here! */ /* Source SKIP_QUERY is not a special, should not get here! */ /* Source MATCH is not a special, should not get here! */ warn("Major problem (!) - in CloneWise matrix to special read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: calculate_hidden_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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_CloneWise(mat,starti,startj,stopi,stopj); CloneWise_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*/ CloneWise_HIDDEN_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; continue; } /* end of Is not in envelope */ /* For state MATCH */ /* setting first movement to score */ score = CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,MATCH) + (mat->match->matrix[i][j]+1); /* From state MATCH to state MATCH */ temp = CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_HIDDEN_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ score += mat->match->matrix[i][j]; CloneWise_HIDDEN_MATRIX(mat,i,j,MATCH) = score; /* Finished calculating state MATCH */ /* For state SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_HIDDEN_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ score += mat->match->skip_iset[i]; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_QUERY) = score; /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_HIDDEN_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ score += mat->match->skip_jset[j]; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_TARGET) = score; /* Finished calculating state SKIP_TARGET */ } } return; } /* Function: init_hidden_CloneWise(mat,starti,startj,stopi,stopj) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * mat,int starti,int startj,int stopi,int stopj) { register int i; register int j; register int hiddenj; hiddenj = startj; for(j=(startj-1);j<=stopj;j++) { for(i=(starti-1);i<=stopi;i++) { CloneWise_HIDDEN_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_HIDDEN_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; } } return; } /* Function: full_dc_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,out,donej,totalj,dpenv) * * Descrip: The main divide-and-conquor routine. Basically, call /PackAln_calculate_small_CloneWise * 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_CloneWise 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 [CloneWise *] * 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_CloneWise(CloneWise * 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_CloneWise"); 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 < 5) { log_full_error(REPORT,0,"[%d,%d][%d,%d] Explicit read off",starti,startj,stopi,stopj);/* Build hidden explicit matrix */ calculate_hidden_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv); *donej += (stopj - startj); /* Now read it off into out */ if( read_hidden_CloneWise(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_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,(int)(*donej*100)/totalj) == FALSE) { warn("In divide and conquor for CloneWise, 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= CloneWise_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,0); lstartj= CloneWise_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,1); lstate = CloneWise_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_CloneWise(mat,CloneWise_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,3),CloneWise_DC_SHADOW_MATRIX_SP(mat,stopi,stopj,stopstate,4),CloneWise_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_CloneWise(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_CloneWise(mat,starti,startj,startstate,stopi,stopj,stopstate,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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_CloneWise(mat); CloneWise_DC_SHADOW_MATRIX(mat,starti,startj,startstate) = 0; run_up_dc_CloneWise(mat,starti,stopi,startj,halfj-1,dpenv,perc_done); push_dc_at_merge_CloneWise(mat,starti,stopi,halfj,&halfj,dpenv); follow_on_dc_CloneWise(mat,starti,stopi,halfj,stopj,dpenv,perc_done); return TRUE; } /* Function: push_dc_at_merge_CloneWise(mat,starti,stopi,startj,stopj,dpenv) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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<1;count++,j++) { for(i=starti;i<=stopi;i++) { if( dpenv != NULL && is_in_DPEnvelope(dpenv,i,j) == FALSE ) { /*Is not in envelope*/ CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = (-100); CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = (-100); CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,0) = (-100); CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,1) = (-100); CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,0) = (-100); CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,1) = (-100); continue; } /* end of Is not in envelope */ /* For state MATCH, pushing when j - offj <= mergej */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + (mat->match->matrix[i][j]+1); if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score) { score = temp; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); } } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score) { score = temp; if( j - 0 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = MATCH; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); } } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score) { score = temp; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = SKIP_QUERY; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_QUERY,k); } } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score) { score = temp; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,2) = SKIP_TARGET; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,5) = MATCH; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_TARGET,k); } } /* Add any movement independant score */ score += mat->match->matrix[i][j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; /* Finished with state MATCH */ /* For state SKIP_QUERY, pushing when j - offj <= mergej */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; if( j - 0 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,1) = j-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,2) = MATCH; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,5) = SKIP_QUERY; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score) { score = temp; if( j - 0 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,1) = j-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,2) = SKIP_TARGET; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,5) = SKIP_QUERY; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_TARGET,k); } } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score) { score = temp; if( j - 0 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,0) = i-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,1) = j-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,2) = SKIP_QUERY; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,5) = SKIP_QUERY; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_QUERY,k); } } /* Add any movement independant score */ score += mat->match->skip_iset[i]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = score; /* Finished with state SKIP_QUERY */ /* For state SKIP_TARGET, pushing when j - offj <= mergej */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,0) = i-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,2) = MATCH; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,5) = SKIP_TARGET; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score) { score = temp; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,0) = i-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,2) = SKIP_QUERY; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,5) = SKIP_TARGET; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_QUERY,k); } } temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score) { score = temp; if( j - 1 <= mergej) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,0) = i-0; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,1) = j-1; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,2) = SKIP_TARGET; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,3) = i; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,4) = j; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,5) = SKIP_TARGET; } else { for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_TARGET,k); } } /* Add any movement independant score */ score += mat->match->skip_jset[j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = score; /* Finished with state SKIP_TARGET */ } } /* 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_CloneWise(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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*/ CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = 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 = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + (mat->match->matrix[i][j]+1); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); } /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_QUERY,k); } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_TARGET,k); } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ score += mat->match->matrix[i][j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; for(k=0;k<7;k++) CloneWise_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 SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_TARGET,k); } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_QUERY,k); } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ score += mat->match->skip_iset[i]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = score; for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_QUERY,k); } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_TARGET,k); } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ score += mat->match->skip_jset[j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = score; for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* Finished calculating state SKIP_TARGET */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: run_up_dc_CloneWise(mat,starti,stopi,startj,stopj,dpenv,perc_done) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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*/ CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = 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 = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,MATCH) + (mat->match->matrix[i][j]+1); /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ score += mat->match->matrix[i][j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; /* Finished calculating state MATCH */ /* For state SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ score += mat->match->skip_iset[i]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = score; /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ score += mat->match->skip_jset[j]; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = score; /* Finished calculating state SKIP_TARGET */ } /* end of this is strip */ } /* end of for each valid j column */ /* Function: init_dc_CloneWise(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * */ } void init_dc_CloneWise(CloneWise * mat) { register int i; register int j; register int k; for(j=0;j<3;j++) { for(i=(-1);iq->length;i++) { CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; for(k=0;k<7;k++) { CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k) = (-1); CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = (-1); CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = (-1); } } } return; } /* Function: dc_start_end_calculate_CloneWise(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 [CloneWise *] * Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean dc_start_end_calculate_CloneWise(CloneWise * 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_CloneWise(mat); leni = mat->q->length; lenj = mat->t->length; total = leni * lenj; for(j=0;jmatch->matrix[i][j]+1) + (mat->match->matrix[i][j]); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,MATCH,k); /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + 0 +(mat->match->matrix[i][j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); } /* From state MATCH to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + 0 +(mat->match->matrix[i][j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0 +(mat->match->matrix[i][j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_QUERY,k); } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0 +(mat->match->matrix[i][j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 1,SKIP_TARGET,k); } /* From state START to state MATCH */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,i-1,j-1,START) + 0 + (mat->match->matrix[i][j]); 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; } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = score; for(k=0;k<7;k++) CloneWise_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 TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,k); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,6) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,6); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,3) = i; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,4) = j; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,5) = MATCH; } /* Finished calculating state MATCH */ /* For state SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start + (mat->match->skip_iset[i]); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,MATCH,k); /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start +(mat->match->skip_iset[i]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_TARGET,k); } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0 +(mat->match->skip_iset[i]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 1,j - 0,SKIP_QUERY,k); } /* From state START to state SKIP_QUERY */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,i-1,j-0,START) + mat->query_skip_start + (mat->match->skip_iset[i]); if( temp > score ) { score = temp; /* This state [START] is a special for SKIP_QUERY... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= SKIP_QUERY; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = score; for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state SKIP_QUERY is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,k); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,6) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,6); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,3) = i; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,4) = j; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,5) = SKIP_QUERY; } /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start + (mat->match->skip_jset[j]); /* shift first shadow numbers */ for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,MATCH,k); /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start +(mat->match->skip_jset[j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_QUERY,k); } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0 +(mat->match->skip_jset[j]); if( temp > score ) { score = temp; for(k=0;k<7;k++) localshadow[k] = CloneWise_DC_SHADOW_MATRIX_SP(mat,i - 0,j - 1,SKIP_TARGET,k); } /* From state START to state SKIP_TARGET */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,i-0,j-1,START) + mat->target_skip_start + (mat->match->skip_jset[j]); if( temp > score ) { score = temp; /* This state [START] is a special for SKIP_TARGET... push top shadow pointers here */ localshadow[0]= i; localshadow[1]= j; localshadow[2]= SKIP_TARGET; localshadow[3]= (-1); localshadow[4]= (-1); localshadow[5]= (-1); localshadow[6]= score; } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ /* Actually, already done inside scores */ CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = score; for(k=0;k<7;k++) CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k) = localshadow[k]; /* Now figure out if any specials need this score */ /* state SKIP_TARGET is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_DC_SHADOW_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; /* Have to push only bottem half of system here */ for(k=0;k<3;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,k) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,k); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,6) = CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,6); CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,3) = i; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,4) = j; CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,5) = SKIP_TARGET; } /* Finished calculating state SKIP_TARGET */ } /* end of for each i position in strip */ /* Special state START has no special to special movements */ /* Special state TRUSTED_SPECIAL has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_DC_SHADOW_SPECIAL(mat,0,j,TRUSTED_SPECIAL); /* Source START is a special source for TRUSTED_SPECIAL */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,k) = CloneWise_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,START,k); } /* Source TRUSTED_SPECIAL is a special source for TRUSTED_SPECIAL */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + ((mat->match->skip_jset[j]-1)) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,TRUSTED_SPECIAL,k) = CloneWise_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,TRUSTED_SPECIAL,k); } /* Source MATCH for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_QUERY for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_TARGET for state TRUSTED_SPECIAL is not special... already calculated */ /* Put back score... (now updated!) */ CloneWise_DC_SHADOW_SPECIAL(mat,0,j,TRUSTED_SPECIAL) = score; /* Finished updating state TRUSTED_SPECIAL */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_DC_SHADOW_SPECIAL(mat,0,j,END); /* Source TRUSTED_SPECIAL is a special source for END */ temp = CloneWise_DC_SHADOW_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + (0) + (0); if( temp > score ) { score = temp; /* Also got to propagate shadows */ for(k=0;k<7;k++) CloneWise_DC_SHADOW_SPECIAL_SP(mat,i,j,END,k) = CloneWise_DC_SHADOW_SPECIAL_SP(mat,i - 0,j - 1,TRUSTED_SPECIAL,k); } /* Put back score... (now updated!) */ CloneWise_DC_SHADOW_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ } /* end of for each j strip */ return TRUE; } /* Function: start_end_find_end_CloneWise(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 [CloneWise *] * Arg: endj [WRITE] position of end in j (meaningless in i) [int *] * * Return [UNKN ] Undocumented return value [int] * */ int start_end_find_end_CloneWise(CloneWise * mat,int * endj) { register int j; register int max; register int maxj; max = CloneWise_DC_SHADOW_SPECIAL(mat,0,mat->t->length-1,END); maxj = mat->t->length-1; for(j= mat->t->length-2 ;j >= 0 ;j--) { if( CloneWise_DC_SHADOW_SPECIAL(mat,0,j,END) > max ) { max = CloneWise_DC_SHADOW_SPECIAL(mat,0,j,END); maxj = j; } } if( endj != NULL) *endj = maxj; return max; } /* Function: init_start_end_linear_CloneWise(mat) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * */ void init_start_end_linear_CloneWise(CloneWise * mat) { register int i; register int j; for(j=0;j<3;j++) { for(i=(-1);iq->length;i++) { CloneWise_DC_SHADOW_MATRIX(mat,i,j,MATCH) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,MATCH,0) = (-1); CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_QUERY) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_QUERY,0) = (-1); CloneWise_DC_SHADOW_MATRIX(mat,i,j,SKIP_TARGET) = NEGI; CloneWise_DC_SHADOW_MATRIX_SP(mat,i,j,SKIP_TARGET,0) = (-1); } } for(j=(-1);jt->length;j++) { CloneWise_DC_SHADOW_SPECIAL(mat,0,j,START) = 0; CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,j,START,0) = j; CloneWise_DC_SHADOW_SPECIAL(mat,0,j,TRUSTED_SPECIAL) = NEGI; CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,j,TRUSTED_SPECIAL,0) = (-1); CloneWise_DC_SHADOW_SPECIAL(mat,0,j,END) = NEGI; CloneWise_DC_SHADOW_SPECIAL_SP(mat,0,j,END,0) = (-1); } return; } /* Function: convert_PackAln_to_AlnBlock_CloneWise(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_CloneWise(PackAln * pal) { AlnConvertSet * acs; AlnBlock * alb; acs = AlnConvertSet_CloneWise(); alb = AlnBlock_from_PackAln(acs,pal); free_AlnConvertSet(acs); return alb; } static char * query_label[] = { "QUERY_MATCH","QUERY_MATCH_PAUSE","QUERY_SKIP","QUERY_PAUSE","NO_QUERY_PAUSE","END" }; /* Function: AlnConvertSet_CloneWise(void) * * Descrip: No Description * * * Return [UNKN ] Undocumented return value [AlnConvertSet *] * */ static char * target_label[] = { "TARGET_MATCH","TARGET_MATCH_PAUSE","TARGET_PAUSE","TARGET_SKIP","END" }; AlnConvertSet * AlnConvertSet_CloneWise(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 = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = MATCH; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[1]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = MATCH; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[0]; acu->label2 = target_label[1]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_QUERY; acu->state2 = MATCH; acu->offi = 1; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_TARGET; acu->state2 = MATCH; acu->offi = 1; acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 3; acu->is_from_special = TRUE; acu->state2 = MATCH; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[0]; acu->label2 = target_label[0]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = SKIP_QUERY; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_TARGET; acu->state2 = SKIP_QUERY; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_QUERY; acu->state2 = SKIP_QUERY; acu->offi = 1; acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 3; acu->is_from_special = TRUE; acu->state2 = SKIP_QUERY; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[2]; acu->label2 = target_label[2]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = SKIP_TARGET; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_QUERY; acu->state2 = SKIP_TARGET; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_TARGET; acu->state2 = SKIP_TARGET; acu->offi = 0; acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 3; acu->is_from_special = TRUE; acu->state2 = SKIP_TARGET; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[3]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = START + 3; acu->state2 = TRUSTED_SPECIAL + 3; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[4]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = TRUSTED_SPECIAL + 3; acu->state2 = TRUSTED_SPECIAL + 3; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[4]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = MATCH; acu->state2 = TRUSTED_SPECIAL + 3; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_QUERY; acu->state2 = TRUSTED_SPECIAL + 3; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = SKIP_TARGET; acu->state2 = TRUSTED_SPECIAL + 3; acu->offi = (-1); acu->offj = 0; acu->label1 = query_label[4]; acu->label2 = target_label[3]; acu = AlnConvertUnit_alloc(); add_AlnConvertSet(out,acu); acu->state1 = TRUSTED_SPECIAL + 3; acu->state2 = END + 3; acu->offi = (-1); acu->offj = 1; acu->label1 = query_label[5]; acu->label2 = target_label[4]; return out; } /* Function: PackAln_read_Expl_CloneWise(mat) * * Descrip: Reads off PackAln from explicit matrix structure * * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * * Return [UNKN ] Undocumented return value [PackAln *] * */ PackAln * PackAln_read_Expl_CloneWise(CloneWise * 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 CloneWise_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_CloneWise(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 CloneWise_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 + 3; prev=pau; while( state != START || isspecial != TRUE) { /*while state != START*/ if( isspecial == TRUE ) max_calc_special_CloneWise(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); else max_calc_CloneWise(mat,i,j,state,isspecial,&i,&j,&state,&isspecial,&cellscore); if(i == CloneWise_READ_OFF_ERROR || j == CloneWise_READ_OFF_ERROR || state == CloneWise_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 CloneWise_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 + 3; prev->score = cellscore; prev = pau; } /* end of while state != START */ invert_PackAln(out); return out; } /* Function: find_end_CloneWise(mat,ri,rj,state,isspecial) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * mat,int * ri,int * rj,int * state,boolean * isspecial) { register int j; register int max; register int maxj; max = CloneWise_EXPL_SPECIAL(mat,0,mat->t->length-1,END); maxj = mat->t->length-1; for(j= mat->t->length-2 ;j >= 0 ;j--) { if( CloneWise_EXPL_SPECIAL(mat,0,j,END) > max ) { max = CloneWise_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: CloneWise_debug_show_matrix(mat,starti,stopi,startj,stopj,ofp) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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 CloneWise_debug_show_matrix(CloneWise * mat,int starti,int stopi,int startj,int stopj,FILE * ofp) { register int i; register int j; for(i=starti;iq->length;i++) { for(j=startj;jt->length;j++) { fprintf(ofp,"Cell [%d - %d]\n",i,j); fprintf(ofp,"State MATCH %d\n",CloneWise_EXPL_MATRIX(mat,i,j,MATCH)); fprintf(ofp,"State SKIP_QUERY %d\n",CloneWise_EXPL_MATRIX(mat,i,j,SKIP_QUERY)); fprintf(ofp,"State SKIP_TARGET %d\n",CloneWise_EXPL_MATRIX(mat,i,j,SKIP_TARGET)); fprintf(ofp,"\n\n"); } } } /* Function: max_calc_CloneWise(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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) = CloneWise_READ_OFF_ERROR; if( i < 0 || j < 0 || i > mat->q->length || j > mat->t->length) { warn("In CloneWise 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 = CloneWise_EXPL_MATRIX(mat,i,j,state); switch(state) { /*Switch state */ case MATCH : /* Has restricted position */ if( (i-1) == 0 && (j-1) == 0 ) { temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 1,j - 1,START) ) { *reti = i - 1; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-1,j-1,START); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,START); } } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,SKIP_TARGET) ) { *reti = i - 1; *retj = j - 1; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-1,SKIP_TARGET); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,SKIP_TARGET); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,SKIP_QUERY) ) { *reti = i - 1; *retj = j - 1; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-1,SKIP_QUERY); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,SKIP_QUERY); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-0,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,MATCH); } temp = cscore - (0) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-1,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,MATCH); } temp = cscore - ((mat->match->matrix[i][j]+1)) - (mat->match->matrix[i][j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,MATCH) ) { *reti = i - 1; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-1,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 1,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_QUERY : /* Has restricted position */ if( (i-1) == 0 && (j-0) == 0 ) { temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 1,j - 0,START) ) { *reti = i - 1; *retj = j - 0; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-1,j-0,START); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,START); } } temp = cscore - (0) - (mat->match->skip_iset[i]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,SKIP_QUERY) ) { *reti = i - 1; *retj = j - 0; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-0,SKIP_QUERY); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,SKIP_QUERY); } temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,SKIP_TARGET) ) { *reti = i - 1; *retj = j - 0; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-0,SKIP_TARGET); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,SKIP_TARGET); } temp = cscore - (mat->query_skip_start) - (mat->match->skip_iset[i]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,MATCH) ) { *reti = i - 1; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-1,j-0,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 1,j - 0,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); case SKIP_TARGET : /* Has restricted position */ if( (i-0) == 0 && (j-1) == 0 ) { temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-0,j-1,START); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,START); } } temp = cscore - (0) - (mat->match->skip_jset[j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,SKIP_TARGET) ) { *reti = i - 0; *retj = j - 1; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-1,SKIP_TARGET); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,SKIP_TARGET); } temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,SKIP_QUERY) ) { *reti = i - 0; *retj = j - 1; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-1,SKIP_QUERY); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,SKIP_QUERY); } temp = cscore - (mat->target_skip_start) - (mat->match->skip_jset[j]); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,MATCH) ) { *reti = i - 0; *retj = j - 1; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-1,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,MATCH); } warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); default: warn("Major problem (!) - in CloneWise read off, position %d,%d state %d no source found!",i,j,state); return (-1); } /* end of Switch state */ } /* Function: max_calc_special_CloneWise(mat,i,j,state,isspecial,reti,retj,retstate,retspecial,cellscore) * * Descrip: No Description * * Arg: mat [UNKN ] Undocumented argument [CloneWise *] * 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_CloneWise(CloneWise * 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) = CloneWise_READ_OFF_ERROR; if( j < 0 || j > mat->t->length) { warn("In CloneWise matrix special read off - out of bounds on matrix [j is %d in special]",j); return -1; } cscore = CloneWise_EXPL_SPECIAL(mat,i,j,state); switch(state) { /*switch on special states*/ case START : case TRUSTED_SPECIAL : /* source SKIP_TARGET is from main matrix */ for(i= mat->q->length-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->target_special_s) - (0); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,SKIP_TARGET) ) { *reti = i - 0; *retj = j - 0; *retstate = SKIP_TARGET; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-0,SKIP_TARGET); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,SKIP_TARGET) ; } } /* end of for i >= 0 */ /* source SKIP_QUERY is from main matrix */ for(i= mat->q->length-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->target_special_s) - (0); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,SKIP_QUERY) ) { *reti = i - 0; *retj = j - 0; *retstate = SKIP_QUERY; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-0,SKIP_QUERY); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,SKIP_QUERY) ; } } /* end of for i >= 0 */ /* source MATCH is from main matrix */ for(i= mat->q->length-1;i >= 0 ;i--) { /*for i >= 0*/ temp = cscore - (mat->target_special_s) - (0); if( temp == CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,MATCH) ) { *reti = i - 0; *retj = j - 0; *retstate = MATCH; *retspecial = FALSE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_MATRIX(mat,i-0,j-0,MATCH); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 0,MATCH) ; } } /* end of for i >= 0 */ /* source TRUSTED_SPECIAL is a special */ temp = cscore - ((mat->match->skip_jset[j]-1)) - (0); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 0,j - 1,TRUSTED_SPECIAL) ) { *reti = i - 0; *retj = j - 1; *retstate = TRUSTED_SPECIAL; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-0,j-1,TRUSTED_SPECIAL); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,TRUSTED_SPECIAL) ; } /* source START is a special */ temp = cscore - (0) - (0); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 0,j - 1,START) ) { *reti = i - 0; *retj = j - 1; *retstate = START; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-0,j-1,START); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,START) ; } case END : /* source TRUSTED_SPECIAL is a special */ temp = cscore - (0) - (0); if( temp == CloneWise_EXPL_SPECIAL(mat,i - 0,j - 1,TRUSTED_SPECIAL) ) { *reti = i - 0; *retj = j - 1; *retstate = TRUSTED_SPECIAL; *retspecial = TRUE; if( cellscore != NULL) { *cellscore = cscore - CloneWise_EXPL_SPECIAL(mat,i-0,j-1,TRUSTED_SPECIAL); } return CloneWise_EXPL_MATRIX(mat,i - 0,j - 1,TRUSTED_SPECIAL) ; } default: warn("Major problem (!) - in CloneWise 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_CloneWise(mat) * * Descrip: This function calculates the CloneWise matrix when in explicit mode * To allocate the matrix use /allocate_Expl_CloneWise * * * Arg: mat [UNKN ] CloneWise which contains explicit basematrix memory [CloneWise *] * * Return [UNKN ] Undocumented return value [boolean] * */ boolean calculate_CloneWise(CloneWise * mat) { int i; int j; int leni; int lenj; int tot; int num; if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT ) { warn("in calculate_CloneWise, passed a non Explicit matrix type, cannot calculate!"); return FALSE; } leni = mat->leni; lenj = mat->lenj; tot = leni * lenj; num = 0; start_reporting("CloneWise Matrix calculation: "); for(j=0;jmatch->matrix[i][j]+1); /* From state MATCH to state MATCH */ temp = CloneWise_EXPL_MATRIX(mat,i-0,j-1,MATCH) + 0; if( temp > score ) { score = temp; } /* From state MATCH to state MATCH */ temp = CloneWise_EXPL_MATRIX(mat,i-1,j-0,MATCH) + 0; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state MATCH */ temp = CloneWise_EXPL_MATRIX(mat,i-1,j-1,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state MATCH */ temp = CloneWise_EXPL_MATRIX(mat,i-1,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-1) == 0 && (j-1) == 0 ) { /* From state START to state MATCH */ temp = CloneWise_EXPL_SPECIAL(mat,i-1,j-1,START) + 0; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for MATCH */ /* Add any movement independant score and put away */ score += mat->match->matrix[i][j]; CloneWise_EXPL_MATRIX(mat,i,j,MATCH) = score; /* state MATCH is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state MATCH */ /* For state SKIP_QUERY */ /* setting first movement to score */ score = CloneWise_EXPL_MATRIX(mat,i-1,j-0,MATCH) + mat->query_skip_start; /* From state SKIP_TARGET to state SKIP_QUERY */ temp = CloneWise_EXPL_MATRIX(mat,i-1,j-0,SKIP_TARGET) + mat->query_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_QUERY to state SKIP_QUERY */ temp = CloneWise_EXPL_MATRIX(mat,i-1,j-0,SKIP_QUERY) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-1) == 0 && (j-0) == 0 ) { /* From state START to state SKIP_QUERY */ temp = CloneWise_EXPL_SPECIAL(mat,i-1,j-0,START) + mat->query_skip_start; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for SKIP_QUERY */ /* Add any movement independant score and put away */ score += mat->match->skip_iset[i]; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_QUERY) = score; /* state SKIP_QUERY is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state SKIP_QUERY */ /* For state SKIP_TARGET */ /* setting first movement to score */ score = CloneWise_EXPL_MATRIX(mat,i-0,j-1,MATCH) + mat->target_skip_start; /* From state SKIP_QUERY to state SKIP_TARGET */ temp = CloneWise_EXPL_MATRIX(mat,i-0,j-1,SKIP_QUERY) + mat->target_skip_start; if( temp > score ) { score = temp; } /* From state SKIP_TARGET to state SKIP_TARGET */ temp = CloneWise_EXPL_MATRIX(mat,i-0,j-1,SKIP_TARGET) + 0; if( temp > score ) { score = temp; } /* Has restricted position */ if( (i-0) == 0 && (j-1) == 0 ) { /* From state START to state SKIP_TARGET */ temp = CloneWise_EXPL_SPECIAL(mat,i-0,j-1,START) + mat->target_skip_start; if( temp > score ) { score = temp; } } /* Ok - finished max calculation for SKIP_TARGET */ /* Add any movement independant score and put away */ score += mat->match->skip_jset[j]; CloneWise_EXPL_MATRIX(mat,i,j,SKIP_TARGET) = score; /* state SKIP_TARGET is a source for special TRUSTED_SPECIAL */ temp = score + (mat->target_special_s) + (0) ; if( temp > CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) ) { CloneWise_EXPL_SPECIAL(mat,i,j,TRUSTED_SPECIAL) = temp; } /* Finished calculating state SKIP_TARGET */ } /* Special state START has no special to special movements */ /* Special state TRUSTED_SPECIAL has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_EXPL_SPECIAL(mat,0,j,TRUSTED_SPECIAL); /* Source START is a special source for TRUSTED_SPECIAL */ /* Has restricted position */ if( (j-1) == 0 ) { temp = CloneWise_EXPL_SPECIAL(mat,0,j - 1,START) + (0) + (0); if( temp > score ) score = temp; } /* Source TRUSTED_SPECIAL is a special source for TRUSTED_SPECIAL */ temp = CloneWise_EXPL_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + ((mat->match->skip_jset[j]-1)) + (0); if( temp > score ) score = temp; /* Source MATCH for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_QUERY for state TRUSTED_SPECIAL is not special... already calculated */ /* Source SKIP_TARGET for state TRUSTED_SPECIAL is not special... already calculated */ /* Put back score... (now updated!) */ CloneWise_EXPL_SPECIAL(mat,0,j,TRUSTED_SPECIAL) = score; /* Finished updating state TRUSTED_SPECIAL */ /* Special state END has special to speical */ /* Set score to current score (remember, state probably updated during main loop */ score = CloneWise_EXPL_SPECIAL(mat,0,j,END); /* Source TRUSTED_SPECIAL is a special source for END */ /* Has restricted position */ if( j == mat->lenj-1 ) { temp = CloneWise_EXPL_SPECIAL(mat,0,j - 1,TRUSTED_SPECIAL) + (0) + (0); if( temp > score ) score = temp; } /* Put back score... (now updated!) */ CloneWise_EXPL_SPECIAL(mat,0,j,END) = score; /* Finished updating state END */ } stop_reporting(); return TRUE; } /* Function: CloneWise_alloc(void) * * Descrip: Allocates structure: assigns defaults if given * * * * Return [UNKN ] Undocumented return value [CloneWise *] * */ CloneWise * CloneWise_alloc(void) { CloneWise * out;/* out is exported at end of function */ /* call ckalloc and see if NULL */ if((out=(CloneWise *) ckalloc (sizeof(CloneWise))) == NULL) { warn("CloneWise_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_CloneWise(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 [CloneWise *] * * Return [UNKN ] Undocumented return value [CloneWise *] * */ CloneWise * free_CloneWise(CloneWise * obj) { if( obj == NULL) { warn("Attempting to free a NULL pointer to a CloneWise 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->q is linked in */ /* obj->t is linked in */ /* obj->match is linked in */ /* obj->target_skip_start is linked in */ /* obj->target_skip is linked in */ /* obj->query_skip_start is linked in */ /* obj->query_skip is linked in */ /* obj->spread is linked in */ /* obj->target_special_s is linked in */ ckfree(obj); return NULL; } #ifdef _cplusplus } #endif