sumatra version 1.0.02
This commit is contained in:
Celine Mercier
317
mtcompare_sumatra.c
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317
mtcompare_sumatra.c
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/*
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* mtcompare.c
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*
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* Created on: 17 ao<61>t 2010
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* Authors: Eric Coissac, Celine Mercier
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*/
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#include <pthread.h>
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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include "sumatra.h"
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#include "../sumalibs/libfasta/sequence.h"
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#include "../sumalibs/libutils/utilities.h"
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#include "../sumalibs/liblcs/upperband.h"
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#include "../sumalibs/liblcs/sse_banded_LCS_alignment.h"
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typedef struct {
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int32_t tocompute; // next line to compute
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int64_t computed; // count of alignment computed
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int32_t thread_count; // count of active thread
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int32_t tokill;
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pthread_t *threads;
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pthread_mutex_t m_tocompute;
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pthread_mutex_t m_thread_count;
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pthread_mutex_t m_incharge;
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pthread_mutex_t m_print;
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pthread_mutex_t m_tokill;
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pthread_mutex_t m_finished;
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int32_t lineset;
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int64_t pairs;
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fastaSeqCount *db1;
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fastaSeqCount *db2;
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BOOL normalize;
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BOOL lcsmode;
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int reference;
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BOOL extradata;
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BOOL always;
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double threshold;
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int16_t** addresses;
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int16_t** iseqs1;
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int16_t** iseqs2;
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int sizeForSeqs;
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} thread_control_t;
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void printLine(fastaSeqPtr seq1, fastaSeqPtr seq2, int32_t seqcount, double *score, BOOL extradata, int64_t pairs)
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{
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int j;
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for (j=0; j < seqcount; j++,seq2++,score++)
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printResults(seq1,seq2,*score,extradata,pairs,(*score >=0));
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}
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void *computeline(void* c)
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{
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thread_control_t *control=(thread_control_t*)c;
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int32_t line;
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int32_t start;
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int32_t end;
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int32_t threadid;
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int32_t i,j;
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double *score;
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double *scores;
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fastaSeqPtr db2;
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fastaSeqPtr db1;
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fastaSeqPtr sq2;
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fastaSeqPtr sq1;
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char* s1;
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int l1;
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int LCSmin;
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threadid = control->thread_count++;
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pthread_mutex_unlock(&(control->m_thread_count));
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db1 = control->db1->fastaSeqs;
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if (control->db2)
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{
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end = control->db2->count;
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db2 = control->db2->fastaSeqs;
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}
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else
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{
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end = control->db1->count;
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db2 = control->db1->fastaSeqs;
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}
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scores = (double*)malloc(end * sizeof(double));
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while (control->tocompute < control->db1->count)
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{
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pthread_mutex_lock(&(control->m_tocompute));
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line = control->tocompute;
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pthread_mutex_unlock(&(control->m_incharge));
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if (line < control->db1->count)
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{
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for (i=0,sq1=db1+line; i < control->lineset && (i+line) < control->db1->count; i++,sq1++)
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{
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s1 = sq1->sequence;
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l1 = sq1->length;
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start = (control->db2) ? 0:line+i+1;
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for (score=scores,j=start; j < end ; j++,score++)
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{
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sq2=db2+j;
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filtersSumatra(sq1, sq2, control->threshold, control->normalize, control->reference, control->lcsmode, score, &LCSmin);
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if (control->always || (*score == -1.0))
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{
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*score = alignForSumathings(s1, *((control->iseqs1)+threadid), sq2->sequence, *((control->iseqs2)+threadid), l1, sq2->length,
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control->normalize, control->reference, control->lcsmode, *((control->addresses)+threadid), control->sizeForSeqs, LCSmin);
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if (!control->always && (((*score < control->threshold) && (control->lcsmode || control->normalize)) || ((!control->lcsmode && !control->normalize) && (*score > control->threshold))))
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*score = -1.0;
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else if (!control->lcsmode && control->normalize)
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*score = 1.0 - *score;
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}
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else if (*score == -2.0)
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*score = -1.0;
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}
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pthread_mutex_lock(&(control->m_print));
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printLine(sq1,db2+start,end-start,scores,control->extradata,control->pairs);
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pthread_mutex_unlock(&(control->m_print));
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}
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}
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}
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pthread_mutex_unlock(&(control->m_incharge));
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free(scores);
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pthread_mutex_lock(&(control->m_finished));
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control->tokill=threadid;
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pthread_mutex_unlock(&(control->m_tokill));
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return (void*)threadid;
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}
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int mt_compare_sumatra(fastaSeqCount *db1, fastaSeqCount *db2, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata, int n)
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{
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int64_t pairs;
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thread_control_t control;
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int32_t i;
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int lmax, lmax1;
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int lmin, lmin1;
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if (db2==NULL)
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{
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fprintf(stderr,"Pairwise alignment of one database against itself\n");
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pairs = (int64_t)(db1->count - 1) * (int64_t)db1->count /2;
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}
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else
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{
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fprintf(stderr,"Pairwise alignment of two databases\n");
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pairs = (int64_t)db1->count * (int64_t)db2->count;
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}
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fprintf(stderr,"Count of alignment to do : %lld\n",pairs);
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control.addresses = (int16_t**) malloc(n*sizeof(int16_t*));
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control.iseqs1 = (int16_t**) malloc(n*sizeof(int16_t*));
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control.iseqs2 = (int16_t**) malloc(n*sizeof(int16_t*));
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calculateMaxAndMinLenDB(*db1, &lmax, &lmin);
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if (!(db2==NULL))
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{
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calculateMaxAndMinLenDB(*db2, &lmax1, &lmin1);
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if (lmax1 > lmax)
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lmax = lmax1;
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if (lmin1 < lmin)
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lmin = lmin1;
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}
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for (i=0; i < n; i++)
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control.sizeForSeqs = prepareTablesForSumathings(lmax, lmin, threshold, normalize, reference, lcsmode, (control.addresses)+i, (control.iseqs1)+i, (control.iseqs2)+i);
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control.db1 = db1;
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control.db2 = db2;
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control.tocompute = 0;
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control.normalize = normalize;
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control.reference = reference;
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control.extradata = extradata;
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control.threshold = threshold;
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control.lcsmode = lcsmode;
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control.computed = 0;
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control.thread_count = 0;
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control.pairs = pairs;
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if (n > control.db1->count/2)
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n = control.db1->count/2;
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control.lineset = control.db1->count / n / 2;
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if (threshold > 0)
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{
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fprintf(stderr,"Compute exact LCS only for score > %lf\n", threshold);
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control.always = FALSE;
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}
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else
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control.always=TRUE;
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if (pthread_mutex_init(&(control.m_thread_count),NULL))
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{
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fprintf(stderr,"m_thread_count mutex init error\n");
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exit(1);
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}
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if (pthread_mutex_init(&(control.m_tocompute),NULL))
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{
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fprintf(stderr,"m_tocompute mutex init error\n");
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exit(1);
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}
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if (pthread_mutex_init(&(control.m_incharge),NULL))
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{
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fprintf(stderr,"m_incharge mutex init error\n");
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exit(1);
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}
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if (pthread_mutex_init(&(control.m_print),NULL))
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{
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fprintf(stderr,"m_print mutex init error\n");
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exit(1);
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}
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if (pthread_mutex_init(&(control.m_tokill),NULL))
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{
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fprintf(stderr,"m_tokill mutex init error\n");
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exit(1);
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}
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if (pthread_mutex_init(&(control.m_finished),NULL))
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{
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fprintf(stderr,"m_finished mutex init error\n");
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exit(1);
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}
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control.threads = (pthread_t*)malloc(n * sizeof(pthread_t));
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if (!control.threads)
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{
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fprintf(stderr,"Cannot allocate memory for threads\n");
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exit(2);
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}
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pthread_mutex_lock(&(control.m_thread_count));
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pthread_mutex_lock(&(control.m_tocompute));
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pthread_mutex_lock(&(control.m_incharge));
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pthread_mutex_unlock(&(control.m_print));
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pthread_mutex_lock(&(control.m_tokill));
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pthread_mutex_unlock(&(control.m_finished));
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fprintf(stderr,"\n");
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for (i=0; i < n; i++)
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{
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fprintf(stderr,"Initializing thread...");
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if (pthread_create(control.threads+i,NULL,computeline,&control))
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{
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fprintf(stderr," : thread %d Error\n",i);
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exit(3);
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}
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pthread_mutex_lock(&(control.m_thread_count));
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fprintf(stderr," : thread %d Ok\n",control.thread_count);
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}
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pthread_mutex_unlock(&(control.m_thread_count));
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for (control.tocompute=0;
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control.tocompute < db1->count+1;
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control.tocompute+=control.lineset)
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{
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pthread_mutex_unlock(&(control.m_tocompute));
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pthread_mutex_lock(&(control.m_incharge));
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}
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pthread_mutex_unlock(&(control.m_tocompute));
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fprintf(stderr,"\n");
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for (i=0; i < n; i++)
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{
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pthread_mutex_lock(&(control.m_tokill));
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fprintf(stderr,"Joining thread %d...",control.tokill);
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pthread_mutex_unlock(&(control.m_tocompute));
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pthread_join(control.threads[control.tokill],NULL);
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fprintf(stderr," : Ok\n");
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pthread_mutex_unlock(&(control.m_finished));
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}
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// Freeing
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for (i=0; i < n; i++)
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{
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free((*((control.iseqs1)+i))-(control.sizeForSeqs)+lmax);
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free((*((control.iseqs2)+i))-(control.sizeForSeqs)+lmax);
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}
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free(control.iseqs1);
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free(control.iseqs2);
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if ((reference == ALILEN) && ((lcsmode && normalize) || (!lcsmode)))
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{
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for (i=0; i < n; i++)
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free(*((control.addresses)+i));
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free(control.addresses);
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}
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return 0;
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}
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