sumatra version 1.0.02

Makefile

+EXEC=sumatra
+
+SUMATRA_SRC= sumatra.c \
+			 mtcompare_sumatra.c
+			              
+SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATRA_SRC))
+
+
+SRCS= $(SUMATRA_SRC)
+
+LIB= -lfasta -llcs -lfile -lutils -lz -lm
+
+include ./global.mk
+
+all: $(EXEC)
+
+
+########
+#
+# sumatra compilation
+#
+########
+
+# executable compilation and link
+
+sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
+	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH) $(LIB)
+	
+########
+#
+# project management
+#
+########
+
+clean:
+	rm -f *.o	
+	rm -f *.P
+	rm -f $(EXEC)
+	$(MAKE) -C ../sumalibs/libfasta clean
+	$(MAKE) -C ../sumalibs/liblcs clean
+	$(MAKE) -C ../sumalibs/libfile clean
+	$(MAKE) -C ../sumalibs/libutils clean
+
+		

global.mk

+
+LIBFASTAPATH = -L../sumalibs/libfasta
+LIBLCSPATH   = -L../sumalibs/liblcs
+LIBFILEPATH  = -L../sumalibs/libfile
+LIBUTILSPATH = -L../sumalibs/libutils
+
+LIBFASTA = ../sumalibs/libfasta/libfasta.a
+LIBLCS   = ../sumalibs/liblcs/liblcs.a
+LIBFILE  = ../sumalibs/libfile/libfile.a
+LIBUTILS = ../sumalibs/libutils/libutils.a
+
+CC=gcc
+LDFLAGS=
+
+
+ifeq ($(CC),gcc)
+        CFLAGS = -O3 -s -DOMP_SUPPORT -fopenmp -w
+else
+        CFLAGS = -O3 -w
+endif
+
+
+default: all
+
+%.o: %.c
+	$(CC) $(CFLAGS) -c -o $@ $< $(LIB)
+
+
+########
+#
+# libraries compilation
+#
+########
+
+../sumalibs/libfasta/libfasta.a:
+	$(MAKE) -C ../sumalibs/libfasta
+
+../sumalibs/liblcs/liblcs.a:
+	$(MAKE) -C ../sumalibs/liblcs
+
+../sumalibs/libfile/libfile.a:
+	$(MAKE) -C ../sumalibs/libfile
+
+../sumalibs/libutils/libutils.a:
+	$(MAKE) -C ../sumalibs/libutils
\ No newline at end of file

mtcompare_sumatra.c

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

mtcompare_sumatra.h

+/*
+ * mtcompare_sumatra.h
+ *
+ *  Created on: 12 mars 2013
+ *      Author: celinemercier
+ */
+
+#ifndef MTCOMPARE_SUMATRA_H_
+#define MTCOMPARE_SUMATRA_H_
+
+int mt_compare_sumatra(fastaSeqCount *db1, fastaSeqCount *db2, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata, int n);
+
+#endif /* MTCOMPARE_SUMATRA_H_ */

sumatra.h

+/*
+ * sumatra.h
+ *
+ *  Created on: 8 aot 2010
+ *      Author: coissac
+ */
+
+#ifndef SUMATRA_H_
+#define SUMATRA_H_
+
+#include "../sumalibs/libfasta/sequence.h"
+
+void printResults(fastaSeqPtr seq1, fastaSeqPtr seq2, double score, BOOL extradata, int64_t pairs, BOOL print);
+
+#endif /* SUMATRA_H_ */