int main( int argc, char * argv[] ){
char * matrixFile = NULL, * queryFile = NULL, * dbFile = NULL;
int i, queryLen;
char * query;
#if defined(__SSE2__)
SWType type = SSE2;
#elif defined(__PS3)
SWType type = PS3;
#elif defined(__ALTIVEC__)
SWType type = ALTIVEC;
#else
SWType type = SCALAR;
#endif
Options options = {-12,-2,DBL_MAX};
int qCount=0, dCount=0, qResidues=0, dResidues=0;
#ifdef HAVE_SYSCONF_NPROCESSORS
int threads = sysconf(_SC_NPROCESSORS_ONLN);
#else
#if defined(__PS3)
int threads = 6;
#else
int threads = 1;
#endif
#endif
SBMatrix matrix;
FastaLib * queryLib;
for ( i=1; i<argc; i++ ){
if (argv[i][0]=='-'){
switch( argv[i][1] ){
case 'h':
matrixFile = NULL;
i = argc; break;
case 's':
type = SCALAR;
break;
case 't':
options.threshold = atoi( argv[++i] );
break;
case 'i':
options.gapOpen = atoi( argv[++i] );
break;
case 'e':
options.gapExt = atoi( argv[++i] );
break;
case 'j':
threads = atoi( argv[++i] );
break;
default:
matrixFile = NULL;
i = argc; break;
}
}else{
if (matrixFile == NULL)
matrixFile = argv[i];
else if (queryFile == NULL)
queryFile = argv[i];
else if (dbFile == NULL)
dbFile = argv[i];
else{
matrixFile = NULL;
i = argc; break;
}
}
}
if ( matrixFile == NULL || queryFile == NULL || dbFile == NULL ){
printf( "Usage: %s [-h] [-s] [-j num] [-i num] [-e num] [-t num] matrix query db\n", argv[0] );
return 0;
}
matrix = swps3_readSBMatrix( matrixFile );
queryLib = swps3_openLib( queryFile );
while ( (query=swps3_readNextSequence( queryLib, &queryLen )) ){
double score = 0;
int *pipes_read;
int *pipes_write;
char **seq_names;
pid_t *children;
int child_id = -1;
int childpipe_read = -1;
int childpipe_write = -1;
FastaLib * dbLib = swps3_openLib( dbFile );
#if defined(__SSE2__)
ProfileByte * profileByte = swps3_createProfileByteSSE( query, queryLen, matrix );
ProfileShort * profileShort = swps3_createProfileShortSSE( query, queryLen, matrix );
#endif
#if defined(__PS3)
SPEProfile * profileByte = swps3_createProfileBytePPU(query, queryLen, matrix, MAX_SEQ_LENGTH);
SPEProfile * profileShort = swps3_createProfileShortPPU(query, queryLen, matrix, MAX_SEQ_LENGTH);
SPEProfile * profileFloat = swps3_createProfileFloatPPU(query, queryLen, matrix, MAX_SEQ_LENGTH);
/* by default byte profile will be loaded */
int current_profile_is_byte = 0;
/* loadProfileByte(profileByte, MAX_SEQ_LENGTH, &options);*/
#endif
#if defined(__ALTIVEC__)
void *profileByteAltivec = swps3_createProfileByteAltivec(query, queryLen, matrix);
void *profileShortAltivec = swps3_createProfileShortAltivec(query, queryLen, matrix);
void *profileFloatAltivec = swps3_createProfileFloatAltivec(query, queryLen, matrix);
#endif
pipes_read = malloc(threads*sizeof(*pipes_read));
pipes_write = malloc(threads*sizeof(*pipes_write));
children = malloc(threads*sizeof(*children));
seq_names = malloc(threads*sizeof(*seq_names));
for(i=0;i<threads;++i) {
pipes_read[i]=-1;
pipes_write[i]=-1;
children[i]=-1;
seq_names[i]=malloc((MAX_SEQ_NAME_LENGTH+1)*sizeof(char));
seq_names[i][MAX_SEQ_NAME_LENGTH]='\0';
}
qCount++; qResidues+=queryLen;
dCount=dResidues=0;
if(threads>1) {
for(i=0; i<threads; ++i) {
int fds[2];
int res;
char *db;
int dbLen;
db=swps3_readNextSequence( dbLib, &dbLen);
strncpy(seq_names[i],swps3_getSequenceName(dbLib),MAX_SEQ_NAME_LENGTH);
if(db == NULL) break;
dResidues+=dbLen;
res = pipe(fds);
if(res < 0) {
perror("error during pipe()");
exit(1);
}
pipes_read[i] = fds[0];
childpipe_write = fds[1];
res = pipe(fds);
if(res < 0) {
perror("error during pipe()");
exit(1);
}
pipes_write[i] = fds[1];
childpipe_read = fds[0];
children[i] = fork();
if(children[i] < 0) {
perror("error during fork()");
exit(1);
} else if(children[i] == 0) {
int j;
for(j=0; j<=i; ++j) {
close(pipes_read[j]);
close(pipes_write[j]);
pipes_read[j] = -1;
pipes_write[j] = -1;
}
child_id = i;
break;
} else {
ssize_t sres;
close(childpipe_read);
close(childpipe_write);
childpipe_read = -1;
childpipe_write = -1;
sres = write_all(pipes_write[i],&dbLen,sizeof(int));
if(sres != sizeof(int)) {
perror("error during write()");
exit(1);
}
sres = write_all(pipes_write[i],db,dbLen);
if(sres != dbLen) {
perror("error during write()");
exit(1);
}
}
}
} else {
childpipe_read = -1;
childpipe_write = -1;
child_id = 0;
}
do {
int dbLen;
char * db;
char * dbName;
if(childpipe_read <= 0) {
db = swps3_readNextSequence( dbLib, &dbLen);
dbName = swps3_getSequenceName(dbLib);
} else {
static char buffer[MAX_SEQ_LENGTH] __ALIGNED__;
ssize_t res;
db = buffer;
res = read_all(childpipe_read,&dbLen,sizeof(int));
if(res != sizeof(int)) {
if(res == 0) exit(0);
perror("error during read()");
exit(1);
}
res = read_all(childpipe_read,db,dbLen);
if(res != dbLen) {
perror("error during read()");
exit(1);
}
dbName = seq_names[child_id];
}
if(child_id == -1) {
fd_set readfds;
int max_fd = -1;
int i;
int res;
FD_ZERO(&readfds);
for(i=0; i<threads; ++i) {
if(pipes_read[i] > 0) FD_SET(pipes_read[i],&readfds);
if(pipes_read[i]>max_fd) max_fd = pipes_read[i];
}
/* all children exited */
if(max_fd == -1) break;
res = select(max_fd+1, &readfds, NULL, NULL, NULL);
if(res <= 0) {
perror("error during select()");
exit(1);
}
for(i=0; i<threads; ++i) {
if(pipes_read[i] > 0 && FD_ISSET(pipes_read[i],&readfds)) {
static char tmpbuff[MAX_SEQ_NAME_LENGTH+1];
char *newName;
res = read_all(pipes_read[i],&score,sizeof(score));
if(res != sizeof(score)) {
perror("error during read()");
exit(1);
}
newName = dbName;
strncpy(tmpbuff,seq_names[i],MAX_SEQ_NAME_LENGTH);
dbName = tmpbuff;
if(db) {
strncpy(seq_names[i],newName,MAX_SEQ_NAME_LENGTH);
res = write_all(pipes_write[i],&dbLen,sizeof(int));
if(res != sizeof(int)) {
perror("error during write()");
exit(1);
}
res = write_all(pipes_write[i],db,dbLen);
if(res != dbLen) {
perror("error during write()");
exit(1);
}
} else {
close(pipes_write[i]);
close(pipes_read[i]);
pipes_write[i] = -1;
pipes_read[i] = -1;
free(seq_names[i]);
seq_names[i] = NULL;
waitpid(children[i],NULL,0);
children[i] = -1;
}
break;
}
}
} else {
if(db == NULL) break;
#ifdef DEBUG
for(i=0; i<queryLen; ++i) printf("\t%c",query[i]);
printf("\n");
#endif
#if defined(__SSE2__)
if(type == SSE2) {
if( (score = swps3_alignmentByteSSE( profileByte, db, dbLen, &options )) >= DBL_MAX ) {
score = swps3_alignmentShortSSE( profileShort, db, dbLen, &options );
assert(score >= 250 && "score too low");
}
}
#endif
#if defined(__PS3)
if(type == PS3) {
#if defined(__ALTIVEC__)
if(child_id == 6) {
#if 0
score = swps3_dynProgrFloatAltivec(db, dbLen, profileFloatAltivec, &options);
#else
score = swps3_dynProgrByteAltivec(db, dbLen, profileByteAltivec, &options);
if(score >= DBL_MAX)
score = swps3_dynProgrShortAltivec(db, dbLen, profileShortAltivec, &options);
#endif
} else {
#endif /* __ALTIVEC__ */
#if 0
loadProfileFloat(profileFloat, MAX_SEQ_LENGTH, &options);
score = alignmentProfileSPE( db, dbLen );
#elif 1
if(!current_profile_is_byte) swps3_loadProfileByte(profileByte, MAX_SEQ_LENGTH, &options);
current_profile_is_byte = 1;
score = swps3_alignmentProfileSPE( db, dbLen );
if( score >= DBL_MAX ) {
if(current_profile_is_byte) swps3_loadProfileShort(profileShort, MAX_SEQ_LENGTH, &options);
current_profile_is_byte = 0;
score = swps3_alignmentProfileSPE( db, dbLen );
}
#elif 1
if(!current_profile_is_byte) swps3_loadProfileShort(profileShort, MAX_SEQ_LENGTH, &options);
current_profile_is_byte = 1;
score = swps3_alignmentProfileSPE( db, dbLen );
#else
score = swps3_alignmentByteSPE( matrix, query, queryLen, db, dbLen, &options );
if( score >= DBL_MAX ) {
score = swps3_alignmentShortSPE( matrix, query, queryLen, db, dbLen, &options );
}
#endif
#if defined(__ALTIVEC__)
}
#endif /* __ALTIVEC__ */
}
#endif /* __PS3 */
#if defined(__ALTIVEC__)
if(type == ALTIVEC) {
#if 0
score = swps3_dynProgrFloatAltivec(db, dbLen, profileFloatAltivec, &options);
#else
score = swps3_dynProgrByteAltivec(db, dbLen, profileByteAltivec, &options);
if(score >= DBL_MAX)
score = swps3_dynProgrShortAltivec(db, dbLen, profileShortAltivec, &options);
}
#endif
#endif /* __ALTIVEC__ */
if(type == SCALAR) {
double dmatrix[MATRIX_DIM*MATRIX_DIM];
for(i=0;i<MATRIX_DIM*MATRIX_DIM;++i) dmatrix[i]=matrix[i];
score = swps3_alignScalar( dmatrix, query, queryLen, db, dbLen, &options);
}
}
if(childpipe_write > 0) {
ssize_t res;
res = write_all(childpipe_write,&score,sizeof(score));
if(res != sizeof(score)) {
perror("error during write()");
exit(1);
}
} else {
if(score >= options.threshold) {
printf(">threshold\t%s\n",dbName);
} else {
printf("%g\t%s\n",score,dbName);
}
}
dCount++; dResidues+=dbLen;
} while(1);
free(pipes_read);
free(pipes_write);
free(children);
free(seq_names);
#if defined(__SSE2__)
swps3_freeProfileByteSSE( profileByte );
swps3_freeProfileShortSSE( profileShort );
#endif
#if defined(__PS3)
swps3_freeProfilePPU( profileByte );
swps3_freeProfilePPU( profileShort );
swps3_freeProfilePPU( profileFloat );
#endif
swps3_closeLib( dbLib );
}
fprintf(stderr,"%d[%d] x %d[%d]\n", qCount, qResidues, dCount, dResidues );
swps3_closeLib( queryLib );
return 0;
}
//changing from const Sequence * known to Sequence * known
int swps3_maxscores ( SBMatrix matrix , Sequence * known, Sequence * test){
int i,queryLen;
const char * query;
//SWType type = SSE2;
Options options = {-12,-2,DBL_MAX};
char * x1;
bool validKnownSeq;
x1 = (char*)malloc(sizeof(char)*known->get_sequence().size());
memcpy(x1, known->get_sequence().c_str(), known->get_sequence().size());
validKnownSeq = swps3_translateSequence(x1,known->get_sequence().size(),NULL);
query = x1;
//query = known->toString().c_str();
queryLen = known->get_sequence().size();
double score = 0;
#ifdef SSE2
ProfileByte * profileByte = swps3_createProfileByteSSE( query, queryLen, matrix );
ProfileShort * profileShort = swps3_createProfileShortSSE( query, queryLen, matrix );
#endif
int dbLen;
const char * db;
char * x2;
bool validTestSeq;
x2 = (char*)malloc(sizeof(char)*test->get_sequence().size());
memcpy(x2, test->get_sequence().c_str(), test->get_sequence().size());
validTestSeq = swps3_translateSequence(x2,test->get_sequence().size(),NULL);
if (validTestSeq) {
db = x2;
//db=test->toString().c_str();
dbLen = test->get_sequence().size();
} else {
printf("sequence %d is corrupt:\nname: %s\ntax_id: %s\nncbi_gi_id: %s\nsequence: %s",
test->get_taxon_name().c_str(),test->get_taxon_name().c_str(),test->get_ncbi_tax_id().c_str(),
test->get_ncbi_gi_number().c_str(),test->get_sequence().c_str());
throw 1;
}
#ifdef DEBUG
for(i=0; i<queryLen; ++i) printf("\t%c",query[i]);
printf("\n");
#endif
#ifdef SSE2
//if(type == SSE2) {
if( (score = swps3_alignmentByteSSE( profileByte, db, dbLen, &options )) >= DBL_MAX ) {
score = swps3_alignmentShortSSE( profileShort, db, dbLen, &options );
//assert(score >= 250 && "score too low");
}
//}
#else
//if(type == SCALAR) {
/*
* doesn't work!!
*/
double dmatrix[MATRIX_DIM*MATRIX_DIM];
for(i=0;i<MATRIX_DIM*MATRIX_DIM;++i) dmatrix[i]=matrix[i];
score = swps3_alignScalar( dmatrix, query, queryLen, db, dbLen, &options);
//}
#endif
#ifdef SSE2
swps3_freeProfileByteSSE( profileByte );
swps3_freeProfileShortSSE( profileShort );
#endif
free(x1);free(x2);
return int(score);
}