/**
* @brief copies an mseq structure
*
* @param[out] prMSeqDest_p
* Copy of mseq structure
* @param[in] prMSeqSrc
* Source mseq structure to copy
*
* @note caller has to free copy by calling FreeMSeq()
*
*/
void
CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc)
{
int i;
assert(prMSeqSrc != NULL && prMSeqDest_p != NULL);
NewMSeq(prMSeqDest_p);
(*prMSeqDest_p)->nseqs = prMSeqSrc->nseqs;
(*prMSeqDest_p)->seqtype = prMSeqSrc->seqtype;
if (prMSeqSrc->filename!=NULL) {
(*prMSeqDest_p)->filename = CkStrdup(prMSeqSrc->filename);
}
(*prMSeqDest_p)->seq = (char **)
CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *));
(*prMSeqDest_p)->orig_seq = (char **)
CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *));
(*prMSeqDest_p)->sqinfo = (SQINFO *)
CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(SQINFO));
for (i=0; i<(*prMSeqDest_p)->nseqs; i++) {
(*prMSeqDest_p)->seq[i] = CkStrdup(prMSeqSrc->seq[i]);
(*prMSeqDest_p)->orig_seq[i] = CkStrdup(prMSeqSrc->orig_seq[i]);
SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[i], &prMSeqSrc->sqinfo[i]);
}
}
/**
*
* @brief the 'real' main function
*
*/
int
MyMain(int argc, char **argv)
{
mseq_t *prMSeq = NULL;
mseq_t *prMSeqProfile1 = NULL;
mseq_t *prMSeqProfile2 = NULL;
cmdline_opts_t cmdline_opts;
/* Must happen first: setup logger */
LogDefaultSetup(&rLog);
/*Log(&rLog, LOG_WARN, "This is a non-public realase of %s. Please do not distribute.", PACKAGE_NAME);*/
/*Log(&rLog, LOG_WARN, "This is a beta version of %s, for protein only.", PACKAGE_NAME);*/ /* FS, r237 -> 238 */
SetDefaultUserOpts(&(cmdline_opts));
ParseCommandLine(&cmdline_opts, argc, argv);
if (NULL != cmdline_opts.pcLogFile) {
prLogFile = fopen(cmdline_opts.pcLogFile, "w");
LogSetFP(&rLog, LOG_INFO, prLogFile);
LogSetFP(&rLog, LOG_VERBOSE, prLogFile);
LogSetFP(&rLog, LOG_DEBUG, prLogFile);
}
InitClustalOmega(cmdline_opts.iThreads);
if (rLog.iLogLevelEnabled < LOG_INFO) {
PrintUserOpts(LogGetFP(&rLog, LOG_INFO), & cmdline_opts);
PrintAlnOpts(LogGetFP(&rLog, LOG_INFO), & (cmdline_opts.aln_opts));
}
/* Read sequence file
*
*/
if (NULL != cmdline_opts.pcSeqInfile) {
NewMSeq(&prMSeq);
if (ReadSequences(prMSeq, cmdline_opts.pcSeqInfile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", cmdline_opts.pcSeqInfile);
}
#if TRACE
{
int iAux;
for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: seq = %s", iAux, prMSeq->seq[iAux]);
LogSqInfo(&prMSeq->sqinfo[iAux]);
}
}
#endif
}
/* k-tuple pairwise distance calculation seg-faults if
* only one sequence, simply exit early.
* note that for profile/profile alignment prMSeq is NULL
* FS, r222->r223 */
if (prMSeq && (prMSeq->nseqs <= 1)){
Log(&rLog, LOG_FATAL, "File '%s' contains %d sequence%s, nothing to align",
cmdline_opts.pcSeqInfile, prMSeq->nseqs, 1==prMSeq->nseqs?"":"s");
}
/* Dealign if requested and neccessary
*/
if (NULL != prMSeq) {
if (TRUE == prMSeq->aligned && cmdline_opts.bDealignInputSeqs) {
Log(&rLog, LOG_INFO, "Dealigning already aligned input sequences as requested.");
DealignMSeq(prMSeq);
}
}
/* Read profile1
*
*/
if (NULL != cmdline_opts.pcProfile1Infile) {
NewMSeq(&prMSeqProfile1);
if (ReadSequences(prMSeqProfile1, cmdline_opts.pcProfile1Infile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile1Infile);
}
/* FIXME: commented out. FS, r240 -> r241
* for explanation see below */
/*if (1==prMSeqProfile1->nseqs) {
Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
cmdline_opts.pcProfile1Infile);
}*/
if (FALSE == prMSeqProfile1->aligned) {
Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
cmdline_opts.pcProfile1Infile);
}
}
/* Read profile2
*
*/
if (NULL != cmdline_opts.pcProfile2Infile) {
NewMSeq(&prMSeqProfile2);
if (ReadSequences(prMSeqProfile2, cmdline_opts.pcProfile2Infile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile2Infile);
}
/* FIXME: there is no (clean) way to align a single sequence to a profile.
* if we go down the -i route, it causes a seg-fault in the pair-wise
* k-tuple distance calculation. However, single sequences can be
* understood as 1-profiles. Therefore we have to allow for 1-profiles.
* FS, r240 -> r241
*/
/*if (1==prMSeqProfile2->nseqs) {
Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
cmdline_opts.pcProfile2Infile);
}*/
if (FALSE == prMSeqProfile1->aligned) {
Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
cmdline_opts.pcProfile2Infile);
}
}
/* Depending on the input we got perform
*
* (i) normal alignment: seq + optional profile
* or
* (ii) profile profile alignment
*
*/
if (NULL != prMSeq) {
if (Align(prMSeq, prMSeqProfile1, & cmdline_opts.aln_opts)) {
Log(&rLog, LOG_FATAL, "An error occured during the alignment");
}
if (WriteAlignment(prMSeq, cmdline_opts.pcAlnOutfile,
cmdline_opts.iAlnOutFormat)) {
Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
}
#if 0
{
bool bSampling = FALSE; /* better set to TRUE for many sequences */
bool bReportAll = TRUE;
AliStat(prMSeq, bSampling, bReportAll);
}
#endif
} else if (NULL != prMSeqProfile1 && NULL != prMSeqProfile2) {
if (AlignProfiles(prMSeqProfile1, prMSeqProfile2,
cmdline_opts.aln_opts.rHhalignPara)) {
Log(&rLog, LOG_FATAL, "An error occured during the alignment");
}
if (WriteAlignment(prMSeqProfile1, cmdline_opts.pcAlnOutfile,
cmdline_opts.iAlnOutFormat)) {
Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
}
}
/* cleanup
*/
if (NULL != prMSeq) {
FreeMSeq(&prMSeq);
}
if (NULL != prMSeqProfile1) {
FreeMSeq(&prMSeqProfile1);
}
if (NULL != prMSeqProfile2) {
FreeMSeq(&prMSeqProfile2);
}
FreeUserOpts(&cmdline_opts);
Log(&rLog, LOG_DEBUG, "Successful program exit");
if (NULL != cmdline_opts.pcLogFile) {
fclose(prLogFile);
}
return EXIT_SUCCESS;
}
