MSADistanceMatrix::MSADistanceMatrix(const MultipleSequenceAlignment& ma, bool _excludeGaps, bool _usePercents)
: usePercents(_usePercents), excludeGaps(_excludeGaps), alignmentLength(ma->getLength()) {
int nSeq = ma->getNumRows();
table.reserve(nSeq);
for (int i = 0; i < nSeq; i++) {
table.append(QVarLengthArray<int>(i + 1));
memset(table[i].data(), 0, (i + 1) * sizeof(int));
seqsUngappedLenghts.append(ma->getMsaRow(i)->getUngappedLength());
}
}
MuscleTask::MuscleTask(const MultipleSequenceAlignment &ma, const MuscleTaskSettings& _config)
: Task(tr("MUSCLE alignment"), TaskFlags_FOSCOE | TaskFlag_MinimizeSubtaskErrorText),
config(_config),
inputMA(ma->getExplicitCopy())
{
GCOUNTER( cvar, tvar, "MuscleTask" );
config.nThreads = (config.nThreads == 0 ? AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount() : config.nThreads);
SAFE_POINT_EXT(config.nThreads > 0,
setError("Incorrect number of max parallel subtasks"), );
setMaxParallelSubtasks(config.nThreads);
algoLog.info(tr("MUSCLE alignment started"));
ctx = new MuscleContext(config.nThreads);
ctx->params.g_bStable = config.stableMode;
ctx->params.g_uMaxIters = config.maxIterations;
ctx->params.g_ulMaxSecs = config.maxSecs;
parallelSubTask = NULL;
//todo: make more precise estimation, use config.op mode
int aliLen = ma->getLength();
int nSeq = ma->getNumRows();
int memUseMB = qint64(aliLen) * qint64(nSeq) * 200 / (1024 * 1024); //200x per char in alignment
TaskResourceUsage tru(RESOURCE_MEMORY, memUseMB);
QString inputAlName = inputMA->getName();
resultMA->setName(inputAlName);
resultSubMA->setName(inputAlName);
inputSubMA = inputMA->getExplicitCopy();
if (config.alignRegion && config.regionToAlign.length != inputMA->getLength()) {
SAFE_POINT_EXT(config.regionToAlign.length > 0,
setError(tr("Incorrect region to align")), );
inputSubMA = inputMA->mid(config.regionToAlign.startPos, config.regionToAlign.length);
CHECK_EXT(inputSubMA != MultipleSequenceAlignment(), setError(tr("Stopping MUSCLE task, because of error in MultipleSequenceAlignment::mid function")), );
}
void convertMAlignment2MSA(MSA& muscleMSA, const MultipleSequenceAlignment& ma, bool fixAlpha) {
MuscleContext *ctx = getMuscleContext();
ctx->fillUidsVectors(ma->getNumRows());
for (int i=0, n = ma->getNumRows(); i<n; i++) {
const MultipleSequenceAlignmentRow row = ma->getMsaRow(i);
int coreLen = row->getCoreLength();
int maLen = ma->getLength();
char* seq = new char[maLen + 1];
memcpy(seq, row->getCore().constData(), coreLen);
memset(seq + coreLen, '-', maLen - coreLen + 1);
seq[maLen] = 0;
char* name = new char[row->getName().length() + 1];
memcpy(name, row->getName().toLocal8Bit().constData(), row->getName().length());
name[row->getName().length()] = '\0';
muscleMSA.AppendSeq(seq, maLen, name);
ctx->tmp_uIds[i] = ctx->input_uIds[i];
}
if (fixAlpha) {
muscleMSA.FixAlpha();
}
}