void BestPositionFindTask::run() {
U2SequenceObject dnaSeq("sequence", sequenceRef);
QByteArray sequence = dnaSeq.getWholeSequenceData(stateInfo);
CHECK_OP(stateInfo, );
if(sequence.isEmpty()) {
return;
}
if(!inputMsa->getAlphabet()->isCaseSensitive()) {
sequence = sequence.toUpper();
}
const int aliLen = inputMsa->getLength();
const int nSeq = inputMsa->getNumRows();
int similarity = 0;
if(referenceRowId >= 0) {
const MultipleSequenceAlignmentRow row = inputMsa->getMsaRow(referenceRowId);
int iterationsNum = aliLen - sequence.length() + 1;
for (int p = 0; p < iterationsNum; p++ ) {
stateInfo.setProgress(100 * p / iterationsNum);
char c = row->charAt(p);
int selLength = 0;
int patternSimilarity = MSAUtils::getPatternSimilarityIgnoreGaps(row, p, sequence, selLength);
if (U2Msa::GAP_CHAR != c && patternSimilarity > similarity) {
similarity = patternSimilarity;
bestPosition = p;
}
}
} else {
int processedRows = 0;
foreach(const MultipleSequenceAlignmentRow &row, inputMsa->getMsaRows()) {
stateInfo.setProgress(100 * processedRows / nSeq);
for (int p = 0; p < ( aliLen - sequence.length() + 1 ); p++ ) {
char c = row->charAt(p);
int selLength = 0;
int patternSimilarity = MSAUtils::getPatternSimilarityIgnoreGaps(row, p, sequence, selLength);
if (U2Msa::GAP_CHAR != c && patternSimilarity > similarity) {
similarity = patternSimilarity;
bestPosition = p;
}
}
processedRows++;
}
}
}
static SearchQuery* createRevComplQuery(SearchQuery* query, DNATranslation* transl) {
SAFE_POINT(query != NULL, "Query is null", NULL);
SAFE_POINT(transl != NULL, "Transl is null", NULL);
QByteArray reversed(query->constSequence());
TextUtils::reverse(reversed.data(), reversed.count());
DNASequence dnaSeq(QString("%1_rev").arg(query->getName()), reversed, NULL);
SearchQuery *rQu = new SearchQuery(&dnaSeq, query);
transl->translate(const_cast<char*>(rQu->constData()), rQu->length());
if (rQu->constSequence() == query->constSequence()) {
delete rQu; rQu = NULL;
return NULL;
}
query->setRevCompl(rQu);
return rQu;
}
