本文整理汇总了C++中DNASequence::getName方法的典型用法代码示例。如果您正苦于以下问题:C++ DNASequence::getName方法的具体用法?C++ DNASequence::getName怎么用?C++ DNASequence::getName使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类DNASequence
的用法示例。
在下文中一共展示了DNASequence::getName方法的3个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: runStep
void CASAVAFilterTask::runStep(){
int ncount = 0;
int ycount = 0;
QScopedPointer<IOAdapter> io (IOAdapterUtils::open(settings.outDir + settings.outName, stateInfo, IOAdapterMode_Append));
//1:N:0:TAAGGG
QRegExp pattern (":Y:[^:]:");
FASTQIterator iter(settings.inputUrl);
while(iter.hasNext()){
if(stateInfo.isCoR()){
return;
}
DNASequence seq = iter.next();
QString comment = DNAInfo::getFastqComment(seq.info);
if(pattern.indexIn(comment) != -1){
ycount++;
}else{
FastqFormat::writeEntry(seq.getName() + " " + comment, seq, io.data(), "Writing error", stateInfo, false);
ncount++;
}
}
algoLog.info(QString("Discarded by CASAVA filter %1").arg(ycount));
algoLog.info(QString("Accepted by CASAVA filter %1").arg(ncount));
algoLog.info(QString("Total by CASAVA FILTER: %1").arg(ncount + ycount));
}
示例2: saveSequence
static void saveSequence(IOAdapter* io, const DNASequence& sequence, U2OpStatus& os) {
writeHeaderToFile( io, sequence.getName( ), os );
CHECK_OP( os, );
const char *seq = sequence.seq.constData( );
const int len = sequence.seq.length( );
for ( int i = 0; i < len; i += SAVE_LINE_LEN ) {
const int chunkSize = qMin( SAVE_LINE_LEN, len - i );
writeBlockToFile( io, seq + i, chunkSize, os );
CHECK_OP( os, );
}
}
示例3: runStep
void FastqQualityTrimTask::runStep(){
int ncount = 0;
int ycount = 0;
QScopedPointer<IOAdapter> io(IOAdapterUtils::open(settings.outDir + settings.outName, stateInfo, IOAdapterMode_Append));
int quality = settings.customParameters.value(QUALITY_ID, 20).toInt();
int minLen = settings.customParameters.value(LEN_ID, 0).toInt();
bool bothEnds = settings.customParameters.value(BOTH_ID, false).toInt();
DNAQualityType qualityType = detectQualityType();
CHECK_OP(stateInfo, );
FASTQIterator iter(settings.inputUrl, stateInfo);
CHECK_OP(stateInfo, );
while (iter.hasNext()) {
CHECK_OP(stateInfo, );
DNASequence dna = iter.next();
dna.quality.type = qualityType;
const U2Region acceptedRegion = DNASequenceUtils::trimByQuality(dna, quality, minLen, bothEnds);
if (0 < acceptedRegion.length) {
ycount++;
} else {
ncount++;
continue;
}
FastqFormat::writeEntry(dna.getName(), dna, io.data(), "Writing error", stateInfo, false);
}
algoLog.info(QString("Discarded by trimmer %1").arg(ncount));
algoLog.info(QString("Accepted by trimmer %1").arg(ycount));
algoLog.info(QString("Total by trimmer %1").arg(ncount + ycount));
}