/*******************************
* Alignment2SequencePrompter
*******************************/
QString Alignment2SequencePrompter::composeRichDoc() {
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_MSA_PORT_ID()));
Actor* producer = input->getProducer(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId());
QString source = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
return tr("Split alignment%1 into sequences.").arg(source);
}
QString ClustalWPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_MSA_PORT_ID()));
Actor* producer = input->getProducer(BasePorts::IN_MSA_PORT_ID());
QString producerName = producer ? tr(" from %1").arg(producer->getLabel()) : "";
QString doc = tr("Aligns each MSA supplied <u>%1</u> with \"<u>ClustalW</u>\".")
.arg(producerName);
return doc;
}
QString MergeFastqPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BaseNGSWorker::INPUT_PORT));
const Actor* producer = input->getProducer(BaseSlots::URL_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
QString doc = tr("Merges input sequences %1.").arg(producerName);
return doc;
}
QString QualityTrimPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BaseNGSWorker::INPUT_PORT));
const Actor* producer = input->getProducer(BaseSlots::URL_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr("<u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
QString doc = tr("Trim input sequence %1 from the end, using the quality threshold.").arg(producerName);
return doc;
}
/*******************************
* FilterSequencePrompter
*******************************/
QString PassFilterPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort("in-data"));
Actor* producer = input->getProducer(BaseSlots::TEXT_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr("<u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
QString passVals = getRequiredParam(BaseSlots::TEXT_SLOT().getId());
passVals = getHyperlink(BaseSlots::TEXT_SLOT().getId(), passVals);
QString res = tr("Filters input data from %1 by value(s) %2.").arg(producerName).arg(passVals);
return res;
}
QString CollocationPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* seqProducer = input->getProducer(SEQ_SLOT);
QString seqName = seqProducer ? tr(" sequence from <u>%1</u>").arg(seqProducer->getLabel()) : "";
QString annName = getProducers(BasePorts::IN_SEQ_PORT_ID(), FEATURE_TABLE_SLOT);
if (!annName.isEmpty()) {
annName = tr(" set of annotations from <u>%1</u>").arg(annName);
}
QString data;
if (seqName.isEmpty() && annName.isEmpty()) {
//return "<font color='red'>"+tr("unset")+"</font>";
} else if (!seqName.isEmpty() && !annName.isEmpty()) {
data = tr("For each %1 and %2,").arg(seqName).arg(annName);
} else {
data = tr("For each %1%2,").arg(seqName).arg(annName);
}
QString annotations;
QStringList names = annotations.split(QRegExp("\\W+"), QString::SkipEmptyParts).toSet().toList();
annotations = names.join(", ");
if (annotations.isEmpty()) {
annotations = getRequiredParam(ANN_ATTR);
}
annotations = getHyperlink(ANN_ATTR, annotations);
int distance = getParameter(LEN_ATTR).toInt();
bool mode = getParameter(FIT_ATTR).toBool();
QString extra;
if (mode) {
extra = tr(" Annotations themselves may not span beyond the region.");
}
QString resultName = getHyperlink(NAME_ATTR, getRequiredParam(NAME_ATTR));
QString doc = tr("%1 look if <u>%2</u> annotations appear collocated within same region of length <u>%3</u>.%4"
"<br>Output the list of found regions annotated as <u>%5</u>.")
.arg(data) //sequence from Read Fasta 1
.arg(annotations)
.arg(getHyperlink(LEN_ATTR, distance))
.arg(extra)
.arg(resultName);
return doc;
}
/******************************
* RepeatPrompter
******************************/
QString RepeatPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* producer = input->getProducer(BaseSlots::DNA_SEQUENCE_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
// TODO extend ?
QString resultName = getRequiredParam(NAME_ATTR);
QString inverted = getParameter(INVERT_ATTR).toBool() ? tr("inverted") : tr("direct");
QString doc = tr("For each sequence%1, find <u>%2</u> repeats."
"<br>Detect <u>%3% identical</u> repeats <u>not shorter than %4 bps</u>."
"<br>Output the list of found regions annotated as <u>%5</u>.")
.arg(producerName) //sequence from Read Fasta 1
.arg(getHyperlink(INVERT_ATTR, inverted))
.arg(getHyperlink(IDENTITY_ATTR, getParameter(IDENTITY_ATTR).toInt()))
.arg(getHyperlink(LEN_ATTR, getParameter(LEN_ATTR).toInt()))
.arg(getHyperlink(NAME_ATTR, resultName));
return doc;
}
/*****************************
* ORFPrompter
*****************************/
QString ORFPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* producer = input->getProducer(BaseSlots::DNA_SEQUENCE_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
ORFAlgorithmSettings cfg;
cfg.strand = getStrand(getParameter(BaseAttributes::STRAND_ATTRIBUTE().getId()).value<QString>());
cfg.minLen = getParameter(LEN_ATTR).toInt();
cfg.mustFit = getParameter(FIT_ATTR).toBool();
cfg.mustInit = getParameter(INIT_ATTR).toBool();
cfg.allowAltStart = getParameter(ALT_ATTR).toBool();
cfg.includeStopCodon = getParameter(ISC_ATTR).toBool();
QString extra;
if (!cfg.mustInit) {
QString anyLink = getHyperlink(INIT_ATTR, tr("starting with any codon"));
extra += tr(", allow ORFs %1 other than terminator").arg(anyLink);
} else if (cfg.allowAltStart) {
QString altLink = getHyperlink(ALT_ATTR, tr("alternative start codons"));
extra += tr(", take into account %1").arg(altLink);
}
if (cfg.mustFit) {
QString mustFitLink = getHyperlink(FIT_ATTR, tr("ignore non-terminated"));
extra += tr(", %1 ORFs").arg(mustFitLink);
}
QString strandName;
switch (cfg.strand) {
case ORFAlgorithmStrand_Both:
strandName = ORFWorker::tr("both strands");
break;
case ORFAlgorithmStrand_Direct:
strandName = ORFWorker::tr("direct strand");
break;
case ORFAlgorithmStrand_Complement:
strandName = ORFWorker::tr("complement strand");
break;
}
strandName = getHyperlink(BaseAttributes::STRAND_ATTRIBUTE().getId(), strandName);
QString resultName = getHyperlink(NAME_ATTR, getRequiredParam(NAME_ATTR));
QString transId = getParameter(ID_ATTR).toString();
QString ttName = AppContext::getDNATranslationRegistry()->
lookupTranslation(AppContext::getDNAAlphabetRegistry()->findById(BaseDNAAlphabetIds::NUCL_DNA_DEFAULT()), DNATranslationType_NUCL_2_AMINO, transId)->getTranslationName();
ttName = getHyperlink(ID_ATTR, ttName);
QString doc = tr("For each nucleotide sequence%1, find ORFs in <u>%2</u> using the <u>%3</u>."
"<br>Detect only ORFs <u>not shorter than %4 bps</u>%5."
"<br>Output the list of found regions annotated as <u>%6</u>.")
.arg(producerName) //sequence from Read Fasta 1
.arg(strandName) //both strands
.arg(ttName) //Standard Genetic Code
.arg(getHyperlink(LEN_ATTR, cfg.minLen)) //100
.arg(extra) // take into account alternative start codons.
.arg(resultName);
return doc;
}