Commit e52ef6a1 authored by Olivier Langella's avatar Olivier Langella
Browse files

write annotations in quantification ODS reports

parent 12c48861
......@@ -7,7 +7,7 @@ DM-Upload-Allowed: yes
Standards-Version: 3.9.1.0
Build-Depends: debhelper (>= 5), cmake (>= 2.6), libx11-dev, libc6-dev, libqt4-dev (>= 4.6.3),
libqwt5-qt4-dev (>=5.2.0), texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended,
texlive-science, hevea, inkscape, doxygen, libpappsomspp-dev (>=0.2.8), libodsstream-dev
texlive-science, hevea, inkscape, doxygen, libpappsomspp-dev (>=0.2.8), libodsstream-dev (>=0.4.4)
Build-Conflicts: qt3-dev-tools
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
......
......@@ -74,31 +74,39 @@ void MonitorComparInterfaceOutput::writeQuantifyBegin(const Quantificator * p_qu
void MonitorComparInterfaceOutput::writeQuantifyEnd() {
qDebug() << "MonitorComparInterfaceOutput::writeQuantifyEnd begin";
//sort quanti items :
sort(_qitem_list.begin(), _qitem_list.end(), [](const QuantiItemBase * l1, const QuantiItemBase * l2) {
return (l1->getMzId() < l2->getMzId());
}
);
);
//sort samples :
sort(_msrun_list.begin(), _msrun_list.end(), [](const Msrun * l1, const Msrun * l2) {
return (l1->getXmlId() < l2->getXmlId());
}
);
);
//write headers
_p_writer->writeLine();
//mzid peptide m/z z sequence mods proteins
_p_writer->writeEmptyCell();
_p_writer->setCellAnnotation("peptide id");
_p_writer->writeCell("peptide");
_p_writer->writeCell("m/z");
_p_writer->setCellAnnotation("peptide charge");
_p_writer->writeCell("z");
_p_writer->setCellAnnotation("natural isotope number");
_p_writer->writeCell("isotope number");
_p_writer->setCellAnnotation("natural isotope rank");
_p_writer->writeCell("isotope rank");
_p_writer->setCellAnnotation("natural isotope theoretical ratio");
_p_writer->writeCell("isotope ratio");
_p_writer->setCellAnnotation("peptide sequence");
_p_writer->writeCell("sequence");
_p_writer->setCellAnnotation("peptide modifications (free text)");
_p_writer->writeCell("mods");
_p_writer->setCellAnnotation("protein ids");
_p_writer->writeCell("proteins");
for (const Msrun * p_msrun : _msrun_list) {
_p_writer->writeCell(p_msrun->getXmlId());
......@@ -108,7 +116,7 @@ void MonitorComparInterfaceOutput::writeQuantifyEnd() {
for (const QuantiItemBase * qitem : _qitem_list) {
_p_writer->writeLine();
_p_writer->writeCell(qitem->getMzId());
qitem->writeOdsComparHeaderLine(*_p_writer);
qitem->writeOdsComparHeaderLine(*_p_writer);
std::map<const QuantiItemBase *, std::map<const Msrun *, pappso::pappso_double>>::const_iterator it_qitem = _compar_table.find(qitem);
if (it_qitem != _compar_table.end()) {
for (const Msrun * p_msrun : _msrun_list) {
......@@ -122,7 +130,7 @@ void MonitorComparInterfaceOutput::writeQuantifyEnd() {
}
}
}
_compar_table.clear();
_msrun_list.clear();
_qitem_list.clear();
......
......@@ -79,20 +79,34 @@ void MonitorOdsInterfaceOutput::writeQuantifyBegin(const Quantificator * p_quant
_p_writer->writeCell("group");
_p_writer->writeCell("msrun");
_p_writer->writeCell("msrunfile");
_p_writer->setCellAnnotation("XIC m/z");
_p_writer->writeCell("mz");
_p_writer->setCellAnnotation("peak maximum intensity retention time");
_p_writer->writeCell("rt");
_p_writer->setCellAnnotation("peak maximum intensity");
_p_writer->writeCell("maxintensity");
_p_writer->setCellAnnotation("peak area");
_p_writer->writeCell("area");
_p_writer->setCellAnnotation("peak start retention time");
_p_writer->writeCell("rtbegin");
_p_writer->setCellAnnotation("peak stop retention time");
_p_writer->writeCell("rtend");
_p_writer->setCellAnnotation("peptide id");
_p_writer->writeCell("peptide");
_p_writer->setCellAnnotation("isotope tags");
_p_writer->writeCell("isotope");
_p_writer->setCellAnnotation("peptide sequence");
_p_writer->writeCell("sequence");
_p_writer->setCellAnnotation("peptide charge");
_p_writer->writeCell("z");
_p_writer->setCellAnnotation("peptide modifications (free text)");
_p_writer->writeCell("mods");
if (p_quantificator->getNiMinimumAbundance() != 0) {
_p_writer->setCellAnnotation("natural isotope number");
_p_writer->writeCell("ninumber");
_p_writer->setCellAnnotation("natural isotope rank");
_p_writer->writeCell("nirank");
_p_writer->setCellAnnotation("natural isotope theoretical ratio");
_p_writer->writeCell("niratio");
}
......
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