Commit f7c02895 authored by Langella Olivier's avatar Langella Olivier
Browse files

#1 solved by accepting obsolete...

#1 solved by accepting obsolete parameters in the read step
parent 4a96afaa
......@@ -129,14 +129,13 @@ TandemParameters::getValue(const QString &label) const
.arg(label)
.arg(_method_name));
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
qDebug();
return it.value();
}
void
TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< label;
qDebug() << label;
// list path
//<note type="input" label="list path, default
// parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
......@@ -147,8 +146,7 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
return;
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< label;
qDebug() << label;
if((label == "spectrum, parent monoisotopic mass error units") ||
(label == "spectrum, fragment monoisotopic mass error units"))
{
......@@ -189,7 +187,9 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "protein, homolog management") ||
(label == "protein, use minimal annotations") ||
(label == "protein, use annotations") ||
(label == "scoring, pluggable scoring"))
(label == "scoring, pluggable scoring") ||
(label == "output, mzid") ||
(label == "spectrum, use noise suppression"))
{
if((value != "yes") && (value != "no"))
{
......@@ -260,7 +260,13 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "scoring, algorithm") || (label == "protein, taxon") ||
(label == "refine, sequence path") || (label == "output, log path") ||
(label == "output, message") || (label == "output, sequence path") ||
(label == "output, path"))
(label == "output, path") ||
(label == "residue, potential modification mass 1") ||
(label == "residue, potential modification mass 2") ||
(label == "residue, potential modification mass 3") ||
(label == "residue, potential modification motif 1") ||
(label == "residue, potential modification motif 2") ||
(label == "residue, potential modification motif 3"))
{
// string
}
......
......@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
#ifndef TANDEMPARAMETERSFILE_H
#define TANDEMPARAMETERSFILE_H
#pragma once
#include <QFileInfo>
#include <QXmlStreamWriter>
......@@ -74,5 +73,3 @@ class TandemParametersFile
QFileInfo _param_source;
bool m_isTandemParameterFile = false;
};
#endif // TANDEMPARAMETERSFILE_H
......@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
#ifndef XTANDEMPARAMSAXHANDLER_H
#define XTANDEMPARAMSAXHANDLER_H
#pragma once
#include <QXmlDefaultHandler>
#include <vector>
......@@ -62,6 +61,7 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString errorString() const;
bool isTandemParameter() const;
private:
bool startElement_note(QXmlAttributes attributes);
bool endElement_note();
......@@ -76,5 +76,3 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString _current_label;
bool m_isTandemParameter = false;
};
#endif // XTANDEMPARAMSAXHANDLER_H
......@@ -8,9 +8,9 @@
set(PAPPSOMSPP_QT5_FOUND 1)
set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
set(PAPPSOMSPP_INCLUDE_DIR "/home/trenne/developpement/git/pappsomspp/src")
set(PAPPSOMSPP_QT5_LIBRARY "/home/trenne/developpement/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/trenne/developpement/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
set(PAPPSOMSPP_INCLUDE_DIR "/home/langella/developpement/git/pappsomspp/src")
set(PAPPSOMSPP_QT5_LIBRARY "/home/langella/developpement/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/langella/developpement/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
......
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