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 ...@@ -129,14 +129,13 @@ TandemParameters::getValue(const QString &label) const
.arg(label) .arg(label)
.arg(_method_name)); .arg(_method_name));
} }
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug();
return it.value(); return it.value();
} }
void void
TandemParameters::setParamLabelValue(const QString &label, const QString &value) TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " qDebug() << label;
<< label;
// list path // list path
//<note type="input" label="list path, default //<note type="input" label="list path, default
// parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note> // 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) ...@@ -147,8 +146,7 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
return; return;
} }
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " qDebug() << label;
<< label;
if((label == "spectrum, parent monoisotopic mass error units") || if((label == "spectrum, parent monoisotopic mass error units") ||
(label == "spectrum, fragment monoisotopic mass error units")) (label == "spectrum, fragment monoisotopic mass error units"))
{ {
...@@ -189,7 +187,9 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value) ...@@ -189,7 +187,9 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "protein, homolog management") || (label == "protein, homolog management") ||
(label == "protein, use minimal annotations") || (label == "protein, use minimal annotations") ||
(label == "protein, use 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")) if((value != "yes") && (value != "no"))
{ {
...@@ -260,7 +260,13 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value) ...@@ -260,7 +260,13 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "scoring, algorithm") || (label == "protein, taxon") || (label == "scoring, algorithm") || (label == "protein, taxon") ||
(label == "refine, sequence path") || (label == "output, log path") || (label == "refine, sequence path") || (label == "output, log path") ||
(label == "output, message") || (label == "output, sequence 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 // string
} }
......
...@@ -28,8 +28,7 @@ ...@@ -28,8 +28,7 @@
*implementation *implementation
******************************************************************************/ ******************************************************************************/
#ifndef TANDEMPARAMETERSFILE_H #pragma once
#define TANDEMPARAMETERSFILE_H
#include <QFileInfo> #include <QFileInfo>
#include <QXmlStreamWriter> #include <QXmlStreamWriter>
...@@ -74,5 +73,3 @@ class TandemParametersFile ...@@ -74,5 +73,3 @@ class TandemParametersFile
QFileInfo _param_source; QFileInfo _param_source;
bool m_isTandemParameterFile = false; bool m_isTandemParameterFile = false;
}; };
#endif // TANDEMPARAMETERSFILE_H
...@@ -28,8 +28,7 @@ ...@@ -28,8 +28,7 @@
*implementation *implementation
******************************************************************************/ ******************************************************************************/
#ifndef XTANDEMPARAMSAXHANDLER_H #pragma once
#define XTANDEMPARAMSAXHANDLER_H
#include <QXmlDefaultHandler> #include <QXmlDefaultHandler>
#include <vector> #include <vector>
...@@ -62,6 +61,7 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler ...@@ -62,6 +61,7 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString errorString() const; QString errorString() const;
bool isTandemParameter() const; bool isTandemParameter() const;
private: private:
bool startElement_note(QXmlAttributes attributes); bool startElement_note(QXmlAttributes attributes);
bool endElement_note(); bool endElement_note();
...@@ -76,5 +76,3 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler ...@@ -76,5 +76,3 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
QString _current_label; QString _current_label;
bool m_isTandemParameter = false; bool m_isTandemParameter = false;
}; };
#endif // XTANDEMPARAMSAXHANDLER_H
...@@ -8,9 +8,9 @@ ...@@ -8,9 +8,9 @@
set(PAPPSOMSPP_QT5_FOUND 1) set(PAPPSOMSPP_QT5_FOUND 1)
set(PAPPSOMSPP_WIDGET_QT5_FOUND 1) set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
set(PAPPSOMSPP_INCLUDE_DIR "/home/trenne/developpement/git/pappsomspp/src") set(PAPPSOMSPP_INCLUDE_DIR "/home/langella/developpement/git/pappsomspp/src")
set(PAPPSOMSPP_QT5_LIBRARY "/home/trenne/developpement/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so") set(PAPPSOMSPP_QT5_LIBRARY "/home/langella/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_WIDGET_QT5_LIBRARY "/home/langella/developpement/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
......
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