diff --git a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
index 8f371534d102e9682474762cf3824bd089f5bc10..697456ff56fd9a216b4df399492ab3a8499b46a2 100644
--- a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
+++ b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
@@ -293,85 +293,6 @@
</item>
</layout>
</widget>
- <widget class="QWidget" name="resultTab">
- <attribute name="title">
- <string>&Result files</string>
- </attribute>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QWidget" name="widget" native="true">
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Peptide quantification result file name</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <property name="spacing">
- <number>6</number>
- </property>
- <item>
- <widget class="QLineEdit" name="outputFileEdit"/>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="comparFileGroupBox">
- <property name="title">
- <string>Compa&r file name</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <property name="spacing">
- <number>6</number>
- </property>
- <item>
- <widget class="QLineEdit" name="comparFileEdit"/>
- </item>
- <item>
- <widget class="QComboBox" name="comparFileFormatComboBox">
- <item>
- <property name="text">
- <string>ODS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>TSV</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
</widget>
</item>
<item>
@@ -398,7 +319,7 @@
</widget>
</item>
<item>
- <widget class="QRadioButton" name="radioButton">
+ <widget class="QRadioButton" name="compar_radioButton">
<property name="text">
<string>Compar file</string>
</property>
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index e95b1f499af01baa03f5853a645760b2025a3164..8f673bb75cba5d253fef3d432bbde14375c28701 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -102,22 +102,13 @@ ExportMasschroqDialog::setMasschroqFileParameters(
ui->zivyParamWidget->setZivyParams(zivy_params);
- ui->outputFileEdit->setText(params.result_file_name);
ui->outputFileFormatComboBox->setCurrentText("ODS");
if(params.result_file_format == TableFileFormat::tsv)
{
ui->outputFileFormatComboBox->setCurrentText("TSV");
}
- ui->comparFileGroupBox->setChecked(params.export_compar_file);
-
- ui->comparFileEdit->setText(params.compar_file_name);
- ui->comparFileFormatComboBox->setCurrentText("ODS");
- if(params.compar_file_format == TableFileFormat::tsv)
- {
- ui->comparFileFormatComboBox->setCurrentText("TSV");
- }
-
+ ui->compar_radioButton->setChecked(params.export_compar_file);
ui->timeCorrectionGroupBox->setChecked(params.write_alignment_times);
ui->timeCorrectionDirectoryEdit->setText(params.alignment_times_directory);
@@ -135,21 +126,21 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
{
MasschroqFileParameters params;
- params.result_file_name = ui->outputFileEdit->text();
params.result_file_format = TableFileFormat::ods;
if(ui->outputFileFormatComboBox->currentText() == "TSV")
{
params.result_file_format = TableFileFormat::tsv;
}
-
- params.export_compar_file = ui->comparFileGroupBox->isChecked();
- params.compar_file_name = ui->comparFileEdit->text();
- params.compar_file_format = TableFileFormat::ods;
- if(ui->comparFileFormatComboBox->currentText() == "TSV")
+ for(int i = 0; i < mp_poModel->rowCount(); i++)
{
- params.compar_file_format = TableFileFormat::tsv;
+ qDebug() << mp_poModel->item(i, 0)->checkState();
+ if(mp_poModel->item(i, 0)->checkState() == Qt::CheckState(Qt::Checked))
+ {
+ params.alignment_groups.push_back(msp_alignmentGroups.at(i));
+ }
}
+ params.export_compar_file = ui->compar_radioButton->isChecked();
params.write_alignment_times = ui->timeCorrectionGroupBox->isChecked();
params.alignment_times_directory = ui->timeCorrectionDirectoryEdit->text();
@@ -190,19 +181,6 @@ void
ExportMasschroqDialog::accept()
{
QString error_message;
- if(ui->outputFileEdit->text().isEmpty())
- {
- error_message = QString(tr("MassChroqML result file name must be set"));
- }
- if(ui->comparFileGroupBox->isChecked())
- {
- if(ui->comparFileEdit->text().isEmpty())
- {
- error_message =
- QString(tr("MassChroqML compar file name must be set"));
- }
- }
-
if(ui->timeCorrectionGroupBox->isChecked())
{
if(ui->timeCorrectionDirectoryEdit->text().isEmpty())
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
index 40eadbefec143b8cd004ac65eeea4168a29adcec..8fef08b58069ac2a15be50234f94be73bc47328f 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
@@ -35,19 +35,12 @@ void
MasschroqFileParameters::save() const
{
QSettings settings;
- settings.setValue("export_masschroqml/result_file_name",
- QString("%1").arg(result_file_name));
settings.setValue("export_masschroqml/result_file_format",
(std::uint8_t)result_file_format);
settings.setValue("export_masschroqml/export_compar_file",
QString("%1").arg(export_compar_file));
- settings.setValue("export_masschroqml/compar_file_name",
- QString("%1").arg(compar_file_name));
- settings.setValue("export_masschroqml/compar_file_format",
- (std::uint8_t)compar_file_format);
-
settings.setValue("export_masschroqml/write_alignment_times",
write_alignment_times);
@@ -73,9 +66,6 @@ void
MasschroqFileParameters::load()
{
QSettings settings;
- result_file_name =
- settings.value("export_masschroqml/result_file_name", QString("results"))
- .toString();
result_file_format =
(TableFileFormat)settings
.value("export_masschroqml/result_file_format",
@@ -87,16 +77,6 @@ MasschroqFileParameters::load()
settings
.value("export_masschroqml/compar_file_name", QString("%1").arg(true))
.toBool();
- compar_file_name =
- settings
- .value("export_masschroqml/compar_file_name", QString("compar_results"))
- .toString();
- compar_file_format =
- (TableFileFormat)settings
- .value("export_masschroqml/compar_file_format",
- QString("%1").arg((std::uint8_t)TableFileFormat::ods))
- .toUInt();
-
write_alignment_times = settings
.value("export_masschroqml/write_alignment_times",
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
index dca3303b7df1c62a828ac9d32223bb0372a39468..55b61563cd6b9e6ee3312fcb1e16306d1390305e 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -41,14 +41,14 @@ struct MasschroqFileParameters
void load();
/** @brief quantification result output file name*/
- QString result_file_name;
+ // QString result_file_name;
/** @brief quantification result output file type*/
TableFileFormat result_file_format = TableFileFormat::ods;
bool export_compar_file = false;
- QString compar_file_name;
- TableFileFormat compar_file_format = TableFileFormat::ods;
+ // QString compar_file_name;
+ // TableFileFormat compar_file_format = TableFileFormat::ods;
bool write_alignment_times;
QString alignment_times_directory;
@@ -62,4 +62,5 @@ struct MasschroqFileParameters
pappso::XicExtractMethod xic_extraction_method; // sum or max
MsRunSp msrun_alignment_reference;
+ std::vector<MsRunAlignmentGroupSp> alignment_groups;
};
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 55aaf40de92dc593c248ac4bef2d798d8e0961df..f3e9299961eb16f00a151cced1f0b153af167d7a 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -664,6 +664,7 @@ MainWindow::doAcceptedExportMasschroqDialog()
MasschroqFileParameters params =
_p_export_masschroq_dialog->getMasschroqFileParameters();
params.save();
+ qDebug() << params.alignment_groups.size();
QSettings settings;
QString default_location = settings.value("path/mcqfile", "").toString();
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index c4ca988d1d67c0472b3a581a13ab2a6eeb21c584..6125a7d650bc402b6da881c6deb90a2859b24f86 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -199,7 +199,8 @@ MassChroQml::writeQuantificationResults()
//<quantification_result output_file="result1"
// format="tsv" />
_output_stream->writeStartElement("quantification_result");
- _output_stream->writeAttribute("output_file", m_params.result_file_name);
+ _output_stream->writeAttribute(
+ "output_file", "result_" + QFileInfo(*_output_file).baseName());
if(m_params.result_file_format == TableFileFormat::ods)
{
_output_stream->writeAttribute("format", "ods");
@@ -219,8 +220,9 @@ MassChroQml::writeQuantificationResults()
if(m_params.export_compar_file)
{
_output_stream->writeStartElement("compar_result");
- _output_stream->writeAttribute("output_file", m_params.compar_file_name);
- if(m_params.compar_file_format == TableFileFormat::ods)
+ _output_stream->writeAttribute(
+ "output_file", "compar_" + QFileInfo(*_output_file).baseName());
+ if(m_params.result_file_format == TableFileFormat::ods)
{
_output_stream->writeAttribute("format", "ods");
}
@@ -456,23 +458,27 @@ MassChroQml::writeAlignments()
_output_stream->writeEndElement();
//<align group_id="G1" method_id="my_ms2" reference_data_id="samp0" />
//<align group_id="G2" method_id="my_obiwarp" reference_data_id="samp2" />
- _output_stream->writeStartElement("align");
- _output_stream->writeAttribute("group_id", "fractiona1");
- _output_stream->writeAttribute("method_id", "my_ms2");
- std::vector<MsRunSp> msrun_list =
- _sp_project.get()->getMsRunStore().getMsRunList();
- if(m_params.msrun_alignment_reference == nullptr)
- {
- _output_stream->writeAttribute("reference_data_id",
- msrun_list.front().get()->getXmlId());
- }
- else
+
+ for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
{
- _output_stream->writeAttribute(
- "reference_data_id",
- m_params.msrun_alignment_reference.get()->getXmlId());
+ _output_stream->writeStartElement("align");
+ _output_stream->writeAttribute("group_id",
+ group_sp->getMsRunAlignmentGroupName());
+ _output_stream->writeAttribute("method_id", "my_ms2");
+ if(group_sp->getMsRunReference() == nullptr)
+ {
+ _output_stream->writeAttribute(
+ "reference_data_id",
+ group_sp->getMsRunsInAlignmentGroup().front().get()->getXmlId());
+ }
+ else
+ {
+ _output_stream->writeAttribute(
+ "reference_data_id",
+ group_sp->getMsRunReference().get()->getXmlId());
+ }
+ _output_stream->writeEndElement();
}
- _output_stream->writeEndElement();
//</alignments>
_output_stream->writeEndElement();
}
@@ -660,17 +666,20 @@ MassChroQml::writeGroups()
//<groups>
_output_stream->writeStartElement("groups");
//<group data_ids="samp0 samp1" id="G1" />
- _output_stream->writeStartElement("group");
- _output_stream->writeAttribute("id", QString("fractiona1"));
- std::vector<MsRunSp> msrun_list =
- _sp_project.get()->getMsRunStore().getMsRunList();
- QStringList list;
- for(MsRunSp &msrun : msrun_list)
+ for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
{
- list << msrun.get()->getXmlId();
+ _output_stream->writeStartElement("group");
+ _output_stream->writeAttribute("id",
+ group_sp->getMsRunAlignmentGroupName());
+ QStringList list;
+ for(MsRunSp &msrun : group_sp->getMsRunsInAlignmentGroup())
+ {
+ list << msrun.get()->getXmlId();
+ }
+ _output_stream->writeAttribute("data_ids", list.join(" "));
+ _output_stream->writeEndElement();
}
- _output_stream->writeAttribute("data_ids", list.join(" "));
- _output_stream->writeEndElement();
+
//<group data_ids="samp2 samp3" id="G2" />
// </groups>
_output_stream->writeEndElement();