diff --git a/src/gui/edit/edit_alignment_param/masschroq_param_view.ui b/src/gui/edit/edit_alignment_param/masschroq_param_view.ui
index f0a7e52ce0792d2777bbb83992fabc1227892a00..9822b3df4b5c50df1281b9062950c3a5cd66c5ce 100644
--- a/src/gui/edit/edit_alignment_param/masschroq_param_view.ui
+++ b/src/gui/edit/edit_alignment_param/masschroq_param_view.ui
@@ -15,19 +15,378 @@
</property>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
- <widget class="QLabel" name="label">
- <property name="font">
- <font>
- <pointsize>20</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Work in Progress</string>
+ <widget class="QTabWidget" name="tabWidget">
+ <property name="currentIndex">
+ <number>0</number>
</property>
+ <widget class="QWidget" name="sumary_tab">
+ <attribute name="title">
+ <string>&Group summary</string>
+ </attribute>
+ <layout class="QVBoxLayout" name="verticalLayout_5">
+ <item>
+ <widget class="QGroupBox" name="groupBox_2">
+ <property name="title">
+ <string>MS runs</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <widget class="QListWidget" name="msruns_list"/>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_3">
+ <property name="title">
+ <string>MS run group reference</string>
+ </property>
+ <layout class="QHBoxLayout" name="horizontalLayout_3">
+ <item>
+ <widget class="QLineEdit" name="reference_line">
+ <property name="placeholderText">
+ <string>No reference selected</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton">
+ <property name="text">
+ <string>Find best</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="alignment_tab">
+ <property name="contextMenuPolicy">
+ <enum>Qt::NoContextMenu</enum>
+ </property>
+ <attribute name="title">
+ <string>&Alignments</string>
+ </attribute>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <widget class="QGroupBox" name="time_correction_group">
+ <property name="title">
+ <string>Score time correction in director&y</string>
+ </property>
+ <property name="checkable">
+ <bool>true</bool>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QLineEdit" name="time_line">
+ <property name="inputMask">
+ <string/>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ <property name="placeholderText">
+ <string>times.d</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="ms2_alignment_group">
+ <property name="title">
+ <string>MS2 alignment parameters</string>
+ </property>
+ <layout class="QFormLayout" name="formLayout">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label">
+ <property name="text">
+ <string>MS2 tendency</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_2">
+ <property name="text">
+ <string>MS2 smoothing</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_3">
+ <property name="text">
+ <string>MS1 smoothing</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="ms2_tendency_spin">
+ <property name="value">
+ <number>10</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="ms2_smoothing_spin">
+ <property name="value">
+ <number>15</number>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QSpinBox" name="ms1_smoothing_spin"/>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>MsRun reference for alignment</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QPushButton" name="best_ref_button">
+ <property name="text">
+ <string>Find best MS run reference for alignment</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="msruns_combo"/>
+ </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>
+ <widget class="QWidget" name="ms_run_tabs">
+ <attribute name="title">
+ <string>&Ms Runs</string>
+ </attribute>
+ </widget>
+ <widget class="QWidget" name="peak_quantification_tab">
+ <attribute name="title">
+ <string>&Peak Quantification</string>
+ </attribute>
+ <layout class="QVBoxLayout" name="verticalLayout_8">
+ <item>
+ <widget class="QGroupBox" name="groupBox_4">
+ <property name="title">
+ <string>XIC extraction parameters</string>
+ </property>
+ <layout class="QFormLayout" name="formLayout_2">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_5">
+ <property name="text">
+ <string>XIC range</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_4">
+ <property name="text">
+ <string>Inside range, take the </string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QComboBox" name="inside_range_combo">
+ <item>
+ <property name="text">
+ <string>max</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>sum</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QDoubleSpinBox" name="xic_range_spin">
+ <property name="decimals">
+ <number>4</number>
+ </property>
+ <property name="value">
+ <double>10.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="xic_range_combo">
+ <property name="currentText">
+ <string>dalton</string>
+ </property>
+ <item>
+ <property name="text">
+ <string>dalton</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>ppm</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>res</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_5">
+ <property name="title">
+ <string>Peak detection parameters</string>
+ </property>
+ <layout class="QFormLayout" name="formLayout_3">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>smoothing</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="smoothing_spin"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_7">
+ <property name="text">
+ <string>minmax half window</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_8">
+ <property name="text">
+ <string>maxmin half window</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_9">
+ <property name="text">
+ <string>minmax threshold</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QLabel" name="label_10">
+ <property name="text">
+ <string>maxmin threshold</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="minmax_win_spin"/>
+ </item>
+ <item row="2" column="1">
+ <widget class="QSpinBox" name="maxmin_win_spin"/>
+ </item>
+ <item row="3" column="1">
+ <widget class="QSpinBox" name="minmax_thre_spin"/>
+ </item>
+ <item row="4" column="1">
+ <widget class="QSpinBox" name="maxmin_thre_spin"/>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_2">
+ <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>
</widget>
</item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="cancel_button">
+ <property name="text">
+ <string>Cancel</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="run_button">
+ <property name="text">
+ <string>Ok</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
</layout>
</widget>
<resources/>
- <connections/>
+ <connections>
+ <connection>
+ <sender>cancel_button</sender>
+ <signal>clicked()</signal>
+ <receiver>MassChroQParamView</receiver>
+ <slot>close()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>386</x>
+ <y>508</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>261</x>
+ <y>265</y>
+ </hint>
+ </hints>
+ </connection>
+ </connections>
</ui>
diff --git a/src/gui/edit/edit_alignment_param/masschroqparam.cpp b/src/gui/edit/edit_alignment_param/masschroqparam.cpp
index 71d988069eb05c4c5cfa579a78324aea4c6cb19f..fc75bfbf3be27a5fd23c26c648f196fe2609a344 100644
--- a/src/gui/edit/edit_alignment_param/masschroqparam.cpp
+++ b/src/gui/edit/edit_alignment_param/masschroqparam.cpp
@@ -29,12 +29,23 @@
#include "../../src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h"
-MassChroQParamWindow::MassChroQParamWindow(MsIdentificationListWindow *parent)
+MassChroQParamWindow::MassChroQParamWindow(
+ MsIdentificationListWindow *parent, MsRunAlignmentGroupSp alignment_group)
: QWidget(), ui(new Ui::MassChroQParamView)
{
mp_identification_list_window = parent;
+ msp_alignment_group = alignment_group;
ui->setupUi(this);
- // msp_alignment_group = alignment_group;
+ foreach(MsRunSp ms_run, msp_alignment_group->getMsRunsInAlignmentGroup())
+ {
+ QListWidgetItem *new_item = new QListWidgetItem(ms_run->getSampleName());
+ ui->msruns_list->insertItem(0, new_item);
+ }
+ MsRunSp reference = msp_alignment_group->getMsRunReference();
+ if(reference != nullptr)
+ {
+ ui->reference_line->setText(reference->getSampleName());
+ }
}
diff --git a/src/gui/edit/edit_alignment_param/masschroqparam.h b/src/gui/edit/edit_alignment_param/masschroqparam.h
index f390503f028d8b6b67a88d51fde58bac51f007d7..e349d2307ceb9c176d92f953a824a35379d6baa5 100644
--- a/src/gui/edit/edit_alignment_param/masschroqparam.h
+++ b/src/gui/edit/edit_alignment_param/masschroqparam.h
@@ -37,7 +37,8 @@ class MassChroQParamWindow : public QWidget
Q_OBJECT
public:
- MassChroQParamWindow(MsIdentificationListWindow *parent);
+ MassChroQParamWindow(MsIdentificationListWindow *parent,
+ MsRunAlignmentGroupSp alignment_group);
~MassChroQParamWindow();
void setAlignmentGroup(MsRunAlignmentGroupSp alignment_group);
diff --git a/src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp b/src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp
index f7f2dd6da306ec7822d9b34b5d83bb6f2ea6c79e..3daf72d704ef8bbc75b183422bc436bde5662eaa 100644
--- a/src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp
+++ b/src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp
@@ -399,8 +399,7 @@ MsIdentificationListWindow::openMassChroQParametersView(
qDebug();
if(mp_massChroQParamWindow == nullptr)
{
- mp_massChroQParamWindow = new MassChroQParamWindow(this);
+ mp_massChroQParamWindow = new MassChroQParamWindow(this, alignment_group);
}
- mp_massChroQParamWindow->setAlignmentGroup(alignment_group);
mp_massChroQParamWindow->show();
}
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 8af29186ee12dc321f560e47a376a4ada385dfb9..3c2dacf863ed8c56295cf1b67c12daaec29d04c7 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -141,6 +141,14 @@ XtpXpipSaxHandler::startElement(const QString &namespaceURI,
{
is_ok = startElement_msrun(attributes);
}
+ else if(qName == "msrun_group")
+ {
+ is_ok = startElement_alignmentGroup(attributes);
+ }
+ else if(qName == "grouped_msrun")
+ {
+ is_ok = startElement_msrunInAlignmentGroup(attributes);
+ }
else if(qName == "peptide")
{
if(_count_total % 100 == 0)
@@ -574,6 +582,29 @@ XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes)
return true;
}
+bool
+XtpXpipSaxHandler::startElement_alignmentGroup(QXmlAttributes attributes)
+{
+ msp_alignment_group = std::make_shared<MsRunAlignmentGroup>(
+ attributes.value("name").simplified());
+ _p_project->addMsRunAlignmentGroupToList(msp_alignment_group);
+ QString reference_id = attributes.value("reference").simplified();
+ if(reference_id != "")
+ {
+ msp_alignment_group->setMsRunReference(_map_msruns.at(reference_id));
+ }
+ return true;
+}
+
+bool
+XtpXpipSaxHandler::startElement_msrunInAlignmentGroup(QXmlAttributes attributes)
+{
+ MsRunSp ms_run = _map_msruns.at(attributes.value("id").simplified());
+ msp_alignment_group->addMsRunToMsRunAlignmentGroupList(ms_run);
+ ms_run->setAlignmentGroup(msp_alignment_group);
+ return true;
+}
+
bool
XtpXpipSaxHandler::startElement_peptide_evidence_list(QXmlAttributes attributes)
{
@@ -837,6 +868,13 @@ XtpXpipSaxHandler::endElement_msrun()
return true;
}
+bool
+XtpXpipSaxHandler::endElement_alignmentGroup()
+{
+ msp_alignment_group = nullptr;
+ return true;
+}
+
bool
XtpXpipSaxHandler::endElement_sequence()
{
diff --git a/src/input/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index 29f8767953cd2be02758081304c1080004e956a7..4f12b05a2cfeb09d5f97679a68ae6e8c768b0698 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -47,10 +47,13 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
XtpXpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
~XtpXpipSaxHandler();
- bool startElement(const QString &namespaceURI, const QString &localName,
- const QString &qName, const QXmlAttributes &attributes);
+ bool startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes);
- bool endElement(const QString &namespaceURI, const QString &localName,
+ bool endElement(const QString &namespaceURI,
+ const QString &localName,
const QString &qName);
bool startDocument();
@@ -77,6 +80,8 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
bool startElement_peptide_evidence_list(QXmlAttributes attributes);
bool startElement_protein(QXmlAttributes attributes);
bool startElement_msrun(QXmlAttributes attributes);
+ bool startElement_alignmentGroup(QXmlAttributes attributes);
+ bool startElement_msrunInAlignmentGroup(QXmlAttributes attributes);
bool startElement_identification_source(QXmlAttributes attributes);
bool startElement_identification_group(QXmlAttributes attributes);
@@ -92,6 +97,7 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
// bool endElement_identification();
bool endElement_sequence();
bool endElement_msrun();
+ bool endElement_alignmentGroup();
bool endElement_protein();
bool endElement_peptide();
bool endElement_protein_match();
@@ -124,6 +130,7 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
IdentificationDataSourceSp _sp_current_identification_source;
LabelingMethodSp _sp_labeling_method;
MsRunSp _sp_msrun;
+ MsRunAlignmentGroupSp msp_alignment_group;
std::map<QString, PeptideXtpSp> _map_peptides;
bool _is_xtpcpp_xpip = false;
QString _current_id;
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 28f01cd96c666bf9334a963d05d90dae644092e5..aae02636f11a5a18864636076b8c89880bbe0944 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -145,6 +145,8 @@ Xpip::write(ProjectSp sp_project)
_output_stream->writeEndElement();
writeMsrunList(_sp_project.get()->getMsRunStore());
+ writeMsrunAlignementGroupsList(
+ _sp_project.get()->getMsRunAlignmentGroupList());
writeIdentificationDataSourceList(
_sp_project.get()->getIdentificationDataSourceStore());
@@ -360,6 +362,39 @@ Xpip::writeMsrunList(const MsRunStore &msrun_store)
_output_stream->writeEndElement();
}
+void
+Xpip::writeMsrunAlignementGroupsList(
+ const std::vector<MsRunAlignmentGroupSp> alignment_groups)
+{
+ _output_stream->writeStartElement("msrun_alignment_group_list");
+ for(const MsRunAlignmentGroupSp group : alignment_groups)
+ {
+ qDebug() << "AAAAAAAAAA";
+ _output_stream->writeStartElement("msrun_group");
+ _output_stream->writeAttribute("name",
+ group.get()->getMsRunAlignmentGroupName());
+ MsRunSp reference = group.get()->getMsRunReference();
+ if(reference != nullptr)
+ {
+ _output_stream->writeAttribute(
+ "reference", group.get()->getMsRunReference().get()->getXmlId());
+ }
+ else
+ {
+ _output_stream->writeAttribute("reference", "");
+ }
+
+ for(const MsRunSp ms_run : group.get()->getMsRunsInAlignmentGroup())
+ {
+ _output_stream->writeStartElement("grouped_msrun");
+ _output_stream->writeAttribute("id", ms_run.get()->getXmlId());
+ _output_stream->writeEndElement();
+ }
+ _output_stream->writeEndElement();
+ }
+ _output_stream->writeEndElement();
+}
+
void
Xpip::writeFastaFileList(const FastaFileStore &fasta_store)
{
diff --git a/src/output/xpip.h b/src/output/xpip.h
index e44d9afa7cc12789dc5bca695dedfeb04ebf2a33..cbd3f5e9bbac4f5be017a926baeb04f28b2e016c 100644
--- a/src/output/xpip.h
+++ b/src/output/xpip.h
@@ -51,6 +51,8 @@ class Xpip
void writeCounts();
void writeMsrunList(const MsRunStore &msrun_store);
+ void writeMsrunAlignementGroupsList(
+ const std::vector<MsRunAlignmentGroupSp> alignment_groups);
void writeIdentificationDataSourceList(
const IdentificationDataSourceStore &ident_store);
void writeFastaFileList(const FastaFileStore &fasta_store);