From 99c148fd1302cee451bc86128e6d45a21bb57ac2 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 14:16:35 +0100
Subject: [PATCH] Use same object for Protein checked in PTM and Protein
windows
---
.../ptmislandlistwindow.cpp | 4 ++
.../ptmislandlistwindow.h | 3 +-
.../ptmislandproxymodel.cpp | 6 +-
.../ptmislandtablemodel.cpp | 4 +-
src/output/masschroqml.cpp | 72 ++++++++++---------
5 files changed, 46 insertions(+), 43 deletions(-)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 2514d5cf..63f1c128 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -198,6 +198,10 @@ PtmIslandListWindow::setColumnMenuList()
}
}
+void PtmIslandListWindow::edited()
+{
+ _project_window->doIdentificationGroupEdited(_p_identification_group);
+}
void
PtmIslandListWindow::doNotCheckedHide(bool hide)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index a4cfea46..6130ba50 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -79,7 +79,8 @@ class PtmIslandListWindow : public QMainWindow
void setPtmIslandListColumnDisplay(PtmIslandListColumn column, bool toggled);
bool getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
void setColumnMenuList();
-
+ void edited();
+
public slots:
void
doIdentificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index bd90592f..a67a3d0c 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -83,10 +83,7 @@ PtmIslandProxyModel::filterAcceptsRow(int source_row,
_p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
.at(source_row);
- ProteinMatch *protein_match =
- _p_ptm_island_table_model->getIdentificationGroup()
- ->getProteinMatchList()
- .at(source_row);
+ ProteinMatch *protein_match = sp_ptm_island->getProteinMatch();
// qDebug() << "Prote
// qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
// << source_row;
@@ -222,6 +219,7 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
{
p_protein_match->setChecked(true);
}
+ _p_ptm_island_list_window->edited();
}
else if((col == (std::int8_t)PtmIslandListColumn::accession) ||
(col == (std::int8_t)PtmIslandListColumn::description))
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index ef47c324..1af9875f 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -234,9 +234,7 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
if(col == (std::int8_t)
PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
{
- if(_p_identification_group->getProteinMatchList()
- .at(row)
- ->isChecked())
+ if(getPtmGroupingExperiment()->getPtmIslandList().at(row)->getProteinMatch()->isChecked())
{
return Qt::Checked;
}
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 3b6fcb9d..10dd89fe 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -263,47 +263,49 @@ MassChroQml::writeQuantificationTraces()
void
MassChroQml::writeQuantify()
{
- for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
+ for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
{
- //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
- _output_stream->writeStartElement("quantify");
- _output_stream->writeAttribute("id", "q1");
-
- _output_stream->writeAttribute("withingroup", group_sp->getMsRunAlignmentGroupName());
- _output_stream->writeAttribute("quantification_method_id", "quant1");
- //<peptides_in_peptide_list mode="real_or_mean" />
- //</quantify>
- //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
- //<peptides_in_peptide_list mode="post_matching"
- // isotope_label_refs="iso1 iso2" />
-
- _output_stream->writeStartElement("peptides_in_peptide_list");
- _output_stream->writeAttribute("mode", "post_matching");
- _output_stream->writeAttribute("ni_min_abundance", "0.8");
+ //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
+ _output_stream->writeStartElement("quantify");
+ _output_stream->writeAttribute("id", "q1");
- LabelingMethod *p_labeling_method =
- _sp_project.get()->getLabelingMethodSp().get();
- if(p_labeling_method != nullptr)
- {
- QStringList isotope_label_ref;
- for(const Label *p_label : p_labeling_method->getLabelList())
+ _output_stream->writeAttribute("withingroup",
+ group_sp->getMsRunAlignmentGroupName());
+ _output_stream->writeAttribute("quantification_method_id", "quant1");
+ //<peptides_in_peptide_list mode="real_or_mean" />
+ //</quantify>
+ //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
+ //<peptides_in_peptide_list mode="post_matching"
+ // isotope_label_refs="iso1 iso2" />
+
+ _output_stream->writeStartElement("peptides_in_peptide_list");
+ _output_stream->writeAttribute("mode", "post_matching");
+ _output_stream->writeAttribute("ni_min_abundance", "0.8");
+
+ LabelingMethod *p_labeling_method =
+ _sp_project.get()->getLabelingMethodSp().get();
+ if(p_labeling_method != nullptr)
{
- isotope_label_ref << p_label->getXmlId();
+ QStringList isotope_label_ref;
+ for(const Label *p_label : p_labeling_method->getLabelList())
+ {
+ isotope_label_ref << p_label->getXmlId();
+ }
+ _output_stream->writeAttribute("isotope_label_refs",
+ isotope_label_ref.join(" "));
}
- _output_stream->writeAttribute("isotope_label_refs",
- isotope_label_ref.join(" "));
- }
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
- _output_stream->writeComment(
- "<mz_list>732.317 449.754 552.234 464.251 "
- "381.577 569.771 575.256</mz_list>");
- _output_stream->writeComment(
- "<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt "
- "mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
+ _output_stream->writeComment(
+ "<mz_list>732.317 449.754 552.234 464.251 "
+ "381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment(
+ "<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n "
+ "<mzrt "
+ "mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
- //</quantify>
- _output_stream->writeEndElement();
+ //</quantify>
+ _output_stream->writeEndElement();
}
}
--
GitLab