From acf0c54c305d3eb3db9cce93def3938072cafd65 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 9 Jun 2017 20:21:40 +0200
Subject: [PATCH] button layout
---
src/core/proteinxtp.cpp | 21 ++++++++++-------
src/core/proteinxtp.h | 10 ++++++--
src/gui/protein_view/protein_detail_view.ui | 20 ++++++++++++++++
src/gui/protein_view/proteinwindow.cpp | 22 +++++++++++++++--
src/gui/protein_view/proteinwindow.h | 1 +
src/output/proticdbml.cpp | 6 ++---
src/utils/types.h | 26 ++++++++++-----------
7 files changed, 77 insertions(+), 29 deletions(-)
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 947eb4149..4dfa3f37a 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -137,31 +137,34 @@ void ProteinXtp::parseAccession2dbxref() {
qDebug() << "ProteinXtp::parseAccession2dbxref accession " << accession;
if (atg.indexIn(accession, 0) != -1) {
QStringList temp = accession.split("\\.");
- _dbxref_list.push_back(std::make_pair(ExternalDatabase::AGI_LocusCode, temp.at(0)));
+ _dbxref_list.push_back(DbXref(ExternalDatabase::AGI_LocusCode, temp.at(0)));
}
if (ncbi_gi.indexIn(accession, 0) != -1) {
- _dbxref_list.push_back(std::make_pair(ExternalDatabase::NCBI_gi, accession));
+ _dbxref_list.push_back(DbXref(ExternalDatabase::NCBI_gi, accession));
}
if (swiss_prot.indexIn(accession, 0) != -1) {
qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt " << accession;
- _dbxref_list.push_back(std::make_pair(ExternalDatabase::SwissProt, accession));
+ _dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
}
if (trembl.indexIn(accession, 0) != -1) {
qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL " << accession;
- _dbxref_list.push_back(std::make_pair(ExternalDatabase::TrEMBL, accession));
+ _dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
}
if (ref.indexIn(accession, 0) != -1) {
- _dbxref_list.push_back(std::make_pair(ExternalDatabase::ref, accession));
+ _dbxref_list.push_back(DbXref(ExternalDatabase::ref, accession));
}
}
if (_dbxref_list.size() > 1) {
- _dbxref_list.sort();
- _dbxref_list.unique([] (const std::pair<ExternalDatabase, QString> & first, const std::pair<ExternalDatabase, QString> & second)
+ _dbxref_list.sort([] (const DbXref & first, const DbXref & second)
{
- return ( first.first == second.first ) && (first.second == second.second);
+ return std::tie(first.database, first.accession) < std::tie(second.database, second.accession);
+ });
+ _dbxref_list.unique([] (const DbXref & first, const DbXref & second)
+ {
+ return ( first.database == second.database ) && (first.accession == second.accession);
});
}
@@ -169,6 +172,6 @@ void ProteinXtp::parseAccession2dbxref() {
}
-const std::list<std::pair<ExternalDatabase, QString>> & ProteinXtp::getDbxrefList() const {
+const std::list<DbXref> & ProteinXtp::getDbxrefList() const {
return _dbxref_list;
}
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index 947ebb593..2bde8ff7b 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -30,6 +30,12 @@
#ifndef PROTEIN_XTP_H
#define PROTEIN_XTP_H
+struct DbXref {
+ DbXref(ExternalDatabase database_in, const QString & accession_in):database(database), accession(accession_in) {
+ };
+ ExternalDatabase database;
+ QString accession;
+};
class ProteinXtp;
@@ -68,13 +74,13 @@ public:
*/
void parseAccession2dbxref();
- const std::list<std::pair<ExternalDatabase, QString>> & getDbxrefList() const;
+ const std::list<DbXref> & getDbxrefList() const;
private:
SequenceDatabase * _p_sequence_database;
bool _is_decoy=false;
bool _is_contaminant=false;
- std::list<std::pair<ExternalDatabase, QString>> _dbxref_list;
+ std::list<DbXref> _dbxref_list;
};
#endif // PROTEIN_XTP_H
diff --git a/src/gui/protein_view/protein_detail_view.ui b/src/gui/protein_view/protein_detail_view.ui
index 9281f5c04..e695d9f50 100644
--- a/src/gui/protein_view/protein_detail_view.ui
+++ b/src/gui/protein_view/protein_detail_view.ui
@@ -47,6 +47,26 @@
</property>
</widget>
</item>
+ <item>
+ <layout class="QHBoxLayout" name="button_space_layout">
+ <item>
+ <layout class="QHBoxLayout" name="dbxref_list_layout"/>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
<item>
<widget class="QLabel" name="description_label">
<property name="text">
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index cb8698c24..1bf378cca 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -27,6 +27,7 @@
#include <pappsomspp/pappsoexception.h>
#include <QMessageBox>
#include <cmath>
+#include <QPushButton>
ProteinWindow::ProteinWindow(ProjectWindow *parent):
QMainWindow(parent),
@@ -56,6 +57,7 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent):
ProteinWindow::~ProteinWindow()
{
+ clearDbXrefLayout();
delete ui;
}
void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
@@ -68,18 +70,34 @@ void ProteinWindow::doPeptideMatchSelected(PeptideMatch * peptide_match) {
}
}
+void ProteinWindow::clearDbXrefLayout() {
+ for (int i = 0; i < ui->dbxref_list_layout->count(); ++i)
+{
+ delete ui->dbxref_list_layout->itemAt(i)->widget();
+}
+}
void ProteinWindow::updateDisplay() {
try {
+ clearDbXrefLayout();
ui->valid_checkbox->setCheckState(Qt::Unchecked);
if (_p_protein_match->isValid()) ui->valid_checkbox->setCheckState(Qt::Checked);
ui->decoy_checkbox->setCheckState(Qt::Unchecked);
if (_p_protein_match->getProteinXtpSp().get()->isDecoy()) ui->decoy_checkbox->setCheckState(Qt::Checked);
ui->accession_label->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
- for (std::pair<ExternalDatabase, QString> dbxref:_p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
- QString accession = ui->accession_label->text().replace(dbxref.second, QString("<a href=\"\" style=\"color:%2;\">%1</a>").arg(dbxref.second).arg("blue"));
+ for (const DbXref & dbxref:_p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
+ QString accession = ui->accession_label->text().replace(dbxref.accession, QString("<span style=\"color:%2;\">%1</span>").arg(dbxref.accession).arg("blue"));
ui->accession_label->setText(accession);
qDebug() << "ProteinWindow::updateDisplay " << accession;
+
+ QPushButton * dbxref_button = new QPushButton(this);
+ dbxref_button->setText(dbxref.accession);
+ ui->dbxref_list_layout->addWidget(dbxref_button);
+ }
+
+ ui->button_space_layout->setEnabled(true);
+ if (ui->dbxref_list_layout->count() == 0) {
+ ui->button_space_layout->setEnabled(false);
}
ui->description_label->setText(_p_protein_match->getProteinXtpSp().get()->getDescription());
ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index a9a147088..ff6d92e5c 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -49,6 +49,7 @@ public slots:
protected :
void updateDisplay();
+ void clearDbXrefLayout();
private:
Ui::ProteinDetailView *ui;
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index b72b08ab0..159bf1612 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -128,11 +128,11 @@ void ProticdbMl::writeSequence(ProteinMatch * p_protein_match) {
// <dbxref key="AT5G16390"
// dbname="AGI_LocusCode"></dbxref>
//if (prot.get_dbxref_type().equals("no") == false) {
- for (const std::pair<ExternalDatabase, QString> & dbxref :p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
+ for (const DbXref & dbxref :p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
_output_stream->writeStartElement("dbxref");
- _output_stream->writeAttribute("dbname", Utils::getDatabaseName(dbxref.first));
+ _output_stream->writeAttribute("dbname", Utils::getDatabaseName(dbxref.database));
_output_stream->writeAttribute("key",
- dbxref.second);
+ dbxref.accession);
_output_stream->writeEndElement();// dbxref
}
_output_stream->writeStartElement("description");
diff --git a/src/utils/types.h b/src/utils/types.h
index 6c6800a1a..e1a894909 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -31,12 +31,12 @@
/** \def ExternalDatabase external database references
*
*/
-enum class ExternalDatabase {
- AGI_LocusCode, ///< AGI_LocusCode
- NCBI_gi, ///< NCBI_gi
- SwissProt, ///< Swiss-Prot
- TrEMBL, ///< TrEMBL
- ref ///< ref
+enum class ExternalDatabase: std::int8_t {
+ SwissProt =1, ///< Swiss-Prot
+ TrEMBL=2, ///< TrEMBL
+ AGI_LocusCode=3, ///< AGI_LocusCode
+ NCBI_gi=4, ///< NCBI_gi
+ ref=5 ///< ref
};
/** \def IdentificationEngine identification engine
@@ -77,10 +77,10 @@ enum class GroupingType {
*/
enum class MzFormat {
- unknown, ///< unknown format
- mzML, ///< mzML
- mzXML, ///< mzXML
- MGF, ///< Mascot format
+ unknown, ///< unknown format
+ mzML, ///< mzML
+ mzXML, ///< mzXML
+ MGF, ///< Mascot format
};
/** \def ValidationState
@@ -89,9 +89,9 @@ enum class MzFormat {
enum class ValidationState: std::int8_t {
notValid = 0,///< notValid : automatic filter validation failed
- valid =1, ///< valid : automatic filter validation passed
- validAndChecked=2, ///< validAndChecked : automatic filter validation passed + manual checking
- grouped=3 ///< grouped : automatic filter validation passed + manual checking + grouped
+ valid =1, ///< valid : automatic filter validation passed
+ validAndChecked=2, ///< validAndChecked : automatic filter validation passed + manual checking
+ grouped=3 ///< grouped : automatic filter validation passed + manual checking + grouped
};
--
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