From 2c3478c87e3fdff065f23f45ad5c0540c6fd793b Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 9 Jun 2017 23:26:23 +0200
Subject: [PATCH] dbxref button works
---
src/core/proteinxtp.cpp | 80 +++++++++++++++++----
src/core/proteinxtp.h | 7 +-
src/gui/protein_view/protein_detail_view.ui | 46 ++++++------
src/gui/protein_view/proteinwindow.cpp | 44 +++++++++---
src/gui/protein_view/proteinwindow.h | 15 +++-
src/utils/types.h | 11 +--
6 files changed, 150 insertions(+), 53 deletions(-)
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 4dfa3f37a..2f24e43a1 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -25,6 +25,44 @@
#include <pappsomspp/protein/enzyme.h>
#include <pappsomspp/pappsoexception.h>
+DbXref::DbXref() {
+}
+DbXref::DbXref(ExternalDatabase database_in, const QString & accession_in):database(database_in), accession(accession_in) {
+}
+
+DbXref::DbXref(const DbXref & other):database(other.database), accession(other.accession) {
+}
+const QUrl DbXref::getUrl() const {
+ QUrl url;
+ qDebug() << "DbXref::getUrl " << accession << " "<< (std::uint8_t)database;
+ switch (database) {
+
+ case ExternalDatabase::AGI_LocusCode :
+ url.setUrl(QString("http://www.arabidopsis.org/servlets/TairObject?type=locus&name=%1").arg(accession));
+ break;
+ case ExternalDatabase::NCBI_gi :
+ url.setUrl(QString("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=protein&dopt=GenBank&list_uids=%1").arg(accession));
+ break;
+
+ case ExternalDatabase::SwissProt :
+ url.setUrl(QString("http://www.uniprot.org/uniprot/%1").arg(accession));
+ break;
+ case ExternalDatabase::TrEMBL :
+ url.setUrl(QString("http://www.uniprot.org/uniprot/%1").arg(accession));
+ break;
+ case ExternalDatabase::ref :
+ break;
+
+ case ExternalDatabase::OboPsiMod :
+ QString iri(QString("http://purl.obolibrary.org/obo/%1").arg(QString(accession).replace(":","_")));
+ url.setUrl(QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
+ break;
+
+ }
+ qDebug() << "DbXref::getUrl end " << url;
+ return url;
+}
+
ProteinXtp::ProteinXtp():pappso::Protein()
{
@@ -132,41 +170,59 @@ void ProteinXtp::parseAccession2dbxref() {
QRegExp swiss_prot("^P[A-Z0-9]{5}$");
QRegExp trembl("^[QOA][A-Z0-9]{5}$");
QRegExp ref ("^[NZ]P\\_[0-9]{5,8}$");
+ QString accession;
- for (QString & accession :access_list) {
+ for (unsigned int i=0; i < access_list.size(); i++) {
+ accession = access_list.at(i);
qDebug() << "ProteinXtp::parseAccession2dbxref accession " << accession;
if (atg.indexIn(accession, 0) != -1) {
QStringList temp = accession.split("\\.");
_dbxref_list.push_back(DbXref(ExternalDatabase::AGI_LocusCode, temp.at(0)));
+ continue;
}
if (ncbi_gi.indexIn(accession, 0) != -1) {
_dbxref_list.push_back(DbXref(ExternalDatabase::NCBI_gi, accession));
+ continue;
}
if (swiss_prot.indexIn(accession, 0) != -1) {
qDebug() << "ProteinXtp::parseAccession2dbxref accession SwissProt " << accession;
_dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
+ continue;
}
if (trembl.indexIn(accession, 0) != -1) {
qDebug() << "ProteinXtp::parseAccession2dbxref accession TrEMBL " << accession;
_dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
+ continue;
}
if (ref.indexIn(accession, 0) != -1) {
_dbxref_list.push_back(DbXref(ExternalDatabase::ref, accession));
+ continue;
+ }
+ if (i > 0) {
+ if ((access_list.at(i-1) == "sp")&&(accession.size() == 6)) {
+ _dbxref_list.push_back(DbXref(ExternalDatabase::SwissProt, accession));
+ }
+
+ if ((access_list.at(i-1) == "tr")&&(accession.size() == 6)) {
+ _dbxref_list.push_back(DbXref(ExternalDatabase::TrEMBL, accession));
+ }
+
+ }
+
+ if (_dbxref_list.size() > 1) {
+ _dbxref_list.sort([] (const DbXref & first, const DbXref & 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);
+ });
}
}
-
- if (_dbxref_list.size() > 1) {
- _dbxref_list.sort([] (const DbXref & first, const DbXref & 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);
- });
- }
+
qDebug() << "ProteinXtp::parseAccession2dbxref end" ;
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index 2bde8ff7b..0e8b916b9 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -24,6 +24,7 @@
#include <pappsomspp/protein/protein.h>
#include <pappsomspp/types.h>
#include <list>
+#include <QUrl>
#include "sequencedatabase.h"
#include "../utils/types.h"
@@ -31,8 +32,10 @@
#define PROTEIN_XTP_H
struct DbXref {
- DbXref(ExternalDatabase database_in, const QString & accession_in):database(database), accession(accession_in) {
- };
+ DbXref();
+ DbXref(const DbXref & other);
+ DbXref(ExternalDatabase database_in, const QString & accession_in);
+ const QUrl getUrl() const;
ExternalDatabase database;
QString accession;
};
diff --git a/src/gui/protein_view/protein_detail_view.ui b/src/gui/protein_view/protein_detail_view.ui
index e695d9f50..9249c676b 100644
--- a/src/gui/protein_view/protein_detail_view.ui
+++ b/src/gui/protein_view/protein_detail_view.ui
@@ -40,7 +40,7 @@
<item>
<widget class="QLabel" name="accession_label">
<property name="text">
- <string>TextLabel</string>
+ <string>TextLa&bel</string>
</property>
<property name="wordWrap">
<bool>true</bool>
@@ -48,24 +48,26 @@
</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>
+ <widget class="QWidget" name="button_layout" native="true">
+ <layout class="QHBoxLayout" name="button_space_layout">
+ <item>
+ <layout class="QHBoxLayout" name="dbxref_list_layout"/>
+ </item>
+ <item>
+ <spacer name="button_spacer">
+ <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>
+ </widget>
</item>
<item>
<widget class="QLabel" name="description_label">
@@ -126,14 +128,14 @@
<item row="0" column="0">
<widget class="QLabel" name="label">
<property name="text">
- <string>coverage</string>
+ <string>cove&rage</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QLabel" name="coverage_label">
<property name="text">
- <string>0%</string>
+ <string>&0%</string>
</property>
</widget>
</item>
@@ -147,7 +149,7 @@
<item row="1" column="1">
<widget class="QLabel" name="mw_label">
<property name="text">
- <string>1Da</string>
+ <string>&1Da</string>
</property>
</widget>
</item>
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 1bf378cca..f66a3898a 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -26,8 +26,30 @@
#include "ui_protein_detail_view.h"
#include <pappsomspp/pappsoexception.h>
#include <QMessageBox>
+#include <QDesktopServices>
#include <cmath>
-#include <QPushButton>
+
+DbXrefButton::DbXrefButton(QWidget * parent, DbXref dbxref): QPushButton(parent) {
+ _dbxref = dbxref;
+#if QT_VERSION >= 0x050000
+ // Qt5 code
+ /*
+ connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
+ connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
+ connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
+ */
+#else
+// Qt4 code
+ QObject::connect(this, SIGNAL(clicked()),this, SLOT(clickedSlot()));
+#endif
+
+ setText(_dbxref.accession);
+}
+
+void DbXrefButton::clickedSlot() {
+ qDebug() << "DbXrefButton::clickedSlot " << _dbxref.getUrl();
+ QDesktopServices::openUrl (_dbxref.getUrl()) ;
+}
ProteinWindow::ProteinWindow(ProjectWindow *parent):
QMainWindow(parent),
@@ -66,17 +88,18 @@ void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identif
void ProteinWindow::doPeptideMatchSelected(PeptideMatch * peptide_match) {
if (_p_protein_match != nullptr) {
- ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_match));
+ ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence(peptide_match));
}
}
void ProteinWindow::clearDbXrefLayout() {
for (int i = 0; i < ui->dbxref_list_layout->count(); ++i)
-{
- delete ui->dbxref_list_layout->itemAt(i)->widget();
+ {
+ delete ui->dbxref_list_layout->itemAt(i)->widget();
+ }
}
+void ProteinWindow::browseUrl(int i) {
}
-
void ProteinWindow::updateDisplay() {
try {
clearDbXrefLayout();
@@ -89,15 +112,14 @@ void ProteinWindow::updateDisplay() {
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);
+
+ DbXrefButton * dbxref_button = new DbXrefButton(this,dbxref);
ui->dbxref_list_layout->addWidget(dbxref_button);
}
-
- ui->button_space_layout->setEnabled(true);
+
+ ui->button_layout->setVisible(true);
if (ui->dbxref_list_layout->count() == 0) {
- ui->button_space_layout->setEnabled(false);
+ ui->button_layout->setVisible(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 ff6d92e5c..f5bbe42dd 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -26,8 +26,19 @@
#include <QMainWindow>
#include <QTextDocument>
+#include <QPushButton>
#include "../../core/proteinmatch.h"
+class DbXrefButton: public QPushButton {
+ Q_OBJECT
+public :
+ DbXrefButton(QWidget * parent, DbXref dbxref);
+protected slots:
+ void clickedSlot();
+private:
+ DbXref _dbxref;
+};
+
class ProjectWindow;
namespace Ui {
@@ -46,7 +57,9 @@ public:
public slots:
void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
void doPeptideMatchSelected(PeptideMatch * peptide_match);
-
+ protected slots:
+ void browseUrl(int i);
+
protected :
void updateDisplay();
void clearDbXrefLayout();
diff --git a/src/utils/types.h b/src/utils/types.h
index e1a894909..222651868 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -32,11 +32,12 @@
*
*/
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
+ OboPsiMod =1, ///< OBO PSI MOD
+ SwissProt =2, ///< Swiss-Prot
+ TrEMBL=3, ///< TrEMBL
+ AGI_LocusCode=4, ///< AGI_LocusCode
+ NCBI_gi=5, ///< NCBI_gi
+ ref=6 ///< ref
};
/** \def IdentificationEngine identification engine
--
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