From 60eeb09cc7a77ff0d068ee0fe095d8fc5811bf19 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 30 Mar 2017 11:09:50 +0200
Subject: [PATCH] html sequence coverage
---
src/CMakeLists.txt | 4 +-
src/core/proteinmatch.cpp | 42 +++++++++++++++++++++
src/core/proteinmatch.h | 4 ++
src/gui/protein_view/protein_detail_view.ui | 4 +-
src/gui/protein_view/proteinwindow.cpp | 2 +-
5 files changed, 51 insertions(+), 5 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 617e2004..46172223 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
- SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 29635494..1dec8423 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -258,6 +258,48 @@ pappso::pappso_double ProteinMatch::getPAI(const pappso::MsRunIdSp & sp_msrun_id
return PAI;
}
+
+const QString ProteinMatch::getHtmlSequence() const
+{
+ size_t prot_size = _protein_sp.get()->size();
+ //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
+ if (prot_size == 0) return 0;
+ bool cover_bool[prot_size] = {false};
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->isValidAndChecked()) {
+ size_t size = p_peptide_match->getPeptideXtpSp().get()->size();
+ size_t offset = p_peptide_match->getStart();
+ if (offset >= 0) {
+ for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
+ cover_bool[offset] = true;
+ }
+ }
+ }
+ }
+ QString sequence = getProteinXtpSp().get()->getSequence();
+ QString sequence_html;
+ for (unsigned int i=0; i < prot_size; i++) {
+
+ if(cover_bool[i]) {
+ sequence_html.append(QString("<span style=\"background-color:yellow;\">%1").arg(sequence[i]));
+ for (;i < prot_size; i++) {
+ if(cover_bool[i]) {
+ sequence_html.append(sequence[i]);
+ }
+ else {
+ sequence_html.append(QString("</span>%1").arg(sequence[i]));
+ break;
+ }
+ }
+ sequence_html.append(QString("</span>"));
+ }
+ else {
+ sequence_html.append(sequence[i]);
+ }
+ }
+ return sequence_html;
+}
+
pappso::pappso_double ProteinMatch::getCoverage() const {
size_t prot_size = _protein_sp.get()->size();
//qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 74ce8c12..9269a875 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -58,6 +58,10 @@ public:
* */
pappso::pappso_double getCoverage() const;
+/** @brief get coverage sequence (html representation)
+ **/
+ const QString getHtmlSequence() const;
+
/** @brief compute Protein Abundance Index (PAI)
* overall sample PAI computation (Rappsilber et al. 2002)
* */
diff --git a/src/gui/protein_view/protein_detail_view.ui b/src/gui/protein_view/protein_detail_view.ui
index c0bd5932..addfcf9f 100644
--- a/src/gui/protein_view/protein_detail_view.ui
+++ b/src/gui/protein_view/protein_detail_view.ui
@@ -40,9 +40,9 @@
</widget>
</item>
<item>
- <widget class="QPlainTextEdit" name="sequenceTextEdit">
+ <widget class="QTextEdit" name="sequenceTextEdit">
<property name="lineWrapMode">
- <enum>QPlainTextEdit::WidgetWidth</enum>
+ <enum>QTextEdit::WidgetWidth</enum>
</property>
</widget>
</item>
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 2fc6f334..8ba96d76 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -55,5 +55,5 @@ ProteinWindow::~ProteinWindow()
void ProteinWindow::setProteinMatch(ProteinMatch * p_protein_match) {
ui->descriptionLabel->setText(p_protein_match->getProteinXtpSp().get()->getAccession());
//ui->sequenceLabel->setText(p_protein_match->getProteinXtpSp().get()->getSequence());
- ui->sequenceTextEdit->setPlainText(p_protein_match->getProteinXtpSp().get()->getSequence());
+ ui->sequenceTextEdit->setText(p_protein_match->getHtmlSequence());
}
--
GitLab