html sequence coverage

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")
 

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();

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)
       * */

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>

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());
 }