ptm sequence color

src/grouping/ptm/ptmsamplescan.cpp

@@ -30,6 +30,12 @@
 #include "ptmsamplescan.h"
 #include "../../grouping/ptm/ptmgroupingexperiment.h"
 
+
+QColor PtmSampleScan::_color_best = QColor("red");
+QColor PtmSampleScan::_color_other_best = QColor("#ff7878");
+QColor PtmSampleScan::_color_no_best = QColor("yellow");
+
+
 PtmSampleScan::PtmSampleScan(const PeptideMatch * p_peptide_match) {
     _peptide_match_list.push_back(p_peptide_match);
 }
@@ -80,3 +86,52 @@ bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
         position_list.erase(last, position_list.end());
         return position_list;
     }
+
+const QString PtmSampleScan::getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const
+{
+    const PeptideMatch * p_representative_peptide = getRepresentativePeptideMatch();
+    size_t pep_size = p_representative_peptide->getPeptideXtpSp().get()->size();
+    //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
+    if (pep_size == 0) return 0;
+    bool best_bool[pep_size] = {false};
+    bool other_best_bool[pep_size] = {false};
+    bool nobest_bool[pep_size] = {false};
+    double best_evalue = p_representative_peptide->getEvalue();
+
+    
+    for (auto & p_peptide_match : _peptide_match_list) {
+        bool is_best= false;
+        if (p_peptide_match->getEvalue() == best_evalue) {
+            is_best= true;
+        }
+        std::vector<unsigned int> position_list = p_ptm_grouping_experiment->getPtmPositions(p_peptide_match);
+        for (unsigned int position :position_list) {
+            if (p_representative_peptide == p_peptide_match) {
+                best_bool[position] = true;
+            }
+            else if (is_best) {
+                other_best_bool[position] = true;
+            }
+            else {
+                nobest_bool[position] = true;
+            }
+        }
+    }
+    QString sequence = p_representative_peptide->getPeptideXtpSp().get()->getSequence();
+    QString sequence_html;
+    for (unsigned int i=0; i < pep_size; i++) {
+        if (best_bool[i]) {
+                sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_best.name()));
+            }
+            else if (other_best_bool[i]) {
+                sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_other_best.name()));
+            }
+            else if (nobest_bool[i]){
+                sequence_html.append(QString("<span style=\"color:%2;\">%1</span>").arg(sequence[i]).arg(_color_no_best.name()));
+            }
+            else {
+                sequence_html.append(sequence[i]);
+            }
+    }
+    return sequence_html;
+}

src/grouping/ptm/ptmsamplescan.h

@@ -52,9 +52,13 @@ public:
     bool add(const PeptideMatch * p_peptide_match);
     std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
     std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
+    const QString getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
     
 private:
     std::vector<const PeptideMatch *> _peptide_match_list;
+    static QColor _color_best;
+    static QColor _color_other_best;
+    static QColor _color_no_best;
 
 };
 

src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp

@@ -50,7 +50,7 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow * parent):QMainWi
     ui->ptm_peptide_tableview->setModel( _ptm_proxy_model_p );
     ui->ptm_peptide_tableview->setSortingEnabled(true);
     ui->ptm_peptide_tableview->setAlternatingRowColors(true);
-    PtmSequenceDelegate * p_sequence_delegate = new PtmSequenceDelegate();
+    PtmSequenceDelegate * p_sequence_delegate = new PtmSequenceDelegate(_p_ptm_island_list_window, this);
     ui->ptm_peptide_tableview->setItemDelegateForColumn((std::int8_t) PtmPeptideListColumn::sequence, p_sequence_delegate);
 
 

src/gui/ptm_peptide_list_view/ptmsequencedelegate.cpp

@@ -28,11 +28,12 @@
 
 #include "ptmsequencedelegate.h"
 #include "../../grouping/ptm/ptmsamplescan.h"
+#include "../ptm_island_list_view/ptmislandlistwindow.h"
 #include <QTextDocument>
 #include <QPainter>
 
-PtmSequenceDelegate::PtmSequenceDelegate(QWidget *parent) : QStyledItemDelegate(parent) {
-    
+PtmSequenceDelegate::PtmSequenceDelegate(PtmIslandListWindow * p_ptm_island_list_window, QWidget *parent) : QStyledItemDelegate(parent) {
+    _p_ptm_island_list_window = p_ptm_island_list_window;
 }
 
 void PtmSequenceDelegate::paint(QPainter *painter, const QStyleOptionViewItem &option,
@@ -45,7 +46,7 @@ void PtmSequenceDelegate::paint(QPainter *painter, const QStyleOptionViewItem &o
         //    painter->fillRect(option.rect, option.palette.highlight());
         QTextDocument document;
      document.setDocumentMargin(2);
-     document.setHtml(p_ptm_sample_scan->getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getSequence());
+     document.setHtml(p_ptm_sample_scan->getHtmlSequence(_p_ptm_island_list_window->getIdentificationGroup()->getPtmGroupingExperiment()));
      painter->translate(option.rect.topLeft());
      document.drawContents(painter);
      painter->translate(-option.rect.topLeft());

src/gui/ptm_peptide_list_view/ptmsequencedelegate.h

@@ -30,13 +30,14 @@
 #define PTMSEQUENCEDELEGATE_H
 
 #include <QStyledItemDelegate>
+class PtmIslandListWindow;
 
 class PtmSequenceDelegate : public QStyledItemDelegate
 {
     Q_OBJECT
 
 public:
-    PtmSequenceDelegate(QWidget *parent = 0);
+    PtmSequenceDelegate(PtmIslandListWindow * p_ptm_island_list_window, QWidget *parent = 0);
 
     void paint(QPainter *painter, const QStyleOptionViewItem &option,
                const QModelIndex &index) const override;
@@ -47,6 +48,7 @@ public:
     //void setEditorData(QWidget *editor, const QModelIndex &index) const override;
     //void setModelData(QWidget *editor, QAbstractItemModel *model,
     //                  const QModelIndex &index) const override;
-
+private:
+    PtmIslandListWindow * _p_ptm_island_list_window;
 };
 #endif // PTMSEQUENCEDELEGATE_H