diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 680c540207cdf882fd93cfd35d2d3003ae8a6520..46b10f6c74012596c4c0b6cd523ee5259fd5318b 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -35,7 +35,7 @@ ProteinTableModel::columnMap ProteinTableModel::_column_assignment = {
(std::int8_t)ProteinListColumn::group,
(std::int8_t)ProteinListColumn::accession,
(std::int8_t)ProteinListColumn::description,
- (std::int8_t)ProteinListColumn::evalue,
+ (std::int8_t)ProteinListColumn::log_evalue,
(std::int8_t)ProteinListColumn::spectrum,
(std::int8_t)ProteinListColumn::specific_spectrum,
(std::int8_t)ProteinListColumn::sequence,
@@ -52,8 +52,6 @@ ProteinTableModel::ProteinTableModel(ProteinListWindow * p_protein_list_window)
{
_p_protein_list_window = p_protein_list_window;
_p_identification_group = nullptr;
-
- _columns << "checked" << "group" << "accession" << "protein description" << "log(Evalue)" << "spectrum" << "specific" << "sequence" << "specific sequence" << "coverage" << "PAI";
}
void ProteinTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
@@ -79,31 +77,111 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::columnCount begin ";
if (_p_identification_group != nullptr) {
- return _columns.size();
+ return 11;
}
return 0;
}
+
+const QString ProteinTableModel::getTitle(std::int8_t column) const {
+ switch (column) {
+
+ case (std::int8_t) ProteinListColumn::checked:
+ return "checked";
+ break;
+
+ case (std::int8_t) ProteinListColumn::group:
+ return "group";
+ break;
+ case (std::int8_t) ProteinListColumn::accession:
+ return "accession";
+ break;
+ case (std::int8_t) ProteinListColumn::description:
+ return "description";
+ break;
+ case (std::int8_t) ProteinListColumn::log_evalue:
+ return "log(Evalue)";
+ break;
+ case (std::int8_t) ProteinListColumn::evalue:
+ return "Evalue";
+ break;
+ case (std::int8_t) ProteinListColumn::spectrum:
+ return "spectrum";
+ break;
+ case (std::int8_t) ProteinListColumn::specific_spectrum:
+ return "specific";
+ break;
+ case (std::int8_t) ProteinListColumn::sequence:
+ return "sequence";
+ break;
+ case (std::int8_t) ProteinListColumn::coverage:
+ return "coverage";
+ break;
+ case (std::int8_t) ProteinListColumn::pai:
+ return "PAI";
+ break;
+ case (std::int8_t) ProteinListColumn::specific_sequence:
+ return "specific sequence";
+
+ }
+ return "";
+}
+
+const QString ProteinTableModel::getDescription(std::int8_t column) const {
+ switch (column) {
+
+ case (std::int8_t) ProteinListColumn::checked:
+ return "manual protein check";
+ break;
+
+ case (std::int8_t) ProteinListColumn::group:
+ return "unique protein grouping identifier";
+ break;
+ case (std::int8_t) ProteinListColumn::accession:
+ return "protein accession";
+ break;
+ case (std::int8_t) ProteinListColumn::description:
+ return "protein description";
+ break;
+ case (std::int8_t) ProteinListColumn::log_evalue:
+ return "log(Evalue)";
+ break;
+ case (std::int8_t) ProteinListColumn::evalue:
+ return "protein Evalue";
+ break;
+ case (std::int8_t) ProteinListColumn::spectrum:
+ return "number of distinct MS spectrum assigned to this protein";
+ break;
+ case (std::int8_t) ProteinListColumn::specific_spectrum:
+ return "number of distinct MS spectrum only assigned to this protein within the group";
+ break;
+ case (std::int8_t) ProteinListColumn::sequence:
+ return "number of unique distinct peptide sequences";
+ break;
+ case (std::int8_t) ProteinListColumn::coverage:
+ return "protein coverage (ratio)";
+ break;
+ case (std::int8_t) ProteinListColumn::pai:
+ return "Protein Abundance Index (Rappsilber et al. 2002)";
+ break;
+ case (std::int8_t) ProteinListColumn::specific_sequence:
+ return "number of unique distinct peptide sequences only assigned to this protein within the group";
+
+ }
+ return "";
+}
QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
if (_p_identification_group == nullptr) return QVariant();
if (orientation == Qt::Horizontal)
{
- if (section < _columns.size())
- {
- if (role == Qt::DisplayRole)
- {
- return QVariant(_columns.at(section));
- }
- else if(role == Qt::SizeHintRole)
- {
- QSize size(1000, 50);
- if (section == 2)
- {
- size.setWidth(400);
- }
-
- return QVariant(size);
- }
+ switch (role) {
+ case Qt::DisplayRole :
+ return QVariant(getTitle(_column_assignment [section]));
+ break;
+ case Qt::ToolTipRole :
+ return QVariant(getDescription(_column_assignment [section]));
+ break;
+
}
}
return QVariant();
@@ -166,9 +244,13 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::description ) {
return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
}
- if (_column_assignment[col] == (std::int8_t) ProteinListColumn::evalue ) {
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::log_evalue ) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getLogEvalue());
}
+
+ if (_column_assignment[col] == (std::int8_t) ProteinListColumn::evalue ) {
+ return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
+ }
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::spectrum ) {
return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countSampleScan(ValidationState::validAndChecked));
}
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index cdf1b33ef1bb49a32ecea038d3a5e866f9190f22..f6cb458292f3c38b98222b5f10108933fc029dee 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -27,6 +27,26 @@
#include <QAbstractTableModel>
#include "../../core/project.h"
+
+/** \def ProteinListColumn list of available fields to display in protein list
+ *
+ */
+
+enum class ProteinListColumn {
+ checked, ///< manual checked
+ group, ///< group id
+ accession, ///< accession
+ description, ///< protein description
+ log_evalue, ///< log(Evalue)
+ evalue, ///< Evalue
+ spectrum, ///< spectrum count
+ specific_spectrum, ///< specific spectrum count
+ sequence, ///< unique sequence count
+ specific_sequence, ///< specific unique sequence
+ coverage, ///< protein coverage
+ pai, ///< PAI
+};
+
class ProteinListWindow;
class ProteinTableModel: public QAbstractTableModel
@@ -39,6 +59,8 @@ public:
virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+ const QString getTitle(std::int8_t column) const;
+ const QString getDescription(std::int8_t column) const;
void setIdentificationGroup(IdentificationGroup * p_identification_group);
IdentificationGroup * getIdentificationGroup();
diff --git a/src/gui/ptm_island_list_view/ptm_island_list_view.ui b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
index 475f2c6a9079e358f324d01e3a53cf8d78a19b14..01d7d80519d8d55e46c900ef15cd54739a693ba4 100644
--- a/src/gui/ptm_island_list_view/ptm_island_list_view.ui
+++ b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>PtmIslandListWindow</class>
- <widget class="QMainWindow" name="ptm_island_list_window">
+ <widget class="QMainWindow" name="PtmIslandListWindow">
<property name="geometry">
<rect>
<x>0</x>
@@ -21,38 +21,6 @@
<enum>Qt::CustomContextMenu</enum>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>hide :</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="hideNotValidCheckBox">
- <property name="text">
- <string>not valid</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="hideNotCheckedCheckBox">
- <property name="text">
- <string>not checked</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="hideNotGroupedCheckBox">
- <property name="text">
- <string>not grouped</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
<item>
<widget class="QTableView" name="ptm_island_tableview">
<property name="contextMenuPolicy">
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 52259a14f27fbdd3e2e18c89aab74b9ed877921f..4c137e57cd55b6ce5b6485b42aa48f3bfe22859a 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -88,6 +88,41 @@ const QString PtmIslandTableModel::getTitle(std::int8_t column) const {
}
return "";
}
+
+const QString PtmIslandTableModel::getDescription(std::int8_t column) const {
+ switch (column) {
+
+ case (std::int8_t) PtmIslandListColumn::spectrum:
+ return "number of distinct spectrum assigned to this PTM island";
+ break;
+
+ case (std::int8_t) PtmIslandListColumn::description:
+ return "protein description";
+ break;
+ case (std::int8_t) PtmIslandListColumn::multiptm:
+ return "number of distinct spectrum containing more than 1 ptm";
+ break;
+ case (std::int8_t) PtmIslandListColumn::sequence:
+ return "number of unique peptide sequence";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+ return "unique PTM island identifier";
+ break;
+ case (std::int8_t) PtmIslandListColumn::accession:
+ return "protein accession";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+ return "PTM positions observed in this PTM island";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_island_start:
+ return "PTM island start on the protein";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_island_length:
+ return "PTM island length";
+
+ }
+ return "";
+}
void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
qDebug() << "PtmIslandTableModel::setIdentificationGroup begin ";
beginResetModel();
@@ -124,9 +159,14 @@ QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientatio
if (getPtmGroupingExperiment() == nullptr) return QVariant();
if (orientation == Qt::Horizontal)
{
- if (role == Qt::DisplayRole)
- {
+ switch (role) {
+ case Qt::DisplayRole :
return QVariant(getTitle(_column_assignment [section]));
+ break;
+ case Qt::ToolTipRole :
+ return QVariant(getDescription(_column_assignment [section]));
+ break;
+
}
}
return QVariant();
@@ -163,7 +203,7 @@ QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
break;
case (std::int8_t) PtmIslandListColumn::ptm_island_start:
- return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getStart());
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getStart()+1);
break;
case (std::int8_t) PtmIslandListColumn::ptm_island_length:
return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->size());
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index c6eeda9b84df1bf86c2e4a1fa55e1af7a8b2ecc9..25b472aa1fd264fd265de93cbef875986e9887b9 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -71,6 +71,7 @@ public:
const QString getTitle(std::int8_t column) const;
+ const QString getDescription(std::int8_t column) const;
using columnMap = std::int8_t[20];
diff --git a/src/utils/types.h b/src/utils/types.h
index 9bf617565658a83712b894d44a73cc3ed75252ad..6c6800a1ad676f7ba22559679716f59fd91fbc53 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -95,22 +95,4 @@ enum class ValidationState: std::int8_t {
};
-/** \def ProteinListColumn list of available fields to display in protein list
- *
- */
-
-enum class ProteinListColumn {
- checked, ///< manual checked
- group, ///< group id
- accession, ///< accession
- description, ///< protein description
- evalue, ///< Evalue
- spectrum, ///< spectrum count
- specific_spectrum, ///< specific spectrum count
- sequence, ///< unique sequence count
- specific_sequence, ///< specific unique sequence
- coverage, ///< protein coverage
- pai, ///< PAI
-};
-
#endif /* _TYPES_H_ */