Merge pull request #2 from jpfeuffer/gui/proteintable

Fixes, cleanups and todos

Author: dhanmoni

src/openms_gui/include/OpenMS/VISUAL/DataSelectionTabs.h

@@ -93,7 +93,7 @@ namespace OpenMS
     /// Tabs which have data to show are automatically enabled. Others are disabled.
     /// If the currently visible tab would have to data to show, we pick the highest (rightmost) tab
     /// which has data and show that instead
-    void update();
+    void callUpdateEntries();
 
     /// invoked when user changes the active tab to @p tab_index
     void currentTabChanged(int tab_index);

src/openms_gui/include/OpenMS/VISUAL/SequenceVisualizer.h

@@ -1,3 +1,38 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
+//
+// This software is released under a three-clause BSD license:
+//  * Redistributions of source code must retain the above copyright
+//    notice, this list of conditions and the following disclaimer.
+//  * Redistributions in binary form must reproduce the above copyright
+//    notice, this list of conditions and the following disclaimer in the
+//    documentation and/or other materials provided with the distribution.
+//  * Neither the name of any author or any participating institution
+//    may be used to endorse or promote products derived from this software
+//    without specific prior written permission.
+// For a full list of authors, refer to the file AUTHORS.
+// --------------------------------------------------------------------------
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
+// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// --------------------------------------------------------------------------
+// $Maintainer: Julianus Pfeuffer $
+// $Authors: Dhanmoni Nath, Julianus Pfeuffer $
+// --------------------------------------------------------------------------
+
+#ifdef QT_WEBENGINEWIDGETS_LIB
 #pragma once
 
 // OpenMS_GUI config
@@ -6,9 +41,6 @@
 #include <QWidget>
 #include <QJsonObject>
 
-#include <unordered_map>
-#include <vector>
-
 namespace Ui
 {
   class SequenceVisualizer;
@@ -23,15 +55,16 @@ namespace OpenMS
     Q_PROPERTY(QJsonObject json_data_obj MEMBER m_json_data_obj)
 
   public:
-    SequenceVisualizer(QWidget* parent = nullptr);
-    ~SequenceVisualizer();
+    explicit SequenceVisualizer(QWidget* parent = nullptr);
+    ~SequenceVisualizer() override;
 
   public slots:
 
-    void setProteinPeptideDataToJsonObj(QString accession_num, QString pro_seq, QJsonArray peptides_data, QJsonArray pep_mod_data);
+    void setProteinPeptideDataToJsonObj(const QString& accession_num, const QString& pro_seq, const QJsonArray& peptides_data, const QJsonArray& pep_mod_data);
 
   private:
     Ui::SequenceVisualizer* ui;
     QJsonObject m_json_data_obj;
   };
-}// namespace OpenMS
+}// namespace OpenMS
+#endif

src/openms_gui/include/OpenMS/VISUAL/SpectraIDViewTab.h

@@ -98,23 +98,20 @@ namespace OpenMS
 
   private:
    /// partially fill the bottom-most row  
-   void fillRow_(const MSSpectrum& spectrum, const int spec_index, const QColor background_color);
+   void fillRow_(const MSSpectrum& spectrum, const int spec_index, const QColor& background_color);
    // extract the required part of the accession 
-   QString extractNumFromAccession_(QString listItem);
+   static static QString extractNumFromAccession_(const QString& listItem);
    //open browser to navigate to uniport site with accession
-   void openUniProtSiteWithAccession_(QString accession);
+   void openUniProtSiteWithAccession_(const QString& accession);
 
     LayerData* layer_ = nullptr;
     QCheckBox* hide_no_identification_ = nullptr;
     QCheckBox* create_rows_for_commmon_metavalue_ = nullptr;
     TableView* table_widget_ = nullptr;
     TableView* protein_table_widget_ = nullptr;
     QTableWidget* fragment_window_ = nullptr;
-    QWidget* protein_window_ = nullptr;
-    QWidget* accession_window_ = nullptr;
-    bool is_ms1_shown_ = false;
     bool is_first_time_loading = true;
-    std::unordered_map<String, std::vector<PeptideIdentification>> protein_to_peptide_id_map;
+    std::unordered_map<String, std::vector<const PeptideIdentification*>> protein_to_peptide_id_map;
   private slots:
     /// Saves the (potentially filtered) IDs as an idXML or mzIdentML file
     void saveIDs_();

src/openms_gui/include/OpenMS/VISUAL/SpectraTreeTab.h

@@ -80,6 +80,9 @@ namespace OpenMS
     /// @param current_type Either DT_PEAK or DT_CHROMATOGRAM, depending on what is currently shown
     bool getSelectedScan(MSExperiment& exp, LayerData::DataType& current_type) const;
 
+    /// received focus e.g. through tabswitching
+    void updateIndexFromCurrentLayer();
+
 signals:
     void spectrumSelected(int);
     void chromsSelected(std::vector<int> indices);
@@ -92,13 +95,15 @@ namespace OpenMS
     QLineEdit* spectra_search_box_ = nullptr;
     QComboBox* spectra_combo_box_ = nullptr;
     TreeView* spectra_treewidget_ = nullptr;
+    LayerData* layer_ = nullptr;
     /// cache to store mapping of chromatogram precursors to chromatogram indices
     std::map<size_t, std::map<Precursor, std::vector<Size>, Precursor::MZLess> > map_precursor_to_chrom_idx_cache_;
     /// remember the last PeakMap that we used to fill the spectra list (and avoid rebuilding it)
     const PeakMap* last_peakmap_ = nullptr;
 
 private slots:
-   /// fill the search-combo-box with current column header names
+
+    /// fill the search-combo-box with current column header names
     void populateSearchBox_();
     /// searches for rows containing a search text (from spectra_search_box_); called when text search box is used
     void spectrumSearchText_();

src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp

@@ -2022,7 +2022,8 @@ namespace OpenMS
     {
       return;
     }
-    selection_view_->currentTabChanged(1); //switch to ID view
+    selection_view_->setCurrentIndex(DataSelectionTabs::IDENT_IDX); //switch to ID view
+    selection_view_->currentTabChanged(DataSelectionTabs::IDENT_IDX);
   }
 
   void TOPPViewBase::annotateWithOSW()

src/openms_gui/source/VISUAL/DataSelectionTabs.cpp

@@ -113,7 +113,7 @@ namespace OpenMS
 
   // called externally
   // and internally by signals
-  void DataSelectionTabs::update()
+  void DataSelectionTabs::callUpdateEntries()
   {
     // prevent infinite loop when calling 'setTabEnabled' -> currentTabChanged() -> update()
     this->blockSignals(true);
@@ -151,7 +151,6 @@ namespace OpenMS
     Size current_index = currentIndex();
     // update the currently visible tab (might be disabled if no data is shown)
     tab_ptrs_[current_index]->updateEntries(layer_ptr);
-    this->update(); // not sure if necessary. Should update itself if changes occurred.
   }
 
   void DataSelectionTabs::currentTabChanged(int tab_index)
@@ -167,9 +166,13 @@ namespace OpenMS
     case IDENT_IDX:
       spectraview_controller_->deactivateBehavior();
       diatab_controller_->deactivateBehavior();
-      if (tv_->getActive2DWidget()) // currently 2D window is open
+      std::cout << "trying to switch to Ident tab" << std::endl;
+      if (tv_->getActive2DWidget()) // currently, 2D window is open
       {
+        std::cout << "2D was open" << std::endl;
         idview_controller_->showSpectrumAsNew1D(0);
+      } else {
+        std::cout << "2D was NOT open" << std::endl;
       }
       idview_controller_->activateBehavior();
       break;
@@ -182,7 +185,12 @@ namespace OpenMS
       std::cerr << "Error: tab_index " << tab_index << " is invalid\n";
       throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
     }
-    update();
+    callUpdateEntries(); //TODO actually this is overkill. Why would you load the entire table again
+    // when you only switched tabs? The TabView should get notified when the layer data changes, so it only
+    // updates when necessary...
+    // The only thing that maybe needs to happen when switching tabs is to sync the index across the tables in the different tabs.
+    // which is the only reason why we need to actually use callUpdateEntries here.
+    // At least we reduced it to only updateEntries during tab switch, not EVERY update() [e.g. when resizing, refocussing...]
   }
 
   void DataSelectionTabs::showSpectrumAsNew1D(int index)

src/openms_gui/source/VISUAL/ICONS/sequence_viz.html

@@ -117,6 +117,7 @@
                 length="${protlen}"
                 displaystart="1"
                 displayend="${protlen}"
+                numberofticks="0"
                 use-ctrl-to-zoom="true"
                 highlight-event="onmouseover"
             />
@@ -132,7 +133,7 @@
             let modProtTrack = `
             <protvista-track id="mod_track"
                 length="${protlen}"
-                displaystart="0"
+                displaystart="1"
                 displayend="${protlen}"
                 use-ctrl-to-zoom="true"
                 tooltip-event="mouseover"

src/openms_gui/source/VISUAL/Plot1DCanvas.cpp

@@ -823,7 +823,7 @@ namespace OpenMS
             }
 
             // Warn if non-empty peak color array present but size doesn't match number of peaks
-            // This indicates a bug but we gracefuly just issue a warning
+            // This indicates a bug but we gracefully just issue a warning
             if (!layer.peak_colors_1d.empty() &&
                 layer.peak_colors_1d.size() < spectrum.size())
             {
@@ -996,7 +996,7 @@ namespace OpenMS
       if (peak.peak >= spec.size())
       {
         // somehow the peak is invalid. This happens from time to time and should be tracked down elsewhere
-        // but its hard to reproduce (changing spectra in 1D view using arrow keys while hovering over the spectrum with the mouse?).
+        // but it's hard to reproduce (changing spectra in 1D view using arrow keys while hovering over the spectrum with the mouse?).
         return;
       }
       const ExperimentType::PeakType& sel = spec[peak.peak];
@@ -2096,6 +2096,7 @@ namespace OpenMS
     // be an in-memory representation in the peak data structure. Using
     // setCurrentSpectrumIndex will select the appropriate spectrum and load it
     // into memory.
+    std::cout << "Current nr. spec: " << getCurrentLayer().getPeakData()->size() << std::endl;
     if (index < getCurrentLayer().getPeakData()->size())
     {
       getCurrentLayer().setCurrentSpectrumIndex(index);

src/openms_gui/source/VISUAL/SequenceVisualizer.cpp

@@ -1,12 +1,42 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
+//
+// This software is released under a three-clause BSD license:
+//  * Redistributions of source code must retain the above copyright
+//    notice, this list of conditions and the following disclaimer.
+//  * Redistributions in binary form must reproduce the above copyright
+//    notice, this list of conditions and the following disclaimer in the
+//    documentation and/or other materials provided with the distribution.
+//  * Neither the name of any author or any participating institution
+//    may be used to endorse or promote products derived from this software
+//    without specific prior written permission.
+// For a full list of authors, refer to the file AUTHORS.
+// --------------------------------------------------------------------------
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
+// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// --------------------------------------------------------------------------
+// $Maintainer: Julianus Pfeuffer $
+// $Authors: Dhanmoni Nath, Julianus Pfeuffer $
+// --------------------------------------------------------------------------
+
+#ifdef QT_WEBENGINEWIDGETS_LIB
 #include <OpenMS/VISUAL/SequenceVisualizer.h>
 #include <ui_SequenceVisualizer.h>
 
-#include <QLabel>
-#include <QDebug>
 #include <QWebChannel>
-#include <QPushButton>
-#include <QMessageBox>
-#include <QJsonArray>
 #include <QString>
 
 #include <QtWebEngineWidgets/QWebEngineView>
@@ -18,8 +48,8 @@ namespace OpenMS
       QWidget(parent), ui(new Ui::SequenceVisualizer)
   {
     ui->setupUi(this);
-    QWebEngineView* view = new QWebEngineView(parent);
-    QWebChannel* channel = new QWebChannel(this);
+    auto* view = new QWebEngineView(parent);
+    auto* channel = new QWebChannel(this);
     view->page()->setWebChannel(channel);
     channel->registerObject(QString("SequenceVisualizer"), this);
     view->load(QUrl("qrc:/new/sequence_viz.html"));
@@ -31,14 +61,15 @@ namespace OpenMS
     delete ui;
   }
 
-  void SequenceVisualizer::setProteinPeptideDataToJsonObj(QString accession_num, 
-      QString pro_seq, 
-      QJsonArray pep_data, 
-      QJsonArray pep_mod_data)
+  void SequenceVisualizer::setProteinPeptideDataToJsonObj(const QString& accession_num,
+      const QString& pro_seq,
+      const QJsonArray& pep_data,
+      const QJsonArray& pep_mod_data)
   {
     m_json_data_obj["accession_num"] = accession_num;
     m_json_data_obj["protein_sequence_data"] = pro_seq;
     m_json_data_obj["peptides_data"] = pep_data;
     m_json_data_obj["peptides_mod_data"] = pep_mod_data;
   }
-}// namespace OpenMS
+}// namespace OpenMS
+#endif