X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=415054ec38313c1a7c525ecdbe6e17f88c2d5b1b;hb=83dd6154fdf5f727bc587ef58790c08e8404b757;hp=06e35cd2f3025941410b359c456d870a017edb03;hpb=933ca77e913c56fc4c71cc0fe534df208bfd742d;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 06e35cd..415054e 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
@@ -32,6 +33,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -46,11 +48,13 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueColourScheme;
+import jalview.util.Comparison;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.StringUtils;
 import jalview.util.UrlLink;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -64,6 +68,7 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
@@ -344,29 +349,33 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
    * 
    * @param ap
+   *              the panel in which the mouse is clicked
    * @param seq
-   * @param features
-   *                   sequence features overlapping the clicked residue
+   *              the sequence under the mouse
+   * @throws NullPointerException
+   *                                if seq is null
    */
-  public PopupMenu(final AlignmentPanel ap, SequenceI seq,
-          List<SequenceFeature> features)
+  public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
   {
-    this(false, ap, seq, features, null);
+    this(false, ap, seq, column, null);
   }
 
   /**
    * Constructor for a PopupMenu for a click in the sequence id panel
    * 
    * @param alignPanel
+   *                     the panel in which the mouse is clicked
    * @param seq
-   * @param features
-   *                     non-positional features for the sequence
+   *                     the sequence under the mouse click
    * @param groupLinks
+   *                     templates for sequence external links
+   * @throws NullPointerException
+   *                                if seq is null
    */
   public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
-          List<SequenceFeature> features, List<String> groupLinks)
+          List<String> groupLinks)
   {
-    this(true, alignPanel, seq, features, groupLinks);
+    this(true, alignPanel, seq, -1, groupLinks);
   }
 
   /**
@@ -376,14 +385,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param fromIdPanel
    * @param alignPanel
    * @param seq
-   * @param features
+   * @param column
+   *                      aligned column position (0...)
    * @param groupLinks
    */
   private PopupMenu(boolean fromIdPanel,
           final AlignmentPanel alignPanel,
-          final SequenceI seq, List<SequenceFeature> features,
-          List<String> groupLinks)
+          final SequenceI seq, final int column, List<String> groupLinks)
   {
+    Objects.requireNonNull(seq);
     this.forIdPanel = fromIdPanel;
     this.ap = alignPanel;
     sequence = seq;
@@ -409,7 +419,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * 'reference annotations' that may be added to the alignment. First for the
      * currently selected sequence (if there is one):
      */
-    final List<SequenceI> selectedSequence = (forIdPanel
+    final List<SequenceI> selectedSequence = (forIdPanel && seq != null
             ? Arrays.asList(seq)
             : Collections.<SequenceI> emptyList());
     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
@@ -701,11 +711,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       rnaStructureMenu.setVisible(false);
     }
 
+    addLinksAndFeatures(seq, column);
+  }
+
+  /**
+   * Adds
+   * <ul>
+   * <li>configured sequence database links (ID panel popup menu)</li>
+   * <li>non-positional feature links (ID panel popup menu)</li>
+   * <li>positional feature links (alignment panel popup menu)</li>
+   * <li>feature details links (alignment panel popup menu)</li>
+   * </ul>
+   * If this panel is also showed complementary (CDS/protein) features, then links
+   * to their feature details are also added.
+   * 
+   * @param seq
+   * @param column
+   */
+  void addLinksAndFeatures(final SequenceI seq, final int column)
+  {
+    List<SequenceFeature> features = null;
+    if (forIdPanel)
+    {
+      features = sequence.getFeatures().getNonPositionalFeatures();
+    }
+    else
+    {
+      features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+              column + 1);
+    }
+
     addLinks(seq, features);
 
     if (!forIdPanel)
     {
-      addFeatureDetails(features);
+      addFeatureDetails(features, seq, column);
     }
   }
 
@@ -713,75 +753,127 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * Add a link to show feature details for each sequence feature
    * 
    * @param features
+   * @param column
+   * @param seq
    */
-  protected void addFeatureDetails(List<SequenceFeature> features)
+  protected void addFeatureDetails(List<SequenceFeature> features,
+          SequenceI seq, int column)
   {
-    if (features == null || features.isEmpty())
+    /*
+     * add features in CDS/protein complement at the corresponding
+     * position if configured to do so
+     */
+    MappedFeatures mf = null;
+    if (ap.av.isShowComplementFeatures())
+    {
+      if (!Comparison.isGap(sequence.getCharAt(column)))
+      {
+        AlignViewportI complement = ap.getAlignViewport()
+                .getCodingComplement();
+        AlignFrame af = Desktop.getAlignFrameFor(complement);
+        FeatureRendererModel fr2 = af.getFeatureRenderer();
+        int seqPos = sequence.findPosition(column);
+        mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
+      }
+    }
+
+    if (features.isEmpty() && mf == null)
     {
+      /*
+       * no features to show at this position
+       */
       return;
     }
+
     JMenu details = new JMenu(
             MessageManager.getString("label.feature_details"));
     add(details);
 
+    String name = seq.getName();
     for (final SequenceFeature sf : features)
     {
-      int start = sf.getBegin();
-      int end = sf.getEnd();
-      String desc = null;
-      if (start == end)
+      addFeatureDetailsMenuItem(details, name, sf);
+    }
+
+    if (mf != null)
+    {
+      name = mf.fromSeq == seq ? mf.mapping.getTo().getName()
+              : mf.fromSeq.getName();
+      for (final SequenceFeature sf : mf.features)
       {
-        desc = String.format("%s %d", sf.getType(), start);
+        addFeatureDetailsMenuItem(details, name, sf);
       }
-      else
+    }
+  }
+
+  /**
+   * A helper method to add one menu item whose action is to show details for one
+   * feature
+   * 
+   * @param details
+   * @param seqName
+   * @param sf
+   */
+  void addFeatureDetailsMenuItem(JMenu details, final String seqName,
+          final SequenceFeature sf)
+  {
+    int start = sf.getBegin();
+    int end = sf.getEnd();
+    String desc = null;
+    if (start == end)
+    {
+      desc = String.format("%s %d", sf.getType(), start);
+    }
+    else
+    {
+      desc = String.format("%s %d-%d", sf.getType(), start, end);
+    }
+    String tooltip = desc;
+    String description = sf.getDescription();
+    if (description != null)
+    {
+      description = StringUtils.stripHtmlTags(description);
+      if (description.length() > 12)
       {
-        desc = String.format("%s %d-%d", sf.getType(), start, end);
+        desc = desc + " " + description.substring(0, 12) + "..";
       }
-      String tooltip = desc;
-      String description = sf.getDescription();
-      if (description != null)
+      else
       {
-        description = StringUtils.stripHtmlTags(description);
-        if (description.length() > 12)
-        {
-          desc = desc + " " + description.substring(0, 12) + "..";
-        }
-        else
-        {
-          desc = desc + " " + description;
-        }
-        tooltip = tooltip + " " + description;
+        desc = desc + " " + description;
       }
-      if (sf.getFeatureGroup() != null)
+      tooltip = tooltip + " " + description;
+    }
+    if (sf.getFeatureGroup() != null)
+    {
+      tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
+    }
+    JMenuItem item = new JMenuItem(desc);
+    item.setToolTipText(tooltip);
+    item.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
+        showFeatureDetails(seqName, sf);
       }
-      JMenuItem item = new JMenuItem(desc);
-      item.setToolTipText(tooltip);
-      item.addActionListener(new ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          showFeatureDetails(sf);
-        }
-      });
-      details.add(item);
-    }
+    });
+    details.add(item);
   }
 
   /**
    * Opens a panel showing a text report of feature dteails
    * 
+   * @param seqName
+   * 
    * @param sf
    */
-  protected void showFeatureDetails(SequenceFeature sf)
+  protected void showFeatureDetails(String seqName, SequenceFeature sf)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
     // it appears Java's CSS does not support border-collapse :-(
     cap.addStylesheetRule("table { border-collapse: collapse;}");
     cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
-    cap.setText(sf.getDetailsReport(sequence));
+    cap.setText(sf.getDetailsReport(seqName));
 
     Desktop.addInternalFrame(cap,
             MessageManager.getString("label.feature_details"), 500, 500);