Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 21db7d7..bc7fb3b 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -49,6 +49,7 @@ import jalview.schemes.PIDColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 
 import java.awt.Color;
@@ -400,9 +401,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
       }
     }
-    // for the case when no sequences are even visible
+
+    /*
+     * offer 'Reveal All'
+     * - in the IdPanel (seq not null) if any sequence is hidden
+     * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+     */
     if (alignPanel.av.hasHiddenRows())
     {
+      boolean addOption = seq != null;
+      if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
+      {
+        addOption = true;
+      }
+      if (addOption)
       {
         menuItem = new JMenuItem(
                 MessageManager.getString("action.reveal_all"));
@@ -418,7 +430,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             }
           }
         });
-
         add(menuItem);
       }
     }
@@ -514,6 +525,89 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     }
 
     addLinks(seq, features);
+
+    if (seq == null)
+    {
+      addFeatureDetails(features);
+    }
+  }
+
+  /**
+   * Add a link to show feature details for each sequence feature
+   * 
+   * @param features
+   */
+  protected void addFeatureDetails(List<SequenceFeature> features)
+  {
+    if (features == null || features.isEmpty())
+    {
+      return;
+    }
+    JMenu details = new JMenu(
+            MessageManager.getString("label.feature_details"));
+    add(details);
+
+    for (final SequenceFeature sf : features)
+    {
+      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 = desc + " " + description.substring(0, 12) + "..";
+        }
+        else
+        {
+          desc = desc + " " + description;
+        }
+        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)
+        {
+          showFeatureDetails(sf);
+        }
+      });
+      details.add(item);
+    }
+  }
+
+  /**
+   * Opens a panel showing a text report of feature dteails
+   * 
+   * @param sf
+   */
+  protected void showFeatureDetails(SequenceFeature sf)
+  {
+    CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+    // it appears Java's CSS does not support border-collaps :-(
+    cap.addStylesheetRule("table { border-collapse: collapse;}");
+    cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+    cap.setText(sf.getDetailsReport());
+
+    Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.feature_details"), 500, 500);
   }
 
   /**
@@ -1477,15 +1571,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-
-    HiddenColumns hidden = new HiddenColumns();
-    BitSet inserts = new BitSet(), mask = new BitSet();
-
-    // set mask to preserve existing hidden columns outside selected group
-    if (ap.av.hasHiddenColumns())
-    {
-      ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
-    }
+    HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+    BitSet inserts = new BitSet();
 
     boolean markedPopup = false;
     // mark inserts in current selection
@@ -1493,10 +1580,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     {
       // mark just the columns in the selection group to be hidden
       inserts.set(ap.av.getSelectionGroup().getStartRes(),
-              ap.av.getSelectionGroup().getEndRes() + 1);
-
-      // and clear that part of the mask
-      mask.andNot(inserts);
+              ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
 
       // now clear columns without gaps
       for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
@@ -1507,29 +1591,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
         inserts.and(sq.getInsertionsAsBits());
       }
-    }
-    else
-    {
-      // initially, mark all columns to be hidden
-      inserts.set(0, ap.av.getAlignment().getWidth());
-
-      // and clear out old hidden regions completely
-      mask.clear();
+      hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+              ap.av.getSelectionGroup().getEndRes());
     }
 
     // now mark for sequence under popup if we haven't already done it
-    if (!markedPopup && sequence != null)
+    else if (!markedPopup && sequence != null)
     {
-      inserts.and(sequence.getInsertionsAsBits());
-    }
-
-    // finally, preserve hidden regions outside selection
-    inserts.or(mask);
+      inserts.or(sequence.getInsertionsAsBits());
 
-    // and set hidden columns accordingly
-    hidden.hideMarkedBits(inserts);
-
-    ap.av.getAlignment().setHiddenColumns(hidden);
+      // and set hidden columns accordingly
+      hidden.hideColumns(inserts);
+    }
     refresh();
   }
 
@@ -1554,10 +1627,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               new Object[]
               { seq.getDisplayId(true) }) + "</h2></p><p>");
       new SequenceAnnotationReport(null).createSequenceAnnotationReport(
-              contents, seq, true, true,
-              (ap.getSeqPanel().seqCanvas.fr != null)
-                      ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
-                      : null);
+              contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
       contents.append("</p>");
     }
     cap.setText("<html>" + contents.toString() + "</html>");
@@ -1767,7 +1837,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
 
     sequence.setDescription(dialog.getDescription());