From 16f0c7f1954c5e59f98fbf2aace6eae3229ad152 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 17 Aug 2015 12:06:22 +0100
Subject: [PATCH] JAL-1800 smarter matching when following mouseover of
 sequence

---
 src/jalview/gui/SeqPanel.java |   76 ++++++++++++++++++++++++++---------------
 1 file changed, 49 insertions(+), 27 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e34a864..41c3ce1 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,27 +20,11 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResults.Match;
@@ -60,6 +44,23 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -128,6 +129,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   StructureSelectionManager ssm;
 
+  SearchResults lastSearchResults;
+
   /**
    * Creates a new SeqPanel object.
    * 
@@ -656,9 +659,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     lastMessage = tmp;
   }
 
+  /**
+   * Highlight the mapped region described by the search results object (unless
+   * unchanged). This supports highlight of protein while mousing over linked
+   * cDNA and vice versa. The status bar is also updated to show the location of
+   * the start of the highlighted region.
+   */
   @Override
   public void highlightSequence(SearchResults results)
   {
+    if (results == null || results.equals(lastSearchResults)) {
+      return;
+    }
+    lastSearchResults = results;
+    
     if (av.isFollowHighlight())
     {
       /*
@@ -868,19 +882,27 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   private void setStatusMessage(SearchResults results)
   {
-    List<Match> matches = results.getResults();
-    if (!matches.isEmpty())
+    AlignmentI al = this.av.getAlignment();
+    int sequenceIndex = al.findIndex(results);
+    if (sequenceIndex == -1)
+    {
+      return;
+    }
+    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    for (Match m : results.getResults())
     {
-      Match m = matches.get(0);
       SequenceI seq = m.getSequence();
-      int sequenceIndex = this.av.getAlignment().findIndex(seq);
 
-      /*
-       * Convert position in sequence (base 1) to sequence character array index
-       * (base 0)
-       */
-      int start = m.getStart() - 1;
-      setStatusMessage(seq, start, sequenceIndex);
+      if (seq == ds)
+      {
+        /*
+         * Convert position in sequence (base 1) to sequence character array
+         * index (base 0)
+         */
+        int start = m.getStart() - 1;
+        setStatusMessage(seq, start, sequenceIndex);
+        return;
+      }
     }
   }
 
-- 
1.7.10.2