JAL-192 show reference sequence position and residue in ruler

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9870e68..479b746 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -481,7 +481,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
          * Convert position in sequence (base 1) to sequence character array
          * index (base 0)
          */
-        int start = m.getStart() - 1;
+        int start = m.getStart() - m.getSequence().getStart();
         setStatusMessage(seq, start, sequenceIndex);
         return true;
       }
@@ -489,6 +489,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return false;
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     lastMousePress = evt.getPoint();
@@ -539,6 +540,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return;
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
@@ -572,6 +574,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
@@ -715,6 +718,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   String lastMessage;
 
+  @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
     String tmp = sequence.hashCode() + index + "";
@@ -726,6 +730,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     lastMessage = tmp;
   }
 
+  @Override
   public void highlightSequence(SearchResults results)
   {
     if (av.isFollowHighlight())
@@ -746,12 +751,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return this.ap == null ? null : this.ap.av;
   }
 
+  @Override
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
     // repaint();
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     int res = findRes(evt);
@@ -912,6 +919,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   Tooltip tooltip;
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (mouseWheelPressed)
@@ -1659,6 +1667,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     seqCanvas.repaint();
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (oldSeq < 0)
@@ -1673,6 +1682,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -1732,6 +1742,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
@@ -1776,6 +1787,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   /**
    * modify current selection according to a received message.
    */
+  @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
           SelectionSource source)
   {
@@ -1821,7 +1833,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         sgroup = seqsel.intersect(av.getAlignment(),
                 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
         if ((sgroup == null || sgroup.getSize() == 0)
-                && (colsel == null || colsel.size() == 0))
+                && (colsel == null || colsel.isEmpty()))
         {
           // don't copy columns if the region didn't intersect.
           copycolsel = false;
@@ -1843,7 +1855,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
-      if (colsel == null || colsel.size() == 0)
+      if (colsel == null || colsel.isEmpty())
       {
         if (av.getColumnSelection() != null)
         {