JAL-2439 Fixes to out-by-one sequence indexing in gui classes

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6ca9499..946fc2a 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -25,8 +25,9 @@ import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -225,16 +226,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      while (seqCanvas.cursorY < av.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > av.getEndSeq())
       {
         ap.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.startRes))
+              .adjustForHiddenColumns(av.getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -243,7 +244,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
       while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.endRes))
+              .adjustForHiddenColumns(av.getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -458,7 +459,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * @param results
    * @return true if results were matched, false if not
    */
-  private boolean setStatusMessage(SearchResults results)
+  private boolean setStatusMessage(SearchResultsI results)
   {
     AlignmentI al = this.av.getAlignment();
     int sequenceIndex = al.findIndex(results);
@@ -467,7 +468,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return false;
     }
     SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
-    for (Match m : results.getResults())
+    for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
       if (seq.getDatasetSequence() != null)
@@ -559,7 +560,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (features != null && features.length > 0)
       {
-        SearchResults highlight = new SearchResults();
+        SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features[0].getBegin(),
                 features[0].getEnd());
         seqCanvas.highlightSearchResults(highlight);
@@ -731,7 +732,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   }
 
   @Override
-  public void highlightSequence(SearchResults results)
+  public void highlightSequence(SearchResultsI results)
   {
     if (av.isFollowHighlight())
     {
@@ -1422,41 +1423,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     stretchGroup = av.getSelectionGroup();
 
-    if (stretchGroup == null)
+    if (stretchGroup == null || !stretchGroup.contains(sequence, res))
     {
-      stretchGroup = av.getAlignment().findGroup(sequence);
-      if (stretchGroup != null && res > stretchGroup.getStartRes()
-              && res < stretchGroup.getEndRes())
+      stretchGroup = av.getAlignment().findGroup(sequence, res);
+      if (stretchGroup != null)
       {
+        // only update the current selection if the popup menu has a group to
+        // focus on
         av.setSelectionGroup(stretchGroup);
       }
-      else
-      {
-        stretchGroup = null;
-      }
-    }
-
-    else if (!stretchGroup.getSequences(null).contains(sequence)
-            || stretchGroup.getStartRes() > res
-            || stretchGroup.getEndRes() < res)
-    {
-      stretchGroup = null;
-
-      SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
-      if (allGroups != null)
-      {
-        for (int i = 0; i < allGroups.length; i++)
-        {
-          if (allGroups[i].getStartRes() <= res
-                  && allGroups[i].getEndRes() >= res)
-          {
-            stretchGroup = allGroups[i];
-            break;
-          }
-        }
-      }
-      av.setSelectionGroup(stretchGroup);
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
@@ -1511,13 +1486,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                "Background");
+        SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+                ap.getViewName());
       }
       if (av.getAbovePIDThreshold())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                "Background");
+        SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+                ap.getViewName());
       }
 
     }
@@ -1544,7 +1519,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                 stretchGroup.getName());
       }
-      else
+      if (stretchGroup.cs.getThreshold() > 0)
       {
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
                 stretchGroup.getName());
@@ -1668,8 +1643,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = -1;
     }
 
-    if (res > av.endRes || res < av.startRes || y < av.startSeq
-            || y > av.endSeq)
+    if (res > av.getEndRes() || res < av.getStartRes()
+            || y < av.getStartSeq() || y > av.getEndSeq())
     {
       mouseExited(evt);
     }
@@ -1915,8 +1890,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollTo(int row, int column)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    column = column < 0 ? ap.av.startRes : column;
+    row = row < 0 ? ap.av.getStartSeq() : row;
+    column = column < 0 ? ap.av.getStartRes() : column;
     ap.scrollTo(column, column, row, true, true);
   }
 
@@ -1928,8 +1903,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToRow(int row)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+    row = row < 0 ? ap.av.getStartSeq() : row;
+    ap.scrollTo(ap.av.getStartRes(), ap.av.getStartRes(), row, true, true);
   }
 
   /**
@@ -1940,8 +1915,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToColumn(int column)
   {
 
-    column = column < 0 ? ap.av.startRes : column;
-    ap.scrollTo(column, column, ap.av.startSeq, true, true);
+    column = column < 0 ? ap.av.getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getStartSeq(), true, true);
   }
 
   /**