X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=8cfd2dcb89d7ad4fd833e17918413fb2933ecd32;hb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;hp=6ca9499618fec362038f5999f4aaf01c822d99a5;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6ca9499..8cfd2dc 100644
--- 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;
@@ -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())
     {
@@ -1424,19 +1425,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (stretchGroup == null)
     {
-      stretchGroup = av.getAlignment().findGroup(sequence);
-      if (stretchGroup != null && res > stretchGroup.getStartRes()
-              && res < stretchGroup.getEndRes())
-      {
-        av.setSelectionGroup(stretchGroup);
-      }
-      else
-      {
-        stretchGroup = null;
-      }
+      stretchGroup = av.getAlignment().findGroup(sequence, res);
+      av.setSelectionGroup(stretchGroup);
     }
 
-    else if (!stretchGroup.getSequences(null).contains(sequence)
+    if (stretchGroup == null
+            || !stretchGroup.getSequences(null).contains(sequence)
             || stretchGroup.getStartRes() > res
             || stretchGroup.getEndRes() < res)
     {
@@ -1511,13 +1505,13 @@ 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 +1538,7 @@ 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());