X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=c1cddaa5e35c6613b383f236c05a5780aaafd811;hb=b5579849960a79b7fc111bdc8f84c8b933632ef0;hp=31bf6a48af3a14ba96afd2d99d026c0171919f19;hpb=e2745a846737920f1ec43b72d271611784503e4c;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 31bf6a4..c1cddaa 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())
     {
@@ -919,6 +920,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   Tooltip tooltip;
 
+  /**
+   * set when the current UI interaction has resulted in a change that requires
+   * overview shading to be recalculated. this could be changed to something
+   * more expressive that indicates what actually has changed, so selective
+   * redraws can be applied
+   */
+  private boolean needOverviewUpdate; // TODO: refactor to avcontroller
+
   @Override
   public void mouseDragged(MouseEvent evt)
   {
@@ -1416,19 +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)
     {
@@ -1503,12 +1505,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+        SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
                 "Background");
       }
       if (av.getAbovePIDThreshold())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+        SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
                 "Background");
       }
 
@@ -1521,9 +1523,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // but defer colourscheme update until hidden sequences are passed in
+    boolean vischange = stretchGroup.recalcConservation(true);
+    // here we rely on stretchGroup == av.getSelection()
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1534,17 +1538,18 @@ 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());
       }
     }
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(true);
     av.sendSelection();
   }
 
@@ -1596,6 +1601,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1603,6 +1609,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1636,6 +1643,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1645,6 +1653,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }