Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9ec1ce4..c1cddaa 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;
@@ -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())
     {
@@ -927,13 +928,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    */
   private boolean needOverviewUpdate; // TODO: refactor to avcontroller
 
-  /**
-   * set if av.getSelectionGroup() refers to a group that is defined on the
-   * alignment view, rather than a transient selection
-   */
-  private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller
-                                               // or viewModel
-
   @Override
   public void mouseDragged(MouseEvent evt)
   {
@@ -1431,21 +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);
-        editingDefinedGroup = true;
-      }
-      else
-      {
-        stretchGroup = null;
-        editingDefinedGroup = false;
-      }
+      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)
     {
@@ -1461,7 +1446,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                   && allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
-            editingDefinedGroup = true;
             break;
           }
         }
@@ -1517,17 +1501,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-      editingDefinedGroup = false;
       stretchGroup = sg;
 
       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");
       }
 
@@ -1543,7 +1526,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && editingDefinedGroup;
+    // here we rely on stretchGroup == av.getSelection()
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1554,7 +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());
@@ -1562,8 +1546,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
     ap.paintAlignment(needOverviewUpdate);
-    needOverviewUpdate =false;
-    editingDefinedGroup = false;
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1618,7 +1601,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1626,7 +1609,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1660,7 +1643,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1670,7 +1653,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1839,9 +1822,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // do we want to thread this ? (contention with seqsel and colsel locks, I
     // suspect)
-    // rules are: colsel is copied if there is a real intersection between
-    // sequence selection
-    boolean repaint = false, copycolsel = true;
+    /*
+     * only copy colsel if there is a real intersection between
+     * sequence selection and this panel's alignment
+     */
+    boolean repaint = false;
+    boolean copycolsel = false;
     if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
     {
       SequenceGroup sgroup = null;
@@ -1858,11 +1844,9 @@ 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.isEmpty()))
+        if ((sgroup != null && sgroup.getSize() > 0))
         {
-          // don't copy columns if the region didn't intersect.
-          copycolsel = false;
+          copycolsel = true;
         }
       }
       if (sgroup != null && sgroup.getSize() > 0)