Merge branch 'develop' into features/JAL-1723_sequenceReport

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bd8959d..885aab2 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -124,7 +124,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   private final SequenceAnnotationReport seqARep;
 
-  StringBuffer tooltipText = new StringBuffer();
+  StringBuilder tooltipText = new StringBuilder();
 
   String tmpString;
 
@@ -616,13 +616,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+    boolean isControlDown = Platform.isControlDown(evt);
+    if (evt.isShiftDown() || isControlDown)
     {
-      if (evt.isAltDown() || evt.isControlDown())
+      editingSeqs = true;
+      if (isControlDown)
       {
         groupEditing = true;
       }
-      editingSeqs = true;
     }
     else
     {
@@ -844,7 +845,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 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
+  // private boolean editingDefinedGroup = false; // TODO: refactor to
+  // avcontroller or viewModel
 
   /**
    * Set status message in alignment panel
@@ -1557,6 +1559,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     final int res = findRes(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
+    needOverviewUpdate = false;
 
     startWrapBlock = wrappedBlock;
 
@@ -1591,12 +1594,10 @@ public class SeqPanel extends JPanel implements MouseListener,
               && (res < stretchGroup.getEndRes()))
       {
         av.setSelectionGroup(stretchGroup);
-        editingDefinedGroup = true;
       }
       else
       {
         stretchGroup = null;
-        editingDefinedGroup = false;
       }
     }
     else if (!stretchGroup.getSequences(null).contains(sequence)
@@ -1615,14 +1616,12 @@ public class SeqPanel extends JPanel implements MouseListener,
                   && (allGroups[i].getEndRes() >= res))
           {
             stretchGroup = allGroups[i];
-            editingDefinedGroup = true;
             break;
           }
         }
       }
 
       av.setSelectionGroup(stretchGroup);
-
     }
 
     if (evt.isPopupTrigger()) // Mac: mousePressed
@@ -1659,7 +1658,6 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1736,7 +1734,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     // 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;
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1755,8 +1753,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     ap.paintAlignment(needOverviewUpdate);
-    needOverviewUpdate =false;
-    editingDefinedGroup = false;
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1810,7 +1807,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1818,7 +1815,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1852,7 +1849,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1862,7 +1859,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= editingDefinedGroup;
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -2016,8 +2013,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (av.getAlignment() == null)
       {
-        Cache.log.warn("alignviewport av SeqSetId="
-                + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+        Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+                + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;
       }