Merge branch 'develop' into features/JAL-1793VCF; lambda Function for

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ad80a3e..282c810 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -214,8 +214,8 @@ public class SeqPanel extends JPanel
               + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
-      y -= hgap;
-      x = Math.max(0, x - seqCanvas.labelWidthWest);
+      y = Math.max(0, y - hgap);
+      x = Math.max(0, x - seqCanvas.getLabelWidthWest());
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
@@ -483,7 +483,7 @@ public class SeqPanel extends JPanel
       av.setSelectionGroup(sg);
     }
 
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -851,11 +851,12 @@ public class SeqPanel extends JPanel
 
   /**
    * 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
+   * shading in overviews and structures to be recalculated. this could be
+   * changed to a something more expressive that indicates what actually has
+   * changed, so selective redraws can be applied (ie. only structures, only
+   * overview, etc)
    */
-  private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
+  private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
 
   /**
    * set if av.getSelectionGroup() refers to a group that is defined on the
@@ -1056,7 +1057,7 @@ public class SeqPanel extends JPanel
         }
         if (newWidth > 0)
         {
-          ap.paintAlignment(false);
+          ap.paintAlignment(false, false);
           if (copyChanges)
           {
             /*
@@ -1655,7 +1656,7 @@ public class SeqPanel extends JPanel
     final int res = findColumn(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
-    needOverviewUpdate = false;
+    updateOverviewAndStructs = false;
 
     startWrapBlock = wrappedBlock;
 
@@ -1809,7 +1810,7 @@ public class SeqPanel extends JPanel
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+    updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
     if (stretchGroup.cs != null)
     {
@@ -1829,8 +1830,10 @@ public class SeqPanel extends JPanel
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
-    needOverviewUpdate = false;
+    // TODO: structure colours only need updating if stretchGroup used to or now
+    // does contain sequences with structure views
+    ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+    updateOverviewAndStructs = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1884,7 +1887,7 @@ public class SeqPanel extends JPanel
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1892,7 +1895,7 @@ public class SeqPanel extends JPanel
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1926,7 +1929,7 @@ public class SeqPanel extends JPanel
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1936,7 +1939,7 @@ public class SeqPanel extends JPanel
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }