Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 54e3db7..ce60be6 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -137,7 +137,7 @@ public class SeqPanel extends JPanel
       MousePos o = (MousePos) obj;
       boolean b = (column == o.column && seqIndex == o.seqIndex
               && annotationIndex == o.annotationIndex);
-      // System.out.println(obj + (b ? "= " : "!= ") + this);
+      // jalview.bin.Console.outPrintln(obj + (b ? "= " : "!= ") + this);
       return b;
     }
 
@@ -881,7 +881,7 @@ public class SeqPanel extends JPanel
 
     if (lastMessage == null || !lastMessage.equals(tmp))
     {
-      // System.err.println("mouseOver Sequence: "+tmp);
+      // jalview.bin.Console.errPrintln("mouseOver Sequence: "+tmp);
       ssm.mouseOverSequence(sequence, index, pos, av);
     }
     lastMessage = tmp;
@@ -1006,7 +1006,7 @@ public class SeqPanel extends JPanel
   @Override
   public void updateColours(SequenceI seq, int index)
   {
-    System.out.println("update the seqPanel colours");
+    jalview.bin.Console.outPrintln("update the seqPanel colours");
     // repaint();
   }
 
@@ -1175,6 +1175,7 @@ public class SeqPanel extends JPanel
     final int column = pos.column;
     final int rowIndex = pos.annotationIndex;
 
+    // TODO - get yOffset for annotation, too
     if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
             || rowIndex < 0)
     {
@@ -1183,8 +1184,9 @@ public class SeqPanel extends JPanel
     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 
     String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
-            anns);
-    if (!tooltip.equals(lastTooltip))
+            anns, 0, av, ap);
+    if (tooltip == null ? tooltip != lastTooltip
+            : !tooltip.equals(lastTooltip))
     {
       lastTooltip = tooltip;
       lastFormattedTooltip = tooltip == null ? null
@@ -1193,7 +1195,7 @@ public class SeqPanel extends JPanel
     }
 
     String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
-            anns[rowIndex]);
+            anns[rowIndex], 0, av);
     ap.alignFrame.setStatus(msg);
   }
 
@@ -2859,7 +2861,7 @@ public class SeqPanel extends JPanel
     if (copycolsel && av.hasHiddenColumns()
             && (av.getAlignment().getHiddenColumns() == null))
     {
-      System.err.println("Bad things");
+      jalview.bin.Console.errPrintln("Bad things");
     }
     if (repaint) // always true!
     {
@@ -2929,6 +2931,8 @@ public class SeqPanel extends JPanel
      * if hidden column selection has changed
      */
     ap.paintAlignment(hiddenChanged, hiddenChanged);
+    // propagate any selection changes
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
 
     return true;
   }