JAL-2759 Changes to getVisibleSequenceStrings after review

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 76c711f..c883071 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -52,6 +52,7 @@ import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -705,7 +706,7 @@ public class AnnotationLabels extends JPanel
         d = ap.annotationSpaceFillerHolder.getPreferredSize();
         ap.annotationSpaceFillerHolder
                 .setPreferredSize(new Dimension(d.width, d.height - dif));
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, false);
       }
 
       ap.addNotify();
@@ -855,7 +856,7 @@ public class AnnotationLabels extends JPanel
               }
             }
 
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
@@ -912,7 +913,7 @@ public class AnnotationLabels extends JPanel
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
@@ -945,8 +946,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };