JAL-2591 simplifying hidden columns usage

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4b774d6..07a5ad9 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -292,33 +292,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh(fullRepaint);
+    ap.refresh(fullRepaint);
 
   }
 
   /**
-   * Redraw sensibly.
-   * 
-   * @adjustHeight if true, try to recalculate panel height for visible
-   *               annotations
-   */
-  protected void refresh(boolean adjustHeight)
-  {
-    ap.validateAnnotationDimensions(adjustHeight);
-    ap.addNotify();
-    if (adjustHeight)
-    {
-      // sort, repaint, update overview
-      ap.paintAlignment(true);
-    }
-    else
-    {
-      // lightweight repaint
-      ap.repaint();
-    }
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param e
@@ -420,7 +398,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh(true);
+            ap.refresh(true);
           }
         });
         pop.add(hideType);
@@ -969,12 +947,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+      omitHidden = av.getAlignment().getHiddenColumns()
+              .getVisibleSequenceStrings(0,
               sq.getLength(), seqs);
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
+    List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
+            .getHiddenRegions();
     if (hiddenCols != null)
     {
       alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
@@ -987,13 +967,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             .setContents(new StringSelection(output), Desktop.instance);
 
     ArrayList<int[]> hiddenColumns = null;
+
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        hiddenColumns.add(new int[] { region[0], region[1] });
-      }
+      av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy(hiddenColumns);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset