X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=96299e7ce9a405bac8d704cdfa89ab7fd1c76da0;hb=1499d3297cf70ff34df05362449dbf36873c5bc1;hp=a23ca683cc26c725bf972852938d48f204c2b912;hpb=ae73ebac0bb62043eb4d0418b99ff238ca3f2e6c;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index a23ca68..96299e7 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,8 +21,7 @@
 
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@ -87,7 +86,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private int actionOption = ACTION_OPTION_SELECT;
 
-  private ColumnSelection oldColumnSelection;
+  private HiddenColumns oldHiddenColumns;
 
   protected int MIN_WIDTH = 420;
 
@@ -111,7 +110,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       return;
     }
-    setOldColumnSelection(av.getColumnSelection());
+    setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
 
     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
@@ -237,26 +236,26 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   @Override
   protected void reset()
   {
-    if (this.getOldColumnSelection() != null)
+    if (this.getOldHiddenColumns() != null)
     {
       av.getColumnSelection().clear();
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        ColumnSelection oldSelection = av
+        HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
-                .getOldColumnSelection();
-        if (oldSelection != null && oldSelection.getHiddenColumns() != null
-                && !oldSelection.getHiddenColumns().isEmpty())
+                .getOldHiddenColumns();
+        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+                && !oldHidden.getHiddenRegions().isEmpty())
         {
-          for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
                   .iterator(); itr.hasNext();)
           {
             int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
-        av.setColumnSelection(oldSelection);
+        av.getAlignment().setHiddenColumns(oldHidden);
       }
       ap.paintAlignment(true);
     }
@@ -334,7 +333,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       // build filter params
       filterParams
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+      if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
                 .setThresholdValue(getCurrentAnnotation().threshold.value);
@@ -409,17 +408,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ap.paintAlignment(true);
   }
 
-
-  public ColumnSelection getOldColumnSelection()
+  public HiddenColumns getOldHiddenColumns()
   {
-    return oldColumnSelection;
+    return oldHiddenColumns;
   }
 
-  public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+  public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
   {
-    if (currentColumnSelection != null)
+    if (currentHiddenColumns != null)
     {
-      this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+      this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
     }
   }
 
@@ -495,8 +493,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
-    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+    if (av.getAlignment()
+            .getAlignmentAnnotation()[annmap[getAnnotations()
+            .getSelectedIndex()]].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }