X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=3a7188ea47d3aa8966a830ed9032bec812a17ad1;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=2acb568025e8156f8da968f62bd9ec2515319807;hpb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 2acb568..3a7188e 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -46,7 +46,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.Iterator;
+import java.util.ArrayList;
 import java.util.Vector;
 
 //import javax.swing.JPanel;
@@ -142,7 +142,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
-    Vector<String> list = new Vector<String>();
+    Vector<String> list = new Vector<>();
     int index = 1;
     for (int i = 0; i < anns.length; i++)
     {
@@ -298,18 +298,19 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getListOfCols() != null
-                && !oldHidden.getListOfCols().isEmpty())
+        if (oldHidden != null)
         {
-          for (Iterator<int[]> itr = oldHidden.getListOfCols()
-                  .iterator(); itr.hasNext();)
+          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
+          for (int[] positions : regions)
           {
-            int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
+        // TODO not clear why we need to hide all the columns (above) if we are
+        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
+      av.sendSelection();
       ap.paintAlignment(true);
     }
 
@@ -428,8 +429,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      // float range = getCurrentAnnotation().graphMax * 1000
+      // - getCurrentAnnotation().graphMin * 1000;
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
@@ -444,7 +445,7 @@ 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);
@@ -504,10 +505,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    // show hidden columns here, before changing the column selection in
+    // filterAnnotations, because showing hidden columns has the side effect of
+    // adding them to the selection
+    av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    av.showAllHiddenColumns();
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();
@@ -515,6 +519,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
+    av.sendSelection();
     ap.paintAlignment(true);
   }
 
@@ -598,7 +603,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
-            .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
+            .getSelectedIndex()].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }