X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=77700d036f2c92ba09196a50a6ec89f009213332;hb=36dceb54710feb97a81f4bd69ad051f316141dc3;hp=32d528c28ebeb62e8bc7b16ab81e4abe3abf8b16;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 32d528c..77700d0 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -150,7 +150,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     String label = "";
     if (av.getColumnSelection() != null
-            && av.getColumnSelection().size() > 0
+            && !av.getColumnSelection().isEmpty()
             && anot[av.getColumnSelection().getMin()] != null)
     {
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
@@ -158,9 +158,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int sel : av.getColumnSelection().getSelected())
       {
-        anot[av.getColumnSelection().columnAt(i)] = null;
+        // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
+        // of
+        // annotation if selection includes hidden columns
+        anot[sel] = null;
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -177,10 +180,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         aa[activeRow].hasText = true;
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
+        // TODO: JAL-2001 - provide a fast method to list visible selected
+        // columns
         if (!av.getColumnSelection().isVisible(index))
         {
           continue;
@@ -201,10 +204,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
       Color col = udc.getColor();
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
         {
           continue;
@@ -262,10 +263,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         }
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
         {
           continue;