JAL-1989 more unit tests and encapsulation for ColumnSelection

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 77d6b51..a70d4b9 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -289,14 +289,14 @@ public class AnnotationPanel extends JPanel 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;
+        anot[sel] = null;
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
     {
-      String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
+      String exMesg = collectAnnotVals(anot, LABEL);
       String label = JOptionPane.showInputDialog(this,
               MessageManager.getString("label.enter_label"), exMesg);
 
@@ -310,10 +310,8 @@ public class AnnotationPanel extends JPanel 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);
-
         if (!av.getColumnSelection().isVisible(index))
         {
           continue;
@@ -338,10 +336,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               MessageManager.getString("label.select_foreground_colour"),
               Color.black);
 
-      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;
@@ -399,10 +395,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           aa[activeRow].showAllColLabels = true;
         }
       }
-      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;
@@ -428,16 +422,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     return;
   }
 
-  private String collectAnnotVals(Annotation[] anot,
-          ColumnSelection columnSelection, String label2)
+  private String collectAnnotVals(Annotation[] anot, String label2)
   {
     String collatedInput = "";
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
     // TODO: refactor and save av.getColumnSelection for efficiency
-    for (int i = 0; i < columnSelection.size(); i++)
+    for (int index : viscols.getSelected())
     {
-      int index = columnSelection.columnAt(i);
       // always check for current display state - just in case
       if (!viscols.isVisible(index))
       {