JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

[jalview.git] / src / jalview / schemes / RNAHelicesColourChooser.java

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..39062e7 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -15,11 +15,13 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-package jalview.gui;
+package jalview.schemes;
 
 import java.util.*;
 import java.awt.event.*;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
@@ -33,9 +35,9 @@ import jalview.schemes.*;
 public class RNAHelicesColourChooser
 {
 
-  AlignViewport av;
+  AlignViewportI av;
 
-  AlignmentPanel ap;
+  AlignmentViewPanel ap;
 
   ColourSchemeI oldcs;
 
@@ -45,17 +47,14 @@ public class RNAHelicesColourChooser
 
   boolean adjusting = false;
 
-  public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+  public RNAHelicesColourChooser(AlignViewportI av, final AlignmentViewPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg:ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         if (sg.cs != null)
         {
           oldgroupColours.put(sg, sg.cs);
@@ -102,17 +101,13 @@ public class RNAHelicesColourChooser
     RNAHelicesColour rhc = null;
 
     rhc = new RNAHelicesColour(currentAnnotation);
-
+   
     av.setGlobalColourScheme(rhc);
 
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg:ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
-
         if (sg.cs == null)
         {
           continue;
@@ -131,11 +126,8 @@ public class RNAHelicesColourChooser
     av.setGlobalColourScheme(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg:ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }