JAL-2446 merged to spike branch

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index fb47d92..15cb157 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -22,10 +22,11 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 
-import java.awt.event.ActionEvent;
 import java.util.Hashtable;
+import java.util.Map;
 import java.util.Vector;
 
 /**
@@ -33,8 +34,9 @@ import java.util.Vector;
  * change colors based on covariation.
  * 
  * @author Lauren Michelle Lui
- * 
+ * @deprecated this seems to be unfinished - just use RNAHelicesColour
  */
+@Deprecated
 public class RNAHelicesColourChooser
 {
 
@@ -44,9 +46,9 @@ public class RNAHelicesColourChooser
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
+  Map<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
@@ -56,44 +58,40 @@ public class RNAHelicesColourChooser
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable();
+      oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        if (sg.cs != null)
+        if (sg.getColourScheme() != null)
         {
-          oldgroupColours.put(sg, sg.cs);
+          oldgroupColours.put(sg, sg.getColourScheme());
         }
       }
     }
     this.av = av;
     this.ap = ap;
 
-    if (oldcs instanceof RNAHelicesColour)
-    {
-      RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
-    }
-
     adjusting = true;
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns != null)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
+      for (int i = 0; i < anns.length; i++)
       {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
+        String label = anns[i].label;
+        if (!list.contains(label))
+        {
+          list.addElement(label);
+        }
+        else
+        {
+          list.addElement(label + "_" + (index++));
+        }
       }
     }
 
     adjusting = false;
-
     changeColour();
-
   }
 
   void changeColour()
@@ -103,44 +101,10 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-    RNAHelicesColour rhc = null;
-
-    rhc = new RNAHelicesColour(av.getAlignment());
+    RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
 
     av.setGlobalColourScheme(rhc);
 
-    if (av.getAlignment().getGroups() != null)
-    {
-      for (SequenceGroup sg : ap.getAlignment().getGroups())
-      {
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        sg.cs = new RNAHelicesColour(sg);
-
-      }
-    }
-
     ap.paintAlignment(true);
   }
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.getAlignment().getGroups() != null)
-    {
-      for (SequenceGroup sg : ap.getAlignment().getGroups())
-      {
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
-      }
-    }
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
 }