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

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index cbd345c..4c7b49d 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -17,6 +17,8 @@
  */
 package jalview.schemes;
 
+import jalview.datamodel.AnnotatedCollectionI;
+
 import java.awt.Color;
 
 /**
@@ -342,26 +344,9 @@ public class ColourSchemeProperty
 
     return ret;
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param al
-   *          DOCUMENT ME!
-   * @param name
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
-          String name)
-  {
-    return getColour(al.getSequences(), al.getWidth(), name);
-  }
-
   /**
    * retrieve or create colourscheme associated with name
-   * 
+   *
    * @param seqs
    *          sequences to colour
    * @param width
@@ -371,7 +356,7 @@ public class ColourSchemeProperty
    *          string to parse as colour for new coloursheme
    * @return Valid Colourscheme
    */
-  public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+  public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
           String name)
   {
     int colindex = getColourIndexFromName(name);
@@ -404,7 +389,7 @@ public class ColourSchemeProperty
         }
       }
     }
-    return getColour(seqs, width, getColourIndexFromName(name));
+    return getColour(alignment, getColourIndexFromName(name));
   }
 
   /**
@@ -419,8 +404,7 @@ public class ColourSchemeProperty
    * 
    * @return null or an instance of the colourscheme configured to colour given sequence set
    */
-  public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-          int index)
+  public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, int index)
   {
     // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
     ColourSchemeI cs = null;
@@ -428,7 +412,7 @@ public class ColourSchemeProperty
     switch (index)
     {
     case CLUSTAL:
-      cs = new ClustalxColourScheme(seqs, width);
+      cs = new ClustalxColourScheme(coll, null);
 
       break;