X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=1e2db769d4f445c30b54505380e9737678e5315c;hb=3b5139b9b736abd652bcd00228a0e85fd8f85615;hp=f06c10f99a2ed021bf71a28fe37fba5654897e22;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index f06c10f..1e2db76 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,33 +1,35 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * 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.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
 
 /**
- * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
+ * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
  * intelligently with mapping unknown names to user defined colourschemes (that
  * exist or can be created from the string representation of the colourscheme
  * name - either a hex RGB triplet or a named colour under java.awt.color ). The
  * values of the colourscheme constants is important for callers of
  * getColourName(int i), since it can be used to enumerate the set of built in
  * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -82,6 +84,9 @@ public class ColourSchemeProperty
 
   public static final int COVARIATION = 14;
 
+  public static final int TCOFFEE = 15;
+
+
   /**
    * index of first colourscheme (includes 'None')
    */
@@ -91,10 +96,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param name
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static int getColourIndexFromName(String name)
@@ -145,6 +150,11 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
+    else if (name.equalsIgnoreCase("T-Coffee Scores"))
+    {
+      ret = TCOFFEE;
+    }
+
     else if (name.equalsIgnoreCase("User Defined"))
     {
       ret = USER_DEFINED;
@@ -167,10 +177,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param cs
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static String getColourName(ColourSchemeI cs)
@@ -226,6 +236,10 @@ public class ColourSchemeProperty
     {
       index = PURINEPYRIMIDINE;
     }
+    else if (cs instanceof TCoffeeColourScheme)
+    {
+      index = TCOFFEE;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -245,10 +259,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param index
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static String getColourName(int index)
@@ -316,9 +330,13 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      ret = "T-Coffee Scores";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
-     * 
+     *
      * break;
      */
     case USER_DEFINED:
@@ -334,26 +352,9 @@ 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
@@ -363,7 +364,7 @@ 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);
@@ -396,30 +397,30 @@ public class ColourSchemeProperty
         }
       }
     }
-    return getColour(seqs, width, getColourIndexFromName(name));
+    return getColour(alignment, getColourIndexFromName(name));
   }
 
   /**
-   * DOCUMENT ME!
-   * 
+   * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
+   *
    * @param seqs
-   *          DOCUMENT ME!
+   *          sequences to be coloured by colourscheme
    * @param width
-   *          DOCUMENT ME!
+   *          geometry of alignment
    * @param index
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   *          colourscheme number
+   *
+   * @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;
 
     switch (index)
     {
     case CLUSTAL:
-      cs = new ClustalxColourScheme(seqs, width);
+      cs = new ClustalxColourScheme(coll, null);
 
       break;
 
@@ -477,6 +478,8 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      cs = new TCoffeeColourScheme(coll);
     // case COVARIATION:
     // cs = new CovariationColourScheme(annotation);