feature colour by label flag/style

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

diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java
index b134968..a99a2f2 100644 (file)
--- a/src/jalview/schemes/GraduatedColor.java
+++ b/src/jalview/schemes/GraduatedColor.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.schemes;
 
@@ -69,6 +84,7 @@ public class GraduatedColor
     thresholdState = oldcs.thresholdState;
     thrsh = oldcs.thrsh;
     autoScale = oldcs.autoScale;
+    colourByLabel = oldcs.colourByLabel; 
   }
   /**
    * make a new gradient from an old one with a different scale range
@@ -120,8 +136,38 @@ public class GraduatedColor
       return rtn; //  ? tolow : !tolow;
     }
   }
+  /**
+   * default implementor of a getColourFromString method.
+   * TODO: abstract an interface enabling pluggable colour from string
+   */
+  private UserColourScheme ucs = null;
+  private boolean colourByLabel=true;
+  /**
+   * 
+   * @return true if colourByLabel style is set
+   */
+  public boolean isColourByLabel()
+  {
+    return colourByLabel;
+  }
+  /**
+   * @param colourByLabel the colourByLabel to set
+   */
+  public void setColourByLabel(boolean colourByLabel)
+  {
+    this.colourByLabel = colourByLabel;
+  }
   public Color findColor(SequenceFeature feature)
-  {     
+  {
+    if (colourByLabel)
+    {
+      //TODO: allow user defined feature label colourschemes. Colour space is {type,regex,%anytype%}x{description string, regex, keyword}
+      if (ucs==null)
+      {
+        ucs = new UserColourScheme();
+      }
+      return ucs.createColourFromName(feature.getDescription());
+    }
     if (range==0.0)
     {
       return getMaxColor();