X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=a40a6901decdb56137fadc5c84e4394065f733d0;hb=488e8b4ff975fbb83eac40f9e9f16d40c5a33d34;hp=bd58273faa3b795e5b8d4bb4c9ad8b0cacefc3b7;hpb=3e943322f9d66e8718316ba8bd03669adce65149;p=jalview.git

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index bd58273..a40a690 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -1,7 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 
+ * 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 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
+import jalview.util.ColorUtils;
 import jalview.util.Format;
 
 import java.awt.Color;
@@ -101,20 +122,20 @@ public class FeatureColour implements FeatureColourI
       /*
        * only a simple colour specification - parse it
        */
-      Color colour = UserColourScheme.getColourFromString(descriptor);
+      Color colour = ColorUtils.parseColourString(descriptor);
       if (colour == null)
       {
-        throw new IllegalArgumentException("Invalid colour descriptor: "
-                + descriptor);
+        throw new IllegalArgumentException(
+                "Invalid colour descriptor: " + descriptor);
       }
       return new FeatureColour(colour);
     }
 
     /*
-     * autoScaled == true: colours range over actual score range; autoScaled ==
-     * false ('abso'): colours range over min/max range
+     * autoScaled == true: colours range over actual score range
+     * autoScaled == false ('abso'): colours range over min/max range
      */
-    boolean autoScaled = false;
+    boolean autoScaled = true;
     String tok = null, minval, maxval;
     if (mincol != null)
     {
@@ -138,15 +159,15 @@ public class FeatureColour implements FeatureColourI
       }
       tok = gcol.nextToken();
       gcol.nextToken(); // skip next '|'
-      if (tok.toLowerCase().indexOf("abso") != 0)
+      if (tok.toLowerCase().startsWith("abso"))
       {
-        minval = tok;
-        autoScaled = true;
+        minval = gcol.nextToken();
+        gcol.nextToken(); // skip next '|'
+        autoScaled = false;
       }
       else
       {
-        minval = gcol.nextToken();
-        gcol.nextToken(); // skip next '|'
+        minval = tok;
       }
       maxval = gcol.nextToken();
       if (gcol.hasMoreTokens())
@@ -192,9 +213,9 @@ public class FeatureColour implements FeatureColourI
     FeatureColour featureColour;
     try
     {
-      featureColour = new FeatureColour(
-              new UserColourScheme(mincol).findColour('A'),
-              new UserColourScheme(maxcol).findColour('A'), min, max);
+      Color minColour = ColorUtils.parseColourString(mincol);
+      Color maxColour = ColorUtils.parseColourString(maxcol);
+      featureColour = new FeatureColour(minColour, maxColour, min, max);
       featureColour.setColourByLabel(labelColour);
       featureColour.setAutoScaled(autoScaled);
       // add in any additional parameters
@@ -215,8 +236,8 @@ public class FeatureColour implements FeatureColourI
         {
           if (!ttype.toLowerCase().startsWith("no"))
           {
-            System.err.println("Ignoring unrecognised threshold type : "
-                    + ttype);
+            System.err.println(
+                    "Ignoring unrecognised threshold type : " + ttype);
           }
         }
       }
@@ -235,8 +256,8 @@ public class FeatureColour implements FeatureColourI
       }
       if (gcol.hasMoreTokens())
       {
-        System.err
-                .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+        System.err.println(
+                "Ignoring additional tokens in parameters in graduated colour specification\n");
         while (gcol.hasMoreTokens())
         {
           System.err.println("|" + gcol.nextToken());
@@ -286,6 +307,14 @@ public class FeatureColour implements FeatureColourI
    */
   public FeatureColour(Color low, Color high, float min, float max)
   {
+    if (low == null)
+    {
+      low = Color.white;
+    }
+    if (high == null)
+    {
+      high = Color.black;
+    }
     graduatedColour = true;
     colour = null;
     minColour = low;
@@ -317,6 +346,7 @@ public class FeatureColour implements FeatureColourI
    */
   public FeatureColour(FeatureColour fc)
   {
+    graduatedColour = fc.graduatedColour;
     colour = fc.colour;
     minColour = fc.minColour;
     maxColour = fc.maxColour;
@@ -335,9 +365,10 @@ public class FeatureColour implements FeatureColourI
     setAutoScaled(fc.isAutoScaled());
     setColourByLabel(fc.isColourByLabel());
   }
-  
+
   /**
    * Copy constructor with new min/max ranges
+   * 
    * @param fc
    * @param min
    * @param max
@@ -359,8 +390,7 @@ public class FeatureColour implements FeatureColourI
    * Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
    * false.
    */
-  @Override
-  public void setGraduatedColour(boolean b)
+  void setGraduatedColour(boolean b)
   {
     graduatedColour = b;
     if (b)
@@ -406,6 +436,7 @@ public class FeatureColour implements FeatureColourI
       setGraduatedColour(false);
     }
   }
+
   @Override
   public boolean isBelowThreshold()
   {
@@ -511,8 +542,7 @@ public class FeatureColour implements FeatureColourI
   {
     if (isColourByLabel())
     {
-      return UserColourScheme
-              .createColourFromName(feature.getDescription());
+      return ColorUtils.createColourFromName(feature.getDescription());
     }
 
     if (!isGraduatedColour())
@@ -543,7 +573,8 @@ public class FeatureColour implements FeatureColourI
     {
       scl = 1f;
     }
-    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen,
+            minBlue + scl * deltaBlue);
   }
 
   /**
@@ -643,7 +674,7 @@ public class FeatureColour implements FeatureColourI
       {
         sb.append(Format.getHexString(getMinColour())).append(BAR);
         sb.append(Format.getHexString(getMaxColour())).append(BAR);
-        if (isAutoScaled())
+        if (!isAutoScaled())
         {
           sb.append("abso").append(BAR);
         }