X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=4eefcda4599c1d94cdd7d68d9679d386875a5c7f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=05776564fd9e1d810b823468a9d52d77da4673ee;hpb=9a94f65ff18342c2505a828e780b9ea38dd51fe4;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 0577656..4eefcda 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,28 +1,32 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
-
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -32,10 +36,11 @@ import jalview.analysis.*;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+  final int[] symbolIndex;
 
   boolean conservationColouring = false;
 
-  Color[] colors=null;
+  Color[] colors = null;
 
   int threshold = 0;
 
@@ -56,22 +61,37 @@ public class ResidueColourScheme implements ColourSchemeI
   /**
    * Creates a new ResidueColourScheme object.
    * 
+   * @param final int[] index table into colors (ResidueProperties.naIndex or
+   *        ResidueProperties.aaIndex)
    * @param colors
-   *                DOCUMENT ME!
+   *          colours for symbols in sequences
    * @param threshold
-   *                DOCUMENT ME!
+   *          threshold for conservation shading
    */
-  public ResidueColourScheme(Color[] colours, int threshold)
+  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+          int threshold)
   {
+    symbolIndex = aaOrnaIndex;
     this.colors = colours;
     this.threshold = threshold;
   }
 
   /**
-   * Creates a new ResidueColourScheme object.
+   * Creates a new ResidueColourScheme object with a lookup table for indexing
+   * the colour map
+   */
+  public ResidueColourScheme(int[] aaOrNaIndex)
+  {
+    symbolIndex = aaOrNaIndex;
+  }
+
+  /**
+   * Creates a new ResidueColourScheme object - default constructor for
+   * non-sequence dependent colourschemes
    */
   public ResidueColourScheme()
   {
+    symbolIndex = null;
   }
 
   /**
@@ -79,16 +99,18 @@ public class ResidueColourScheme implements ColourSchemeI
    */
   public Color findColour(char c)
   {
-    return colors==null ? Color.white : colors[ResidueProperties.aaIndex[c]];
+    return colors == null ? Color.white : colors[symbolIndex[c]];
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 
-    if ((threshold == 0) || aboveThreshold(c, j))
+    if (colors != null && symbolIndex != null && (threshold == 0)
+            || aboveThreshold(c, j))
     {
-      currentColour = colors[ResidueProperties.aaIndex[c]];
+      currentColour = colors[symbolIndex[c]];
     }
     else
     {
@@ -117,7 +139,7 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param ct
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setThreshold(int ct, boolean ignoreGaps)
   {
@@ -136,9 +158,9 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param j
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -172,6 +194,11 @@ public class ResidueColourScheme implements ColourSchemeI
   {
     return conservationColouring;
   }
+  @Override
+  public void setConservationApplied(boolean conservationApplied)
+  {
+    conservationColouring = conservationApplied;
+  }
 
   public void setConservationInc(int i)
   {
@@ -187,7 +214,7 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param consensus
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setConsensus(Hashtable[] consensus)
   {
@@ -224,9 +251,9 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -278,4 +305,22 @@ public class ResidueColourScheme implements ColourSchemeI
     return currentColour;
   }
 
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+  }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    try {
+      return getClass().newInstance();
+    }
+    catch (Exception q)
+    {
+      throw new Error("Serious implementation error: cannot duplicate colourscheme "+getClass().getName(), q);
+    }
+  }
 }