JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 666834e..3164748 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- * 
+ * 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/>.
+ * 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;
 
@@ -22,6 +25,7 @@ import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.util.Hashtable;
@@ -36,6 +40,7 @@ import java.util.Map;
 public class ResidueColourScheme implements ColourSchemeI
 {
   final int[] symbolIndex;
+
   boolean conservationColouring = false;
 
   Color[] colors = null;
@@ -58,13 +63,16 @@ public class ResidueColourScheme implements ColourSchemeI
 
   /**
    * Creates a new ResidueColourScheme object.
-   * @param final int[] index table into colors (ResidueProperties.naIndex or ResidueProperties.aaIndex)
+   * 
+   * @param final int[] index table into colors (ResidueProperties.naIndex or
+   *        ResidueProperties.aaIndex)
    * @param colors
    *          colours for symbols in sequences
    * @param threshold
    *          threshold for conservation shading
    */
-  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, int threshold)
+  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+          int threshold)
   {
     symbolIndex = aaOrnaIndex;
     this.colors = colours;
@@ -72,14 +80,17 @@ public class ResidueColourScheme implements ColourSchemeI
   }
 
   /**
-   * Creates a new ResidueColourScheme object with a lookup table for indexing the colour map
+   * 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
+   * Creates a new ResidueColourScheme object - default constructor for
+   * non-sequence dependent colourschemes
    */
   public ResidueColourScheme()
   {
@@ -91,8 +102,7 @@ public class ResidueColourScheme implements ColourSchemeI
    */
   public Color findColour(char c)
   {
-    return colors == null ? Color.white
-            : colors[symbolIndex[c]];
+    return colors == null ? Color.white : colors[symbolIndex[c]];
   }
 
   @Override
@@ -100,7 +110,8 @@ public class ResidueColourScheme implements ColourSchemeI
   {
     Color currentColour;
 
-    if (colors!=null && symbolIndex!=null && (threshold == 0) || aboveThreshold(c, j))
+    if (colors != null && symbolIndex != null && (threshold == 0)
+            || aboveThreshold(c, j))
     {
       currentColour = colors[symbolIndex[c]];
     }
@@ -116,6 +127,7 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
+
   /**
    * Get the percentage threshold for this colour scheme
    * 
@@ -186,6 +198,12 @@ public class ResidueColourScheme implements ColourSchemeI
     return conservationColouring;
   }
 
+  @Override
+  public void setConservationApplied(boolean conservationApplied)
+  {
+    conservationColouring = conservationApplied;
+  }
+
   public void setConservationInc(int i)
   {
     inc = i;
@@ -297,4 +315,18 @@ public class ResidueColourScheme implements ColourSchemeI
   {
   }
 
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    try
+    {
+      return getClass().newInstance();
+    } catch (Exception q)
+    {
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_cannot_duplicate_colour_scheme",
+              new String[] { getClass().getName() }), q);
+    }
+  }
 }