X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=d7665969700ae443eae03cf4ba26a387771ab057;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=5f9f8f0954497f96877f5e572df791b1c9572d64;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 5f9f8f0..d766596 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,31 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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 java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 public class ClustalxColourScheme extends ResidueColourScheme // implements
-                                                              // IParameterizable
+// IParameterizable
 {
   public static Hashtable colhash = new Hashtable();
 
@@ -52,23 +58,25 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
-    colhash
-            .put("MAGENTA",
-                    new Color((float) 0.8, (float) 0.3, (float) 0.8));
+    colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
-  public ClustalxColourScheme(Vector seqs, int maxWidth)
+  public ClustalxColourScheme(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    resetClustalX(seqs, maxWidth);
+    alignmentChanged(alignment, hiddenReps);
   }
 
-  public void resetClustalX(Vector seqs, int maxWidth)
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
+    int maxWidth = alignment.getWidth();
+    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
     cons2 = new int[maxWidth][24];
     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
-                                    // get the current setting of the
-                                    // includeGaps param.
+    // get the current setting of the
+    // includeGaps param.
     int start = 0;
 
     // Initialize the array
@@ -85,9 +93,9 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     int j = 0;
     char[] seq;
 
-    while (j < seqs.size())
+    for (SequenceI sq : seqs)
     {
-      seq = ((SequenceI) seqs.elementAt(j)).getSequence();
+      seq = sq.getSequence();
 
       int end_j = seq.length - 1;
 
@@ -213,12 +221,13 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     tmp5[3] = conses[19]; // Q
     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 
-    Consensus[] tmp6 = new Consensus[5];
+    Consensus[] tmp6 = new Consensus[6];
     tmp6[0] = conses[3]; // -
     tmp6[1] = conses[29]; // D
     tmp6[2] = conses[10]; // E
-    tmp6[3] = conses[6]; // q
+    tmp6[3] = conses[6]; // QE
     tmp6[4] = conses[19]; // Q
+    tmp6[5] = conses[2]; // DE
     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 
     Consensus[] tmp7 = new Consensus[5];
@@ -253,12 +262,14 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     ResidueColour[19] = colours[0]; // V
   }
 
+  @Override
   public Color findColour(char c)
   {
     return Color.pink;
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 
@@ -312,12 +323,22 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
 
   /**
    * @param includeGaps
-   *                the includeGaps to set
+   *          the includeGaps to set
    */
   protected void setIncludeGaps(boolean includeGaps)
   {
     this.includeGaps = includeGaps;
   }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    ClustalxColourScheme css = new ClustalxColourScheme(sg,
+            hiddenRepSequences);
+    css.includeGaps = includeGaps;
+    return css;
+  }
 }
 
 class ConsensusColour