JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index c556bb2..d363764 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * This file is part of Jalview.
  * 
@@ -17,11 +17,15 @@
  */
 package jalview.schemes;
 
-import java.util.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
-
-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
@@ -51,19 +55,17 @@ 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
@@ -84,9 +86,9 @@ 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;
 
@@ -212,12 +214,13 @@ 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];
@@ -252,12 +255,14 @@ 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;