X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=6eb2ac1ef3b98862193381831be86d3c1a7dd0d0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=bc2f9ead956ec33d61ec4098ec2d35f98500ba1b;hpb=067a6494124d4f1d0fe8b6d758b593145393b7dd;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bc2f9ea..6eb2ac1 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,62 +1,82 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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 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 jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
-import jalview.datamodel.*;
-
-public class ClustalxColourScheme
-    extends ResidueColourScheme // implements IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme // implements
+// IParameterizable
 {
   public static Hashtable colhash = new Hashtable();
+
   Hashtable[] cons;
+
   int[][] cons2;
+
   ConsensusColour[] colours;
+
   ConsensusColour[] ResidueColour;
+
   int size;
+
   Consensus[] conses = new Consensus[32];
+
   Vector colourTable = new Vector();
-  private boolean includeGaps=true;
-  
+
+  private boolean includeGaps = true;
+
   {
-    colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
-    colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
-    colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
-    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("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
+    colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
+    colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
+    colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
+    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("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.
+    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
+    // get the current setting of the
+    // includeGaps param.
     int start = 0;
 
     // Initialize the array
@@ -73,15 +93,15 @@ public class ClustalxColourScheme
     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;
 
       for (i = start; i <= end_j; i++)
       {
-        if ( (seq.length - 1) < i)
+        if ((seq.length - 1) < i)
         {
           res = 23;
         }
@@ -95,7 +115,7 @@ public class ClustalxColourScheme
 
       j++;
     }
-    
+
     this.size = seqs.size();
     makeColours();
   }
@@ -140,82 +160,83 @@ public class ClustalxColourScheme
     colours = new ConsensusColour[11];
 
     Consensus[] tmp8 = new Consensus[1];
-    tmp8[0] = conses[30]; //G
-    colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+    tmp8[0] = conses[30]; // G
+    colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 
     Consensus[] tmp9 = new Consensus[1];
-    tmp9[0] = conses[31]; //P
-    colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+    tmp9[0] = conses[31]; // P
+    colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 
     Consensus[] tmp10 = new Consensus[1];
-    tmp10[0] = conses[27]; //C
-    colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+    tmp10[0] = conses[27]; // C
+    colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 
     Consensus[] tmp1 = new Consensus[14];
-    tmp1[0] = conses[0]; //%
-    tmp1[1] = conses[1]; //#
-    tmp1[2] = conses[26]; //A
-    tmp1[3] = conses[27]; //C
-    tmp1[4] = conses[11]; //F
-    tmp1[5] = conses[13]; //H
-    tmp1[6] = conses[14]; //I
-    tmp1[7] = conses[15]; //L
-    tmp1[8] = conses[16]; //M
-    tmp1[9] = conses[23]; //V
-    tmp1[10] = conses[24]; //W
-    tmp1[11] = conses[25]; //Y
-    tmp1[12] = conses[18]; //P
-    tmp1[13] = conses[19]; //p
-    colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
-
-    colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+    tmp1[0] = conses[0]; // %
+    tmp1[1] = conses[1]; // #
+    tmp1[2] = conses[26]; // A
+    tmp1[3] = conses[27]; // C
+    tmp1[4] = conses[11]; // F
+    tmp1[5] = conses[13]; // H
+    tmp1[6] = conses[14]; // I
+    tmp1[7] = conses[15]; // L
+    tmp1[8] = conses[16]; // M
+    tmp1[9] = conses[23]; // V
+    tmp1[10] = conses[24]; // W
+    tmp1[11] = conses[25]; // Y
+    tmp1[12] = conses[18]; // P
+    tmp1[13] = conses[19]; // p
+    colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
+
+    colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 
     Consensus[] tmp2 = new Consensus[5];
-    tmp2[0] = conses[8]; //t
-    tmp2[1] = conses[21]; //S
-    tmp2[2] = conses[22]; //T
-    tmp2[3] = conses[0]; //%
-    tmp2[4] = conses[1]; //#
-    colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+    tmp2[0] = conses[8]; // t
+    tmp2[1] = conses[21]; // S
+    tmp2[2] = conses[22]; // T
+    tmp2[3] = conses[0]; // %
+    tmp2[4] = conses[1]; // #
+    colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 
     Consensus[] tmp3 = new Consensus[3];
 
-    tmp3[0] = conses[17]; //N
-    tmp3[1] = conses[29]; //D
-    tmp3[2] = conses[5]; //n
-    colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+    tmp3[0] = conses[17]; // N
+    tmp3[1] = conses[29]; // D
+    tmp3[2] = conses[5]; // n
+    colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 
     Consensus[] tmp4 = new Consensus[6];
     tmp4[0] = conses[6]; // q = QE
-    tmp4[1] = conses[19]; //Q
-    tmp4[2] = conses[22]; //E
-    tmp4[3] = conses[3]; //+
-    tmp4[4] = conses[28]; //K
-    tmp4[5] = conses[20]; //R
-    colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+    tmp4[1] = conses[19]; // Q
+    tmp4[2] = conses[22]; // E
+    tmp4[3] = conses[3]; // +
+    tmp4[4] = conses[28]; // K
+    tmp4[5] = conses[20]; // R
+    colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 
     Consensus[] tmp5 = new Consensus[4];
-    tmp5[0] = conses[3]; //+
-    tmp5[1] = conses[28]; //K
-    tmp5[2] = conses[20]; //R
-    tmp5[3] = conses[19]; //Q
-    colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
-
-    Consensus[] tmp6 = new Consensus[5];
-    tmp6[0] = conses[3]; //-
-    tmp6[1] = conses[29]; //D
-    tmp6[2] = conses[10]; //E
-    tmp6[3] = conses[6]; //q
-    tmp6[4] = conses[19]; //Q
-    colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+    tmp5[0] = conses[3]; // +
+    tmp5[1] = conses[28]; // K
+    tmp5[2] = conses[20]; // R
+    tmp5[3] = conses[19]; // Q
+    colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
+
+    Consensus[] tmp6 = new Consensus[6];
+    tmp6[0] = conses[3]; // -
+    tmp6[1] = conses[29]; // D
+    tmp6[2] = conses[10]; // E
+    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];
-    tmp7[0] = conses[3]; //-
-    tmp7[1] = conses[29]; //D
-    tmp7[2] = conses[10]; //E
-    tmp7[3] = conses[17]; //N
-    tmp7[4] = conses[2]; //DE
-    colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+    tmp7[0] = conses[3]; // -
+    tmp7[1] = conses[29]; // D
+    tmp7[2] = conses[10]; // E
+    tmp7[3] = conses[17]; // N
+    tmp7[4] = conses[2]; // DE
+    colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 
     // Now attach the ConsensusColours to the residue letters
     ResidueColour = new ConsensusColour[20];
@@ -241,16 +262,19 @@ public class ClustalxColourScheme
     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;
 
-    if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    if (cons2.length <= j
+            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
@@ -266,7 +290,8 @@ public class ClustalxColourScheme
 
     for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
+              includeGaps))
       {
         currentColour = ResidueColour[i].c;
       }
@@ -297,24 +322,36 @@ public class ClustalxColourScheme
   }
 
   /**
-   * @param includeGaps the includeGaps to set
+   * @param includeGaps
+   *          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
 {
   Consensus[] conses;
+
   Color c;
 
   public ConsensusColour(Color c, Consensus[] conses)
   {
     this.conses = conses;
 
-    //    this.list = list;
+    // this.list = list;
     this.c = c;
   }
 }