X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=19723ca64f67b020e6ba2bcf78852d1c2dd8460d;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=bc2f9ead956ec33d61ec4098ec2d35f98500ba1b;hpb=067a6494124d4f1d0fe8b6d758b593145393b7dd;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bc2f9ea..19723ca 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,137 +1,166 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
-import java.awt.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
 
-import jalview.datamodel.*;
-
-public class ClustalxColourScheme
-    extends ResidueColourScheme // implements IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme
 {
-  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;
-  
-  {
-    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));
-  }
+  private static final int EIGHTY_FIVE = 85;
+
+  private static final int FIFTY = 50;
 
-  public ClustalxColourScheme(Vector seqs, int maxWidth)
+  private static final int EIGHTY = 80;
+
+  private static final int SIXTY = 60;
+
+  enum ClustalColour
   {
-    resetClustalX(seqs, maxWidth);
+    RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
+    ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
+    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+    YELLOW(0.8f, 0.8f, 0.0f);
+
+    final Color colour;
+
+    ClustalColour(float r, float g, float b)
+    {
+      colour = new Color(r, g, b);
+    }
   }
 
-  public void resetClustalX(Vector seqs, int maxWidth)
+  private class ConsensusColour
   {
-    cons2 = new int[maxWidth][24];
-    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
-    int start = 0;
+    Consensus[] cons;
+
+    Color c;
 
-    // Initialize the array
-    for (int j = 0; j < 24; j++)
+    public ConsensusColour(ClustalColour col, Consensus[] conses)
     {
-      for (int i = 0; i < maxWidth; i++)
-      {
-        cons2[i][j] = 0;
-      }
+      this.cons = conses;
+      this.c = col.colour;
     }
+  }
 
-    int res;
-    int i;
-    int j = 0;
-    char[] seq;
+  private int[][] cons2;
 
-    while (j < seqs.size())
-    {
-      seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+  private ConsensusColour[] colours;
+
+  private ConsensusColour[] residueColour;
+
+  private int size;
+
+  private Consensus[] conses = new Consensus[32];
 
-      int end_j = seq.length - 1;
+  private boolean includeGaps = true;
+
+  /**
+   * Default constructor (required for Class.newInstance())
+   */
+  public ClustalxColourScheme()
+  {
+
+  }
 
-      for (i = start; i <= end_j; i++)
+  public ClustalxColourScheme(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    alignmentChanged(alignment, hiddenReps);
+  }
+
+  @Override
+  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.
+    int res = 0;
+
+    for (SequenceI sq : seqs)
+    {
+      int end_j = sq.getLength() - 1;
+      int length = sq.getLength();
+
+      for (int i = 0; i <= end_j; i++)
       {
-        if ( (seq.length - 1) < i)
+        if (length - 1 < i)
         {
           res = 23;
         }
         else
         {
-          res = ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[sq.getCharAt(i)];
         }
-
         cons2[i][res]++;
       }
-
-      j++;
     }
-    
+
     this.size = seqs.size();
     makeColours();
   }
 
-  public void makeColours()
+  void makeColours()
   {
-    conses[0] = new Consensus("WLVIMAFCYHP", 60);
-    conses[1] = new Consensus("WLVIMAFCYHP", 80);
-    conses[2] = new Consensus("ED", 50);
-    conses[3] = new Consensus("KR", 60);
-    conses[4] = new Consensus("G", 50);
-    conses[5] = new Consensus("N", 50);
-    conses[6] = new Consensus("QE", 50);
-    conses[7] = new Consensus("P", 50);
-    conses[8] = new Consensus("TS", 50);
-
-    conses[26] = new Consensus("A", 85);
-    conses[27] = new Consensus("C", 85);
-    conses[10] = new Consensus("E", 85);
-    conses[11] = new Consensus("F", 85);
-    conses[12] = new Consensus("G", 85);
-    conses[13] = new Consensus("H", 85);
-    conses[14] = new Consensus("I", 85);
-    conses[15] = new Consensus("L", 85);
-    conses[16] = new Consensus("M", 85);
-    conses[17] = new Consensus("N", 85);
-    conses[18] = new Consensus("P", 85);
-    conses[19] = new Consensus("Q", 85);
-    conses[20] = new Consensus("R", 85);
-    conses[21] = new Consensus("S", 85);
-    conses[22] = new Consensus("T", 85);
-    conses[23] = new Consensus("V", 85);
-    conses[24] = new Consensus("W", 85);
-    conses[25] = new Consensus("Y", 85);
-    conses[28] = new Consensus("K", 85);
-    conses[29] = new Consensus("D", 85);
+    conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
+    conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
+    conses[2] = new Consensus("ED", FIFTY);
+    conses[3] = new Consensus("KR", SIXTY);
+    conses[4] = new Consensus("G", FIFTY);
+    conses[5] = new Consensus("N", FIFTY);
+    conses[6] = new Consensus("QE", FIFTY);
+    conses[7] = new Consensus("P", FIFTY);
+    conses[8] = new Consensus("TS", FIFTY);
+
+    conses[26] = new Consensus("A", EIGHTY_FIVE);
+    conses[27] = new Consensus("C", EIGHTY_FIVE);
+    conses[10] = new Consensus("E", EIGHTY_FIVE);
+    conses[11] = new Consensus("F", EIGHTY_FIVE);
+    conses[12] = new Consensus("G", EIGHTY_FIVE);
+    conses[13] = new Consensus("H", EIGHTY_FIVE);
+    conses[14] = new Consensus("I", EIGHTY_FIVE);
+    conses[15] = new Consensus("L", EIGHTY_FIVE);
+    conses[16] = new Consensus("M", EIGHTY_FIVE);
+    conses[17] = new Consensus("N", EIGHTY_FIVE);
+    conses[18] = new Consensus("P", EIGHTY_FIVE);
+    conses[19] = new Consensus("Q", EIGHTY_FIVE);
+    conses[20] = new Consensus("R", EIGHTY_FIVE);
+    conses[21] = new Consensus("S", EIGHTY_FIVE);
+    conses[22] = new Consensus("T", EIGHTY_FIVE);
+    conses[23] = new Consensus("V", EIGHTY_FIVE);
+    conses[24] = new Consensus("W", EIGHTY_FIVE);
+    conses[25] = new Consensus("Y", EIGHTY_FIVE);
+    conses[28] = new Consensus("K", EIGHTY_FIVE);
+    conses[29] = new Consensus("D", EIGHTY_FIVE);
 
     conses[30] = new Consensus("G", 0);
     conses[31] = new Consensus("P", 0);
@@ -140,152 +169,153 @@ 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(ClustalColour.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(ClustalColour.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(ClustalColour.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(ClustalColour.BLUE, tmp1);
+
+    colours[10] = new ConsensusColour(ClustalColour.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(ClustalColour.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(ClustalColour.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(ClustalColour.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(ClustalColour.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(ClustalColour.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(ClustalColour.MAGENTA, tmp7);
 
     // Now attach the ConsensusColours to the residue letters
-    ResidueColour = new ConsensusColour[20];
-    ResidueColour[0] = colours[0]; // A
-    ResidueColour[1] = colours[4]; // R
-    ResidueColour[2] = colours[2]; // N
-    ResidueColour[3] = colours[6]; // D
-    ResidueColour[4] = colours[0]; // C
-    ResidueColour[5] = colours[3]; // Q
-    ResidueColour[6] = colours[5]; // E
-    ResidueColour[7] = colours[7]; // G
-    ResidueColour[8] = colours[10]; // H
-    ResidueColour[9] = colours[0]; // I
-    ResidueColour[10] = colours[0]; // L
-    ResidueColour[11] = colours[4]; // K
-    ResidueColour[12] = colours[0]; // M
-    ResidueColour[13] = colours[0]; // F
-    ResidueColour[14] = colours[8]; // P
-    ResidueColour[15] = colours[1]; // S
-    ResidueColour[16] = colours[1]; // T
-    ResidueColour[17] = colours[0]; // W
-    ResidueColour[18] = colours[10]; // Y
-    ResidueColour[19] = colours[0]; // V
+    residueColour = new ConsensusColour[20];
+    residueColour[0] = colours[0]; // A
+    residueColour[1] = colours[4]; // R
+    residueColour[2] = colours[2]; // N
+    residueColour[3] = colours[6]; // D
+    residueColour[4] = colours[0]; // C
+    residueColour[5] = colours[3]; // Q
+    residueColour[6] = colours[5]; // E
+    residueColour[7] = colours[7]; // G
+    residueColour[8] = colours[10]; // H
+    residueColour[9] = colours[0]; // I
+    residueColour[10] = colours[0]; // L
+    residueColour[11] = colours[4]; // K
+    residueColour[12] = colours[0]; // M
+    residueColour[13] = colours[0]; // F
+    residueColour[14] = colours[8]; // P
+    residueColour[15] = colours[1]; // S
+    residueColour[16] = colours[1]; // T
+    residueColour[17] = colours[0]; // W
+    residueColour[18] = colours[10]; // Y
+    residueColour[19] = colours[0]; // V
   }
 
+  @Override
   public Color findColour(char c)
   {
     return Color.pink;
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  protected Color findColour(char c, int j, SequenceI seq)
   {
-    Color currentColour;
-
-    if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    // TODO why the test for includeGaps here?
+    if (cons2.length <= j || Comparison.isGap(c)
+    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
     }
 
     int i = ResidueProperties.aaIndex[c];
 
-    currentColour = Color.white;
+    Color colour = Color.white;
 
     if (i > 19)
     {
-      return currentColour;
+      return colour;
     }
 
-    for (int k = 0; k < ResidueColour[i].conses.length; k++)
+    for (int k = 0; k < residueColour[i].cons.length; k++)
     {
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+      if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = ResidueColour[i].c;
+        colour = residueColour[i].c;
       }
     }
 
     if (i == 4)
     {
+      /*
+       * override to colour C pink if >85% conserved
+       */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = (Color) colhash.get("PINK");
+        colour = ClustalColour.PINK.colour;
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+    return colour;
   }
 
   /**
@@ -297,24 +327,39 @@ public class ClustalxColourScheme
   }
 
   /**
-   * @param includeGaps the includeGaps to set
+   * @param includeGaps
+   *          the includeGaps to set
    */
   protected void setIncludeGaps(boolean includeGaps)
   {
     this.includeGaps = includeGaps;
   }
-}
 
-class ConsensusColour
-{
-  Consensus[] conses;
-  Color c;
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
+  {
+    ClustalxColourScheme css = new ClustalxColourScheme(sg,
+            view == null ? null : view.getHiddenRepSequences());
+    css.includeGaps = includeGaps;
+    return css;
+  }
+
+  @Override
+  public boolean isPeptideSpecific()
+  {
+    return true;
+  }
 
-  public ConsensusColour(Color c, Consensus[] conses)
+  @Override
+  public String getSchemeName()
   {
-    this.conses = conses;
+    return JalviewColourScheme.Clustal.toString();
+  }
 
-    //    this.list = list;
-    this.c = c;
+  @Override
+  public boolean isSimple()
+  {
+    return false;
   }
 }