X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=2ba06dc54a05b9e5bf73b644057d4d619c8b0f98;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bbca4deb11ca70628f43f34d6e2d62e9d3b35c5f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bbca4de..2ba06dc 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,282 +1,363 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* 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.
-*
-* 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
-*/
-
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import java.util.*;
-import java.awt.*;
-
-public class ClustalxColourScheme extends ResidueColourScheme
-{
-  Hashtable[] cons;
-  int[][] cons2;
-  ConsensusColour[] colours;
-  ConsensusColour[] ResidueColour;
-  int size;
-    Consensus[] conses = new Consensus[32];
-    public static Hashtable colhash = new Hashtable();
-
-    {
-        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));
-
-    }
-  Vector colourTable = new Vector();
-
-  public ClustalxColourScheme(Vector seqs, int maxWidth)
-  {
-    resetClustalX(seqs, maxWidth);
-  }
-
-  public void resetClustalX(Vector seqs, int maxWidth)
-  {
-    cons2 = new int[maxWidth][24];
-    int start = 0;
-
-    // Initialize the array
-    for (int j=0;j<24;j++)
-      for (int i=0; i < maxWidth;i++)
-        cons2[i][j] = 0;
-
-      int res,i, j = 0;
-      String seq;
-      while(j < seqs.size())
-      {
-        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
-        int end_j = seq.length()-1;
-        for (i = start; i <= end_j; i++)
-        {
-          if(seq.length()-1<i)
-            res = 23;
-          else
-            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
-          cons2[i][res]++;
-        }
-        j++;
-      }
-
-    this.size = seqs.size();
-    makeColours();
-  }
-  public 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[30] = new Consensus("G",0);
-    conses[31] = new Consensus("P",0);
-
-    // We now construct the colours
-    colours = new ConsensusColour[11];
-
-
-    Consensus[] tmp8 = new Consensus[1];
-    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);
-
-    Consensus[] tmp10 = new Consensus[1];
-    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);
-
-    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);
-
-    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);
-
-    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);
-    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);
-
-    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);
-
-    // 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
-  }
-
-  public Color findColour(String s)
-  {
-    return Color.pink;
-  }
-
-  public Color findColour(String s, int j)
-   {
-     if( threshold!=0 && !aboveThreshold(s,j))
-      return Color.white;
-
-
-     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
-
-     Color c = Color.white;
-
-     if(i>19)
-       return c;
-
-     for (int k=0; k < ResidueColour[i].conses.length ; k++)
-       if (ResidueColour[i].conses[k].isConserved(cons2,j,size))
-         c =  ResidueColour[i].c;
-
-     if (i == 4)
-    {
-      if (conses[27].isConserved(cons2, j, size))
-        c = (Color) colhash.get("PINK");
-    }
-
-
-     return c;
-
-   }
-}
-
-class ConsensusColour {
-
-  Consensus[] conses;
-  Color c;
-
-  public ConsensusColour(Color c,Consensus[] conses) {
-    this.conses = conses;
-    //    this.list = list;
-    this.c = c;
-  }
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ClustalxColourScheme extends ResidueColourScheme
+{
+  private static final int EIGHTY_FIVE = 85;
+
+  private static final int FIFTY = 50;
+
+  private static final int EIGHTY = 80;
+
+  private static final int SIXTY = 60;
+
+  /*
+   * Map from conventional colour names to Clustal version of the same
+   */
+  private static Map<Color, Color> colhash = new HashMap<Color, Color>();
+
+  private int[][] cons2;
+
+  private ConsensusColour[] colours;
+
+  private ConsensusColour[] residueColour;
+
+  private int size;
+
+  private Consensus[] conses = new Consensus[32];
+
+  private boolean includeGaps = true;
+
+  static
+  {
+    colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
+    colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
+    colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
+    colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
+    colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
+    colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
+    colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
+    colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
+  }
+
+  public ClustalxColourScheme(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    alignmentChanged(alignment, hiddenReps);
+  }
+
+  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 start = 0;
+
+    // Initialize the array
+    for (int j = 0; j < 24; j++)
+    {
+      for (int i = 0; i < maxWidth; i++)
+      {
+        cons2[i][j] = 0;
+      }
+    }
+
+    int res;
+    int i;
+    int j = 0;
+    char[] seq;
+
+    for (SequenceI sq : seqs)
+    {
+      seq = sq.getSequence();
+
+      int end_j = seq.length - 1;
+
+      for (i = start; i <= end_j; i++)
+      {
+        if ((seq.length - 1) < i)
+        {
+          res = 23;
+        }
+        else
+        {
+          res = ResidueProperties.aaIndex[seq[i]];
+        }
+
+        cons2[i][res]++;
+      }
+
+      j++;
+    }
+
+    this.size = seqs.size();
+    makeColours();
+  }
+
+  public void makeColours()
+  {
+    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);
+
+    // We now construct the colours
+    colours = new ConsensusColour[11];
+
+    Consensus[] tmp8 = new Consensus[1];
+    tmp8[0] = conses[30]; // G
+    colours[7] = new ConsensusColour(colhash.get(Color.ORANGE), tmp8);
+
+    Consensus[] tmp9 = new Consensus[1];
+    tmp9[0] = conses[31]; // P
+    colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
+
+    Consensus[] tmp10 = new Consensus[1];
+    tmp10[0] = conses[27]; // C
+    colours[9] = new ConsensusColour(colhash.get(Color.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(colhash.get(Color.BLUE), tmp1);
+
+    colours[10] = new ConsensusColour(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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
+  }
+
+  @Override
+  public Color findColour(char c)
+  {
+    return Color.pink;
+  }
+
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    Color currentColour;
+
+    if (cons2.length <= j
+            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    {
+      return Color.white;
+    }
+
+    int i = ResidueProperties.aaIndex[c];
+
+    currentColour = Color.white;
+
+    if (i > 19)
+    {
+      return currentColour;
+    }
+
+    for (int k = 0; k < residueColour[i].conses.length; k++)
+    {
+      if (residueColour[i].conses[k].isConserved(cons2, j, size,
+              includeGaps))
+      {
+        currentColour = residueColour[i].c;
+      }
+    }
+
+    if (i == 4)
+    {
+      if (conses[27].isConserved(cons2, j, size, includeGaps))
+      {
+        currentColour = colhash.get(Color.PINK);
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * @return the includeGaps
+   */
+  protected boolean isIncludeGaps()
+  {
+    return includeGaps;
+  }
+
+  /**
+   * @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.c = c;
+  }
+}