X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=353accf324cfd95f26d2677f9db04f4778f6f285;hb=a6cd54c46366acd8bc3350a79374b18f9eb0b240;hp=bbca4deb11ca70628f43f34d6e2d62e9d3b35c5f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bbca4de..353accf 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,51 +1,52 @@
 /*
-* 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
-*/
-
+ * 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
+import jalview.datamodel.*;
+
+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];
-    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));
-
-    }
+  Consensus[] conses = new Consensus[32];
   Vector colourTable = new Vector();
 
+  {
+    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)
   {
     resetClustalX(seqs, maxWidth);
@@ -54,83 +55,101 @@ public class ClustalxColourScheme extends ResidueColourScheme
   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++)
+    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;
+    String seq;
+
+    while (j < seqs.size())
+    {
+      seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
 
-      int res,i, j = 0;
-      String seq;
-      while(j < seqs.size())
+      int end_j = seq.length() - 1;
+
+      for (i = start; i <= end_j; i++)
       {
-        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
         {
-          if(seq.length()-1<i)
-            res = 23;
-          else
-            res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();
-          cons2[i][res]++;
+          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
+              "")).intValue();
         }
-        j++;
+
+        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);
+
+  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);
+    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]; //%
@@ -147,54 +166,56 @@ public class ClustalxColourScheme extends ResidueColourScheme
     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[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
 
-    colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);
+    colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
 
     Consensus[] tmp2 = new Consensus[5];
-    tmp2[0] = conses[8];  //t
+    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[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[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[0] = conses[6]; // q = QE
     tmp4[1] = conses[19]; //Q
     tmp4[2] = conses[22]; //E
-    tmp4[3] = conses[3];  //+
+    tmp4[3] = conses[3]; //+
     tmp4[4] = conses[28]; //K
     tmp4[5] = conses[20]; //R
-    colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);
+    colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+
     Consensus[] tmp5 = new Consensus[4];
-    tmp5[0] = conses[3];  //+
+    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);
+    colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
+
     Consensus[] tmp6 = new Consensus[5];
-    tmp6[0] = conses[3];  //-
+    tmp6[0] = conses[3]; //-
     tmp6[1] = conses[29]; //D
     tmp6[2] = conses[10]; //E
-    tmp6[3] = conses[6];  //q
+    tmp6[3] = conses[6]; //q
     tmp6[4] = conses[19]; //Q
-    colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);
+    colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
 
     Consensus[] tmp7 = new Consensus[5];
-    tmp7[0] = conses[3];  //-
+    tmp7[0] = conses[3]; //-
     tmp7[1] = conses[29]; //D
     tmp7[2] = conses[10]; //E
-    tmp7[3] = conses[17];  //N
+    tmp7[3] = conses[17]; //N
     tmp7[4] = conses[2]; //DE
-    colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);
+    colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
 
     // Now attach the ConsensusColours to the residue letters
     ResidueColour = new ConsensusColour[20];
@@ -226,57 +247,54 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   public Color findColour(String s, int j)
-   {
-     if( threshold!=0 && !aboveThreshold(s,j))
+  {
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
       return Color.white;
+    }
 
+    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
 
-     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
-
-     Color c = Color.white;
+    currentColour = Color.white;
 
-     if(i>19)
-       return c;
+    if (i > 19)
+    {
+      return currentColour;
+    }
 
-     for (int k=0; k < ResidueColour[i].conses.length ; k++)
-       if (ResidueColour[i].conses[k].isConserved(cons2,j,size))
-         c =  ResidueColour[i].c;
+    for (int k = 0; k < ResidueColour[i].conses.length; k++)
+    {
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+      {
+        currentColour = ResidueColour[i].c;
+      }
+    }
 
-     if (i == 4)
+    if (i == 4)
     {
       if (conses[27].isConserved(cons2, j, size))
-        c = (Color) colhash.get("PINK");
+      {
+        currentColour = (Color) colhash.get("PINK");
+      }
     }
 
+    if(conservationColouring)
+         applyConservation(j);
 
-     return c;
-
-   }
+    return currentColour;
+  }
 }
 
-class ConsensusColour {
-
+class ConsensusColour
+{
   Consensus[] conses;
   Color c;
 
-  public ConsensusColour(Color c,Consensus[] conses) {
+  public ConsensusColour(Color c, Consensus[] conses)
+  {
     this.conses = conses;
+
     //    this.list = list;
     this.c = c;
   }
 }
-
-
-
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-