From: jprocter <Jim Procter>
Date: Mon, 30 Jun 2008 09:48:06 +0000 (+0000)
Subject: included includeGaps flag in clustalW colour calculation - behaviour for includeGaps... 
X-Git-Tag: Release_2_4~92
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=067a6494124d4f1d0fe8b6d758b593145393b7dd;p=jalview.git

included includeGaps flag in clustalW colour calculation - behaviour for includeGaps=false is not verified to match ClustalX as yet.
---

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 8dd8994..bc2f9ea 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,303 +1,320 @@
-/*
- * 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
- * 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 java.util.*;
-
-import java.awt.*;
-
-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];
-  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);
-  }
-
-  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;
-    int i;
-    int j = 0;
-    char[] 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 = ResidueProperties.aaIndex[seq[i]];
-        }
-
-        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(char c)
-  {
-    return Color.pink;
-  }
-
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-
-    if (cons2.length <= j || (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))
-      {
-        currentColour = ResidueColour[i].c;
-      }
-    }
-
-    if (i == 4)
-    {
-      if (conses[27].isConserved(cons2, j, size))
-      {
-        currentColour = (Color) colhash.get("PINK");
-      }
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
-
-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
+ * 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
+ * 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 java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+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;
+  
+  {
+    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);
+  }
+
+  public void resetClustalX(Vector seqs, int maxWidth)
+  {
+    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;
+
+    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 = ResidueProperties.aaIndex[seq[i]];
+        }
+
+        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(char c)
+  {
+    return Color.pink;
+  }
+
+  public Color findColour(char c, int j)
+  {
+    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 = (Color) colhash.get("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;
+  }
+}
+
+class ConsensusColour
+{
+  Consensus[] conses;
+  Color c;
+
+  public ConsensusColour(Color c, Consensus[] conses)
+  {
+    this.conses = conses;
+
+    //    this.list = list;
+    this.c = c;
+  }
+}
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 8aa59e3..5cd7b52 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,79 +1,91 @@
-/*
- * 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
- * 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;
-
-////////////////////////////////////////////
-// This does nothing at all at the moment!!!!!!!!!!
-// AW 15th Dec 2004
-/////////////////////////////////////////
-public class Consensus
-{
-  int[] mask;
-  double threshold;
-  String maskstr;
-
-  public Consensus(String mask, double threshold)
-  {
-    // this.id = id;
-    //    this.mask = mask;
-    this.maskstr = mask;
-    setMask(mask);
-    this.threshold = threshold;
-  }
-
-  public void setMask(String s)
-  {
-    this.mask = setNums(s);
-
-    //   for (int i=0; i < mask.length; i++) {
-    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
-    // }
-  }
-
-  public boolean isConserved(int[][] cons2, int col, int size)
-  {
-    int tot = 0;
-
-    for (int i = 0; i < mask.length; i++)
-    {
-      tot += cons2[col][mask[i]];
-    }
-
-    if ( (double) tot > ( (threshold * size) / 100))
-    {
-      return true;
-    }
-
-    return false;
-  }
-
-  int[] setNums(String s)
-  {
-    int[] out = new int[s.length()];
-    int i = 0;
-
-    while (i < s.length())
-    {
-      out[i] = ResidueProperties.aaIndex[s.charAt(i)];
-      i++;
-    }
-
-    return out;
-  }
-}
+/*
+ * 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
+ * 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;
+
+////////////////////////////////////////////
+// This does nothing at all at the moment!!!!!!!!!!
+// AW 15th Dec 2004
+/////////////////////////////////////////
+public class Consensus
+{
+  int[] mask;
+  double threshold;
+  String maskstr;
+
+  public Consensus(String mask, double threshold)
+  {
+    // this.id = id;
+    //    this.mask = mask;
+    this.maskstr = mask;
+    setMask(mask);
+    this.threshold = threshold;
+  }
+
+  public void setMask(String s)
+  {
+    this.mask = setNums(s);
+
+    //   for (int i=0; i < mask.length; i++) {
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // }
+  }
+
+  /**
+   * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
+   */
+  public boolean isConserved(int[][] cons2, int col, int size)
+  {
+    return isConserved(cons2, col, size, true);
+  }
+
+  public boolean isConserved(int[][] cons2, int col, int size, boolean includeGaps)
+  {
+    int tot = 0;
+    if (!includeGaps)
+    {
+      size -= cons2[col][cons2[col].length-1]; 
+    }
+    for (int i = 0; i < mask.length; i++)
+    {
+      tot += cons2[col][mask[i]];
+    }
+
+    if ( (double) tot > ( (threshold * size) / 100))
+    {
+        // System.out.println("True conserved "+tot+" from "+threshold+" out of "+size+" : "+maskstr);
+      return true;
+    }
+
+    return false;
+  }
+
+  int[] setNums(String s)
+  {
+    int[] out = new int[s.length()];
+    int i = 0;
+
+    while (i < s.length())
+    {
+      out[i] = ResidueProperties.aaIndex[s.charAt(i)];
+      i++;
+    }
+
+    return out;
+  }
+}