X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=895ee86c5f56684a7446d88240610889dfb319a3;hb=aa213924876640ba82e866da5a750d9cdaa816d2;hp=03b6778cf32828bef78cdbc71423111c633c6f2a;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..895ee86 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,28 +1,57 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
 package jalview.schemes;
 
-public class ScoreMatrix {
+public class ScoreMatrix
+{
   String name;
+
   /**
    * reference to integer score matrix
    */
   int[][] matrix;
+
   /**
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
-  ScoreMatrix(String name, int[][] matrix, int type) {
-    this.matrix=matrix;
-    this.type=type;
+
+  ScoreMatrix(String name, int[][] matrix, int type)
+  {
+    this.matrix = matrix;
+    this.type = type;
   }
-  public boolean isDNA() {
-    return type==1;
+
+  public boolean isDNA()
+  {
+    return type == 1;
   }
-  public boolean isProtein() {
-    return type==0;
+
+  public boolean isProtein()
+  {
+    return type == 0;
   }
-  public int[][] getMatrix() {
+
+  public int[][] getMatrix()
+  {
     return matrix;
   }
+
   /**
    * 
    * @param A1
@@ -31,24 +60,81 @@ public class ScoreMatrix {
    */
   public int getPairwiseScore(String A1, String A2)
   {
-    return getPairwiseScore(A1.charAt(0),A2.charAt(0));
+    return getPairwiseScore(A1.charAt(0), A2.charAt(0));
   }
-  public int getPairwiseScore(char c, char d) {
+
+  public int getPairwiseScore(char c, char d)
+  {
     int pog = 0;
 
     try
     {
-      int a = (type==0) ? ResidueProperties.aaIndex[c] : ResidueProperties.nucleotideIndex[c];
-      int b = (type==0) ? ResidueProperties.aaIndex[d] : ResidueProperties.nucleotideIndex[d];
+      int a = (type == 0) ? ResidueProperties.aaIndex[c]
+              : ResidueProperties.nucleotideIndex[c];
+      int b = (type == 0) ? ResidueProperties.aaIndex[d]
+              : ResidueProperties.nucleotideIndex[d];
 
       pog = matrix[a][b];
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
-      //System.out.println("Unknown residue in " + A1 + " " + A2);
+      // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
     return pog;
   }
 
+  /**
+   * pretty print the matrix
+   */
+  public String toString()
+  {
+    return outputMatrix(false);
+  }
+  public String outputMatrix(boolean html)
+  {
+    StringBuffer sb=new StringBuffer();
+    int[] symbols=(type==0) ? ResidueProperties.aaIndex : ResidueProperties.nucleotideIndex;
+    int symMax = (type==0) ? ResidueProperties.maxProteinIndex :ResidueProperties.maxNucleotideIndex;
+    boolean header=true;
+    if (html)
+    {
+      sb.append("<table>");
+    }
+    for (char sym='A';sym<='Z';sym++)
+    {
+      if (symbols[sym]>=0 && symbols[sym]<symMax)
+      {
+        if (header) {
+          sb.append(html ? "<tr><td></td>" : "");
+        for (char sym2='A';sym2<='Z';sym2++)
+        {
+          if (symbols[sym2]>=0 && symbols[sym2]<symMax)
+          {
+            sb.append((html ? "<td>&nbsp;" : "\t")+sym2 +(html ? "&nbsp;</td>": ""));
+          }
+        }
+        header=false;
+        sb.append(html ? "</tr>\n" : "\n");
+        } 
+        if (html)
+        {
+          sb.append("<tr>");
+        }
+        sb.append((html ? "<td>" : "")+sym+(html ? "</td>" : ""));
+        for (char sym2='A';sym2<='Z';sym2++)
+        {
+          if (symbols[sym2]>=0 && symbols[sym2]<symMax)
+          {
+            sb.append((html ? "<td>" : "\t")+matrix[symbols[sym]][symbols[sym2]]+(html ? "</td>" : ""));
+          }
+        }
+        sb.append(html ? "</tr>\n" : "\n");
+      }
+    }
+    if (html)
+    {
+      sb.append("</table>");
+    }
+    return sb.toString();
+  }
 }