X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=895ee86c5f56684a7446d88240610889dfb319a3;hb=cd05157564b53f68ca9eb3ade15d0e687b57572d;hp=6a4ceec9e5e979561d4c2c1f6e9f93bc89eb1bd7;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 6a4ceec..895ee86 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -83,4 +83,58 @@ public class ScoreMatrix
     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();
+  }
 }