X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=895ee86c5f56684a7446d88240610889dfb319a3;hb=cd05157564b53f68ca9eb3ade15d0e687b57572d;hp=a5a5ed374074c5f9b972e4193b78190001615555;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index a5a5ed3..895ee86 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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 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;
 
@@ -84,4 +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();
+  }
 }