formatting

[jalview.git] / src / jalview / schemes / ScoreMatrix.java

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..9341509 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,28 +1,57 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
 package jalview.schemes;\r
 \r
-public class ScoreMatrix {\r
+public class ScoreMatrix\r
+{\r
   String name;\r
+\r
   /**\r
    * reference to integer score matrix\r
    */\r
   int[][] matrix;\r
+\r
   /**\r
    * 0 for Protein Score matrix. 1 for dna score matrix\r
    */\r
   int type;\r
-  ScoreMatrix(String name, int[][] matrix, int type) {\r
-    this.matrix=matrix;\r
-    this.type=type;\r
+\r
+  ScoreMatrix(String name, int[][] matrix, int type)\r
+  {\r
+    this.matrix = matrix;\r
+    this.type = type;\r
   }\r
-  public boolean isDNA() {\r
-    return type==1;\r
+\r
+  public boolean isDNA()\r
+  {\r
+    return type == 1;\r
   }\r
-  public boolean isProtein() {\r
-    return type==0;\r
+\r
+  public boolean isProtein()\r
+  {\r
+    return type == 0;\r
   }\r
-  public int[][] getMatrix() {\r
+\r
+  public int[][] getMatrix()\r
+  {\r
     return matrix;\r
   }\r
+\r
   /**\r
    * \r
    * @param A1\r
@@ -31,24 +60,88 @@ public class ScoreMatrix {
    */\r
   public int getPairwiseScore(String A1, String A2)\r
   {\r
-    return getPairwiseScore(A1.charAt(0),A2.charAt(0));\r
+    return getPairwiseScore(A1.charAt(0), A2.charAt(0));\r
   }\r
-  public int getPairwiseScore(char c, char d) {\r
+\r
+  public int getPairwiseScore(char c, char d)\r
+  {\r
     int pog = 0;\r
 \r
     try\r
     {\r
-      int a = (type==0) ? ResidueProperties.aaIndex[c] : ResidueProperties.nucleotideIndex[c];\r
-      int b = (type==0) ? ResidueProperties.aaIndex[d] : ResidueProperties.nucleotideIndex[d];\r
+      int a = (type == 0) ? ResidueProperties.aaIndex[c]\r
+              : ResidueProperties.nucleotideIndex[c];\r
+      int b = (type == 0) ? ResidueProperties.aaIndex[d]\r
+              : ResidueProperties.nucleotideIndex[d];\r
 \r
       pog = matrix[a][b];\r
-    }\r
-    catch (Exception e)\r
+    } catch (Exception e)\r
     {\r
-      //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+      // System.out.println("Unknown residue in " + A1 + " " + A2);\r
     }\r
 \r
     return pog;\r
   }\r
 \r
+  /**\r
+   * pretty print the matrix\r
+   */\r
+  public String toString()\r
+  {\r
+    return outputMatrix(false);\r
+  }\r
+\r
+  public String outputMatrix(boolean html)\r
+  {\r
+    StringBuffer sb = new StringBuffer();\r
+    int[] symbols = (type == 0) ? ResidueProperties.aaIndex\r
+            : ResidueProperties.nucleotideIndex;\r
+    int symMax = (type == 0) ? ResidueProperties.maxProteinIndex\r
+            : ResidueProperties.maxNucleotideIndex;\r
+    boolean header = true;\r
+    if (html)\r
+    {\r
+      sb.append("<table>");\r
+    }\r
+    for (char sym = 'A'; sym <= 'Z'; sym++)\r
+    {\r
+      if (symbols[sym] >= 0 && symbols[sym] < symMax)\r
+      {\r
+        if (header)\r
+        {\r
+          sb.append(html ? "<tr><td></td>" : "");\r
+          for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
+          {\r
+            if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
+            {\r
+              sb.append((html ? "<td>&nbsp;" : "\t") + sym2\r
+                      + (html ? "&nbsp;</td>" : ""));\r
+            }\r
+          }\r
+          header = false;\r
+          sb.append(html ? "</tr>\n" : "\n");\r
+        }\r
+        if (html)\r
+        {\r
+          sb.append("<tr>");\r
+        }\r
+        sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));\r
+        for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
+        {\r
+          if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
+          {\r
+            sb.append((html ? "<td>" : "\t")\r
+                    + matrix[symbols[sym]][symbols[sym2]]\r
+                    + (html ? "</td>" : ""));\r
+          }\r
+        }\r
+        sb.append(html ? "</tr>\n" : "\n");\r
+      }\r
+    }\r
+    if (html)\r
+    {\r
+      sb.append("</table>");\r
+    }\r
+    return sb.toString();\r
+  }\r
 }\r