From 213bb03dc91ef5af6aacbfc641d82420d0bdbb5a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 14:37:35 +0100
Subject: [PATCH] JAL-1167 method and simple tests for printing score matrices
 as tab or html formatted tables

---
 src/jalview/schemes/ScoreMatrix.java         |   54 ++++++++++++++++++++++++++
 test/jalview/schemes/ScoreMatrixPrinter.java |   29 ++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 test/jalview/schemes/ScoreMatrixPrinter.java

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index f5d30a9..895ee86 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -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();
+  }
 }
diff --git a/test/jalview/schemes/ScoreMatrixPrinter.java b/test/jalview/schemes/ScoreMatrixPrinter.java
new file mode 100644
index 0000000..099db3c
--- /dev/null
+++ b/test/jalview/schemes/ScoreMatrixPrinter.java
@@ -0,0 +1,29 @@
+package jalview.schemes;
+
+import java.util.Map;
+
+import org.junit.Test;
+
+
+public class ScoreMatrixPrinter 
+{
+  @Test
+  public void printAllMatrices()
+  {
+    for (Map.Entry<String,ScoreMatrix> sm:((Map<String, ScoreMatrix>) ResidueProperties.scoreMatrices).entrySet())
+    {
+      System.out.println("Matrix "+sm.getKey());
+      System.out.println(sm.getValue().toString());
+    }
+  }
+  @Test
+  public void printHTMLMatrices()
+  {
+    for (Map.Entry<String,ScoreMatrix> sm:((Map<String, ScoreMatrix>) ResidueProperties.scoreMatrices).entrySet())
+    {
+      System.out.println("Matrix "+sm.getKey());
+      System.out.println(sm.getValue().outputMatrix(true));
+    }
+  }
+
+}
-- 
1.7.10.2