X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=d0817946f6cccae0b1725ace72a4358f8da85e5d;hb=d0a3c7594380d978b0d3bf3cbdba55a016b9d920;hp=4aea4b1a08395f3fb078295415145ec3e6bad269;hpb=427421de47dacacac55ac29deca78e2f0a1c5408;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 4aea4b1..d081794 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -83,7 +83,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];
-    double totscore = 0;
+    double totscore = 0D;
     int count = seqs.length;
     boolean first = true;
 
@@ -121,26 +121,53 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     if (count > 2)
     {
-      System.out.println(
-              "Pairwise alignment scaled similarity score matrix\n");
+      printScoreMatrix(seqs, scores, totscore);
+    }
+  }
 
-      for (int i = 0; i < count; i++)
-      {
-        System.out.println(String.format("%d %s", i,
-                seqs[i].getDisplayId(true)));
-      }
+  /**
+   * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
+   * 
+   * @param seqs
+   * @param scores
+   * @param totscore
+   */
+  protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
+          double totscore)
+  {
+    System.out
+            .println("Pairwise alignment scaled similarity score matrix\n");
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.println(String.format("%3d %s", i + 1,
+              seqs[i].getDisplayId(true)));
+    }
 
-      for (int i = 0; i < count; i++)
+    /*
+     * table heading columns for sequences 1, 2, 3...
+     */
+    System.out.print("\n ");
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.print(String.format("%7d", i + 1));
+    }
+    System.out.println();
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.print(String.format("%3d", i + 1));
+      for (int j = 0; j < i; j++)
       {
-        for (int j = 0; j < i; j++)
-        {
-          System.out.print(String.format("%7.3f", scores[i][j] / totscore));
-        }
-        System.out.println();
+        /*
+         * as a fraction of tot score, outputs are 0 <= score <= 1
+         */
+        System.out.print(String.format("%7.3f", scores[i][j] / totscore));
       }
-
-      System.out.println("\n");
+      System.out.println();
     }
+
+    System.out.println("\n");
   }
 
   /**