X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=c4b53675abfa3830ed371f5826ebe175d5207ba6;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=4aea4b1a08395f3fb078295415145ec3e6bad269;hpb=427421de47dacacac55ac29deca78e2f0a1c5408;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 4aea4b1..c4b5367 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -65,14 +65,14 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             && selectionGroup.getSize() > 0;
     AlignmentView view = viewport.getAlignmentView(isSelection);
     // String[] seqStrings = viewport.getViewAsString(true);
-    String[] seqStrings = view.getSequenceStrings(viewport
-            .getGapCharacter());
+    String[] seqStrings = view
+            .getSequenceStrings(viewport.getGapCharacter());
 
     SequenceI[] seqs;
     if (isSelection)
     {
-      seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
-              .getGapCharacter())[0];
+      seqs = (SequenceI[]) view
+              .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
     }
     else
     {
@@ -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;
 
@@ -109,8 +109,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
         first = false;
         as.printAlignment(System.out);
-        scores[i][j] = as.getMaxScore()
-                / as.getASeq1().length;
+        scores[i][j] = as.getMaxScore() / as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
@@ -121,26 +120,53 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     if (count > 2)
     {
+      printScoreMatrix(seqs, scores, totscore);
+    }
+  }
+
+  /**
+   * 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(
-              "Pairwise alignment scaled similarity score matrix\n");
+              String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
+    }
 
-      for (int i = 0; i < count; i++)
-      {
-        System.out.println(String.format("%d %s", i,
-                seqs[i].getDisplayId(true)));
-      }
+    /*
+     * 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 < count; i++)
+    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");
   }
 
   /**