Merge branch 'develop' into features/mchmmer

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 4aea4b1..e736a11 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,13 +21,13 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -43,7 +43,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private static final String DASHES = "---------------------\n";
 
-  AlignmentViewport av;
+  AlignViewportI av;
 
   Vector<SequenceI> sequences;
 
@@ -51,14 +51,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
-   *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignmentViewport viewport)
+  public PairwiseAlignPanel(AlignViewportI viewport)
   {
     super();
     this.av = viewport;
 
-    sequences = new Vector<SequenceI>();
+    sequences = new Vector<>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
     boolean isSelection = selectionGroup != null
@@ -83,7 +82,7 @@ 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 +120,53 @@ 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 < count; i++)
+    for (int i = 0; i < seqs.length; i++)
+    {
+      System.out.println(String.format("%3d %s", i + 1,
+              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 < 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");
   }
 
   /**