Alogirthm working, but still giving slightly off results

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index c4b5367..2379e27 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -43,21 +43,38 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private static final String DASHES = "---------------------\n";
 
+  private float[][] scores;
+
+  private float[][] alignmentScores;   // scores used by PaSiMap
+
+  private int GAP_OPEN_COST;
+
+  private int GAP_EXTEND_COST;
+
   AlignmentViewport av;
 
   Vector<SequenceI> sequences;
 
+  private String alignmentOutput;
+
   /**
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
    *          DOCUMENT ME!
+   * @param endGaps ~ toggle gaps and the beginning and end of sequences
    */
   public PairwiseAlignPanel(AlignmentViewport viewport)
   {
+    this(viewport, false, 120, 20);    // default penalties used in AlignSeq
+  }
+  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
+  {
     super();
     this.av = viewport;
 
+    StringBuilder sb = new StringBuilder(1024);
+
     sequences = new Vector<SequenceI>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
@@ -83,16 +100,21 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];
+    float[][] alignmentScores = new float[seqs.length][seqs.length];
     double totscore = 0D;
     int count = seqs.length;
     boolean first = true;
+    //AlignSeq as = new AlignSeq(seqs[1], seqStrings[1], seqs[0], seqStrings[0], type, gapOpenCost, gapExtendCost);
 
     for (int i = 1; i < count; i++)
     {
+      // fill diagonal alignmentScores with Float.NaN
+      alignmentScores[i-1][i-1] = Float.NaN;
       for (int j = 0; j < i; j++)
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
-                seqStrings[j], type);
+                seqStrings[j], type, gapOpenCost, gapExtendCost);
+//     as.seqInit(seqs[i], seqStrings[i], seqs[j], seqStrings[j], type);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
@@ -100,28 +122,59 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
 
         as.calcScoreMatrix();
-        as.traceAlignment();
+       if (endGaps)
+       {
+          as.traceAlignmentWithEndGaps();
+       } else {
+         as.traceAlignment();
+       }
+       as.scoreAlignment();
 
         if (!first)
         {
           System.out.println(DASHES);
           textarea.append(DASHES);
+         sb.append(DASHES);
         }
         first = false;
         as.printAlignment(System.out);
         scores[i][j] = as.getMaxScore() / as.getASeq1().length;
+System.out.println(String.format("%s x %s -> [%d][%d] (%f)", seqs[i].getName(), seqs[j].getName(), i, j, as.getAlignmentScore()));
+        alignmentScores[i][j] = as.getAlignmentScore();
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
+       sb.append(as.getOutput());
         sequences.add(as.getAlignedSeq1());
         sequences.add(as.getAlignedSeq2());
       }
     }
+    alignmentScores[count-1][count-1] = Float.NaN;
+
+    this.scores = scores;
+    this.alignmentScores = alignmentScores;
 
     if (count > 2)
     {
       printScoreMatrix(seqs, scores, totscore);
     }
+
+    alignmentOutput = sb.toString();
+  }
+
+  public float[][] getScores()
+  {
+    return this.scores;
+  }
+
+  public float[][] getAlignmentScores()
+  {
+    return this.alignmentScores;
+  }
+
+  public String getAlignmentOutput()
+  {
+    return this.alignmentOutput;
   }
 
   /**