New GPCAPanel button : output pairwise alignments (pasimap only)

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index a499365..a84c449 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -55,6 +55,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   Vector<SequenceI> sequences;
 
+  private String alignmentOutput;
+
   /**
    * Creates a new PairwiseAlignPanel object.
    * 
@@ -71,6 +73,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     super();
     this.av = viewport;
 
+    StringBuilder sb = new StringBuilder(1024);
+
     sequences = new Vector<SequenceI>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
@@ -128,6 +132,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         {
           System.out.println(DASHES);
           textarea.append(DASHES);
+         sb.append(DASHES);
         }
         first = false;
         as.printAlignment(System.out);
@@ -136,6 +141,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
+       sb.append(as.getOutput());
         sequences.add(as.getAlignedSeq1());
         sequences.add(as.getAlignedSeq2());
       }
@@ -149,6 +155,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     {
       printScoreMatrix(seqs, scores, totscore);
     }
+
+    alignmentOutput = sb.toString();
   }
 
   public float[][] getScores()
@@ -161,6 +169,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     return this.alignmentScores;
   }
 
+  public String getAlignmentOutput()
+  {
+    return this.alignmentOutput;
+  }
+
   /**
    * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
    *