JAL-674 JAL-207 getTers for aligned sequences in dataset context

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9815b97..dd29d73 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -270,6 +270,34 @@ public class AlignSeq
   }
 
   /**
+   * 
+   * @return aligned instance of Seq 1
+   */
+  public SequenceI getAlignedSeq1()
+  {
+    SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
+    alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
+    alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
+    alSeq1.setDatasetSequence(s1.getDatasetSequence() == null ? s1 : s1
+            .getDatasetSequence());
+    return alSeq1;
+  }
+
+  /**
+   * 
+   * @return aligned instance of Seq 2
+   */
+  public SequenceI getAlignedSeq2()
+  {
+    SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
+    alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
+    alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
+    alSeq2.setDatasetSequence(s2.getDatasetSequence() == null ? s2 : s2
+            .getDatasetSequence());
+    return alSeq2;
+  }
+
+  /**
    * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
    * 
    * @param s1
@@ -614,7 +642,7 @@ public class AlignSeq
       output = output.append("\n\n");
     }
 
-    pid = pid / (float) (aseq1.length - count) * 100;
+    pid = pid / (aseq1.length - count) * 100;
     output = output.append(new Format("Percentage ID = %2.2f\n\n")
             .form(pid));