- AlignViewport av;
- Vector sequences;
-
- /**
- * Creates a new PairwiseAlignPanel object.
- *
- * @param av DOCUMENT ME!
- */
- public PairwiseAlignPanel(AlignViewport av)
+ private static final String DASHES = "---------------------\n";
+
+ AlignmentViewport av;
+
+ Vector<SequenceI> sequences;
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param viewport
+ * contains selected sequences to align
+ */
+ public PairwiseAlignPanel(AlignmentViewport viewport)
+ {
+ this(viewport,null);
+ }
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param viewport
+ * contains selected sequences to align
+ */
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)
+ {
+ super();
+ this.av = viewport;
+
+ sequences = new Vector<SequenceI>();
+
+ SequenceGroup selectionGroup = viewport.getSelectionGroup();
+ boolean isSelection = selectionGroup != null
+ && selectionGroup.getSize() > 0;
+ AlignmentView view = viewport.getAlignmentView(isSelection);
+ // String[] seqStrings = viewport.getViewAsString(true);
+ String[] seqStrings = view
+ .getSequenceStrings(viewport.getGapCharacter());
+
+ SequenceI[] seqs;
+ if (isSelection)