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;
private static final String DASHES = "---------------------\n";
- AlignmentViewport av;
+ AlignViewportI av;
Vector<SequenceI> sequences;
* 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
&& selectionGroup.getSize() > 0;
AlignmentView view = viewport.getAlignmentView(isSelection);
// String[] seqStrings = viewport.getViewAsString(true);
- String[] seqStrings = view.getSequenceStrings(viewport
- .getGapCharacter());
+ String[] seqStrings = view
+ .getSequenceStrings(viewport.getGapCharacter());
SequenceI[] seqs;
if (isSelection)
{
- seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
- .getGapCharacter())[0];
+ seqs = (SequenceI[]) view
+ .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
}
else
{
}
first = false;
as.printAlignment(System.out);
- scores[i][j] = as.getMaxScore()
- / as.getASeq1().length;
+ scores[i][j] = as.getMaxScore() / as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
for (int i = 0; i < seqs.length; i++)
{
- System.out.println(String.format("%3d %s", i + 1,
- seqs[i].getDisplayId(true)));
+ System.out.println(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
}
/*