import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.List;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- refresh(fullRepaint);
+ ap.refresh(fullRepaint);
}
/**
- * Redraw sensibly.
- *
- * @adjustHeight if true, try to recalculate panel height for visible
- * annotations
- */
- protected void refresh(boolean adjustHeight)
- {
- ap.validateAnnotationDimensions(adjustHeight);
- ap.addNotify();
- if (adjustHeight)
- {
- // sort, repaint, update overview
- ap.paintAlignment(true);
- }
- else
- {
- // lightweight repaint
- ap.repaint();
- }
- }
-
- /**
* DOCUMENT ME!
*
* @param e
// ann.visible = false;
// }
// }
- refresh(true);
+ ap.refresh(true);
}
});
pop.add(hideType);
Alignment ds = new Alignment(dseqs);
if (av.hasHiddenColumns())
{
- omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+ omitHidden = av.getAlignment().getHiddenColumns()
+ .getVisibleSequenceStrings(0,
sq.getLength(), seqs);
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
- List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
- if (hiddenCols != null)
+ if (av.hasHiddenColumns())
{
- alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
- hiddenCols);
+ alignmentStartEnd = av.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
}
+
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
seqs, omitHidden, alignmentStartEnd);
.setContents(new StringSelection(output), Desktop.instance);
ArrayList<int[]> hiddenColumns = null;
+
if (av.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<int[]>();
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
+ hiddenColumns = av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset