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;
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
- List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
- .getHiddenRegions();
- 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.getAlignment().getHiddenColumns()
- .getHiddenRegions())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
+ hiddenColumns = av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset