case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ ranges.scrollUp(true);
}
else
{
- alignPanel.setScrollValues(ranges.getStartRes(),
- 2 * ranges.getStartSeq() - ranges.getEndSeq());
+ ranges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ ranges.scrollUp(false);
}
else
{
- alignPanel
- .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
+ ranges.pageDown();
}
break;
return null;
}
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
if (displayTextbox)
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new Vector<SequenceI>();
+ List<SequenceI> sg = new Vector<>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static Vector<int[]> copiedHiddenColumns;
protected void copy_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector();
+ copiedHiddenColumns = new Vector<>(viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getAlignment().getHiddenColumns()
- .getHiddenRegions())
+ for (int[] region : copiedHiddenColumns)
{
- copiedHiddenColumns.addElement(new int[] {
- region[0] - hiddenOffset, region[1] - hiddenOffset });
+ region[0] = region[0] - hiddenOffset;
+ region[1] = region[1] - hiddenOffset;
}
}
else
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+ int[] region = copiedHiddenColumns.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}