import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
- AlignViewport viewport;
+ AlignmentViewPanel alignpanel;
+
+ AlignViewportI viewport;
FileParse source = null;
public CutAndPasteTransfer()
/**
* DOCUMENT ME!
*/
- public void setForInput(AlignViewport viewport)
+ public void setForInput(AlignmentViewPanel viewpanel)
{
- this.viewport = viewport;
+ this.alignpanel = viewpanel;
+ if (alignpanel != null)
+ {
+ this.viewport = alignpanel.getAlignViewport();
+ }
if (viewport != null)
{
ok.setText(MessageManager.getString("action.add"));
{
String format = new IdentifyFile().Identify(getText(), "Paste");
// TODO: identify feature, annotation or tree file and parse appropriately.
- Alignment al = null;
+ AlignmentI al = null;
if (FormatAdapter.isValidFormat(format))
{
try
{
- FormatAdapter fa = new FormatAdapter(viewport);
+ FormatAdapter fa = new FormatAdapter(alignpanel);
al = fa.readFile(getText(), "Paste", format);
source = fa.getAlignFile();
{ format });
if (viewport != null)
{
- viewport.addAlignment(al, title);
+ ((AlignViewport) viewport).addAlignment(al, title);
}
else
{
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
-
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+ af.getViewport().setFeaturesDisplayed(fd);
af.changeColour(cs);
}
else