*/
package jalview.gui;
+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;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.DataFlavor;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
/**
* Cut'n'paste files into the desktop See JAL-1105
*
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