*/
package jalview.gui;
-import jalview.datamodel.Alignment;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.HtmlFile;
-import jalview.io.IdentifyFile;
-import jalview.io.JSONFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-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
*
}
else
{
- AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- af.currentFileFormat = format;
- Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
- .getString("label.successfully_pasted_alignment_file"));
- if (source instanceof HtmlFile)
+ AlignFrame af;
+ if (source instanceof ComplexAlignFile)
{
- ((HtmlFile) source).applySettingsToAlignmentView(af);
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+ af.changeColour(cs);
}
- else if (source instanceof JSONFile)
+ else
{
- ((JSONFile) source).applySettingsToAlignmentView(af);
+ af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
+ af.currentFileFormat = format;
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{