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JAL-1705 parse 'description' from GFF as sequence description
[jalview.git]
/
src
/
jalview
/
gui
/
CutAndPasteTransfer.java
diff --git
a/src/jalview/gui/CutAndPasteTransfer.java
b/src/jalview/gui/CutAndPasteTransfer.java
index
4541fc2
..
c0e59a4
100644
(file)
--- a/
src/jalview/gui/CutAndPasteTransfer.java
+++ b/
src/jalview/gui/CutAndPasteTransfer.java
@@
-24,6
+24,7
@@
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeaturesDisplayedI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
@@
-72,6
+73,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
SwingUtilities.invokeLater(new Runnable()
{
{
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
textarea.requestFocus();
public void run()
{
textarea.requestFocus();
@@
-124,6
+126,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
textarea.append(text);
}
textarea.append(text);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
public void save_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
@@
-160,6
+163,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void copyItem_actionPerformed(ActionEvent e)
{
textarea.getSelectedText();
public void copyItem_actionPerformed(ActionEvent e)
{
textarea.getSelectedText();
@@
-173,6
+177,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@
-198,6
+203,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
String text = getText();
public void ok_actionPerformed(ActionEvent e)
{
String text = getText();
@@
-206,7
+212,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
return;
}
return;
}
- String format = new IdentifyFile().Identify(text, "Paste");
+ String format = new IdentifyFile().identify(text, "Paste");
if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
{
System.err.println(MessageManager
if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
{
System.err.println(MessageManager
@@
-247,7
+253,11
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
String title = MessageManager.formatMessage(
"label.input_cut_paste_params", new String[] { format });
{
String title = MessageManager.formatMessage(
"label.input_cut_paste_params", new String[] { format });
- if (viewport != null)
+ /*
+ * if the view panel was closed its alignment is nulled
+ * and this is an orphaned cut and paste window
+ */
+ if (viewport != null && viewport.getAlignment() != null)
{
((AlignViewport) viewport).addAlignment(al, title);
}
{
((AlignViewport) viewport).addAlignment(al, title);
}
@@
-282,6
+292,10
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
{
af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ af.getViewport().setShowSequenceFeatures(true);
+ }
}
af.currentFileFormat = format;
}
af.currentFileFormat = format;
@@
-319,6
+333,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
try
public void cancel_actionPerformed(ActionEvent e)
{
try
@@
-329,6
+344,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
}
}
}
}
+ @Override
public void textarea_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
public void textarea_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
@@
-339,6
+355,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copyItem_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
copyItem_actionPerformed(e);
@@
-348,6
+365,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
item = new JMenuItem(MessageManager.getString("action.paste"));
item.addActionListener(new ActionListener()
{
item = new JMenuItem(MessageManager.getString("action.paste"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteMenu_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
pasteMenu_actionPerformed(e);