package jalview.gui;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
public class PymolViewer extends StructureViewerBase
{
private static final int myWidth = 500;
openNewPymol(ap, pe, seqs);
}
+ /**
+ * Constructor given a session file to be restored
+ *
+ * @param sessionFile
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByPymol
+ * @param colourBySequence
+ * @param newViewId
+ */
+ public PymolViewer(String sessionFile, AlignmentPanel alignPanel,
+ PDBEntry[] pdbArray, SequenceI[][] seqsArray,
+ boolean colourByPymol, boolean colourBySequence, String newViewId)
+ {
+ // TODO convert to base/factory class method
+ this();
+ setViewId(newViewId);
+ this.pymolSessionFile = sessionFile;
+ openNewPymol(alignPanel, pdbArray, seqsArray);
+ if (colourByPymol)
+ {
+ binding.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (colourBySequence)
+ {
+ binding.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
+ }
+
private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
SequenceI[][] seqs)
{
binding.setColourBySequence(true);
setSize(myWidth, myHeight);
initMenus();
+ viewerActionMenu.setText("PyMOL");
+ updateTitleAndMenus();
addingStructures = false;
worker = new Thread(this);
if (!binding.launchPymol())
{
JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pymol_failed"),
+ MessageManager.formatMessage("label.open_viewer_failed",
+ getViewerName()),
MessageManager.getString("label.error_loading_file"),
JvOptionPane.ERROR_MESSAGE);
this.dispose();
}
@Override
- public void closeViewer(boolean closePymol)
+ public ViewerType getViewerType()
{
- if (binding != null && binding.isPymolRunning())
- {
- if (!closePymol)
- {
- // TODO i18n (and pull up)
- String prompt = MessageManager
- .formatMessage("label.confirm_close_pymol", new Object[]
- { binding.getViewerTitle(getViewerName(), false) });
- prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JvOptionPane.showConfirmDialog(this, prompt,
- MessageManager.getString("label.close_viewer"),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- /*
- * abort closure if user hits escape or Cancel
- */
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
- {
- return;
- }
- closePymol = confirm == JvOptionPane.YES_OPTION;
- }
- binding.closeViewer(closePymol);
- }
- setAlignmentPanel(null);
- _aps.clear();
- _alignwith.clear();
- _colourwith.clear();
- // TODO: check for memory leaks where instance isn't finalised because
- // binding
- // holds a reference to the window
- binding = null;
- dispose();
+ return ViewerType.PYMOL;
}
@Override
- public String getStateInfo()
+ protected String getViewerName()
{
- return null;
+ return "PyMOL";
}
@Override
- public ViewerType getViewerType()
+ protected void initMenus()
{
- return ViewerType.PYMOL;
+ super.initMenus();
+
+ savemenu.setVisible(false); // not yet implemented
+ viewMenu.add(fitToWindow);
+
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_viewer_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_viewer_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sendFeaturesToPymol();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
}
- @Override
- protected String getViewerName()
+ protected void sendFeaturesToPymol()
{
- return "PyMOL";
+ int count = binding.sendFeaturesToViewer(getAlignmentPanel());
+ statusBar.setText(
+ MessageManager.formatMessage("label.attributes_set", count));
}
}