package jalview.gui;
+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;
+
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)
{
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)
- {
- 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();
- }
-
- @Override
- public String getStateInfo()
- {
- return null;
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.PYMOL;