import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.ws.dbsources.Pdb;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import java.util.Random;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
{
createProgressBar();
// FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
- String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
- null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
}
- /**
- * Retrieve chains for sequences by inspecting their PDB refs. The hope is
- * that the first will be to the sequence's own chain. Really need a more
- * managed way of doing this.
- *
- * @param seqs
- * @return
- */
- protected String[][] extractChains(SequenceI[][] seqs)
- {
- String[][] chains = new String[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- chains[i] = new String[seqs[i].length];
- int seqno = 0;
- for (SequenceI seq : seqs[i])
- {
- String chain = null;
- if (seq.getDatasetSequence() != null)
- {
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbrefs != null && pdbrefs.size() > 0)
- {
- // FIXME: SequenceI.PDBEntry[0] chain mapping used for
- // ChimeraViewFrame. Is this even used ???
- chain = pdbrefs.get(0).getChainCode();
- }
- }
- chains[i][seqno++] = chain;
- }
- }
- return chains;
- }
/**
* Create a new viewer from saved session state data including Chimera session
setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
}
- /**
- * Returns a list of any Chimera viewers in the desktop. The list is
- * restricted to those linked to the given alignment panel if it is not null.
- */
- @Override
- protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
- {
- List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
- {
- result.add((StructureViewerBase) frame);
- }
- }
- }
- return result;
- }
/**
* Launch Chimera. If we have a chimera session file name, send Chimera the
if (!jmb.launchChimera())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
this.dispose();
return;
}
jmb.startChimeraListener();
}
- /**
- * If the list is not empty, add menu items for 'All' and each individual
- * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
- *
- * @param chainNames
- */
- void setChainMenuItems(List<String> chainNames)
- {
- chainMenu.removeAll();
- if (chainNames == null || chainNames.isEmpty())
- {
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- }
- showSelectedChains();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
-
- for (String chainName : chainNames)
- {
- menuItem = new JCheckBoxMenuItem(chainName, true);
- menuItem.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- showSelectedChains();
- }
- }
- });
-
- chainMenu.add(menuItem);
- }
- }
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
* option to close the associated Chimera window (process). They may wish to
* keep it open until they have had an opportunity to save any work.
*
- * @param closeChimera
+ * @param forceCloseChimera
* if true, close any linked Chimera process; if false, prompt first
*/
@Override
- public void closeViewer(boolean closeChimera)
+ public void closeViewer(boolean forceCloseChimera)
{
- if (jmb != null && jmb.isChimeraRunning())
+ if (jmb != null)
{
- if (!closeChimera)
+ if (jmb.isChimeraRunning())
{
- String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle("Chimera", false) });
- prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
- MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (confirm == JOptionPane.CANCEL_OPTION)
+ /*
+ * force close, or prompt to close, Chimera
+ */
+ if (!forceCloseChimera)
{
- return;
+ String prompt = MessageManager.formatMessage(
+ "label.confirm_close_chimera",
+ new Object[] { jmb.getViewerTitle("Chimera", 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;
+ }
+ forceCloseChimera = confirm == JvOptionPane.YES_OPTION;
}
- closeChimera = confirm == JOptionPane.YES_OPTION;
}
- jmb.closeViewer(closeChimera);
+
+ /*
+ * close the viewer plus any side-effects e.g. remove mappings
+ * note we do this also if closing Chimera triggered this method
+ */
+ jmb.closeViewer(forceCloseChimera);
}
+
setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
List<Integer> filePDBpos = new ArrayList<Integer>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new Object[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Throwable e)
{
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
jmb.getChains()[pos], pe.getFile(), protocol);
+ stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
}
}
}
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
* @return
* @throws Exception
*/
+
+ private void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
+ jmb.getChainNames().add(chid);
+ jmb.getChainFile().put(chid, file);
+ }
+ }
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
// FIXME: this is duplicated code with Jmol frame ?