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;
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
// TODO Auto-generated method stub
}
});
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sendFeaturesToChimera();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
+ }
+
+ /**
+ * Send a command to Chimera to create residue attributes for Jalview features
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ */
+ protected void sendFeaturesToChimera()
+ {
+ jmb.sendFeaturesToChimera(getAlignmentPanel());
}
/**
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
- super();
+ this();
String pdbId = pdbentry.getId();
/*
SequenceI[][] seqs)
{
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,
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
String chain = null;
if (seq.getDatasetSequence() != null)
{
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
+ 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();
}
}
* @param newViewId
*/
public ChimeraViewFrame(String chimeraSessionFile,
- AlignmentPanel alignPanel,
- PDBEntry[] pdbArray,
+ AlignmentPanel alignPanel, PDBEntry[] pdbArray,
SequenceI[][] seqsArray, boolean colourByChimera,
boolean colourBySequence, String newViewId)
{
- super();
+ this();
setViewId(newViewId);
this.chimeraSessionFile = chimeraSessionFile;
openNewChimera(alignPanel, pdbArray, seqsArray);
public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
AlignmentPanel ap)
{
- super();
+ this();
openNewChimera(ap, pe, seqs);
}
- public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
- AlignmentPanel alignPanel)
+ /**
+ * Default constructor
+ */
+ public ChimeraViewFrame()
{
super();
/*
- * Convert the map of sequences per pdb entry into the tied arrays expected
- * by openNewChimera
- *
- * TODO pass the Map down to openNewChimera and its callees instead
+ * closeViewer will decide whether or not to close this frame
+ * depending on whether user chooses to Cancel or not
*/
- final Set<PDBEntry> pdbEntries = toView.keySet();
- PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
- SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
- for (int i = 0; i < pdbs.length; i++)
- {
- final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
- seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
- }
-
- openNewChimera(alignPanel, pdbs, seqsForPdbs);
+ setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
}
/**
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
if (!jmb.launchChimera())
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
+ JOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
JOptionPane.ERROR_MESSAGE);
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
* @param closeChimera
* if true, close any linked Chimera process; if false, prompt first
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
if (jmb != null && jmb.isChimeraRunning())
if (!closeChimera)
{
String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", false) });
+ "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_OPTION);
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ /*
+ * abort closure if user hits escape or Cancel
+ */
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
closeChimera = confirm == JOptionPane.YES_OPTION;
}
jmb.closeViewer(closeChimera);
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
+ dispose();
}
/**
* Open any newly added PDB structures in Chimera, having first fetched data
* from PDB (if not already saved).
*/
+ @Override
public void run()
{
_started = true;
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
{
int pos = filePDBpos.get(num).intValue();
long startTime = startProgressBar("Chimera "
- + MessageManager.getString("status.opening_file"));
+ + MessageManager.getString("status.opening_file_for")
+ + " " + pe.getId());
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
}
// Explicitly map to the filename used by Chimera ;
jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos],
- pe.getFile(),
- protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
alignStructs_withAllAlignPanels();
*/
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
+ // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
+ new Object[] { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- msg = pdbid + " "
- + MessageManager.getString("label.state_completed");
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// stopProgressBar(msg, hdl);
}
setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle("Chimera", true));
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
+ // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+ // {
viewerActionMenu.setVisible(true);
- }
+ // }
if (!jmb.isLoadingFromArchive())
{
seqColour_actionPerformed(null);
}
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
git://source.jalview.org / jalview.git / blobdiff