*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Random;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
+
/**
* Base class with common functionality for JMol, Chimera or other structure
* viewers.
/**
* list of alignment panels to use for superposition
*/
- protected Vector<AlignmentPanel> _alignwith = new Vector<>();
+ protected Vector<AlignmentViewPanel> _alignwith = new Vector<>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- protected Vector<AlignmentPanel> _colourwith = new Vector<>();
+ protected Vector<AlignmentViewPanel> _colourwith = new Vector<>();
private String viewId = null;
protected boolean alignAddedStructures = false;
- protected boolean _started = false;
+ protected volatile boolean _started = false;
- protected boolean addingStructures = false;
+ protected volatile boolean addingStructures = false;
protected Thread worker = null;
protected JMenu viewSelectionMenu;
/**
+ * set after sequence colouring has been applied for this structure viewer.
+ * used to determine if the final sequence/structure mapping has been
+ * determined
+ */
+ protected volatile boolean seqColoursApplied = false;
+
+ private IProgressIndicator progressBar = null;
+
+ private Random random = new Random();
+
+ /**
* Default constructor
*/
public StructureViewerBase()
}
/**
+ * @return true if added structures should be aligned to existing one(s)
+ */
+ @Override
+ public boolean isAlignAddedStructures()
+ {
+ return alignAddedStructures;
+ }
+
+ /**
+ *
+ * @param true
+ * if added structures should be aligned to existing one(s)
+ */
+ @Override
+ public void setAlignAddedStructures(boolean alignAdded)
+ {
+ alignAddedStructures = alignAdded;
+ }
+
+ /**
+ * called by the binding model to indicate when adding structures is happening
+ * or has been completed
+ *
+ * @param addingStructures
+ */
+ public synchronized void setAddingStructures(boolean addingStructures)
+ {
+ this.addingStructures = addingStructures;
+ }
+
+ /**
*
* @param ap2
* @return true if this Jmol instance is linked with the given alignPanel
return _aps.contains(ap2.av.getSequenceSetId());
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ public boolean isUsedforaligment(AlignmentViewPanel ap2)
{
return (_alignwith != null) && _alignwith.contains(ap2);
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ public boolean isUsedForColourBy(AlignmentViewPanel ap2)
{
return (_colourwith != null) && _colourwith.contains(ap2);
}
this.viewId = viewId;
}
- public abstract String getStateInfo();
-
protected void buildActionMenu()
{
if (_alignwith == null)
_alignwith.add(ap);
}
;
+ // TODO: refactor to allow concrete classes to register buttons for adding
+ // here
+ // currently have to override to add buttons back in after they are cleared
+ // in this loop
for (Component c : viewerActionMenu.getMenuComponents())
{
if (c != alignStructs)
}
}
+ @Override
public AlignmentPanel getAlignmentPanel()
{
return ap;
*
* @param nap
*/
- public void removeAlignmentPanel(AlignmentPanel nap)
+ @Override
+ public void removeAlignmentPanel(AlignmentViewPanel nap)
{
try
{
public abstract ViewerType getViewerType();
- protected abstract IProgressIndicator getIProgressIndicator();
-
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
*/
protected void addStructure(final PDBEntry pdbentry,
final SequenceI[] seqs, final String[] chains,
- final boolean align, final IProgressIndicator alignFrame)
+ final IProgressIndicator alignFrame)
{
if (pdbentry.getFile() == null)
{
}
}
// and call ourselves again.
- addStructure(pdbentry, seqs, chains, align, alignFrame);
+ addStructure(pdbentry, seqs, chains, alignFrame);
}
}, "Adding3DStructureQueue").start();
return;
{ seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
- alignAddedStructures = align;
worker = new Thread(this, "Adding3DStructure");
worker.start();
return;
}
- /**
- * Presents a dialog with the option to add an align a structure to an
- * existing structure view
- *
- * @param pdbId
- * @param view
- * @return YES, NO or CANCEL JvOptionPane code
- */
- protected int chooseAlignStructureToViewer(String pdbId,
- StructureViewerBase view)
- {
- int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbId, view.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- return option;
- }
-
protected boolean hasPdbId(String pdbId)
{
return getBinding().hasPdbId(pdbId);
}
- protected abstract List<StructureViewerBase> getViewersFor(
- AlignmentPanel alp);
-
/**
- * Check for any existing views involving this alignment and give user the
- * option to add and align this molecule to one of them
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param apanel
- * @param pdbId
- * @return true if user adds to a view, or cancels entirely, else false
+ * Returns a list of any viewer of the instantiated type. The list is
+ * restricted to those linked to the given alignment panel if it is not null.
*/
- protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbId)
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
{
- for (StructureViewerBase view : getViewersFor(apanel))
- {
- // TODO: highlight the view somehow
- /*
- * JAL-1742 exclude view with this structure already mapped (don't offer
- * to align chain B to chain A of the same structure)
- */
- if (view.hasPdbId(pdbId))
- {
- continue;
- }
- int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JvOptionPane.CANCEL_OPTION)
- {
- return true;
- }
- else if (option == JvOptionPane.YES_OPTION)
- {
- view.useAlignmentPanelForSuperposition(apanel);
- view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
- return true;
- }
- else
- {
- // NO_OPTION - offer the next viewer if any
- }
- }
+ return Desktop.instance.getStructureViewers(alp, this.getClass());
+ }
+ @Override
+ public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel apanel, String pdbId)
+ {
/*
- * nothing offered and selected
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure); code may defend
+ * against this possibility before we reach here
*/
- return false;
+ if (hasPdbId(pdbId))
+ {
+ return;
+ }
+ AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error
+ // if this
+ // cast fails
+ useAlignmentPanelForSuperposition(alignPanel);
+ addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
}
/**
* @param apanel
* @param pdbFilename
*/
- protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ public void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel alpanel,
+ String pdbFilename)
{
+ AlignmentPanel apanel = (AlignmentPanel) alpanel;
+
// TODO : Fix multiple seq to one chain issue here.
/*
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE, getIProgressIndicator());
+ pdbFilename, DataSourceType.FILE, getProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
}
}
- /**
- * Check if the PDB file is already loaded, if so offer to add it to the
- * existing viewer
- *
- * @param seq
- * @param chains
- * @param apanel
- * @param pdbId
- * @return true if the user chooses to add to a viewer, or to cancel entirely
- */
- protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
- final AlignmentPanel apanel, String pdbId)
+ @Override
+ public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentViewPanel apanel, String pdbId)
{
- boolean finished = false;
String alreadyMapped = apanel.getStructureSelectionManager()
.alreadyMappedToFile(pdbId);
- if (alreadyMapped != null)
- {
- /*
- * the PDB file is already loaded
- */
- int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbId }),
- MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbId }),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JvOptionPane.CANCEL_OPTION)
- {
- finished = true;
- }
- else if (option == JvOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
- finished = true;
- }
+ if (alreadyMapped == null)
+ {
+ return false;
}
- return finished;
+
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ return true;
}
void setChainMenuItems(List<String> chainNames)
}
}
- abstract void showSelectedChains();
-
/**
* Action on selecting one of Jalview's registered colour schemes
*/
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
- ColourSchemeI cs = ColourSchemes.getInstance()
- .getColourScheme(colourSchemeName, al, null);
- getBinding().setJalviewColourScheme(cs);
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
+ colourSchemeName, getAlignmentPanel().av, al, null);
+ getBinding().colourByJalviewColourScheme(cs);
}
/**
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- viewerColour_actionPerformed(actionEvent);
+ viewerColour_actionPerformed();
}
});
colourMenu.add(viewerColour);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- background_actionPerformed(actionEvent);
+ background_actionPerformed();
}
});
colourMenu.add(backGround);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- seqColour_actionPerformed(actionEvent);
+ seqColour_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- chainColour_actionPerformed(actionEvent);
+ chainColour_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- chargeColour_actionPerformed(actionEvent);
+ chargeColour_actionPerformed();
}
});
viewerColour = new JRadioButtonMenuItem();
- // text is set in overrides of this method
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_viewer"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_viewer_manage_structure_colours"));
viewerColour.setName(ViewerColour.ByViewer.name());
viewerColour.setSelected(!binding.isColourBySequence());
}
else
{
- // update the Chimera display now.
- seqColour_actionPerformed(null);
+ // update the viewer display now.
+ seqColour_actionPerformed();
}
}
});
@Override
public void itemStateChanged(ItemEvent e)
{
- alignStructs.setEnabled(!_alignwith.isEmpty());
- alignStructs.setToolTipText(MessageManager.formatMessage(
- "label.align_structures_using_linked_alignment_views",
- _alignwith.size()));
+ if (_alignwith.isEmpty())
+ {
+ alignStructs.setEnabled(false);
+ alignStructs.setToolTipText(null);
+ }
+ else
+ {
+ alignStructs.setEnabled(true);
+ alignStructs.setToolTipText(MessageManager.formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ _alignwith.size()));
+ }
}
};
viewSelectionMenu = new ViewSelectionMenu(
}
});
- buildColourMenu();
- }
+ viewerActionMenu.setText(getViewerName());
+ helpItem.setText(MessageManager.formatMessage("label.viewer_help",
+ getViewerName()));
- @Override
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- getBinding().setJalviewColourScheme(cs);
+ buildColourMenu();
}
/**
* the operation.
*/
@Override
- protected String alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- return alignStructs_withAllAlignPanels();
- }
-
- protected String alignStructs_withAllAlignPanels()
+ protected String alignStructsWithAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
String reply = null;
try
{
- AlignmentI[] als = new Alignment[_alignwith.size()];
- HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getAlignment().getHiddenColumns();
- }
- reply = getBinding().superposeStructures(als, alm, alc);
- if (reply != null)
+ reply = getBinding().superposeStructures(_alignwith);
+ if (reply != null && !reply.isEmpty())
{
String text = MessageManager
.formatMessage("error.superposition_failed", reply);
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
+ for (AlignmentViewPanel alignPanel : _alignwith)
{
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ sp.append("'" + alignPanel.getViewName() + "' ");
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
+ Console.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
return reply;
}
+ /**
+ * Opens a colour chooser dialog, and applies the chosen colour to the
+ * background of the structure viewer
+ */
@Override
- public void background_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- null);
- if (col != null)
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- getBinding().setBackgroundColour(col);
- }
+ @Override
+ public void colourSelected(Color c)
+ {
+ getBinding().setBackgroundColour(c);
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, null, listener);
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ public void viewerColour_actionPerformed()
{
if (viewerColour.isSelected())
{
}
@Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
+ public void chainColour_actionPerformed()
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
@Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ public void chargeColour_actionPerformed()
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
@Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
+ public void seqColour_actionPerformed()
{
AAStructureBindingModel binding = getBinding();
binding.setColourBySequence(seqColour.isSelected());
}
}
// Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel alignPanel : _colourwith)
{
- binding.colourBySequence(ap);
+ binding.colourBySequence(alignPanel);
}
+ seqColoursApplied = true;
}
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ public void pdbFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
}
@Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ public void viewMapping_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
/**
* Configures the title and menu items of the viewer panel.
*/
+ @Override
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
* enable 'Superpose with' if more than one mapped structure
*/
viewSelectionMenu.setEnabled(false);
- if (getBinding().getStructureFiles().length > 1
+ if (getBinding().getMappedStructureCount() > 1
&& getBinding().getSequence().length > 1)
{
viewSelectionMenu.setEnabled(true);
if (!binding.isLoadingFromArchive())
{
- seqColour_actionPerformed(null);
+ seqColour_actionPerformed();
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return getTitle();
+ }
+
+ @Override
+ public boolean hasMapping()
+ {
+ if (worker != null && (addingStructures || _started))
+ {
+ return false;
+ }
+ if (getBinding() == null)
+ {
+ if (_aps == null || _aps.size() == 0)
+ {
+ // viewer has been closed, but we did at some point run.
+ return true;
+ }
+ return false;
+ }
+ String[] pdbids = getBinding().getStructureFiles();
+ if (pdbids == null)
+ {
+ return false;
+ }
+ int p = 0;
+ for (String pdbid : pdbids)
+ {
+ StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+ if (sm != null && sm.length > 0 && sm[0] != null)
+ {
+ p++;
+ }
+ }
+ // only return true if there is a mapping for every structure file we have
+ // loaded
+ if (p == 0 || p != pdbids.length)
+ {
+ return false;
+ }
+ // and that coloring has been applied
+ return seqColoursApplied;
+ }
+
+ @Override
+ public void raiseViewer()
+ {
+ toFront();
+ }
+
+ @Override
+ public long startProgressBar(String msg)
+ {
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, tm);
+ }
+ return tm;
+ }
+
+ @Override
+ public void stopProgressBar(String msg, long handle)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, handle);
+ }
+ }
+
+ protected IProgressIndicator getProgressIndicator()
+ {
+ return progressBar;
+ }
+
+ protected void setProgressIndicator(IProgressIndicator pi)
+ {
+ progressBar = pi;
+ }
+
+ public void setProgressMessage(String message, long id)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+ }
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ // default does nothing
+ }
+
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ protected void showSelectedChains()
+ {
+ List<String> toshow = new ArrayList<>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.add(item.getText());
+ }
+ }
}
+ getBinding().showChains(toshow);
+ }
+
+ /**
+ * Tries to fetch a PDB file and save to a temporary local file. Returns the
+ * saved file path if successful, or null if not.
+ *
+ * @param processingEntry
+ * @return
+ */
+ protected String fetchPdbFile(PDBEntry processingEntry)
+ {
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ EBIAlfaFold afclient = new EBIAlfaFold();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ long handle = System.currentTimeMillis()
+ + Thread.currentThread().hashCode();
+
+ /*
+ * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+ */
+ String msg = MessageManager.formatMessage("status.fetching_pdb",
+ new Object[]
+ { pdbid });
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // long hdl = startProgressBar(MessageManager.formatMessage(
+ // "status.fetching_pdb", new Object[]
+ // { pdbid }));
+ try
+ {
+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid,
+ processingEntry.getRetrievalUrl());
+ }
+ else
+ {
+ if (processingEntry.hasRetrievalUrl())
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbid, "UTF-8")
+ .replace("%", "__");
+
+ // retrieve from URL to new local tmpfile
+ File tmpFile = File.createTempFile(safePDBId,
+ "." + (PDBEntry.Type.MMCIF.toString().equals(
+ processingEntry.getType().toString()) ? "cif"
+ : "pdb"));
+ String fromUrl = processingEntry.getRetrievalUrl();
+ UrlDownloadClient.download(fromUrl, tmpFile);
+
+ // may not need this check ?
+ String file = tmpFile.getAbsolutePath();
+ if (file != null)
+ {
+ pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,
+ tmpFile, pdbid, null, null, null);
+ }
+ }
+ else
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
+ } finally
+ {
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
+ }
+ /*
+ * If PDB data were saved and are not invalid (empty alignment), return the
+ * file path.
+ */
+ if (pdbseq != null && pdbseq.getHeight() > 0)
+ {
+ // just use the file name from the first sequence's first PDBEntry
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ processingEntry.setFile(filePath);
+ }
+ return filePath;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file, else returns null
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ if (getBinding() == null)
+ {
+ return null;
+ }
+ File session = getBinding().saveSession();
+ long l = session.length();
+ int wait = 50;
+ do
+ {
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException e)
+ {
+ }
+ long nextl = session.length();
+ if (nextl != l)
+ {
+ wait = 50;
+ l = nextl;
+ }
+ } while (--wait > 0);
+ return session;
+ }
+
+ /**
+ * Close down this instance of Jalview's Chimera viewer, giving the user the
+ * 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 forceClose
+ * if true, close any linked Chimera process; if false, prompt first
+ */
+ @Override
+ public void closeViewer(boolean forceClose)
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding != null && binding.isViewerRunning())
+ {
+ if (!forceClose)
+ {
+ String viewerName = getViewerName();
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_viewer", new Object[]
+ { binding.getViewerTitle(viewerName, false), viewerName });
+ 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;
+ }
+ forceClose = confirm == JvOptionPane.YES_OPTION;
+ }
+ }
+ if (binding != null)
+ {
+ binding.closeViewer(forceClose);
+ }
+ setAlignmentPanel(null);
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ // jmb = null;
+ dispose();
+ }
+
+ @Override
+ public void showHelp_actionPerformed()
+ {
+ /*
+ try
+ {
+ */
+ String url = getBinding().getHelpURL();
+ if (url != null)
+ {
+ BrowserLauncher.openURL(url);
+ }
+ /*
+ }
+ catch (IOException ex)
+ {
+ System.err
+ .println("Show " + getViewerName() + " failed with: "
+ + ex.getMessage());
+ }
+ */
+ }
+
+ @Override
+ public boolean hasViewerActionsMenu()
+ {
+ return viewerActionMenu != null && viewerActionMenu.isEnabled()
+ && viewerActionMenu.getItemCount() > 0
+ && viewerActionMenu.isVisible();
}
}
git://source.jalview.org / jalview.git / blobdiff