*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
+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.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+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.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Collections;
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.event.MenuEvent;
import javax.swing.event.MenuListener;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
/**
* GUI elements for handling an external chimera display
*
private boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
- /*
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
- private boolean addingStructures = false;
-
private IProgressIndicator progressBar = null;
/*
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /*
* Path to Chimera session file. This is set when an open Jalview/Chimera
* session is saved, or on restore from a Jalview project (if it holds the
* filename of any saved Chimera sessions).
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);
+
+ final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes");
+ fetchAttributes
+ .setToolTipText("Copy Chimera attribute to Jalview feature");
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
+
}
/**
- * add a single PDB structure to a new or existing Chimera view
+ * Query Chimera for its residue attribute names and add them as items off the
+ * attributes menu
*
- * @param pdbentry
- * @param seq
- * @param chains
- * @param ap
+ * @param attributesMenu
*/
- public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final AlignmentPanel ap)
+ protected void buildAttributesMenu(JMenu attributesMenu)
{
- super();
-
- /*
- * is the pdb file already loaded?
- */
- String pdbId = pdbentry.getId();
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbId);
-
- if (alreadyMapped != null)
+ List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+ if (atts == null)
{
- int option = chooseAddSequencesToViewer(pdbId);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped);
- return;
- }
+ return;
}
-
- /*
- * Check if there are other Chimera views involving this alignment and give
- * user the option to add and align this molecule to one of them
- */
- List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame view : existingViews)
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (String att : atts)
{
- // TODO: highlight view somehow
+ final String attName = att.split(" ")[1];
+
/*
- * JAL-1742 exclude view with this structure already mapped (don't offer
- * to align chain B to chain A of the same structure)
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
*/
- if (view.hasPdbId(pdbId))
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- continue;
- }
- int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- view.useAlignmentPanelForSuperposition(ap);
- view.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
+ JMenuItem menuItem = new JMenuItem(attName);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getChimeraAttributes(attName);
+ }
+ });
+ attributesMenu.add(menuItem);
}
}
-
- /*
- * If the options above are declined or do not apply, open a new viewer
- */
- openNewChimera(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
}
/**
- * Presents a dialog with the option to add an align a structure to an
- * existing Chimera view
+ * Read residues in Chimera with the given attribute name, and set as features
+ * on the corresponding sequence positions (if any)
*
- * @param pdbId
- * @param view
- * @return YES, NO or CANCEL JOptionPane code
+ * @param attName
*/
- protected int chooseAlignStructureToViewer(String pdbId,
- ChimeraViewFrame view)
+ protected void getChimeraAttributes(String attName)
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbId, view.getTitle() }), MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- return option;
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
}
/**
- * Presents a dialog with the option to add sequences to a viewer which
- * already has their structure open
- *
- * @param pdbId
- * @return YES, NO or CANCEL JOptionPane code
+ * 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 int chooseAddSequencesToViewer(String pdbId)
+ protected void sendFeaturesToChimera()
{
- int option = JOptionPane.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 }), JOptionPane.YES_NO_CANCEL_OPTION);
- return option;
+ jmb.sendFeaturesToViewer(getAlignmentPanel());
}
/**
- * Adds mappings for the given sequences to an already opened PDB structure,
- * and updates any viewers that have the PDB file
+ * add a single PDB structure to a new or existing Chimera view
*
+ * @param pdbentry
* @param seq
* @param chains
* @param ap
- * @param pdbFilename
*/
- protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel ap, String pdbFilename)
+ public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap)
{
- // TODO : Fix multiple seq to one chain issue here.
- /*
- * create the mappings
- */
- ap.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
- AppletFormatAdapter.FILE);
+ this();
+ String pdbId = pdbentry.getId();
/*
- * alert the FeatureRenderer to show new (PDB RESNUM) features
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
*/
- if (ap.getSeqPanel().seqCanvas.fr != null)
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
+ return;
}
/*
- * add the sequences to any other Chimera viewers for this pdb file
+ * Check if there are other Chimera views involving this alignment and give
+ * user the option to add and align this molecule to one of them (or cancel)
*/
- // JBPNOTE: this looks like a binding routine, rather than a gui routine
- for (JInternalFrame frame : Desktop.instance.getAllFrames())
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- if (frame instanceof ChimeraViewFrame)
- {
- ChimeraViewFrame chimeraView = ((ChimeraViewFrame) frame);
- for (int pe = 0; pe < chimeraView.jmb.getPdbCount(); pe++)
- {
- if (chimeraView.jmb.getPdbEntry(pe).getFile().equals(pdbFilename))
- {
- chimeraView.jmb.addSequence(pe, seq);
- chimeraView.addAlignmentPanel(ap);
- /*
- * add it to the set of alignments used for colouring structure by
- * sequence
- */
- chimeraView.useAlignmentPanelForColourbyseq(ap);
- chimeraView.buildActionMenu();
- ap.getStructureSelectionManager().sequenceColoursChanged(ap);
- break;
- }
- }
- }
+ return;
}
+
+ /*
+ * If the options above are declined or do not apply, show the structure in
+ * a new viewer
+ */
+ openNewChimera(ap, new PDBEntry[] { pdbentry },
+ new SequenceI[][] { seq });
}
/**
}
}
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
protected boolean hasPdbId(String pdbId)
{
return jmb.hasPdbId(pdbId);
SequenceI[][] seqs)
{
createProgressBar();
- 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)
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
/**
- * 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)
- {
- chain = pdbrefs.get(0).getChainCode();
- }
- }
- chains[i][seqno++] = chain;
- }
- }
- return chains;
- }
-
- /**
* Create a new viewer from saved session state data including Chimera session
* file
*
* @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);
}
/**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
+ * 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.
*/
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
- {
- if (worker != null && worker.isAlive())
- {
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
- {
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
-
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- // progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
{
- List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof ChimeraViewFrame)
{
- if (((StructureViewerBase) frame).isLinkedWith(apanel))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- result.add((ChimeraViewFrame) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
*/
void initChimera()
{
- jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
+ Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
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;
}
+ chimeraSessionFile);
}
}
- jmb.setFinishedInit(true);
jmb.startChimeraListener();
}
*
* @param chainNames
*/
+ @Override
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
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)
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
* @param closeChimera
* if true, close any linked Chimera process; if false, prompt first
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
- if (jmb.isChimeraRunning())
+ 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,
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_OPTION);
- closeChimera = confirm == JOptionPane.YES_OPTION;
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ /*
+ * abort closure if user hits escape or Cancel
+ */
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ closeChimera = confirm == JvOptionPane.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;
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);
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
{
+ jmb.setFinishedInit(false);
if (!addingStructures)
{
try
{
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());
- 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],
- jmb.getChains()[pos],
- pe.getFile(),
- protocol);
+ 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);
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();
* @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 ?
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);
{
return ViewerType.CHIMERA;
}
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
}
git://source.jalview.org / jalview.git / blobdiff