*/
package jalview.gui;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.structures.JalviewStructureDisplayI;
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.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
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.Component;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
+import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
-import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
*
*/
public class ChimeraViewFrame extends GStructureViewer implements Runnable,
- ViewSetProvider, JalviewStructureDisplayI
-
+ ViewSetProvider
{
- JalviewChimeraBindingModel jmb;
+ private JalviewChimeraBinding jmb;
+
+ private boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
AlignmentPanel ap;
- Vector atomsPicked = new Vector();
+ /*
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
private boolean addingStructures = false;
- ViewSelectionMenu seqColourBy;
+ private IProgressIndicator progressBar = null;
+
+ /*
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
/**
- *
- * @param files
- * @param ids
- * @param seqs
- * @param ap
- * @param usetoColour
- * - add the alignment panel to the list used for colouring these
- * structures
- * @param useToAlign
- * - add the alignment panel to the list used for aligning these
- * structures
- * @param leaveColouringToJmol
- * - do not update the colours from any other source. Jmol is
- * handling them
- * @param loadStatus
- * @param bounds
- * @param viewid
- *
- * public ChimeraViewFrame(String[] files, String[] ids,
- * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour,
- * boolean useToAlign, boolean leaveColouringToJmol, String
- * loadStatus, Rectangle bounds, String viewid) { PDBEntry[]
- * pdbentrys = new PDBEntry[files.length]; for (int i = 0; i <
- * pdbentrys.length; i++) { PDBEntry pdbentry = new PDBEntry();
- * pdbentry.setFile(files[i]); pdbentry.setId(ids[i]); pdbentrys[i] =
- * pdbentry; } // / TODO: check if protocol is needed to be set, and
- * if chains are // autodiscovered. jmb = new
- * JalviewChimeraBindingModel(this,
- * ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
- *
- * jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if
- * (useToAlign) { useAlignmentPanelForSuperposition(ap); } if
- * (leaveColouringToJmol || !usetoColour) {
- * jmb.setColourBySequence(false); seqColour.setSelected(false);
- * jmolColour.setSelected(true); } if (usetoColour) {
- * useAlignmentPanelForColourbyseq(ap);
- * jmb.setColourBySequence(true); seqColour.setSelected(true);
- * jmolColour.setSelected(false); } this.setBounds(bounds);
- * initMenus(); viewId = viewid; //
- * jalview.gui.Desktop.addInternalFrame(this, "Loading File", //
- * bounds.width,bounds.height);
- *
- * this.addInternalFrameListener(new InternalFrameAdapter() { public
- * void internalFrameClosing(InternalFrameEvent internalFrameEvent) {
- * closeViewer(); } }); initJmol(loadStatus); // pdbentry, seq,
- * JBPCHECK!
- *
- * }
+ * Initialise menu options.
*/
private void initMenus()
{
+ viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+ viewerColour.setText(MessageManager
+ .getString("label.colour_with_chimera"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_chimera_manage_structure_colours"));
+ helpItem.setText(MessageManager.getString("label.chimera_help"));
seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
if (_colourwith == null)
{
_colourwith = new Vector<AlignmentPanel>();
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ // save As not yet implemented
+ savemenu.setVisible(false);
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
-
@Override
public void itemStateChanged(ItemEvent e)
{
}
else
{
- // update the jmol display now.
+ // update the Chimera display now.
seqColour_actionPerformed(null);
}
}
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
-
@Override
public void itemStateChanged(ItemEvent e)
{
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[]
+ new Object[]
{ new Integer(_alignwith.size()).toString() }));
}
});
handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
public void menuDeselected(MenuEvent e)
{
// TODO Auto-generated method stub
-
}
@Override
public void menuCanceled(MenuEvent e)
{
// TODO Auto-generated method stub
-
}
});
}
- IProgressIndicator progressBar = null;
-
/**
- * add a single PDB structure to a new or existing Jmol view
+ * add a single PDB structure to a new or existing Chimera view
*
* @param pdbentry
* @param seq
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
+ super();
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new String[]
+ "label.pdb_entry_is_already_displayed", new Object[]
{ pdbentry.getId() }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new String[]
- { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbentry.getId() }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
if (option == JOptionPane.YES_OPTION)
{
// TODO : Fix multiple seq to one chain issue here.
ap.getStructureSelectionManager().setMapping(seq, chains,
alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
+ if (ap.getSeqPanel().seqCanvas.fr != null)
{
- ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.getSeqPanel().seqCanvas.fr.featuresAdded();
ap.paintAlignment(true);
}
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
+ // Now this ChimeraViewFrame is mapped to new sequences. We must add
+ // them to the existing array
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ for (JInternalFrame frame : frames)
{
- if (frames[i] instanceof ChimeraViewFrame)
+ if (frame instanceof ChimeraViewFrame)
{
- final ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
+ final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
+ for (int pe = 0; pe < topView.jmb.getPdbCount(); pe++)
{
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ if (topView.jmb.getPdbEntry(pe).getFile()
+ .equals(
+ alreadyMapped))
{
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
+ topView.jmb.addSequence(pe, seq);
+ topView.addAlignmentPanel(ap);
// add it to the set used for colouring
- topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildChimeraActionMenu();
+ topView.useAlignmentPanelForColourbyseq(ap);
+ topView.buildChimeraActionMenu();
ap.getStructureSelectionManager()
.sequenceColoursChanged(ap);
break;
}
}
// /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
+ // Check if there are other Chimera views involving this alignment
// and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
+ List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
+ for (ChimeraViewFrame topView : existingViews)
{
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
+ // TODO: highlight topView in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[]
+ { pdbentry.getId(), topView.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
{
- ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement();
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.formatMessage(
- "label.add_pdbentry_to_view", new String[]
- { pdbentry.getId(), topJmol.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ return;
+ }
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topView.useAlignmentPanelForSuperposition(ap);
+ topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
}
}
// /////////////////////////////////
- openNewJmol(ap, new PDBEntry[]
+ openNewChimera(ap, new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq });
}
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
progressBar = ap.alignFrame;
}
/**
- * create a new Jmol containing several structures superimposed using the
+ * create a new viewer containing several structures superimposed using the
* given alignPanel.
*
* @param ap
public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
SequenceI[][] seqs)
{
- openNewJmol(ap, pe, seqs);
+ super();
+ openNewChimera(ap, pe, seqs);
}
- /**
- * list of sequenceSet ids associated with the view
- */
- ArrayList<String> _aps = new ArrayList();
-
public AlignmentPanel[] getAllAlignmentPanels()
{
AlignmentPanel[] t, list = new AlignmentPanel[0];
}
/**
- * list of alignment panels to use for superposition
- */
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
- /**
* set the primary alignmentPanel reference and add another alignPanel to the
* list of ones to use for colouring and aligning
*
useAlignmentPanelForColourbyseq(nap);
jmb.setColourBySequence(enableColourBySeq);
seqColour.setSelected(enableColourBySeq);
- jmolColour.setSelected(!enableColourBySeq);
+ viewerColour.setSelected(!enableColourBySeq);
}
public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
}
/**
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
*
return;
}
- private Vector getJmolsFor(AlignmentPanel ap2)
+ private List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
{
- Vector otherJmols = new Vector();
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
+ List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ for (JInternalFrame frame : frames)
{
- if (frames[i] instanceof ChimeraViewFrame)
+ if (frame instanceof ChimeraViewFrame)
{
- ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
- if (topJmol.isLinkedWith(ap2))
+ if (((ChimeraViewFrame) frame).isLinkedWith(apanel))
{
- otherJmols.addElement(topJmol);
+ result.add((ChimeraViewFrame) frame);
}
}
}
- return otherJmols;
+ return result;
}
void initChimera(String command)
jmb.setFinishedInit(false);
// TODO: consider waiting until the structure/view is fully loaded before
// displaying
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
if (command == null)
{
command = "";
}
- jmb.evalStateCommand(command);
+ jmb.evalStateCommand(command, false);
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
- if (chains == null)
+ if (chainNames == null)
{
return;
}
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
}
centerViewer();
allChainsSelected = false;
chainMenu.add(menuItem);
- for (int c = 0; c < chains.size(); c++)
+ for (String chainName : chainNames)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
+ {
centerViewer();
+ }
}
});
}
}
- boolean allChainsSelected = false;
-
- private boolean alignAddedStructures = false;
-
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ List<String> toshow = new ArrayList<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
{
- toshow.addElement(item.getText());
+ toshow.add(item.getText());
}
}
}
jmb.centerViewer(toshow);
}
+ /**
+ * 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.
+ */
public void closeViewer()
{
- jmb.closeViewer();
+ 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_OPTION);
+ jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+ }
ap = null;
_aps.clear();
_alignwith.clear();
}
/**
- * state flag for PDB retrieval thread
+ * Open any newly added PDB structures in Chimera, having first fetched data
+ * from PDB (if not already saved).
*/
- private boolean _started = false;
-
public void run()
{
_started = true;
- String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
- List<String> fileToLoad=new ArrayList<String>();
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder(128);
+ StringBuilder files = new StringBuilder(128);
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
- List<Integer> filePDBpos =new ArrayList<Integer>();
+ List<Integer> filePDBpos = new ArrayList<Integer>();
+ PDBEntry thePdbEntry = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = null;
- if (jmb.pdbentry[pi].getFile()==null)
+ thePdbEntry = jmb.getPdbEntry(pi);
+ if (thePdbEntry.getFile() == null)
{
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.pdbentry[pi].getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
+ /*
+ * Retrieve PDB data, save to file, attach to PDBEntry
+ */
+ file = fetchPdbFile(thePdbEntry);
+ if (file == null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
- }
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
- {
- progressBar.setProgressBar("Finished.", hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
- jmb.pdbentry[pi].setFile(file);
-
- files.append(" \"" + Platform.escapeString(file) + "\"");
- }
- else
- {
- errormsgs.append("'" + pdbid + "' ");
+ errormsgs.append("'" + thePdbEntry.getId() + "' ");
}
}
else
{
- file = new File(jmb.pdbentry[pi].getFile())
- .getAbsoluteFile().getPath();
+ /*
+ * Got file already - ignore if already loaded in Chimera.
+ */
+ file = new File(thePdbEntry.getFile()).getAbsoluteFile()
+ .getPath();
if (curfiles != null && curfiles.length > 0)
{
addingStructures = true; // already files loaded.
}
}
}
-
- if (file != null)
- {
- fileToLoad.add(file);
- filePDB.add(jmb.pdbentry[pi]);
- filePDBpos.add(Integer.valueOf(pi));
- files.append(" \"" + Platform.escapeString(file) + "\"");
- }
+ }
+ if (file != null)
+ {
+ filePDB.add(thePdbEntry);
+ filePDBpos.add(Integer.valueOf(pi));
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(),
+ oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ errormsgs.append("When retrieving pdbfiles for '"
+ + thePdbEntry.getId() + "'");
}
if (errormsgs.length() > 0)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[]
+ new Object[]
{ errormsgs.toString() }), MessageManager
.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
-
}
- long lastnotify = jmb.getLoadNotifiesHandled();
+
if (files.length() > 0)
{
if (!addingStructures)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
}
- }
- int num=-1;
+ }
+ int num = -1;
for (PDBEntry pe : filePDB)
{
num++;
{
try
{
- int pos=filePDBpos.get(num).intValue();
+ int pos = filePDBpos.get(num).intValue();
jmb.openFile(pe);
- jmb.addSequence(pos, jmb.sequence[pos]);
- File fl=new File(pe.getFile());
+ jmb.addSequence(pos, jmb.getSequence()[pos]);
+ File fl = new File(pe.getFile());
String protocol = AppletFormatAdapter.URL;
try
{
if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
{
+ protocol = AppletFormatAdapter.FILE;
}
- // Explicitly map to the filename used by Jmol ;
- jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
- protocol);
- // pdbentry[pe].getFile(), protocol);
+ } catch (Throwable e)
+ {
+ }
+ // Explicitly map to the filename used by Chimera ;
+ // TODO: use pe.getId() instead of pe.getFile() ?
+ jmb.getSsm().setMapping(jmb.getSequence()[pos], null,
+ pe.getFile(),
+ protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
}
}
}
- // jmb.getPdbFile();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
-
+
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
// do superposition if asked to
if (alignAddedStructures)
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ new Thread(new Runnable()
{
public void run()
{
alignStructs_withAllAlignPanels();
}
- });
+ }).start();
alignAddedStructures = false;
}
addingStructures = false;
worker = null;
}
+ /**
+ * Fetch PDB data and save to a local file. Returns the full path to the file,
+ * or null if fetch fails.
+ *
+ * @param processingEntry
+ * @return
+ * @throws Exception
+ */
+ private String fetchPdbFile(PDBEntry processingEntry) throws Exception
+ {
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new Object[]
+ { pdbid }), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } finally
+ {
+ if (progressBar != null)
+ {
+ progressBar
+ .setProgressBar(
+ pdbid
+ + " "
+ + MessageManager
+ .getString("label.state_completed"),
+ 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(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ processingEntry.setFile(filePath);
+ }
+ return filePath;
+ }
+
+ @Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
+ BufferedReader in = null;
try
{
// TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
}
}
}
+ @Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
{
- cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
+ cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
cap.appendText("\n");
}
} catch (OutOfMemoryError e)
600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- throw new Error("EPS Generation not yet implemented.");
+ throw new Error(
+ MessageManager
+ .getString("error.eps_generation_not_implemented"));
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- throw new Error("PNG Generation not yet implemented.");
+ throw new Error(
+ MessageManager
+ .getString("error.png_generation_not_implemented"));
}
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
- if (jmolColour.isSelected())
+ if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
+ @Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
}
}
+ @Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
jmb.colourByChain();
}
+ @Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
jmb.colourByCharge();
}
+ @Override
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
zappoColour.setSelected(true);
jmb.setJalviewColourScheme(new ZappoColourScheme());
}
+ @Override
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
taylorColour.setSelected(true);
jmb.setJalviewColourScheme(new TaylorColourScheme());
}
+ @Override
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
hydroColour.setSelected(true);
jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
+ @Override
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
helixColour.setSelected(true);
jmb.setJalviewColourScheme(new HelixColourScheme());
}
+ @Override
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
strandColour.setSelected(true);
jmb.setJalviewColourScheme(new StrandColourScheme());
}
+ @Override
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
turnColour.setSelected(true);
jmb.setJalviewColourScheme(new TurnColourScheme());
}
+ @Override
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ @Override
public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
+ @Override
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
new UserDefinedColours(this, null);
}
+ @Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
}
}
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
}
setChainMenuItems(jmb.chainNames);
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ this.setTitle(jmb.getViewerTitle("Chimera", true));
+ if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
{
- jmolActionMenu.setVisible(true);
+ viewerActionMenu.setVisible(true);
}
if (!jmb.isLoadingFromArchive())
{
_alignwith.add(ap);
}
;
- for (Component c : jmolActionMenu.getMenuComponents())
+ for (Component c : viewerActionMenu.getMenuComponents())
{
if (c != alignStructs)
{
- jmolActionMenu.remove((JMenuItem) c);
+ viewerActionMenu.remove((JMenuItem) c);
}
}
- final ItemListener handler;
}
/*
return ap;
}
- /**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
- {
- return _aps.contains(ap2.av.getSequenceSetId());
- }
-
- public boolean isUsedforaligment(AlignmentPanel ap2)
- {
-
- return (_alignwith != null) && _alignwith.contains(ap2);
- }
-
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ public AAStructureBindingModel getBinding()
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return jmb;
}
/**
+ * Ask Chimera to save its session to the designated file path. Returns true
+ * if successful, else false.
*
- * @return TRUE if the view is NOT being coloured by sequence associations.
+ * @param filepath
*/
- public boolean isColouredByJmol()
+ public boolean saveSession(String filepath)
{
- return !jmb.isColourBySequence();
+ return jmb.saveSession(filepath);
}
-
- public SequenceStructureBinding getBinding()
- {
- return jmb;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff