/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.api.FeatureRenderer;
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.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-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.ext.rbvi.chimera.ChimeraCommands;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
-import java.awt.Component;
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.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
+import java.io.FileInputStream;
import java.io.IOException;
-import java.io.PrintWriter;
+import java.io.InputStream;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
-import java.util.Vector;
+import java.util.Random;
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;
-import javax.swing.event.MenuListener;
/**
- * GUI elements for handlnig an external chimera display
+ * GUI elements for handling an external chimera display
*
* @author jprocter
*
*/
-public class ChimeraViewFrame extends GStructureViewer implements Runnable,
- ViewSetProvider, JalviewStructureDisplayI
-
+public class ChimeraViewFrame extends StructureViewerBase
{
- private JalviewChimeraBindingModel jmb;
-
- /*
- * list of sequenceSet ids associated with the view
- */
- private ArrayList<String> _aps = new ArrayList<String>();
-
- /*
- * list of alignment panels to use for superposition
- */
- private Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+ private JalviewChimeraBinding jmb;
- /*
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- private Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
- private boolean allChainsSelected = false;
-
- private boolean alignAddedStructures = false;
-
- AlignmentPanel ap;
+ private IProgressIndicator progressBar = null;
/*
- * state flag for PDB retrieval thread
+ * 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).
*/
- private boolean _started = false;
-
- private boolean addingStructures = false;
+ private String chimeraSessionFile = null;
- private IProgressIndicator progressBar = null;
+ private Random random = new Random();
- private String viewId = null;
+ private int myWidth = 500;
- /*
- * pdb retrieval thread.
- */
- private Thread worker = null;
+ private int myHeight = 150;
/**
* Initialise menu options.
*/
- private void initMenus()
+ @Override
+ protected void initMenus()
{
+ super.initMenus();
+
viewerActionMenu.setText(MessageManager.getString("label.chimera"));
- viewerColour.setText(MessageManager
- .getString("label.colour_with_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());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
+ savemenu.setVisible(false); // not yet implemented
+ viewMenu.add(fitToWindow);
+
+ /*
+ * exchange of Jalview features and Chimera attributes is for now
+ * an optionally enabled experimental feature
+ */
+ if (Desktop.instance.showExperimental())
{
- _colourwith = new Vector<AlignmentPanel>();
+ 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(
+ MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes.setToolTipText(MessageManager
+ .getString("label.fetch_chimera_attributes_tip"));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
}
- if (_alignwith == null)
+ }
+
+ /**
+ * Query Chimera for its residue attribute names and add them as items off the
+ * attributes menu
+ *
+ * @param attributesMenu
+ */
+ protected void buildAttributesMenu(JMenu attributesMenu)
+ {
+ List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+ if (atts == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ return;
}
-
- // 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)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the Chimera display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (String att : atts)
{
+ final String attName = att.split(" ")[1];
- @Override
- public void menuSelected(MenuEvent e)
+ /*
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- handler.itemStateChanged(null);
+ JMenuItem menuItem = new JMenuItem(attName);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getChimeraAttributes(attName);
+ }
+ });
+ attributesMenu.add(menuItem);
}
+ }
+ }
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
- }
+ /**
+ * Read residues in Chimera with the given attribute name, and set as features
+ * on the corresponding sequence positions (if any)
+ *
+ * @param attName
+ */
+ protected void getChimeraAttributes(String attName)
+ {
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+ }
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
- }
- });
+ /**
+ * 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()
+ {
+ int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
+ statusBar.setText(
+ MessageManager.formatMessage("label.attributes_set", count));
}
/**
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
- super();
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ this();
+ String pdbId = pdbentry.getId();
- if (alreadyMapped != null)
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbentry.getId() }), MessageManager.formatMessage(
- "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.getSeqPanel().seqCanvas.fr != null)
- {
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
+ return;
+ }
- // Now this ChimeraViewFrame is mapped to new sequences. We must add
- // them to the existing array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ /*
+ * 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)
+ */
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
+ {
+ return;
+ }
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topView.jmb.pdbentry.length; pe++)
- {
- if (topView.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildChimeraActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
+ /*
+ * 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 });
+ }
- return;
- }
- }
- // /////////////////////////////////
- // Check if there are other Chimera views involving this alignment
- // and prompt user about adding this molecule to one of them
- List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame topView : existingViews)
+ /**
+ * Create a helper to manage progress bar display
+ */
+ protected void createProgressBar()
+ {
+ if (progressBar == null)
{
- // 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)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- topView.useAlignmentPanelForSuperposition(ap);
- topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ progressBar = new ProgressBar(statusPanel, statusBar);
}
- // /////////////////////////////////
- openNewChimera(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
}
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
- progressBar = ap.alignFrame;
+ createProgressBar();
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
jmb.setColourBySequence(true);
- setSize(400, 400); // probably should be a configurable/dynamic default here
+ setSize(myWidth, myHeight);
initMenus();
- worker = null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- }
-
- /**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
- *
- * @param ap
- * @param pe
- * @param seqs
- */
- public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
- SequenceI[][] seqs)
- {
- super();
- openNewChimera(ap, pe, seqs);
- }
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
- public AlignmentPanel[] getAllAlignmentPanels()
- {
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
+ this.addInternalFrameListener(new InternalFrameAdapter()
{
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
+ closeViewer(false);
}
- }
+ });
- return list;
}
/**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
+ * Create a new viewer from saved session state data including Chimera session
+ * file
*
- * @param nap
+ * @param chimeraSessionFile
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByChimera
+ * @param colourBySequence
+ * @param newViewId
*/
- public void addAlignmentPanel(AlignmentPanel nap)
+ public ChimeraViewFrame(String chimeraSessionFile,
+ AlignmentPanel alignPanel, PDBEntry[] pdbArray,
+ SequenceI[][] seqsArray, boolean colourByChimera,
+ boolean colourBySequence, String newViewId)
{
- if (ap == null)
+ this();
+ setViewId(newViewId);
+ this.chimeraSessionFile = chimeraSessionFile;
+ openNewChimera(alignPanel, pdbArray, seqsArray);
+ if (colourByChimera)
{
- ap = nap;
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
}
- if (!_aps.contains(nap.av.getSequenceSetId()))
+ else if (colourBySequence)
{
- _aps.add(nap.av.getSequenceSetId());
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
}
}
/**
- * remove any references held to the given alignment panel
+ * create a new viewer containing several structures superimposed using the
+ * given alignPanel.
*
- * @param nap
+ * @param pe
+ * @param seqs
+ * @param ap
*/
- public void removeAlignmentPanel(AlignmentPanel nap)
- {
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildChimeraActionMenu();
- }
- }
-
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- if (_alignwith.contains(nap))
- {
- _alignwith.remove(nap);
- }
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
- boolean enableColourBySeq)
- {
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- viewerColour.setSelected(!enableColourBySeq);
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ AlignmentPanel ap)
{
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
- {
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
+ this();
+ openNewChimera(ap, pe, seqs);
}
/**
- * 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
+ * Default constructor
*/
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
+ public ChimeraViewFrame()
{
- 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)
- {
- }
+ super();
- }
- // 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;
+ /*
+ * closeViewer will decide whether or not to close this frame
+ * depending on whether user chooses to Cancel or not
+ */
+ setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
}
- private List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ /**
+ * 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<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ List<StructureViewerBase> result = new ArrayList<>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof ChimeraViewFrame)
{
- if (((ChimeraViewFrame) frame).isLinkedWith(apanel))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- result.add((ChimeraViewFrame) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
return result;
}
- void initChimera(String command)
+ /**
+ * Launch Chimera. If we have a chimera session file name, send Chimera the
+ * command to open its saved session file.
+ */
+ void initChimera()
{
jmb.setFinishedInit(false);
- // TODO: consider waiting until the structure/view is fully loaded before
- // displaying
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(true),
- getBounds().width, getBounds().height);
- if (command == null)
- {
- command = "";
- }
- jmb.evalStateCommand(command, false);
- jmb.setFinishedInit(true);
- }
+ Desktop.addInternalFrame(this,
+ jmb.getViewerTitle(getViewerName(), true), getBounds().width,
+ getBounds().height);
- void setChainMenuItems(List<String> chainNames)
- {
- chainMenu.removeAll();
- if (chainNames == null)
+ if (!jmb.launchChimera())
{
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.chimera_failed"),
+ MessageManager.getString("label.error_loading_file"),
+ JvOptionPane.ERROR_MESSAGE);
+ this.dispose();
return;
}
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- 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);
- }
- }
- centerViewer();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
- for (String chainName : chainNames)
+ if (this.chimeraSessionFile != null)
{
- menuItem = new JCheckBoxMenuItem(chainName, true);
- menuItem.addItemListener(new ItemListener()
+ boolean opened = jmb.openSession(chimeraSessionFile);
+ if (!opened)
{
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- centerViewer();
- }
- }
- });
-
- chainMenu.add(menuItem);
+ System.err.println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
+ }
}
+
+ jmb.startChimeraListener();
}
- void centerViewer()
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ @Override
+ void showSelectedChains()
{
- List<String> toshow = new ArrayList<String>();
+ List<String> toshow = new ArrayList<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(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.
+ *
+ * @param closeChimera
+ * if true, close any linked Chimera process; if false, prompt first
*/
- public void closeViewer()
+ @Override
+ public void closeViewer(boolean closeChimera)
{
- if (jmb.isChimeraRunning())
+ if (jmb != null && jmb.isChimeraRunning())
{
- String prompt = MessageManager
- .formatMessage("label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle(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);
+ if (!closeChimera)
+ {
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle(getViewerName(), 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;
+ }
+ closeChimera = confirm == JvOptionPane.YES_OPTION;
+ }
+ jmb.closeViewer(closeChimera);
}
- ap = null;
+ 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();
}
/**
* Open any newly added PDB structures in Chimera, having first fetched data
* from PDB (if not already saved).
*/
+ @Override
public void run()
{
_started = true;
// 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<PDBEntry> filePDB = new ArrayList<>();
+ List<Integer> filePDBpos = new ArrayList<>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = null;
- thePdbEntry = jmb.pdbentry[pi];
+ thePdbEntry = jmb.getPdbEntry(pi);
if (thePdbEntry.getFile() == null)
{
/*
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles for '"
- + thePdbEntry.getId() + "'");
+ 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 Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new Object[]
+ { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
{
+ jmb.setFinishedInit(false);
if (!addingStructures)
{
try
{
- initChimera("");
+ initChimera();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
try
{
int pos = filePDBpos.get(num).intValue();
+ long startTime = startProgressBar(getViewerName() + " "
+ + MessageManager.getString("status.opening_file_for")
+ + " " + pe.getId());
jmb.openFile(pe);
- jmb.addSequence(pos, jmb.sequence[pos]);
+ 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)
{
+ } finally
+ {
+ stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- // TODO: use pe.getId() instead of pe.getFile() ?
- jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
- protocol);
+
+ pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ progressBar);
+ stashFoundChains(pdb, pe.getFile());
+
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
oomerror);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open " + pe.getFile()
- + " in Chimera viewer!", ex);
+ Cache.log.error(
+ "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+ ex);
} finally
{
Cache.log.debug("File locations are " + files);
}
}
}
+
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
+ /*
+ * ensure that any newly discovered features (e.g. RESNUM)
+ * are added to any open feature settings dialog
+ */
+ FeatureRenderer fr = getBinding().getFeatureRenderer(null);
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
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();
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @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;
String pdbid = processingEntry.getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new Object[]
- { pdbid }), hdl);
- }
+ 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
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- if (progressBar != null)
- {
- progressBar
- .setProgressBar(
- pdbid
- + " "
- + MessageManager
- .getString("label.state_completed"),
- hdl);
- }
+ 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
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();
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
processingEntry.setFile(filePath);
}
return filePath;
}
- @Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ /**
+ * Convenience method to update the progress bar if there is one. Be sure to
+ * call stopProgressBar with the returned handle to remove the message.
+ *
+ * @param msg
+ * @param handle
+ */
+ public long startProgressBar(String msg)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
{
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- e.printStackTrace();
- }
- }
- }
+ progressBar.setProgressBar(msg, tm);
}
+ return tm;
}
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ /**
+ * End the progress bar with the specified handle, leaving a message (if not
+ * null) on the status bar
+ *
+ * @param msg
+ * @param handle
+ */
+ public void stopProgressBar(String msg, long handle)
{
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
- {
- cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }
- } catch (OutOfMemoryError e)
+ if (progressBar != null)
{
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
+ progressBar.setProgressBar(msg, handle);
}
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
}
@Override
public void eps_actionPerformed(ActionEvent e)
{
- throw new Error(
- MessageManager
- .getString("error.eps_generation_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.eps_generation_not_implemented"));
}
@Override
public void png_actionPerformed(ActionEvent e)
{
- throw new Error(
- MessageManager
- .getString("error.png_generation_not_implemented"));
- }
-
- @Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && ap != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
- }
- }
- }
-
- @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, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
+ throw new Error(MessageManager
+ .getString("error.png_generation_not_implemented"));
}
@Override
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
- } catch (Exception ex)
+ } catch (IOException ex)
{
}
}
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
-
- this.setTitle(jmb.getViewerTitle(true));
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- protected void buildChimeraActionMenu()
+ @Override
+ public AAStructureBindingModel getBinding()
{
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : viewerActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- viewerActionMenu.remove((JMenuItem) c);
- }
- }
+ return jmb;
}
- /*
- * (non-Javadoc)
+ /**
+ * Ask Chimera to save its session to the designated file path, or to a
+ * temporary file if the path is null. Returns the file path if successful,
+ * else null.
*
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
+ * @param filepath
+ * @see getStateInfo
*/
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
+ protected String saveSession(String filepath)
{
- if (ap == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(ap);
- }
- ;
+ String pathUsed = filepath;
try
{
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
+ if (pathUsed == null)
{
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
+ File tempFile = File.createTempFile("chimera", ".py");
+ tempFile.deleteOnExit();
+ pathUsed = tempFile.getPath();
}
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
+ boolean result = jmb.saveSession(pathUsed);
+ if (result)
{
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ this.chimeraSessionFile = pathUsed;
+ return pathUsed;
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
+ } catch (IOException e)
+ {
}
-
- }
-
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
+ return null;
}
/**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
+ * Returns a string representing the state of the Chimera session. This is
+ * done by requesting Chimera to save its session to a temporary file, then
+ * reading the file contents. Returns an empty string on any error.
*/
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ @Override
+ public String getStateInfo()
{
- for (AlignmentPanel ap : getAllAlignmentPanels())
+ String sessionFile = saveSession(null);
+ if (sessionFile == null)
+ {
+ return "";
+ }
+ InputStream is = null;
+ try
+ {
+ File f = new File(sessionFile);
+ byte[] bytes = new byte[(int) f.length()];
+ is = new FileInputStream(sessionFile);
+ is.read(bytes);
+ return new String(bytes);
+ } catch (IOException e)
{
- if (ap.av.getAlignment() == alignment)
+ return "";
+ } finally
+ {
+ if (is != null)
{
- return ap;
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
}
}
- return ap;
}
- /**
- *
- * @param ap2
- * @return true if this Chimera instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
+ @Override
+ protected void fitToWindow_actionPerformed()
{
- return _aps.contains(ap2.av.getSequenceSetId());
+ jmb.focusView();
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ @Override
+ public ViewerType getViewerType()
{
-
- return (_alignwith != null) && _alignwith.contains(ap2);
+ return ViewerType.CHIMERA;
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ protected String getViewerName()
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return "Chimera";
}
/**
+ * Sends commands to align structures according to associated alignment(s).
*
- * @return TRUE if the view is NOT being coloured by sequence associations.
+ * @return
*/
- public boolean isColouredByChimera()
+ @Override
+ protected String alignStructs_withAllAlignPanels()
{
- return !jmb.isColourBySequence();
+ String reply = super.alignStructs_withAllAlignPanels();
+ if (reply != null)
+ {
+ statusBar.setText("Superposition failed: " + reply);
+ }
+ return reply;
}
- public SequenceStructureBinding getBinding()
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
{
- return jmb;
+ return progressBar;
}
-
}