package jalview.ext.rbvi.chimera;
import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.gui.Preferences;
import jalview.gui.StructureViewer.ViewerType;
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureCommandsI.SuperposeData;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.ColorUtils;
import jalview.util.MessageManager;
-import java.awt.Color;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Collections;
-import java.util.Hashtable;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
// Chimera clause to exclude alternate locations in atom selection
private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
- private static final String COLOURING_CHIMERA = MessageManager
- .getString("status.colouring_chimera");
-
private static final boolean debug = false;
private static final String PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
- private List<String> chainNames = new ArrayList<>();
-
- private Hashtable<String, String> chainFile = new Hashtable<>();
-
/*
* Object through which we talk to Chimera
*/
- private ChimeraManager viewer;
+ private ChimeraManager chimeraManager;
/*
* Object which listens to Chimera notifications
private AbstractRequestHandler chimeraListener;
/*
- * set if chimera state is being restored from some source - instructs binding
- * not to apply default display style when structure set is updated for first
- * time.
- */
- private boolean loadingFromArchive = false;
-
- /*
- * flag to indicate if the Chimera viewer should ignore sequence colouring
- * events from the structure manager because the GUI is still setting up
- */
- private boolean loadingFinished = true;
-
- /*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
String lastHighlightCommand;
- /*
- * incremented every time a load notification is successfully handled -
- * lightweight mechanism for other threads to detect when they can start
- * referring to new structures.
- */
- private long loadNotifiesHandled = 0;
-
private Thread chimeraMonitor;
/**
try
{
List<ChimeraModel> modelsToMap = new ArrayList<>();
- List<ChimeraModel> oldList = viewer.getModelList();
+ List<ChimeraModel> oldList = chimeraManager.getModelList();
boolean alreadyOpen = false;
/*
*/
if (!alreadyOpen)
{
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- if (viewer.isChimeraX())
- {
- /*
- * ChimeraX hack: force chimera model name to pdbId
- */
- int modelNumber = chimeraMaps.size() + 1;
- String command = "setattr #" + modelNumber + " models name "
- + pe.getId();
- sendChimeraCommand(command, false);
- modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
- modelNumber, 0));
- }
- else
- {
- /*
- * Chimera: query for actual models and find the one with
- * matching model name - set in viewer.openModel()
- */
- List<ChimeraModel> newList = viewer.getModelList();
- // JAL-1728 newList.removeAll(oldList) does not work
- for (ChimeraModel cm : newList)
- {
- if (cm.getModelName().equals(pe.getId()))
- {
- modelsToMap.add(cm);
- }
- }
- }
+ chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ addChimeraModel(pe, modelsToMap);
}
chimeraMaps.put(file, modelsToMap);
}
/**
+ * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
+ * name matching PDB id
+ *
+ * @param pe
+ * @param modelsToMap
+ */
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
+ {
+ /*
+ * Chimera: query for actual models and find the one with
+ * matching model name - already set in viewer.openModel()
+ */
+ List<ChimeraModel> newList = chimeraManager.getModelList();
+ // JAL-1728 newList.removeAll(oldList) does not work
+ for (ChimeraModel cm : newList)
+ {
+ if (cm.getModelName().equals(pe.getId()))
+ {
+ modelsToMap.add(cm);
+ }
+ }
+ }
+
+ /**
* Constructor
*
* @param ssm
DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
- viewer = new ChimeraManager(new StructureManager(true));
- String viewerType = Cache.getProperty(Preferences.STRUCTURE_DISPLAY);
- viewer.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
+ chimeraManager = new ChimeraManager(new StructureManager(true));
+ chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType()));
+ setStructureCommands(new ChimeraCommands());
+ }
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
}
/**
*/
protected void startChimeraProcessMonitor()
{
- final Process p = viewer.getChimeraProcess();
+ final Process p = chimeraManager.getChimeraProcess();
chimeraMonitor = new Thread(new Runnable()
{
try
{
chimeraListener = new ChimeraListener(this);
- viewer.startListening(chimeraListener.getUri());
+ chimeraManager.startListening(chimeraListener.getUri());
} catch (BindException e)
{
System.err.println(
}
/**
- * Tells Chimera to display only the specified chains
- *
- * @param toshow
- */
- public void showChains(List<String> toshow)
- {
- /*
- * Construct a chimera command like
- *
- * ~display #*;~ribbon #*;ribbon :.A,:.B
- */
- StringBuilder cmd = new StringBuilder(64);
- boolean first = true;
- for (String chain : toshow)
- {
- int modelNumber = getModelNoForChain(chain);
- String showChainCmd = modelNumber == -1 ? ""
- : modelNumber + ":." + chain.split(":")[1];
- if (!first)
- {
- cmd.append(",");
- }
- cmd.append(showChainCmd);
- first = false;
- }
-
- /*
- * could append ";focus" to this command to resize the display to fill the
- * window, but it looks more helpful not to (easier to relate chains to the
- * whole)
- */
- final String command = "~display #*; ~ribbon #*; ribbon :"
- + cmd.toString();
- sendChimeraCommand(command, false);
- }
-
- /**
* Close down the Jalview viewer and listener, and (optionally) the associated
* Chimera window.
*/
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
- viewer.exitChimera();
+ chimeraManager.exitChimera();
}
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
- viewer = null;
+ chimeraManager = null;
if (chimeraMonitor != null)
{
releaseUIResources();
}
- @Override
- public void colourByChain()
- {
- colourBySequence = false;
- sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
- }
-
- /**
- * Constructs and sends a Chimera command to colour by charge
- * <ul>
- * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
- * <li>Lysine and Arginine (positive charge) blue</li>
- * <li>Cysteine - yellow</li>
- * <li>all others - white</li>
- * </ul>
- */
- @Override
- public void colourByCharge()
- {
- colourBySequence = false;
- String command = viewer.isChimeraX()
- ? "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"
- : "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
-
/**
* {@inheritDoc}
*/
- @Override
public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
+ // TODO delete method
StringBuilder allComs = new StringBuilder(128);
String[] files = getStructureFiles();
refreshPdbEntries();
StringBuilder selectioncom = new StringBuilder(256);
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
for (int a = 0; a < _alignment.length; a++)
{
int refStructure = _refStructure[a];
SuperposeData[] structures = new SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
- structures[f] = new SuperposeData(alignment.getWidth());
+ structures[f] = new SuperposeData(alignment.getWidth(), f);
}
/*
}
else
{
- allComs.append("chain @CA|P; ribbon ; focus");
- allComs.append(selectioncom.toString());
+ allComs.append("chain @CA|P; ribbon ");
+ allComs.append(selectioncom.toString()).append("; focus");
}
// allComs.append("; ~display all; chain @CA|P; ribbon ")
// .append(selectioncom.toString()).append("; focus");
- List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
+ List<String> chimeraReplies = executeCommand(allComs.toString(),
true);
for (String reply : chimeraReplies)
{
*/
public boolean launchChimera()
{
- if (viewer.isChimeraLaunched())
+ if (chimeraManager.isChimeraLaunched())
{
return true;
}
- boolean launched = viewer.launchChimera(
- StructureManager.getChimeraPaths(viewer.isChimeraX()));
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
}
/**
+ * Returns a list of candidate paths to the Chimera program executable
+ *
+ * @return
+ */
+ protected List<String> getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(false);
+ }
+
+ /**
* Answers true if the Chimera process is still running, false if ended or not
* started.
*
*/
public boolean isChimeraRunning()
{
- return viewer.isChimeraLaunched();
+ return chimeraManager.isChimeraLaunched();
}
/**
* Send a command to Chimera, and optionally log and return any responses.
- * <p>
- * Does nothing, and returns null, if the command is the same as the last one
- * sent [why?].
*
* @param command
* @param getResponse
*/
- public List<String> sendChimeraCommand(final String command,
+ @Override
+ public List<String> executeCommand(final String command,
boolean getResponse)
{
- if (viewer == null)
+ if (chimeraManager == null || command == null)
{
// ? thread running after viewer shut down
return null;
}
List<String> reply = null;
- viewerCommandHistory(false);
- if (true /*lastCommand == null || !lastCommand.equals(command)*/)
+ // trim command or it may never find a match in the replyLog!!
+ List<String> lastReply = chimeraManager
+ .sendChimeraCommand(command.trim(), getResponse);
+ if (getResponse)
{
- // trim command or it may never find a match in the replyLog!!
- List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
- getResponse);
- if (getResponse)
+ reply = lastReply;
+ if (debug)
{
- reply = lastReply;
- if (debug)
- {
- log("Response from command ('" + command + "') was:\n"
- + lastReply);
- }
+ log("Response from command ('" + command + "') was:\n" + lastReply);
}
}
- viewerCommandHistory(true);
return reply;
}
/**
- * Send a Chimera command asynchronously in a new thread. If the progress
- * message is not null, display this message while the command is executing.
- *
- * @param command
- * @param progressMsg
- */
- protected abstract void sendAsynchronousCommand(String command,
- String progressMsg);
-
- /**
- * Sends a set of colour commands to the structure viewer
- *
- * @param colourBySequenceCommands
- */
- @Override
- protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
- {
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
- {
- for (String command : cpdbbyseq.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
- }
- }
-
- /**
- * @param files
- * @param sr
- * @param viewPanel
- * @return
- */
- @Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
- {
- return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel, viewer.isChimeraX());
- }
-
- /**
* @param command
*/
protected void executeWhenReady(String command)
{
waitForChimera();
- sendChimeraCommand(command, false);
+ executeCommand(command, false);
waitForChimera();
}
private void waitForChimera()
{
- while (viewer != null && viewer.isBusy())
+ while (chimeraManager != null && chimeraManager.isBusy())
{
try
{
}
}
- // End StructureListener
- // //////////////////////////
-
- /**
- * instruct the Jalview binding to update the pdbentries vector if necessary
- * prior to matching the viewer's contents to the list of structure files
- * Jalview knows about.
- */
- public abstract void refreshPdbEntries();
-
- /**
- * map between index of model filename returned from getPdbFile and the first
- * index of models from this file in the viewer. Note - this is not trimmed -
- * use getPdbFile to get number of unique models.
- */
- private int _modelFileNameMap[];
-
- // ////////////////////////////////
- // /StructureListener
@Override
public synchronized String[] getStructureFiles()
{
- if (viewer == null)
+ if (chimeraManager == null)
{
return new String[0];
}
return;
}
- boolean forChimeraX = viewer.isChimeraX();
+ boolean forChimeraX = chimeraManager.isChimeraX();
StringBuilder cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
*/
if (lastHighlightCommand != null)
{
- viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
}
if (found)
{
- viewer.sendChimeraCommand(command, false);
+ chimeraManager.sendChimeraCommand(command, false);
}
this.lastHighlightCommand = command;
}
/*
* Ask Chimera for its current selection
*/
- List<String> selection = viewer.getSelectedResidueSpecs();
+ List<String> selection = chimeraManager.getSelectedResidueSpecs();
/*
* Parse model number, residue and chain for each selected position,
protected List<AtomSpec> convertStructureResiduesToAlignment(
List<String> structureSelection)
{
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
List<AtomSpec> atomSpecs = new ArrayList<>();
for (String atomSpec : structureSelection)
{
System.err.println("## Chimera log: " + message);
}
- private void viewerCommandHistory(boolean enable)
- {
- // log("(Not yet implemented) History "
- // + ((debug || enable) ? "on" : "off"));
- }
-
- public long getLoadNotifiesHandled()
- {
- return loadNotifiesHandled;
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- viewerCommandHistory(false);
- StringBuilder command = new StringBuilder(128);
-
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
-
- /*
- * concatenate colour commands, one per residue symbol
- * Chimera format: color colorCode ::VAL
- * ChimeraX format: color :VAL colourCode
- */
- boolean chimeraX = viewer.isChimeraX();
- for (String resName : residueSet)
- {
- char res = resName.length() == 3
- ? ResidueProperties.getSingleCharacterCode(resName)
- : resName.charAt(0);
- Color col = cs.findColour(res, 0, null, null, 0f);
- command.append("color ");
- String colorSpec = ColorUtils.toTkCode(col);
- if (chimeraX)
- {
- command.append(":").append(resName).append(" ").append(colorSpec);
- }
- else
- {
- command.append(colorSpec).append(" ::").append(resName);
- }
- command.append(";");
- }
-
- sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
- viewerCommandHistory(true);
- }
-
- /**
- * called when the binding thinks the UI needs to be refreshed after a Chimera
- * state change. this could be because structures were loaded, or because an
- * error has occurred.
- */
- public abstract void refreshGUI();
-
- @Override
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
- }
-
- /**
- *
- * @return true if Chimeral is still restoring state or loading is still going
- * on (see setFinsihedLoadingFromArchive)
- */
- @Override
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive && !loadingFinished;
- }
-
- /**
- * modify flag which controls if sequence colouring events are honoured by the
- * binding. Should be true for normal operation
- *
- * @param finishedLoading
- */
- @Override
- public void setFinishedLoadingFromArchive(boolean finishedLoading)
- {
- loadingFinished = finishedLoading;
- }
-
- /**
- * Send the Chimera 'background solid <color>" command.
- *
- * @see https
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
- * .html
- * @param col
- */
- @Override
- public void setBackgroundColour(Color col)
- {
- viewerCommandHistory(false);
- String command = "set bgColor " + ColorUtils.toTkCode(col);
- viewer.sendChimeraCommand(command, false);
- viewerCommandHistory(true);
- }
-
/**
* Ask Chimera to save its session to the given file. Returns true if
* successful, else false.
* Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
*/
- String command = isChimeraX() ? "save session " : "save ";
- List<String> reply = viewer.sendChimeraCommand(command + filepath,
- true);
+ String command = getCommandGenerator().saveSession(filepath);
+ List<String> reply = chimeraManager.sendChimeraCommand(command, true);
if (reply.contains("Session written"))
{
return true;
* Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
*/
- sendChimeraCommand("open " + filepath, true);
+ executeCommand("open " + filepath, true);
// todo: test for failure - how?
return true;
}
/**
- * Returns a list of chains mapped in this viewer. Note this list is not
- * currently scoped per structure.
- *
- * @return
- */
- @Override
- public List<String> getChainNames()
- {
- return chainNames;
- }
-
- /**
- * Send a 'focus' command to Chimera to recentre the visible display
- */
- public void focusView()
- {
- sendChimeraCommand(viewer.isChimeraX() ? "view" : "focus", false);
- }
-
- /**
* Send a 'show' command for all atoms in the currently selected columns
*
* TODO: pull up to abstract structure viewer interface
public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
// TODO refactor as required to pull up to an interface
- AlignmentI alignment = avp.getAlignment();
-
String[] files = getStructureFiles();
if (files == null)
{
return 0;
}
- StructureMappingcommandSet commandSet = ChimeraCommands
- .getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), avp, viewer.isChimeraX());
- String[] commands = commandSet.commands;
+ String[] commands = getCommandGenerator()
+ .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
if (commands.length > 10)
{
sendCommandsByFile(commands);
*/
protected void sendCommandsByFile(String[] commands)
{
- boolean toChimeraX = viewer.isChimeraX();
try
{
- File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
tmp.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
for (String command : commands)
out.flush();
out.close();
String path = tmp.getAbsolutePath();
- String command = "open " + (toChimeraX ? "" : "cmd:") + path;
+ String command = getCommandGenerator().openCommandFile(path);
sendAsynchronousCommand(command, null);
} catch (IOException e)
{
}
/**
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
+ * @return
+ */
+ protected String getCommandFileExtension()
+ {
+ return ".com";
+ }
+
+ /**
* Get Chimera residues which have the named attribute, find the mapped
* positions in the Jalview sequence(s), and set as sequence features
*
// fails for 'average.bfactor' (which is bad):
String cmd = "list residues attr '" + attName + "'";
- List<String> residues = sendChimeraCommand(cmd, true);
+ List<String> residues = executeCommand(cmd, true);
boolean featureAdded = createFeaturesForAttributes(attName, residues);
if (featureAdded)
{
boolean featureAdded = false;
String featureGroup = getViewerFeatureGroup();
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
for (String residue : residues)
{
return CHIMERA_FEATURE_GROUP;
}
- public Hashtable<String, String> getChainFile()
- {
- return chainFile;
- }
-
- public List<ChimeraModel> getChimeraModelByChain(String chain)
- {
- return chimeraMaps.get(chainFile.get(chain));
- }
-
- public int getModelNoForChain(String chain)
+ @Override
+ public int getModelNoForFile(String pdbFile)
{
- List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+ List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
if (foundModels != null && !foundModels.isEmpty())
{
return foundModels.get(0).getModelNumber();
*/
public List<String> getChimeraAttributes()
{
- List<String> atts = viewer.getAttrList();
+ List<String> atts = chimeraManager.getAttrList();
Iterator<String> it = atts.iterator();
while (it.hasNext())
{
return atts;
}
- public boolean isChimeraX()
+ /**
+ * Returns the file extension to use for a saved viewer session file
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return ".py";
+ }
+
+ public String getHelpURL()
{
- return viewer.isChimeraX();
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
}
}
git://source.jalview.org / jalview.git / blobdiff