import java.net.BindException;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
public static final String CHIMERA_FEATURE_GROUP = "Chimera";
- // Chimera clause to exclude alternate locations in atom selection
- private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
-
- private static final boolean debug = false;
-
- private static final String PHOSPHORUS = "P";
-
- private static final String ALPHACARBON = "CA";
-
/*
* Object through which we talk to Chimera
*/
String lastHighlightCommand;
- private Thread chimeraMonitor;
+ /**
+ * Returns a model of the structure positions described by the Chimera format atomspec
+ * @param atomSpec
+ * @return
+ */
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraAtomspec(atomSpec);
+ }
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
- chimeraManager = new ChimeraManager(new StructureManager(true));
- chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType()));
- setStructureCommands(new ChimeraCommands());
+ boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
+ chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true));
+ setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
}
@Override
}
/**
- * Starts a thread that waits for the Chimera process to finish, so that we can
- * then close the associated resources. This avoids leaving orphaned Chimera
- * viewer panels in Jalview if the user closes Chimera.
- */
- protected void startChimeraProcessMonitor()
- {
- final Process p = chimeraManager.getChimeraProcess();
- chimeraMonitor = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- try
- {
- p.waitFor();
- JalviewStructureDisplayI display = getViewer();
- if (display != null)
- {
- display.closeViewer(false);
- }
- } catch (InterruptedException e)
- {
- // exit thread if Chimera Viewer is closed in Jalview
- }
- }
- });
- chimeraMonitor.start();
- }
-
- /**
* Start a dedicated HttpServer to listen for Chimera notifications, and tell it
* to start listening
*/
try
{
chimeraListener = new ChimeraListener(this);
- chimeraManager.startListening(chimeraListener.getUri());
+ startListening(chimeraListener.getUri());
} catch (BindException e)
{
System.err.println(
* Close down the Jalview viewer and listener, and (optionally) the associated
* Chimera window.
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- if (closeChimera)
- {
- chimeraManager.exitChimera();
- }
+ super.closeViewer(closeChimera);
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
- chimeraManager = null;
-
- if (chimeraMonitor != null)
+
+ /*
+ * the following call is added to avoid a stack trace error in Chimera
+ * after "stop really" is sent; Chimera > 1.14 will not need it; see also
+ * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597
+ */
+ if (closeChimera && (getViewerType() == ViewerType.CHIMERA))
{
- chimeraMonitor.interrupt();
+ chimeraManager.getChimeraProcess().destroy();
}
- releaseUIResources();
+
+ chimeraManager.clearOnChimeraExit();
+ chimeraManager = null;
}
/**
boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
- startChimeraProcessMonitor();
+ startExternalViewerMonitor(chimeraManager.getChimeraProcess());
}
else
{
*
* @return
*/
- public boolean isChimeraRunning()
+ @Override
+ public boolean isViewerRunning()
{
- return chimeraManager.isChimeraLaunched();
+ return chimeraManager!=null && chimeraManager.isChimeraLaunched();
}
/**
if (getResponse)
{
reply = lastReply;
- if (debug)
+ if (Console.isDebugEnabled()) {
+ Console.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
+ }
+ }
+ else
+ {
+ if (Console.isDebugEnabled())
{
- log("Response from command ('" + cmd + "') was:\n" + lastReply);
+ Console.debug("Command executed: " + cmd);
}
}
{
return;
}
-
+ if (!found)
+ {
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
+ }
/*
- * unshow the label for the previous residue
+ * prepend with command
+ * to unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
- chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
+ cmd.insert(0, ";");
+ cmd.insert(0,lastHighlightCommand);
+ cmd.insert(0,"~");
+
}
- if (found)
- {
- chimeraManager.sendChimeraCommand(command, false);
+ if (cmd.length()>0) {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
+ }
+
+ if (found) {
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
/*
* Ask Chimera for its current selection
*/
- List<String> selection = chimeraManager.getSelectedResidueSpecs();
+ StructureCommandI command = getCommandGenerator().getSelectedResidues();
+
+ Runnable action = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ List<String> chimeraReply = executeCommand(command, true);
+
+ List<String> selectedResidues = new ArrayList<>();
+ if (chimeraReply != null)
+ {
+ /*
+ * expect 0, 1 or more lines of the format either
+ * Chimera:
+ * residue id #0:43.A type GLY
+ * ChimeraX:
+ * residue id /A:89 name THR index 88
+ * We are only interested in the atomspec (third token of the reply)
+ */
+ for (String inputLine : chimeraReply)
+ {
+ String[] inputLineParts = inputLine.split("\\s+");
+ if (inputLineParts.length >= 5)
+ {
+ selectedResidues.add(inputLineParts[2]);
+ }
+ }
+ }
- /*
- * Parse model number, residue and chain for each selected position,
- * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
- */
- List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
- selection);
+ /*
+ * Parse model number, residue and chain for each selected position,
+ * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
+ */
+ List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selectedResidues);
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
+ /*
+ * Broadcast the selection (which may be empty, if the user just cleared all
+ * selections)
+ */
+ getSsm().mouseOverStructure(atomSpecs);
+
+ }
+ };
+ new Thread(action).start();
}
/**
- * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
+ * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the
* corresponding residues (if any) in Jalview
*
* @param structureSelection
protected List<AtomSpec> convertStructureResiduesToAlignment(
List<String> structureSelection)
{
- boolean chimeraX = chimeraManager.isChimeraX();
List<AtomSpec> atomSpecs = new ArrayList<>();
for (String atomSpec : structureSelection)
{
try
{
- AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX);
+ AtomSpec spec = parseAtomSpec(atomSpec);
String pdbfilename = getPdbFileForModel(spec.getModelNumber());
spec.setPdbFile(pdbfilename);
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- System.err.println("Failed to parse atomspec: " + atomSpec);
+ Console.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
}
/**
- * Ask Chimera to save its session to the given file. Returns true if
- * successful, else false.
- *
- * @param filepath
- * @return
- */
- public boolean saveSession(String filepath)
- {
- if (isChimeraRunning())
- {
- /*
- * 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 = getCommandGenerator().saveSession(filepath)
- .getCommand();
- List<String> reply = chimeraManager.sendChimeraCommand(command, true);
- if (reply.contains("Session written"))
- {
- return true;
- }
- else
- {
- Cache.log
- .error("Error saving Chimera session: " + reply.toString());
- }
- }
- return false;
- }
-
- /**
- * Ask Chimera to open a session file. Returns true if successful, else false.
- * The filename must have a .py (Chimera) or .cxs (ChimeraX) extension for
- * this command to work.
- *
- * @param filepath
- * @return
- */
- public boolean openSession(String filepath)
- {
- /*
- * 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
- */
- executeCommand(getCommandGenerator().loadFile(filepath), true);
- // todo: test for failure - how?
- return true;
- }
-
- /**
- * Send a 'show' command for all atoms in the currently selected columns
- *
- * TODO: pull up to abstract structure viewer interface
- *
- * @param vp
- */
- public void highlightSelection(AlignmentViewPanel vp)
- {
- List<Integer> cols = vp.getAlignViewport().getColumnSelection()
- .getSelected();
- AlignmentI alignment = vp.getAlignment();
- StructureSelectionManager sm = getSsm();
- for (SequenceI seq : alignment.getSequences())
- {
- /*
- * convert selected columns into sequence positions
- */
- int[] positions = new int[cols.size()];
- int i = 0;
- for (Integer col : cols)
- {
- positions[i++] = seq.findPosition(col);
- }
- sm.highlightStructure(this, seq, positions);
- }
- }
-
- /**
* Constructs and send commands to Chimera to set attributes on residues for
- * features visible in Jalview
+ * features visible in Jalview.
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
*
* @param avp
* @return
public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
// TODO refactor as required to pull up to an interface
- String[] files = getStructureFiles();
- if (files == null)
- {
- return 0;
- }
+ Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+ avp);
List<StructureCommandI> commands = getCommandGenerator()
- .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
+ .setAttributes(featureValues);
if (commands.size() > 10)
{
sendCommandsByFile(commands);
}
else
{
- for (StructureCommandI command : commands)
- {
- sendAsynchronousCommand(command, null);
- }
+ executeCommands(commands, false, null);
}
return commands.size();
}
String path = tmp.getAbsolutePath();
StructureCommandI command = getCommandGenerator()
.openCommandFile(path);
- sendAsynchronousCommand(command, null);
+ executeCommand(false, null, command);
} catch (IOException e)
{
System.err.println("Sending commands to Chimera via file failed with "
}
/**
- * Get Chimera residues which have the named attribute, find the mapped
- * positions in the Jalview sequence(s), and set as sequence features
- *
- * @param attName
- * @param alignmentPanel
- */
- public void copyStructureAttributesToFeatures(String attName,
- AlignmentViewPanel alignmentPanel)
- {
- // todo pull up to AAStructureBindingModel (and interface?)
-
- /*
- * ask Chimera to list residues with the attribute, reporting its value
- */
- // this alternative command
- // list residues spec ':*/attName' attr attName
- // doesn't report 'None' values (which is good), but
- // fails for 'average.bfactor' (which is bad):
-
- String cmd = "list residues attr '" + attName + "'";
- List<String> residues = executeCommand(new StructureCommand(cmd), true);
-
- boolean featureAdded = createFeaturesForAttributes(attName, residues);
- if (featureAdded)
- {
- alignmentPanel.getFeatureRenderer().featuresAdded();
- }
- }
-
- /**
* Create features in Jalview for the given attribute name and structure
* residues.
*
*
* @param attName
* @param residues
- * @return
+ * @return the number of features added
*/
- protected boolean createFeaturesForAttributes(String attName,
+ protected int createFeaturesForAttributes(String attName,
List<String> residues)
{
- boolean featureAdded = false;
+ int featuresAdded = 0;
String featureGroup = getViewerFeatureGroup();
- boolean chimeraX = chimeraManager.isChimeraX();
for (String residue : residues)
{
try
{
- spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX);
+ spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- System.err.println("Problem parsing atomspec " + atomSpec);
+ Console.error("Problem parsing atomspec " + atomSpec);
continue;
}
start, end, score, featureGroup);
// todo: should SequenceFeature have an explicit property for chain?
// note: repeating the action shouldn't duplicate features
- featureAdded |= seq.addSequenceFeature(sf);
+ if (seq.addSequenceFeature(sf))
+ {
+ featuresAdded++;
+ }
}
}
- return featureAdded;
+ return featuresAdded;
}
/**
*/
public List<String> getChimeraAttributes()
{
- List<String> atts = chimeraManager.getAttrList();
- Iterator<String> it = atts.iterator();
- while (it.hasNext())
+ List<String> attributes = new ArrayList<>();
+ StructureCommandI command = getCommandGenerator().listResidueAttributes();
+ final List<String> reply = executeCommand(command, true);
+ if (reply != null)
{
- if (it.next().startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ for (String inputLine : reply)
{
- /*
- * attribute added from Jalview - exclude it
- */
- it.remove();
+ String[] lineParts = inputLine.split("\\s");
+ if (lineParts.length == 2 && lineParts[0].equals("resattr"))
+ {
+ String attName = lineParts[1];
+ /*
+ * exclude attributes added from Jalview
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ {
+ attributes.add(attName);
+ }
+ }
}
}
- return atts;
+ return attributes;
}
/**
return CHIMERA_SESSION_EXTENSION;
}
+ @Override
public String getHelpURL()
{
return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
git://source.jalview.org / jalview.git / blobdiff