*/
package jalview.ext.rbvi.chimera;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.httpserver.AbstractRequestHandler;
-import jalview.io.DataSourceType;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommandsI.SuperposeData;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintWriter;
import java.net.BindException;
import java.util.ArrayList;
-import java.util.BitSet;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedHashMap;
import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+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;
+import jalview.structures.models.AAStructureBindingModel;
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
- 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";
+ public static final String CHIMERA_SESSION_EXTENSION = ".py";
- private static final String ALPHACARBON = "CA";
+ public static final String CHIMERA_FEATURE_GROUP = "Chimera";
/*
* Object through which we talk to Chimera
String lastHighlightCommand;
- private Thread chimeraMonitor;
-
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
}
/**
- * 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
*/
* 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.clearOnChimeraExit();
chimeraManager = null;
-
- if (chimeraMonitor != null)
- {
- chimeraMonitor.interrupt();
- }
- releaseUIResources();
- }
-
- /**
- * {@inheritDoc}
- */
- public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, HiddenColumns[] _hiddenCols)
- {
- StringBuilder allComs = new StringBuilder(128);
- String[] files = getStructureFiles();
-
- if (!waitForFileLoad(files))
- {
- return null;
- }
-
- refreshPdbEntries();
- StringBuilder selectioncom = new StringBuilder(256);
- boolean chimeraX = chimeraManager.isChimeraX();
- for (int a = 0; a < _alignment.length; a++)
- {
- int refStructure = _refStructure[a];
- AlignmentI alignment = _alignment[a];
- HiddenColumns hiddenCols = _hiddenCols[a];
-
- if (refStructure >= files.length)
- {
- System.err.println("Ignoring invalid reference structure value "
- + refStructure);
- refStructure = -1;
- }
-
- /*
- * 'matched' bit i will be set for visible alignment columns i where
- * all sequences have a residue with a mapping to the PDB structure
- */
- BitSet matched = new BitSet();
- for (int m = 0; m < alignment.getWidth(); m++)
- {
- if (hiddenCols == null || hiddenCols.isVisible(m))
- {
- matched.set(m);
- }
- }
-
- SuperposeData[] structures = new SuperposeData[files.length];
- for (int f = 0; f < files.length; f++)
- {
- structures[f] = new SuperposeData(alignment.getWidth(), f);
- }
-
- /*
- * Calculate the superposable alignment columns ('matched'), and the
- * corresponding structure residue positions (structures.pdbResNo)
- */
- int candidateRefStructure = findSuperposableResidues(alignment,
- matched, structures);
- if (refStructure < 0)
- {
- /*
- * If no reference structure was specified, pick the first one that has
- * a mapping in the alignment
- */
- refStructure = candidateRefStructure;
- }
-
- int nmatched = matched.cardinality();
- if (nmatched < 4)
- {
- return MessageManager.formatMessage("label.insufficient_residues",
- nmatched);
- }
-
- /*
- * Generate select statements to select regions to superimpose structures
- */
- String[] selcom = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- final int modelNo = pdbfnum + (chimeraX ? 1 : 0);
- // todo correct resolution to model number
- String chainCd = "." + structures[pdbfnum].chain;
- int lpos = -1;
- boolean run = false;
- StringBuilder molsel = new StringBuilder();
- if (chimeraX)
- {
- molsel.append("/" + structures[pdbfnum].chain + ":");
- }
-
- int nextColumnMatch = matched.nextSetBit(0);
- while (nextColumnMatch != -1)
- {
- int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
- if (lpos != pdbResNum - 1)
- {
- /*
- * discontiguous - append last residue now
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- if (!chimeraX)
- {
- molsel.append(chainCd);
- }
- molsel.append(",");
- }
- run = false;
- }
- else
- {
- /*
- * extending a contiguous run
- */
- if (!run)
- {
- /*
- * start the range selection
- */
- molsel.append(String.valueOf(lpos));
- molsel.append("-");
- }
- run = true;
- }
- lpos = pdbResNum;
- nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
- }
-
- /*
- * and terminate final selection
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- if (!chimeraX)
- {
- molsel.append(chainCd);
- }
- }
- if (molsel.length() > 1)
- {
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("#").append(String.valueOf(modelNo));
- if (!chimeraX)
- {
- selectioncom.append(":");
- }
- selectioncom.append(selcom[pdbfnum]);
- // selectioncom.append(" ");
- if (pdbfnum < files.length - 1)
- {
- selectioncom.append("|");
- }
- }
- else
- {
- selcom[pdbfnum] = null;
- }
- }
-
- StringBuilder command = new StringBuilder(256);
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- final int modelNo = pdbfnum + (chimeraX ? 1 : 0);
- if (pdbfnum == refStructure || selcom[pdbfnum] == null
- || selcom[refStructure] == null)
- {
- continue;
- }
- if (command.length() > 0)
- {
- command.append(";");
- }
-
- /*
- * Form Chimera match command, from the 'new' structure to the
- * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
- *
- * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
- *
- * @see
- * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
- */
- command.append(chimeraX ? "align " : "match ");
- command.append(getModelSpec(modelNo));
- if (!chimeraX)
- {
- command.append(":");
- }
- command.append(selcom[pdbfnum]);
- command.append("@").append(
- structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
- // JAL-1757 exclude alternate CA locations - ChimeraX syntax tbd
- if (!chimeraX)
- {
- command.append(NO_ALTLOCS);
- }
- command.append(chimeraX ? " toAtoms " : " ")
- .append(getModelSpec(refStructure + (chimeraX ? 1 : 0)));
- if (!chimeraX)
- {
- command.append(":");
- }
- command.append(selcom[refStructure]);
- command.append("@").append(
- structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
- if (!chimeraX)
- {
- command.append(NO_ALTLOCS);
- }
- }
- if (selectioncom.length() > 0)
- {
- if (debug)
- {
- System.out.println("Select regions:\n" + selectioncom.toString());
- System.out.println(
- "Superimpose command(s):\n" + command.toString());
- }
- // allComs.append("~display all; ");
- // if (chimeraX)
- // {
- // allComs.append("show ").append(selectioncom.toString())
- // .append(" pbonds");
- // }
- // else
- // {
- // allComs.append("chain @CA|P; ribbon ");
- // allComs.append(selectioncom.toString());
- // }
- if (allComs.length() > 0) {
- allComs.append(";");
- }
- allComs.append(command.toString());
- }
- }
-
- String error = null;
- if (selectioncom.length() > 0)
- {
- // TODO: visually distinguish regions that were superposed
- if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
- {
- selectioncom.setLength(selectioncom.length() - 1);
- }
- if (debug)
- {
- System.out.println("Select regions:\n" + selectioncom.toString());
- }
- allComs.append(";~display all; ");
- if (chimeraX)
- {
- allComs.append("show @CA|P pbonds; show ")
- .append(selectioncom.toString()).append(" ribbons; view");
- }
- else
- {
- 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 = executeCommand(allComs.toString(),
- true);
- for (String reply : chimeraReplies)
- {
- if (reply.toLowerCase().contains("unequal numbers of atoms"))
- {
- error = reply;
- }
- }
- }
- return error;
}
/**
boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
- startChimeraProcessMonitor();
+ startExternalViewerMonitor(chimeraManager.getChimeraProcess());
}
else
{
*
* @return
*/
- public boolean isChimeraRunning()
+ @Override
+ public boolean isViewerRunning()
{
return chimeraManager.isChimeraLaunched();
}
* @param getResponse
*/
@Override
- public List<String> executeCommand(final String command,
+ public List<String> executeCommand(final StructureCommandI command,
boolean getResponse)
{
if (chimeraManager == null || command == null)
}
List<String> reply = null;
// trim command or it may never find a match in the replyLog!!
+ String cmd = command.getCommand().trim();
List<String> lastReply = chimeraManager
- .sendChimeraCommand(command.trim(), getResponse);
+ .sendChimeraCommand(cmd, getResponse);
if (getResponse)
{
reply = lastReply;
- if (debug)
- {
- log("Response from command ('" + command + "') was:\n" + lastReply);
- }
+ Cache.log.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
}
return reply;
}
- /**
- * @param command
- */
- protected void executeWhenReady(String command)
- {
- waitForChimera();
- executeCommand(command, false);
- waitForChimera();
- }
-
- private void waitForChimera()
- {
- while (chimeraManager != null && chimeraManager.isBusy())
- {
- try
- {
- Thread.sleep(15);
- } catch (InterruptedException q)
- {
- }
- }
- }
-
@Override
public synchronized String[] getStructureFiles()
{
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- System.err.println("Failed to parse atomspec: " + atomSpec);
+ Cache.log.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);
- 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("open " + 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
/**
* 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;
- }
- String[] commands = getCommandGenerator()
- .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
- if (commands.length > 10)
+ Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+ avp);
+ List<StructureCommandI> commands = getCommandGenerator()
+ .setAttributes(featureValues);
+ if (commands.size() > 10)
{
sendCommandsByFile(commands);
}
else
{
- for (String command : commands)
+ for (StructureCommandI command : commands)
{
sendAsynchronousCommand(command, null);
}
}
- return commands.length;
+ return commands.size();
}
/**
*
* @param commands
*/
- protected void sendCommandsByFile(String[] commands)
+ protected void sendCommandsByFile(List<StructureCommandI> commands)
{
try
{
File tmp = File.createTempFile("chim", getCommandFileExtension());
tmp.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
- for (String command : commands)
+ for (StructureCommandI command : commands)
{
- out.println(command);
+ out.println(command.getCommand());
}
out.flush();
out.close();
String path = tmp.getAbsolutePath();
- String command = getCommandGenerator().openCommandFile(path);
+ StructureCommandI command = getCommandGenerator()
+ .openCommandFile(path);
sendAsynchronousCommand(command, null);
} catch (IOException e)
{
// fails for 'average.bfactor' (which is bad):
String cmd = "list residues attr '" + attName + "'";
- List<String> residues = executeCommand(cmd, true);
+ List<String> residues = executeCommand(new StructureCommand(cmd), true);
boolean featureAdded = createFeaturesForAttributes(attName, residues);
if (featureAdded)
}
@Override
- public int getModelNoForFile(String pdbFile)
+ public String getModelIdForFile(String pdbFile)
{
List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
if (foundModels != null && !foundModels.isEmpty())
{
- return foundModels.get(0).getModelNumber();
+ return String.valueOf(foundModels.get(0).getModelNumber());
}
- return -1;
+ return "";
}
/**
}
/**
- * Returns the file extension to use for a saved viewer session file
+ * Returns the file extension to use for a saved viewer session file (.py)
*
* @return
*/
+ @Override
public String getSessionFileExtension()
{
- return ".py";
+ return CHIMERA_SESSION_EXTENSION;
}
+ @Override
public String getHelpURL()
{
return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
git://source.jalview.org / jalview.git / blobdiff