*/
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 java.util.List;
import java.util.Map;
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.Console;
+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";
+ public static final String CHIMERA_SESSION_EXTENSION = ".py";
- private static final boolean debug = false;
-
- private static final String PHOSPHORUS = "P";
-
- 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;
+ /**
+ * 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.
*
- * We check if the PDB model id is already loaded in Chimera, if so don't reopen
- * it. This is the case if Chimera has opened a saved session file.
+ * We check if the PDB model id is already loaded in Chimera, if so don't
+ * reopen it. This is the case if Chimera has opened a saved session file.
*
* @param pe
* @return
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
+ * Start a dedicated HttpServer to listen for Chimera notifications, and tell
+ * it to start listening
*/
public void startChimeraListener()
{
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)
- {
- chimeraMonitor.interrupt();
- }
- releaseUIResources();
- }
-
- /**
- * {@inheritDoc}
- */
- public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, HiddenColumns[] _hiddenCols)
- {
- StringBuilder allComs = new StringBuilder(128);
- String[] files = getStructureFiles();
-
- if (!waitForFileLoad(files))
+ /*
+ * 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))
{
- return null;
+ chimeraManager.getChimeraProcess().destroy();
}
- 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;
+ 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();
}
/**
* @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!!
- List<String> lastReply = chimeraManager
- .sendChimeraCommand(command.trim(), getResponse);
+ String cmd = command.getCommand().trim();
+ List<String> lastReply = chimeraManager.sendChimeraCommand(cmd,
+ getResponse);
if (getResponse)
{
reply = lastReply;
- if (debug)
+ if (Console.isDebugEnabled())
{
- log("Response from command ('" + command + "') was:\n" + lastReply);
+ Console.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())
+ else
{
- try
- {
- Thread.sleep(15);
- } catch (InterruptedException q)
+ if (Console.isDebugEnabled())
{
+ Console.debug("Command executed: " + cmd);
}
}
+
+ return reply;
}
@Override
}
/**
- * Construct and send a command to highlight zero, one or more atoms. We do this
- * by sending an "rlabel" command to show the residue label at that position.
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
first = false;
if (forChimeraX)
{
- cmd.append(cms.get(0).getModelNumber())
- .append("/").append(chain).append(":").append(pdbResNum);
+ cmd.append(cms.get(0).getModelNumber()).append("/").append(chain)
+ .append(":").append(pdbResNum);
}
else
{
- cmd.append(cms.get(0).getModelNumber())
- .append(":").append(pdbResNum);
+ cmd.append(cms.get(0).getModelNumber()).append(":")
+ .append(pdbResNum);
if (!chain.equals(" ") && !forChimeraX)
{
cmd.append(".").append(chain);
{
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 (cmd.length() > 0)
+ {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
}
+
if (found)
{
- chimeraManager.sendChimeraCommand(command, false);
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
/*
* Ask Chimera for its current selection
*/
- List<String> selection = chimeraManager.getSelectedResidueSpecs();
+ StructureCommandI command = getCommandGenerator().getSelectedResidues();
- /*
- * 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);
+ Runnable action = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ List<String> chimeraReply = executeCommand(command, true);
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
+ 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(
+ selectedResidues);
+
+ /*
+ * 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
- * corresponding residues (if any) in Jalview
+ * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing
+ * the corresponding residues (if any) in Jalview
*
* @param structureSelection
* @return
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);
- 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
- *
- * @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;
- }
- 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)
- {
- sendAsynchronousCommand(command, null);
- }
+ executeCommands(commands, false, null);
}
- return commands.length;
+ return commands.size();
}
/**
- * Write commands to a temporary file, and send a command to Chimera to open the
- * file as a commands script. For use when sending a large number of separate
- * commands would overload the REST interface mechanism.
+ * Write commands to a temporary file, and send a command to Chimera to open
+ * the file as a commands script. For use when sending a large number of
+ * separate commands would overload the REST interface mechanism.
*
* @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);
- sendAsynchronousCommand(command, null);
+ StructureCommandI command = getCommandGenerator()
+ .openCommandFile(path);
+ executeCommand(false, null, command);
} catch (IOException e)
{
System.err.println("Sending commands to Chimera via file failed with "
/**
* Returns the file extension required for a file of commands to be read by
* the structure viewer
+ *
* @return
*/
protected String getCommandFileExtension()
}
/**
- * 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(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;
}
/**
}
@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 "";
}
/**
*/
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;
}
/**
- * 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