*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-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.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+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.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
+import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureCommandsI.SuperposeData;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.Comparison;
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.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
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 ALPHACARBON = "CA";
- private StructureManager csm;
-
/*
* 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;
-
- /*
- * state flag used to check if the Chimera viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
- private List<String> atomsPicked = new ArrayList<String>();
-
- private List<String> chainNames;
-
- private Map<String, String> chainFile;
-
- public String fileLoadingError;
-
- /*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
- /*
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- private int frameNo = 0;
+ String lastHighlightCommand;
- private String lastCommand;
-
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
- String lastMousedOverAtomSpec;
-
- private List<String> lastReply;
-
- /*
- * 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;
/**
* 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
String file = pe.getFile();
try
{
- List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
- List<ChimeraModel> oldList = viewer.getModelList();
+ List<ChimeraModel> modelsToMap = new ArrayList<>();
+ List<ChimeraModel> oldList = chimeraManager.getModelList();
boolean alreadyOpen = false;
/*
*/
if (!alreadyOpen)
{
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- 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);
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
}
return true;
} catch (Exception q)
}
/**
- * Constructor
+ * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
+ * name matching PDB id
*
- * @param ssm
- * @param pdbentry
- * @param sequenceIs
- * @param chains
- * @param protocol
+ * @param pe
+ * @param modelsToMap
*/
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
- viewer = new ChimeraManager(
- csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
- }
-
- /**
- * Start a dedicated HttpServer to listen for Chimera notifications, and tell
- * it to start listening
- */
- public void startChimeraListener()
- {
- try
- {
- chimeraListener = new ChimeraListener(this);
- viewer.startListening(chimeraListener.getUri());
- } catch (BindException e)
+ /*
+ * 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)
{
- System.err.println("Failed to start Chimera listener: "
- + e.getMessage());
+ if (cm.getModelName().equals(pe.getId()))
+ {
+ modelsToMap.add(cm);
+ }
}
}
* Constructor
*
* @param ssm
- * @param theViewer
+ * @param pdbentry
+ * @param sequenceIs
+ * @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- ChimeraManager theViewer)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, protocol);
+ chimeraManager = new ChimeraManager(new StructureManager(true));
+ chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType()));
+ setStructureCommands(new ChimeraCommands());
+ }
+
+ @Override
+ protected ViewerType getViewerType()
{
- super(ssm, null);
- viewer = theViewer;
- csm = viewer.getStructureManager();
+ return ViewerType.CHIMERA;
}
/**
- * Construct a title string for the viewer window based on the data Jalview
- * knows about
- *
- * @param verbose
- * @return
+ * 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.
*/
- public String getViewerTitle(boolean verbose)
+ protected void startChimeraProcessMonitor()
{
- return getViewerTitle("Chimera", verbose);
+ 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();
}
/**
- * prepare the view for a given set of models/chains. chainList contains
- * strings of the form 'pdbfilename:Chaincode'
- *
- * @param toshow
- * list of chains to make visible
+ * Start a dedicated HttpServer to listen for Chimera notifications, and tell it
+ * to start listening
*/
- public void centerViewer(List<String> toshow)
+ public void startChimeraListener()
{
- StringBuilder cmd = new StringBuilder(64);
- int mlength, p;
- for (String lbl : toshow)
+ try
{
- mlength = 0;
- do
- {
- p = mlength;
- mlength = lbl.indexOf(":", p);
- } while (p < mlength && mlength < (lbl.length() - 2));
- // TODO: lookup each pdb id and recover proper model number for it.
- cmd.append("#" + getModelNum(chainFile.get(lbl)) + "."
- + lbl.substring(mlength + 1) + " or ");
- }
- if (cmd.length() > 0)
+ chimeraListener = new ChimeraListener(this);
+ chimeraManager.startListening(chimeraListener.getUri());
+ } catch (BindException e)
{
- cmd.setLength(cmd.length() - 4);
+ System.err.println(
+ "Failed to start Chimera listener: " + e.getMessage());
}
- String cmdstring = cmd.toString();
- evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring
- + ";focus " + cmdstring, false);
}
/**
*/
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
- viewer.exitChimera();
+ chimeraManager.exitChimera();
}
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
- lastCommand = null;
- viewer = null;
+ chimeraManager = null;
+ if (chimeraMonitor != null)
+ {
+ chimeraMonitor.interrupt();
+ }
releaseUIResources();
}
- public void colourByChain()
- {
- colourBySequence = false;
- evalStateCommand("rainbow chain", false);
- }
-
- public void colourByCharge()
- {
- colourBySequence = false;
- evalStateCommand(
- "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS",
- false);
- }
-
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions.
- */
- public void superposeStructures(AlignmentI alignment)
- {
- superposeStructures(alignment, -1, null);
- }
-
- /**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
+ * Helper method to construct model spec in Chimera format:
+ * <ul>
+ * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
+ * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
+ * <ul>
+ * Note for now we only ever choose the first of multiple models. This
+ * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
+ * future if there is a need to select specific sub-models.
*
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
+ * @param pdbfnum
+ * @return
*/
- public void superposeStructures(AlignmentI alignment, int refStructure)
+ protected String getModelSpec(int pdbfnum)
{
- superposeStructures(alignment, refStructure, null);
+ if (pdbfnum < 0 || pdbfnum >= getPdbCount())
+ {
+ return "#" + pdbfnum; // temp hack for ChimeraX
+ }
+
+ /*
+ * For now, the test for having sub-models is whether multiple Chimera
+ * models are mapped for the PDB file; the models are returned as a response
+ * to the Chimera command 'list models type molecule', see
+ * ChimeraManager.getModelList().
+ */
+ List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
+ boolean hasSubModels = maps != null && maps.size() > 1;
+ return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
+ * Launch Chimera, unless an instance linked to this object is already
+ * running. Returns true if Chimera is successfully launched, or already
+ * running, else false.
*
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
- * @param hiddenCols
- * TODO
+ * @return
*/
- public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
+ public boolean launchChimera()
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
- }
-
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
- {
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
- StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd
- String[] files = getPdbFile();
- // check to see if we are still waiting for Chimera files
- long starttime = System.currentTimeMillis();
- boolean waiting = true;
- do
+ if (chimeraManager.isChimeraLaunched())
{
- waiting = false;
- for (String file : files)
- {
- try
- {
- // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
- // every possible exception
- StructureMapping[] sm = getSsm().getMapping(file);
- if (sm == null || sm.length == 0)
- {
- waiting = true;
- }
- } catch (Exception x)
- {
- waiting = true;
- } catch (Error q)
- {
- waiting = true;
- }
- }
- // we wait around for a reasonable time before we give up
- } while (waiting
- && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
- if (waiting)
- {
- System.err
- .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures.");
- return;
- }
- refreshPdbEntries();
- StringBuffer selectioncom = new StringBuffer();
- for (int a = 0; a < _alignment.length; a++)
- {
- int refStructure = _refStructure[a];
- AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
- if (a > 0
- && selectioncom.length() > 0
- && !selectioncom.substring(selectioncom.length() - 1).equals(
- " "))
- {
- selectioncom.append(" ");
- }
- // process this alignment
- if (refStructure >= files.length)
- {
- System.err.println("Invalid reference structure value "
- + refStructure);
- refStructure = -1;
- }
- if (refStructure < -1)
- {
- refStructure = -1;
- }
-
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
- {
-
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
- }
-
- int commonrpositions[][] = new int[files.length][alignment.getWidth()];
- String isel[] = new String[files.length];
- String[] targetC = new String[files.length];
- String[] chainNames = new String[files.length];
- String[] atomSpec = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
- // RACE CONDITION - getMapping only returns Jmol loaded filenames once
- // Jmol callback has completed.
- if (mapping == null || mapping.length < 1)
- {
- throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data"));
- }
- int lastPos = -1;
- final int seqCountForPdbFile = getSequence()[pdbfnum].length;
- for (int s = 0; s < seqCountForPdbFile; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI theSequence = getSequence()[pdbfnum][s];
- if (mapping[m].getSequence() == theSequence
- && (sp = alignment.findIndex(theSequence)) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- if (!matched[r])
- {
- continue;
- }
- matched[r] = false; // assume this is not a good site
- if (r >= asp.getLength())
- {
- continue;
- }
-
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- // no mapping to gaps in sequence
- continue;
- }
- int t = asp.findPosition(r); // sequence position
- int apos = mapping[m].getAtomNum(t);
- int pos = mapping[m].getPDBResNum(t);
-
- if (pos < 1 || pos == lastPos)
- {
- // can't align unmapped sequence
- continue;
- }
- matched[r] = true; // this is a good ite
- lastPos = pos;
- // just record this residue position
- commonrpositions[pdbfnum][r] = pos;
- }
- // create model selection suffix
- isel[pdbfnum] = "#" + pdbfnum;
- if (mapping[m].getChain() == null
- || mapping[m].getChain().trim().length() == 0)
- {
- targetC[pdbfnum] = "";
- }
- else
- {
- targetC[pdbfnum] = "." + mapping[m].getChain();
- }
- chainNames[pdbfnum] = mapping[m].getPdbId()
- + targetC[pdbfnum];
- atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON;
- // move on to next pdb file
- s = seqCountForPdbFile;
- break;
- }
- }
- }
- }
-
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
-
- String[] selcom = new String[files.length];
- int nmatched = 0;
- String sep = "";
- // generate select statements to select regions to superimpose structures
- {
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- String chainCd = targetC[pdbfnum];
- int lpos = -1;
- boolean run = false;
- StringBuffer molsel = new StringBuffer();
- for (int r = 0; r < matched.length; r++)
- {
- if (matched[r])
- {
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append((run ? "" : ":") + lpos);
- molsel.append(chainCd);
- molsel.append(",");
- }
- }
- else
- {
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(":" + lpos);
- molsel.append("-");
- }
- run = true;
- }
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
- }
- }
- // add final selection phrase
- if (lpos != -1)
- {
- molsel.append((run ? "" : ":") + lpos);
- molsel.append(chainCd);
- // molsel.append("");
- }
- if (molsel.length() > 1)
- {
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("#" + pdbfnum);
- 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++)
- {
- 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. (residues 1-91, chain B/A, alphacarbons):
- *
- * match #1:1-91.B@CA #0:1-91.A@CA
- *
- * @see
- * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
- */
- command.append("match #" + pdbfnum /* +".1" */);
- // TODO: handle sub-models
- command.append(selcom[pdbfnum]);
- command.append("@" + atomSpec[pdbfnum]);
- command.append(" #" + refStructure /* +".1" */);
- command.append(selcom[refStructure]);
- command.append("@" + atomSpec[refStructure]);
- }
- 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; chain @CA|P; ribbon "
- + selectioncom.toString() + ";"+command.toString());
- // selcom.append("; ribbons; ");
- }
- }
- if (selectioncom.length() > 0)
- {// finally, mark all 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; chain @CA|P; ribbon "
- + selectioncom.toString() + "; focus");
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
- evalStateCommand(allComs.toString(), true /* false */);
+ return true;
}
-
- }
- private void checkLaunched()
- {
- if (!viewer.isChimeraLaunched())
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
+ if (launched)
{
- viewer.launchChimera(StructureManager.getChimeraPaths());
+ startChimeraProcessMonitor();
}
- if (!viewer.isChimeraLaunched())
+ else
{
log("Failed to launch Chimera!");
}
+ return launched;
}
/**
- * Answers true if the Chimera process is still running, false if ended or not
- * started.
+ * Returns a list of candidate paths to the Chimera program executable
*
* @return
*/
- public boolean isChimeraRunning()
+ protected List<String> getChimeraPaths()
{
- return viewer.isChimeraLaunched();
+ return StructureManager.getChimeraPaths(false);
}
/**
- * Send a command to Chimera, launching it first if necessary, and optionally
- * log any responses.
+ * Answers true if the Chimera process is still running, false if ended or not
+ * started.
*
- * @param command
- * @param logResponse
+ * @return
*/
- public void evalStateCommand(final String command, boolean logResponse)
+ public boolean isChimeraRunning()
{
- viewerCommandHistory(false);
- checkLaunched();
- if (lastCommand == null || !lastCommand.equals(command))
- {
- // trim command or it may never find a match in the replyLog!!
- lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
- if (debug && logResponse)
- {
- log("Response from command ('" + command + "') was:\n" + lastReply);
- }
- }
- viewerCommandHistory(true);
- lastCommand = command;
+ return chimeraManager.isChimeraLaunched();
}
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Send a command to Chimera, and optionally log and return any responses.
+ *
+ * @param command
+ * @param getResponse
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ @Override
+ public List<String> executeCommand(final String command,
+ boolean getResponse)
{
- if (!colourBySequence || !loadingFinished)
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
+ if (chimeraManager == null || command == null)
{
- fr = getFeatureRenderer(alignmentv);
+ // ? thread running after viewer shut down
+ return null;
}
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ List<String> reply = null;
+ // trim command or it may never find a match in the replyLog!!
+ List<String> lastReply = chimeraManager
+ .sendChimeraCommand(command.trim(), getResponse);
+ if (getResponse)
{
- for (String command : cpdbbyseq.commands)
+ reply = lastReply;
+ if (debug)
{
- executeWhenReady(command);
+ log("Response from command ('" + command + "') was:\n" + lastReply);
}
}
- }
- /**
- * @param files
- * @param sr
- * @param fr
- * @param alignment
- * @return
- */
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
- {
- return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, alignment);
+ return reply;
}
/**
protected void executeWhenReady(String command)
{
waitForChimera();
- evalStateCommand(command, false);
+ executeCommand(command, false);
waitForChimera();
}
private void waitForChimera()
{
- while (viewer != null && viewer.isBusy())
+ while (chimeraManager != null && chimeraManager.isBusy())
{
- try {
+ try
+ {
Thread.sleep(15);
} catch (InterruptedException q)
- {}
+ {
+ }
}
}
-
-
- // End StructureListener
- // //////////////////////////
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ @Override
+ public synchronized String[] getStructureFiles()
{
- if (getModelNum(pdbfile) < 0)
+ if (chimeraManager == null)
{
- return null;
+ return new String[0];
}
- log("get model / residue colour attribute unimplemented");
- return null;
- }
- /**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
+ }
/**
- * instruct the Jalview binding to update the pdbentries vector if necessary
- * prior to matching the jmol view's contents to the list of structure files
- * Jalview knows about.
+ * 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.
*/
- public abstract void refreshPdbEntries();
-
- private int getModelNum(String modelFileName)
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- String[] mfn = getPdbFile();
- if (mfn == null)
+ if (atoms == null || atoms.size() == 0)
{
- return -1;
+ return;
}
- for (int i = 0; i < mfn.length; i++)
+
+ boolean forChimeraX = chimeraManager.isChimeraX();
+ StringBuilder cmd = new StringBuilder(128);
+ boolean first = true;
+ boolean found = false;
+
+ for (AtomSpec atom : atoms)
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+ String pdbfile = atom.getPdbFile();
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
+ if (cms != null && !cms.isEmpty())
{
- return i;
+ if (first)
+ {
+ cmd.append(forChimeraX ? "label #" : "rlabel #");
+ }
+ else
+ {
+ cmd.append(",");
+ }
+ first = false;
+ if (forChimeraX)
+ {
+ cmd.append(cms.get(0).getModelNumber())
+ .append("/").append(chain).append(":").append(pdbResNum);
+ }
+ else
+ {
+ cmd.append(cms.get(0).getModelNumber())
+ .append(":").append(pdbResNum);
+ if (!chain.equals(" ") && !forChimeraX)
+ {
+ cmd.append(".").append(chain);
+ }
+ }
+ found = true;
}
}
- return -1;
- }
+ String command = cmd.toString();
- /**
- * 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[];
+ /*
+ * avoid repeated commands for the same residue
+ */
+ if (command.equals(lastHighlightCommand))
+ {
+ return;
+ }
- // ////////////////////////////////
- // /StructureListener
- public synchronized String[] getPdbFile()
- {
- if (viewer == null)
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- return new String[0];
+ chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
}
- // if (modelFileNames == null)
- // {
- // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
- // _modelFileNameMap = new int[chimodels.size()];
- // int j = 0;
- // for (ChimeraModel chimodel : chimodels)
- // {
- // String mdlName = chimodel.getModelName();
- // }
- // modelFileNames = new String[j];
- // // System.arraycopy(mset, 0, modelFileNames, 0, j);
- // }
-
- return chimeraMaps.keySet().toArray(
- modelFileNames = new String[chimeraMaps.size()]);
+ if (found)
+ {
+ chimeraManager.sendChimeraCommand(command, false);
+ }
+ this.lastHighlightCommand = command;
}
/**
- * map from string to applet
+ * Query Chimera for its current selection, and highlight it on the alignment
*/
- public Map getRegistryInfo()
+ public void highlightChimeraSelection()
{
- // TODO Auto-generated method stub
- return null;
+ /*
+ * Ask Chimera for its current selection
+ */
+ List<String> selection = chimeraManager.getSelectedResidueSpecs();
+
+ /*
+ * 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);
+
+ /*
+ * Broadcast the selection (which may be empty, if the user just cleared all
+ * selections)
+ */
+ getSsm().mouseOverStructure(atomSpecs);
}
/**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
+ * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
+ * corresponding residues (if any) in Jalview
*
+ * @param structureSelection
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
- /**
- * Construct and send a command to highlight an atom.
- *
- * <pre>
- * Done by generating a command like (to 'highlight' position 44)
- * ~show #0:43.C;show #0:44.C
- * Note this removes the highlight from the previous position.
- * </pre>
- */
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ protected List<AtomSpec> convertStructureResiduesToAlignment(
+ List<String> structureSelection)
{
- List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
- if (cms != null)
+ boolean chimeraX = chimeraManager.isChimeraX();
+ List<AtomSpec> atomSpecs = new ArrayList<>();
+ for (String atomSpec : structureSelection)
{
- StringBuilder sb = new StringBuilder();
- sb.append(" #" + cms.get(0).getModelNumber());
- sb.append(":" + pdbResNum);
- if (!chain.equals(" "))
+ try
{
- sb.append("." + chain);
- }
- String atomSpec = sb.toString();
-
- StringBuilder command = new StringBuilder(32);
- if (lastMousedOverAtomSpec != null)
- {
- command.append("~show " + lastMousedOverAtomSpec + ";");
- }
- viewerCommandHistory(false);
- command.append("show ").append(atomSpec);
- String cmd = command.toString();
- if (cmd.length() > 0)
+ AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX);
+ String pdbfilename = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbfilename);
+ atomSpecs.add(spec);
+ } catch (IllegalArgumentException e)
{
- viewer.stopListening(chimeraListener.getUri());
- viewer.sendChimeraCommand(cmd, false);
- viewer.startListening(chimeraListener.getUri());
+ System.err.println("Failed to parse atomspec: " + atomSpec);
}
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
}
+ return atomSpecs;
}
/**
- * Query Chimera for its current selection, and highlight it on the alignment
+ * @param modelId
+ * @return
*/
- public void highlightChimeraSelection()
+ protected String getPdbFileForModel(int modelId)
{
/*
- * Ask Chimera for its current selection
+ * Work out the pdbfilename from the model number
*/
- List<String> selection = viewer.getSelectedResidueSpecs();
-
- /*
- * 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 = new ArrayList<AtomSpec>();
- for (String atomSpec : selection)
+ String pdbfilename = modelFileNames[0];
+ findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
{
- int colonPos = atomSpec.indexOf(":");
- if (colonPos == -1)
- {
- continue; // malformed
- }
-
- int hashPos = atomSpec.indexOf("#");
- String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
- int dotPos = modelSubmodel.indexOf(".");
- int modelId = 0;
- try {
- modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
- : modelSubmodel.substring(0, dotPos));
- } catch (NumberFormatException e) {
- // ignore, default to model 0
- }
-
- String residueChain = atomSpec.substring(colonPos + 1);
- dotPos = residueChain.indexOf(".");
- int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
- : residueChain.substring(0, dotPos));
-
- String chainId = dotPos == -1 ? "" : residueChain
- .substring(dotPos + 1);
-
- /*
- * Work out the pdbfilename from the model number
- */
- String pdbfilename = modelFileNames[frameNo];
- findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+ for (ChimeraModel cm : chimeraMaps.get(pdbfile))
{
- for (ChimeraModel cm : chimeraMaps.get(pdbfile))
+ if (cm.getModelNumber() == modelId)
{
- if (cm.getModelNumber() == modelId)
- {
- pdbfilename = pdbfile;
- break findfileloop;
- }
+ pdbfilename = pdbfile;
+ break findfileloop;
}
}
- atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
}
-
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
+ return pdbfilename;
}
private void log(String message)
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;
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
+ /**
+ * Ask Chimera to save its session to the given file. Returns true if
+ * successful, else false.
+ *
+ * @param filepath
+ * @return
+ */
+ public boolean saveSession(String filepath)
{
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- // Chimera expects RBG values in the range 0-1
- final double normalise = 255D;
- viewerCommandHistory(false);
- StringBuilder command = new StringBuilder(128);
-
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
- for (String res : residueSet)
+ if (isChimeraRunning())
{
- Color col = cs.findColour(res.charAt(0));
- command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
+ /*
+ * 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());
+ }
}
-
- evalStateCommand(command.toString(),false);
- viewerCommandHistory(true);
+ return false;
}
/**
- * 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.
+ * 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 abstract void refreshGUI();
-
- public void setLoadingFromArchive(boolean loadingFromArchive)
+ public boolean openSession(String filepath)
{
- this.loadingFromArchive = loadingFromArchive;
+ /*
+ * 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
*
- * @return true if Chimeral is still restoring state or loading is still going
- * on (see setFinsihedLoadingFromArchive)
+ * TODO: pull up to abstract structure viewer interface
+ *
+ * @param vp
*/
- public boolean isLoadingFromArchive()
+ public void highlightSelection(AlignmentViewPanel vp)
{
- return loadingFromArchive && !loadingFinished;
+ 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);
+ }
}
/**
- * modify flag which controls if sequence colouring events are honoured by the
- * binding. Should be true for normal operation
+ * Constructs and send commands to Chimera to set attributes on residues for
+ * features visible in Jalview
*
- * @param finishedLoading
+ * @param avp
+ * @return
*/
- public void setFinishedLoadingFromArchive(boolean finishedLoading)
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
- loadingFinished = finishedLoading;
+ // 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)
+ {
+ sendCommandsByFile(commands);
+ }
+ else
+ {
+ for (String command : commands)
+ {
+ sendAsynchronousCommand(command, null);
+ }
+ }
+ return commands.length;
}
/**
- * Send the Chimera 'background solid <color>" command.
+ * 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.
*
- * @see https
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
- * .html
- * @param col
+ * @param commands
+ */
+ protected void sendCommandsByFile(String[] commands)
+ {
+ try
+ {
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
+ tmp.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+ for (String command : commands)
+ {
+ out.println(command);
+ }
+ out.flush();
+ out.close();
+ String path = tmp.getAbsolutePath();
+ String command = getCommandGenerator().openCommandFile(path);
+ sendAsynchronousCommand(command, null);
+ } catch (IOException e)
+ {
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
+ * @return
*/
- public void setBackgroundColour(Color col)
+ protected String getCommandFileExtension()
{
- viewerCommandHistory(false);
- double normalise = 255D;
- final String command = "background solid " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + ";";
- viewer.sendChimeraCommand(command, false);
- viewerCommandHistory(true);
+ return ".com";
}
/**
+ * Get Chimera residues which have the named attribute, find the mapped
+ * positions in the Jalview sequence(s), and set as sequence features
*
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
+ * @param attName
+ * @param alignmentPanel
*/
- public String printMapping(String pdbfile)
+ public void copyStructureAttributesToFeatures(String attName,
+ AlignmentViewPanel alignmentPanel)
{
- return getSsm().printMapping(pdbfile);
+ // 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();
+ }
}
/**
- * Ask Chimera to save its session to the given file. Returns true if
- * successful, else false.
+ * Create features in Jalview for the given attribute name and structure
+ * residues.
*
- * @param filepath
+ * <pre>
+ * The residue list should be 0, 1 or more reply lines of the format:
+ * residue id #0:5.A isHelix -155.000836316 index 5
+ * or
+ * residue id #0:6.A isHelix None
+ * </pre>
+ *
+ * @param attName
+ * @param residues
* @return
*/
- public boolean saveSession(String filepath)
+ protected boolean createFeaturesForAttributes(String attName,
+ List<String> residues)
{
- if (isChimeraRunning())
+ boolean featureAdded = false;
+ String featureGroup = getViewerFeatureGroup();
+ boolean chimeraX = chimeraManager.isChimeraX();
+
+ for (String residue : residues)
{
- List<String> reply = viewer.sendChimeraCommand("save " + filepath,
- true);
- if (reply.contains("Session written"))
+ AtomSpec spec = null;
+ String[] tokens = residue.split(" ");
+ if (tokens.length < 5)
{
- return true;
+ continue;
}
- else
+ String atomSpec = tokens[2];
+ String attValue = tokens[4];
+
+ /*
+ * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
+ */
+ if ("None".equalsIgnoreCase(attValue)
+ || "False".equalsIgnoreCase(attValue))
{
- Cache.log
- .error("Error saving Chimera session: " + reply.toString());
+ continue;
+ }
+
+ try
+ {
+ spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX);
+ } catch (IllegalArgumentException e)
+ {
+ System.err.println("Problem parsing atomspec " + atomSpec);
+ continue;
+ }
+
+ String chainId = spec.getChain();
+ String description = attValue;
+ float score = Float.NaN;
+ try
+ {
+ score = Float.valueOf(attValue);
+ description = chainId;
+ } catch (NumberFormatException e)
+ {
+ // was not a float value
+ }
+
+ String pdbFile = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbFile);
+
+ List<AtomSpec> atoms = Collections.singletonList(spec);
+
+ /*
+ * locate the mapped position in the alignment (if any)
+ */
+ SearchResultsI sr = getSsm()
+ .findAlignmentPositionsForStructurePositions(atoms);
+
+ /*
+ * expect one matched alignment position, or none
+ * (if the structure position is not mapped)
+ */
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ int start = m.getStart();
+ int end = m.getEnd();
+ SequenceFeature sf = new SequenceFeature(attName, description,
+ 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);
}
}
- return false;
+ return featureAdded;
}
/**
- * Ask Chimera to open a session file. Returns true if successful, else false.
- * The filename must have a .py extension for this command to work.
+ * Answers the feature group name to apply to features created in Jalview from
+ * Chimera attributes
*
- * @param filepath
* @return
*/
- public boolean openSession(String filepath)
+ protected String getViewerFeatureGroup()
{
- evalStateCommand("open " + filepath, true);
- // todo: test for failure - how?
- return true;
+ // todo pull up to interface
+ return CHIMERA_FEATURE_GROUP;
}
- public boolean isFinishedInit()
+ @Override
+ public int getModelNoForFile(String pdbFile)
{
- return finishedInit;
+ List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
+ if (foundModels != null && !foundModels.isEmpty())
+ {
+ return foundModels.get(0).getModelNumber();
+ }
+ return -1;
}
- public void setFinishedInit(boolean finishedInit)
+ /**
+ * Answers a (possibly empty) list of attribute names in Chimera[X], excluding
+ * any which were added from Jalview
+ *
+ * @return
+ */
+ public List<String> getChimeraAttributes()
{
- this.finishedInit = finishedInit;
+ List<String> atts = chimeraManager.getAttrList();
+ Iterator<String> it = atts.iterator();
+ while (it.hasNext())
+ {
+ if (it.next().startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ {
+ /*
+ * attribute added from Jalview - exclude it
+ */
+ it.remove();
+ }
+ }
+ return atts;
}
- public List<String> getChainNames()
+ /**
+ * Returns the file extension to use for a saved viewer session file
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
{
- return chainNames;
+ return ".py";
}
+ public String getHelpURL()
+ {
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+ }
}