/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.rbvi.chimera;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.SequenceStructureBindingModel;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.awt.event.ComponentEvent;
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.Enumeration;
-import java.util.HashMap;
+import java.util.Collections;
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
- SequenceStructureBindingModel implements StructureListener,
- SequenceStructureBinding, StructureSelectionManagerProvider
-
+public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
+ 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";
- private StructureManager csm;
-
- private ChimeraManager viewer;
-
- /**
- * 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.
+ /*
+ * Object through which we talk to Chimera
*/
- private boolean loadingFromArchive = false;
+ private ChimeraManager chimeraManager;
- /**
- * second flag to indicate if the Chimera viewer should ignore sequence
- * colouring events from the structure manager because the GUI is still
- * setting up
+ /*
+ * Object which listens to Chimera notifications
*/
- private boolean loadingFinished = true;
+ private AbstractRequestHandler chimeraListener;
- /**
- * state flag used to check if the Chimera viewer's paint method can be called
+ /*
+ * Map of ChimeraModel objects keyed by PDB full local file name
*/
- private boolean finishedInit = false;
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
- boolean allChainsSelected = false;
+ String lastHighlightCommand;
/**
- * when true, try to search the associated datamodel for sequences that are
- * associated with any unknown structures in the Chimera view.
- */
- private boolean associateNewStructs = false;
-
- List<String> atomsPicked = new ArrayList<String>();
-
- public List<String> chainNames;
-
- private Map<String, String> chainFile;
-
- /**
- * array of target chains for sequences - tied to pdbentry and sequence[]
+ * Returns a model of the structure positions described by the Chimera format
+ * atomspec
+ *
+ * @param atomSpec
+ * @return
*/
- protected String[][] chains;
-
- boolean colourBySequence = true;
-
- StringBuffer eval = new StringBuffer();
-
- public String fileLoadingError;
-
- private Map<String, List<ChimeraModel>> chimmaps = new LinkedHashMap<String, List<ChimeraModel>>();
-
- private List<String> mdlToFile = new ArrayList<String>();
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraAtomspec(atomSpec);
+ }
/**
- * the default or current model displayed if the model cannot be identified
- * from the selection message
+ * 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.
+ *
+ * @param pe
+ * @return
*/
- int frameNo = 0;
-
- String lastCommand;
-
- String lastMessage;
-
- boolean loadedInline;
-
public boolean openFile(PDBEntry pe)
{
String file = pe.getFile();
try
{
- List<ChimeraModel> oldList = viewer.getModelList();
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- List<ChimeraModel> newList = viewer.getModelList();
- if (oldList.size() < newList.size())
+ List<ChimeraModel> modelsToMap = new ArrayList<>();
+ List<ChimeraModel> oldList = chimeraManager.getModelList();
+ boolean alreadyOpen = false;
+
+ /*
+ * If Chimera already has this model, don't reopen it, but do remap it.
+ */
+ for (ChimeraModel open : oldList)
{
- while (oldList.size() > 0)
- {
- oldList.remove(0);
- newList.remove(0);
- }
- chimmaps.put(file, newList);
- for (ChimeraModel cm : newList)
+ if (open.getModelName().equals(pe.getId()))
{
- while (mdlToFile.size() < 1 + cm.getModelNumber())
- {
- mdlToFile.add(new String(""));
- }
- mdlToFile.set(cm.getModelNumber(), file);
+ alreadyOpen = true;
+ modelsToMap.add(open);
}
+ }
- File fl = new File(file);
- String protocol = AppletFormatAdapter.URL;
- try
- {
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
- {
- }
- // Explicitly map to the filename used by Chimera ;
- // pdbentry[pe].getFile(), protocol);
+ /*
+ * If Chimera doesn't yet have this model, ask it to open it, and retrieve
+ * the model name(s) added by Chimera.
+ */
+ if (!alreadyOpen)
+ {
+ chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ addChimeraModel(pe, modelsToMap);
+ }
- if (ssm != null)
- {
- ssm.addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
- }
- return true;
+ chimeraMaps.put(file, modelsToMap);
+
+ if (getSsm() != null)
+ {
+ getSsm().addStructureViewerListener(this);
}
+ return true;
} catch (Exception q)
{
log("Exception when trying to open model " + file + "\n"
}
/**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
- public PDBEntry[] pdbentry;
-
- /**
- * datasource protocol for access to PDBEntrylatest
- */
- String protocol = null;
-
- StringBuffer resetLastRes = new StringBuffer();
-
- /**
- * sequences mapped to each pdbentry
+ * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
+ * name matching PDB id
+ *
+ * @param pe
+ * @param modelsToMap
*/
- public SequenceI[][] sequence;
-
- public StructureSelectionManager ssm;
-
- private List<String> lastReply;
-
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
{
- this.ssm = ssm;
- this.sequence = sequenceIs;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
- if (chains == null)
+ /*
+ * 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)
{
- this.chains = new String[pdbentry.length][];
+ if (cm.getModelName().equals(pe.getId()))
+ {
+ modelsToMap.add(cm);
+ }
}
- viewer = new ChimeraManager(
- csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
- }
-
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- ChimeraManager viewer2)
- {
- this.ssm = ssm;
- viewer = viewer2;
- csm = viewer.getStructureManager();
}
/**
- * Construct a title string for the viewer window based on the data Jalview
- * knows about
+ * Constructor
*
- * @param verbose
- * @return
+ * @param ssm
+ * @param pdbentry
+ * @param sequenceIs
+ * @param protocol
*/
- public String getViewerTitle(boolean verbose)
+ public JalviewChimeraBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- if (sequence == null || pdbentry == null || sequence.length < 1
- || pdbentry.length < 1 || sequence[0].length < 1)
- {
- return ("Jalview Chimera Window");
- }
- // TODO: give a more informative title when multiple structures are
- // displayed.
- StringBuilder title = new StringBuilder(64);
- title.append("Chimera view for " + sequence[0][0].getName() + ":"
- + pdbentry[0].getId());
+ super(ssm, pdbentry, sequenceIs, protocol);
+ boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
+ chimeraManager = chimeraX
+ ? new ChimeraXManager(new StructureManager(true))
+ : new ChimeraManager(new StructureManager(true));
+ setStructureCommands(
+ chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
+ }
- if (verbose)
- {
- if (pdbentry[0].getProperty() != null)
- {
- if (pdbentry[0].getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry[0].getProperty().get("method"));
- }
- if (pdbentry[0].getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry[0].getProperty().get("chains"));
- }
- }
- }
- return title.toString();
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
}
/**
- * 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);
+ 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);
}
/**
- * Close down the Jalview viewer, and (optionally) the associate Chimera
- * window.
+ * Close down the Jalview viewer and listener, and (optionally) the associated
+ * Chimera window.
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
- ssm.removeStructureViewerListener(this, this.getPdbFile());
- if (closeChimera)
+ super.closeViewer(closeChimera);
+ if (this.chimeraListener != null)
{
- viewer.exitChimera();
+ chimeraListener.shutdown();
+ chimeraListener = null;
}
- lastCommand = null;
- viewer = null;
- releaseUIResources();
- }
-
- /**
- * called by JalviewChimerabinding after closeViewer is called - release any
- * resources and references so they can be garbage collected.
- */
- protected abstract void 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);
- }
+ /*
+ * 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))
+ {
+ chimeraManager.getChimeraProcess().destroy();
+ }
- /**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions.
- */
- public void superposeStructures(AlignmentI alignment)
- {
- superposeStructures(alignment, -1, null);
+ chimeraManager.clearOnChimeraExit();
+ chimeraManager = 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)
- {
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
- }
-
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ public boolean launchChimera()
{
- 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 = ssm.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;
+ return true;
}
- 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 = ssm.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;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -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 (jalview.util.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 = sequence[pdbfnum].length;
- 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 */);
- }
-
- }
-
- private void checkLaunched()
- {
- if (!viewer.isChimeraLaunched())
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
+ if (launched)
{
- viewer.launchChimera(csm.getChimeraPaths());
+ startExternalViewerMonitor(chimeraManager.getChimeraProcess());
}
- 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, 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)
+ @Override
+ public boolean isViewerRunning()
{
- viewerCommandHistory(false);
- checkLaunched();
- if (lastCommand == null || !lastCommand.equals(command))
- {
-// Thread t = new Thread(new Runnable()
-// {
-// @Override
-// public void run()
-// {
- // 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);
- }
-// }
-// });
- // TODO - use j7/8 thread management
-// try
-// {
-// t.join();
-// } catch (InterruptedException foo)
-// {
-// }
-// ;
- }
- viewerCommandHistory(true);
- lastCommand = command;
+ return chimeraManager != null && 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 StructureCommandI command,
+ boolean getResponse)
{
- if (!colourBySequence || !loadingFinished)
- {
- return;
- }
- if (ssm == null)
+ if (chimeraManager == null || command == null)
{
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
+ // ? thread running after viewer shut down
+ return null;
}
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands
- .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
- alignment))
+ 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(cmd,
+ getResponse);
+ if (getResponse)
{
- for (String cbyseq : cpdbbyseq.commands)
+ reply = lastReply;
+ if (Console.isDebugEnabled())
{
- waitForChimera();
- evalStateCommand(cbyseq, false);
- waitForChimera();
+ Console.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
- }
-
- private void waitForChimera()
- {
- while (viewer != null && viewer.isBusy())
- {
- try {
- Thread.sleep(15);
- } catch (InterruptedException q)
- {}
- }
- }
-
- public boolean isColourBySequence()
- {
- return colourBySequence;
- }
-
- public void setColourBySequence(boolean colourBySequence)
- {
- this.colourBySequence = colourBySequence;
- }
-
- // End StructureListener
- // //////////////////////////
-
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- {
- return null;
- }
- 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);
-
- /**
- * 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.
- */
- public abstract void refreshPdbEntries();
-
- private int getModelNum(String modelFileName)
- {
- String[] mfn = getPdbFile();
- if (mfn == null)
- {
- return -1;
- }
- for (int i = 0; i < mfn.length; i++)
+ else
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
+ if (Console.isDebugEnabled())
{
- return i;
+ Console.debug("Command executed: " + cmd);
}
}
- return -1;
- }
- /**
- * 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[];
+ return reply;
+ }
- // ////////////////////////////////
- // /StructureListener
- public synchronized String[] getPdbFile()
+ @Override
+ public synchronized String[] getStructureFiles()
{
- if (viewer == null)
+ if (chimeraManager == null)
{
return new String[0];
}
- // 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 chimmaps.keySet().toArray(
- modelFileNames = new String[chimmaps.size()]);
- }
- /**
- * map from string to applet
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
}
/**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
+ * 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 SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
- // jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- List<ChimeraModel> cms = chimmaps.get(pdbfile);
- if (cms != null)
- {
- int mdlNum = cms.get(0).getModelNumber();
-
- viewerCommandHistory(false);
- // viewer.stopListening();
- if (resetLastRes.length() > 0)
- {
- eval.setLength(0);
- eval.append(resetLastRes.toString() + ";");
- }
-
- eval.append("display "); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("~display ");
- {
- eval.append(" #" + (mdlNum));
- resetLastRes.append(" #" + (mdlNum));
- }
- // complete select string
-
- eval.append(":" + pdbResNum);
- resetLastRes.append(":" + pdbResNum);
- if (!chain.equals(" "))
- {
- eval.append("." + chain);
- resetLastRes.append("." + chain);
- }
-
- viewer.sendChimeraCommand(eval.toString(), false);
- viewerCommandHistory(true);
- // viewer.startListening();
- }
- }
-
- private void log(String message)
- {
- System.err.println("## Chimera log: " + message);
- }
-
- private void viewerCommandHistory(boolean enable)
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- // log("(Not yet implemented) History "
- // + ((debug || enable) ? "on" : "off"));
- }
-
- public void loadInline(String string)
- {
- loadedInline = true;
- // TODO: re JAL-623
- // viewer.loadInline(strModel, isAppend);
- // could do this:
- // construct fake fullPathName and fileName so we can identify the file
- // later.
- // Then, construct pass a reader for the string to Jmol.
- // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
- // fileName, null, reader, false, null, null, 0);
- // viewer.openStringInline(string);
- log("cannot load inline in Chimera, yet");
- }
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- // function to parse a mouseOver event from Chimera
- //
- int pdbResNum;
- int alocsep = strInfo.indexOf("^");
- int mdlSep = strInfo.indexOf("/");
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
- if (chainSeparator == -1)
+ if (atoms == null || atoms.size() == 0)
{
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
- {
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
- }
+ return;
}
- // handle insertion codes
- if (alocsep != -1)
- {
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, alocsep));
- }
- else
- {
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
- }
- String chainId;
+ boolean forChimeraX = chimeraManager.isChimeraX();
+ StringBuilder cmd = new StringBuilder(128);
+ boolean first = true;
+ boolean found = false;
- if (strInfo.indexOf(":") > -1)
+ for (AtomSpec atom : atoms)
{
- chainId = strInfo.substring(strInfo.indexOf(":") + 1,
- strInfo.indexOf("."));
- }
- else
- {
- chainId = " ";
- }
-
- String pdbfilename = modelFileNames[frameNo]; // default is first or current
- // model
- if (mdlSep > -1)
- {
- if (chainSeparator1 == -1)
- {
- chainSeparator1 = strInfo.indexOf(".", mdlSep);
- }
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
- try
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+ String pdbfile = atom.getPdbFile();
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
+ if (cms != null && !cms.isEmpty())
{
- // recover PDB filename for the model hovered over.
- int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
- .intValue() - 1;
- while (mnumber < _modelFileNameMap[_mp])
+ if (first)
{
- _mp--;
+ cmd.append(forChimeraX ? "label #" : "rlabel #");
}
- pdbfilename = modelFileNames[_mp];
- if (pdbfilename == null)
+ else
{
- // pdbfilename = new File(viewer.getModelFileName(mnumber))
- // .getAbsolutePath();
+ cmd.append(",");
}
-
- } catch (Exception e)
- {
+ 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;
}
- ;
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
}
+ String command = cmd.toString();
- lastMessage = strInfo;
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
- {
- /**
- * this implements the toggle label behaviour copied from the original
- * structure viewer, MCView
+ /*
+ * avoid repeated commands for the same residue
*/
- if (strData != null)
+ if (command.equals(lastHighlightCommand))
{
- System.err.println("Ignoring additional pick data string " + strData);
+ return;
}
- // rewrite these selections for chimera (DNA, RNA and protein)
- int chainSeparator = strInfo.indexOf(":");
- int p = 0;
- if (chainSeparator == -1)
+ if (!found)
{
- chainSeparator = strInfo.indexOf(".");
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
}
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
- String mdlString = "";
- if ((p = strInfo.indexOf(":")) > -1)
+ /*
+ * prepend with command
+ * to unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
- }
+ cmd.insert(0, ";");
+ cmd.insert(0, lastHighlightCommand);
+ cmd.insert(0, "~");
- if ((p = strInfo.indexOf("/")) > -1)
- {
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
}
- picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
- + mdlString + "))";
- viewerCommandHistory(false);
-
- if (!atomsPicked.contains(picked))
+ if (cmd.length() > 0)
{
- viewer.select(picked);
- atomsPicked.add(picked);
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
}
- else
+
+ if (found)
{
- viewer.select("not " + picked);
- atomsPicked.remove(picked);
+ this.lastHighlightCommand = command;
}
- viewerCommandHistory(true);
- // TODO: in application this happens
- //
- // if (scriptWindow != null)
- // {
- // scriptWindow.sendConsoleMessage(strInfo);
- // scriptWindow.sendConsoleMessage("\n");
- // }
-
}
- // 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;
-
- public long getLoadNotifiesHandled()
+ /**
+ * Query Chimera for its current selection, and highlight it on the alignment
+ */
+ public void highlightChimeraSelection()
{
- return loadNotifiesHandled;
- }
+ /*
+ * Ask Chimera for its current selection
+ */
+ StructureCommandI command = getCommandGenerator().getSelectedResidues();
- public void notifyFileLoaded(String fullPathName, String fileName2,
- String modelName, String errorMsg, int modelParts)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- refreshGUI();
- return;
- }
- // TODO: deal sensibly with models loaded inLine:
- // modelName will be null, as will fullPathName.
-
- // the rest of this routine ignores the arguments, and simply interrogates
- // the Jmol view to find out what structures it contains, and adds them to
- // the structure selection manager.
- fileLoadingError = null;
- String[] oldmodels = modelFileNames;
- modelFileNames = null;
- chainNames = new ArrayList<String>();
- chainFile = new HashMap<String, String>();
- boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
- // first check if we've lost any structures
- if (oldmodels != null && oldmodels.length > 0)
+ Runnable action = new Runnable()
{
- int oldm = 0;
- for (int i = 0; i < oldmodels.length; i++)
+ @Override
+ public void run()
{
- for (int n = 0; n < modelfilenames.length; n++)
- {
- if (modelfilenames[n] == oldmodels[i])
- {
- oldmodels[i] = null;
- break;
- }
- }
- if (oldmodels[i] != null)
- {
- oldm++;
- }
- }
- if (oldm > 0)
- {
- String[] oldmfn = new String[oldm];
- oldm = 0;
- for (int i = 0; i < oldmodels.length; i++)
+ List<String> chimeraReply = executeCommand(command, true);
+
+ List<String> selectedResidues = new ArrayList<>();
+ if (chimeraReply != null)
{
- if (oldmodels[i] != 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)
{
- oldmfn[oldm++] = oldmodels[i];
+ String[] inputLineParts = inputLine.split("\\s+");
+ if (inputLineParts.length >= 5)
+ {
+ selectedResidues.add(inputLineParts[2]);
+ }
}
}
- // deregister the Jmol instance for these structures - we'll add
- // ourselves again at the end for the current structure set.
- ssm.removeStructureViewerListener(this, oldmfn);
- }
- }
- // register ourselves as a listener and notify the gui that it needs to
- // update itself.
- ssm.addStructureViewerListener(this);
+ /*
+ * 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);
- if (notifyLoaded)
- {
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
}
- refreshGUI();
- loadNotifiesHandled++;
- }
- setLoadingFromArchive(false);
+ };
+ new Thread(action).start();
}
- public void setJalviewColourScheme(ColourSchemeI cs)
+ /**
+ * 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)
{
- colourBySequence = false;
-
- if (cs == null)
+ List<AtomSpec> atomSpecs = new ArrayList<>();
+ for (String atomSpec : structureSelection)
{
- return;
- }
-
- String res;
- int index;
- Color col;
- // Chimera expects RBG values in the range 0-1
- final double normalise = 255D;
- viewerCommandHistory(false);
- // TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuilder command = new StringBuilder(128);
- command.append("color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
+ try
{
- continue;
+ AtomSpec spec = parseAtomSpec(atomSpec);
+ String pdbfilename = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbfilename);
+ atomSpecs.add(spec);
+ } catch (IllegalArgumentException e)
+ {
+ Console.error("Failed to parse atomspec: " + atomSpec);
}
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
- command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
}
-
- evalStateCommand(command.toString(),false);
- viewerCommandHistory(true);
+ return atomSpecs;
}
/**
- * 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.
+ * @param modelId
+ * @return
*/
- public abstract void refreshGUI();
-
- public void componentResized(ComponentEvent e)
- {
-
- }
-
- public void componentMoved(ComponentEvent e)
- {
-
- }
-
- public void componentShown(ComponentEvent e)
- {
- }
-
- public void componentHidden(ComponentEvent e)
+ protected String getPdbFileForModel(int modelId)
{
+ /*
+ * Work out the pdbfilename from the model number
+ */
+ String pdbfilename = modelFileNames[0];
+ findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+ {
+ for (ChimeraModel cm : chimeraMaps.get(pdbfile))
+ {
+ if (cm.getModelNumber() == modelId)
+ {
+ pdbfilename = pdbfile;
+ break findfileloop;
+ }
+ }
+ }
+ return pdbfilename;
}
- public void setLoadingFromArchive(boolean loadingFromArchive)
+ private void log(String message)
{
- this.loadingFromArchive = loadingFromArchive;
+ System.err.println("## Chimera log: " + message);
}
/**
+ * Constructs and send commands to Chimera to set attributes on residues for
+ * 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
*
- * @return true if Chimeral is still restoring state or loading is still going
- * on (see setFinsihedLoadingFromArchive)
+ * @param avp
+ * @return
*/
- public boolean isLoadingFromArchive()
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
- return loadingFromArchive && !loadingFinished;
+ // TODO refactor as required to pull up to an interface
+
+ Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+ avp);
+ List<StructureCommandI> commands = getCommandGenerator()
+ .setAttributes(featureValues);
+ if (commands.size() > 10)
+ {
+ sendCommandsByFile(commands);
+ }
+ else
+ {
+ executeCommands(commands, false, null);
+ }
+ return commands.size();
}
/**
- * modify flag which controls if sequence colouring events are honoured by the
- * binding. Should be true for normal operation
+ * 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 finishedLoading
+ * @param commands
*/
- public void setFinishedLoadingFromArchive(boolean finishedLoading)
+ protected void sendCommandsByFile(List<StructureCommandI> commands)
{
- loadingFinished = finishedLoading;
+ try
+ {
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
+ tmp.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+ for (StructureCommandI command : commands)
+ {
+ out.println(command.getCommand());
+ }
+ out.flush();
+ out.close();
+ String path = tmp.getAbsolutePath();
+ StructureCommandI command = getCommandGenerator()
+ .openCommandFile(path);
+ executeCommand(false, null, command);
+ } catch (IOException e)
+ {
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
+ }
}
/**
- * Send the Chimera 'background solid <color>" command.
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
*
- * @see https
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
- * .html
- * @param col
+ * @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";
}
/**
- * add structures and any known sequence associations
+ * Create features in Jalview for the given attribute name and structure
+ * residues.
+ *
+ * <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>
*
- * @returns the pdb entries added to the current set.
+ * @param attName
+ * @param residues
+ * @return the number of features added
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
+ protected int createFeaturesForAttributes(String attName,
+ List<String> residues)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
- for (int i = 0; i < pdbentry.length; i++)
- {
- v.add(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
+ int featuresAdded = 0;
+ String featureGroup = getViewerFeatureGroup();
+
+ for (String residue : residues)
{
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
+ AtomSpec spec = null;
+ String[] tokens = residue.split(" ");
+ if (tokens.length < 5)
{
- rtn.add(new int[]
- { v.size(), i });
- v.add(pdbe[i]);
+ 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))
{
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
+ continue;
}
- }
- pdbe = v.toArray(new PDBEntry[v.size()]);
- pdbentry = pdbe;
- if (rtn.size() > 0)
- {
- // expand the tied sequence[] and string[] arrays
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];
- String[][] sch = new String[pdbentry.length][];
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);
- System.arraycopy(chains, 0, sch, 0, this.chains.length);
- sequence = sqs;
- chains = sch;
- pdbe = new PDBEntry[rtn.size()];
- for (int r = 0; r < pdbe.length; r++)
+
+ try
{
- int[] stri = (rtn.get(r));
- // record the pdb file as a new addition
- pdbe[r] = pdbentry[stri[0]];
- // and add the new sequence/chain entries
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+ spec = parseAtomSpec(atomSpec);
+ } catch (IllegalArgumentException e)
+ {
+ Console.error("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
+ if (seq.addSequenceFeature(sf))
+ {
+ featuresAdded++;
+ }
}
}
- else
- {
- pdbe = null;
- }
- return pdbe;
+ return featuresAdded;
}
/**
- * Adds sequences to the pe'th pdbentry's sequence set.
+ * Answers the feature group name to apply to features created in Jalview from
+ * Chimera attributes
*
- * @param pe
- * @param seq
+ * @return
*/
- public void addSequence(int pe, SequenceI[] seq)
+ protected String getViewerFeatureGroup()
{
- addSequenceAndChain(pe, seq, null);
+ // todo pull up to interface
+ return CHIMERA_FEATURE_GROUP;
}
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ @Override
+ public String getModelIdForFile(String pdbFile)
{
- if (pe < 0 || pe >= pdbentry.length)
+ List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
+ if (foundModels != null && !foundModels.isEmpty())
{
- throw new Error(MessageManager.formatMessage(
- "error.implementation_error_no_pdbentry_from_index",
- new Object[]
- { Integer.valueOf(pe).toString() }));
+ return String.valueOf(foundModels.get(0).getModelNumber());
}
- final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
- if (chains == null)
- {
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
+ return "";
+ }
+
+ /**
+ * Answers a (possibly empty) list of attribute names in Chimera[X], excluding
+ * any which were added from Jalview
+ *
+ * @return
+ */
+ public List<String> getChimeraAttributes()
+ {
+ List<String> attributes = new ArrayList<>();
+ StructureCommandI command = getCommandGenerator()
+ .listResidueAttributes();
+ final List<String> reply = executeCommand(command, true);
+ if (reply != null)
{
- for (int i = 0; i < sequence[pe].length; i++)
+ for (String inputLine : reply)
{
- s.add(sequence[pe][i]);
- if (chains[pe] != null)
+ String[] lineParts = inputLine.split("\\s");
+ if (lineParts.length == 2 && lineParts[0].equals("resattr"))
{
- if (i < chains[pe].length)
- {
- c.add(chains[pe][i]);
- }
- else
+ String attName = lineParts[1];
+ /*
+ * exclude attributes added from Jalview
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- c.add(nullChain);
+ attributes.add(attName);
}
}
- else
- {
- if (tchain != null && tchain.length > 0)
- {
- c.add(nullChain);
- }
- }
- }
- }
- for (int i = 0; i < seq.length; i++)
- {
- if (!s.contains(seq[i]))
- {
- s.add(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.add(tchain[i] == null ? nullChain : tchain[i]);
- }
}
}
- SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
- sequence[pe] = tmp;
- if (c.size() > 0)
- {
- String[] tch = c.toArray(new String[c.size()]);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
- chains[pe] = tch;
- }
- else
- {
- chains[pe] = null;
- }
+ return attributes;
}
/**
+ * Returns the file extension to use for a saved viewer session file (.py)
*
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
+ * @return
*/
- public String printMapping(String pdbfile)
+ @Override
+ public String getSessionFileExtension()
{
- return ssm.printMapping(pdbfile);
+ return CHIMERA_SESSION_EXTENSION;
}
+ @Override
+ public String getHelpURL()
+ {
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+ }
}
git://source.jalview.org / jalview.git / blobdiff