/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
*
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
import java.awt.Color;
+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.Collections;
+import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
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 String ALPHACARBON = "CA";
+ private List<String> chainNames = new ArrayList<String>();
+
+ private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+
/*
* Object through which we talk to Chimera
*/
*/
private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
- /*
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- private int frameNo = 0;
-
- private String lastCommand;
-
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
- String lastMousedOverAtomSpec;
-
- private List<String> lastReply;
+ String lastHighlightCommand;
/*
* incremented every time a load notification is successfully handled -
* @param ssm
* @param pdbentry
* @param sequenceIs
- * @param chains
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(
new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
boolean first = true;
for (String chain : toshow)
{
+ int modelNumber = getModelNoForChain(chain);
+ String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
+ + chain.split(":")[1];
if (!first)
{
cmd.append(",");
}
- cmd.append(":.").append(chain);
+ cmd.append(showChainCmd);
first = false;
}
* window, but it looks more helpful not to (easier to relate chains to the
* whole)
*/
- final String command = "~display #*; ~ribbon #*; ribbon "
+ final String command = "~display #*; ~ribbon #*; ribbon :"
+ cmd.toString();
sendChimeraCommand(command, false);
}
chimeraListener.shutdown();
chimeraListener = null;
}
- lastCommand = null;
viewer = null;
releaseUIResources();
}
/**
- * Send a command to Chimera, and optionally log any responses.
+ * Send a command to Chimera, and optionally log and return any responses.
+ * <p>
+ * Does nothing, and returns null, if the command is the same as the last one
+ * sent [why?].
*
* @param command
- * @param logResponse
+ * @param getResponse
*/
- public void sendChimeraCommand(final String command, boolean logResponse)
+ public List<String> sendChimeraCommand(final String command,
+ boolean getResponse)
{
if (viewer == null)
{
// ? thread running after viewer shut down
- return;
+ return null;
}
+ List<String> reply = null;
viewerCommandHistory(false);
- if (lastCommand == null || !lastCommand.equals(command))
+ if (true /*lastCommand == null || !lastCommand.equals(command)*/)
{
// trim command or it may never find a match in the replyLog!!
- lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
- if (logResponse && debug)
+ List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ getResponse);
+ if (getResponse)
{
- log("Response from command ('" + command + "') was:\n" + lastReply);
+ reply = lastReply;
+ if (debug)
+ {
+ log("Response from command ('" + command + "') was:\n"
+ + lastReply);
+ }
}
}
viewerCommandHistory(true);
- lastCommand = command;
+
+ return reply;
}
/**
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
+ .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
+ fr, alignment);
+ for (String command : colourBySequenceCommands.commands)
{
- for (String command : cpdbbyseq.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
/**
- * @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);
- }
-
- /**
* @param command
*/
protected void executeWhenReady(String command)
// End StructureListener
// //////////////////////////
- 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
*/
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++)
- {
- if (mfn[i].equalsIgnoreCase(modelFileName))
- {
- return i;
- }
- }
- 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[];
-
// ////////////////////////////////
// /StructureListener
@Override
{
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 chimeraMaps.keySet().toArray(
modelFileNames = new String[chimeraMaps.size()]);
}
/**
- * map from string to applet
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
* returns the current sequenceRenderer that should be used to colour the
* structures
*
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight zero, one or more atoms.
- *
- * <pre>
- * Done by generating a command like (to 'highlight' position 44)
- * show #0:44.C
- * </pre>
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
- if (atoms == null)
+ if (atoms == null || atoms.size() == 0)
{
return;
}
- StringBuilder atomSpecs = new StringBuilder();
+
+ StringBuilder cmd = new StringBuilder(128);
boolean first = true;
+ boolean found = false;
+
for (AtomSpec atom : atoms)
{
int pdbResNum = atom.getPdbResNum();
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
- /*
- * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
- * concatenate multiple 'show' commands
- */
- atomSpecs.append(first ? "" : ";show ");
+ if (first)
+ {
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
+ .append(":");
+ }
+ else
+ {
+ cmd.append(",");
+ }
first = false;
- atomSpecs.append("#" + cms.get(0).getModelNumber());
- atomSpecs.append(":" + pdbResNum);
+ cmd.append(pdbResNum);
if (!chain.equals(" "))
{
- atomSpecs.append("." + chain);
+ cmd.append(".").append(chain);
}
+ found = true;
}
}
- String atomSpec = atomSpecs.toString();
+ String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
- if (atomSpec.equals(lastMousedOverAtomSpec))
+ if (command.equals(lastHighlightCommand))
{
return;
}
- StringBuilder command = new StringBuilder(32);
- viewerCommandHistory(false);
- if (atomSpec.length() > 0)
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- command.append("show ").append(atomSpec);
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
}
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ if (found)
+ {
+ viewer.sendChimeraCommand(command, false);
+ }
+ this.lastHighlightCommand = command;
}
/**
* 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);
+ }
+
+ /**
+ * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
+ * corresponding residues (if any) in Jalview
+ *
+ * @param structureSelection
+ * @return
+ */
+ protected List<AtomSpec> convertStructureResiduesToAlignment(
+ List<String> structureSelection)
+ {
List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
- for (String atomSpec : selection)
+ for (String atomSpec : structureSelection)
{
- 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)
+ AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
+ String pdbfilename = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbfilename);
+ atomSpecs.add(spec);
+ } catch (IllegalArgumentException e)
{
- // ignore, default to model 0
+ System.err.println("Failed to parse atomspec: " + atomSpec);
}
+ }
+ return atomSpecs;
+ }
- 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())
+ /**
+ * @param modelId
+ * @return
+ */
+ 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))
{
- 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)
*/
public abstract void refreshGUI();
+ @Override
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
* @return true if Chimeral is still restoring state or loading is still going
* on (see setFinsihedLoadingFromArchive)
*/
+ @Override
public boolean isLoadingFromArchive()
{
return loadingFromArchive && !loadingFinished;
*
* @param finishedLoading
*/
+ @Override
public void setFinishedLoadingFromArchive(boolean finishedLoading)
{
loadingFinished = finishedLoading;
*
* @return
*/
+ @Override
public List<String> getChainNames()
{
- List<String> names = new ArrayList<String>();
- String[][] allNames = getChains();
- if (allNames != null)
+ return chainNames;
+ }
+
+ /**
+ * Send a 'focus' command to Chimera to recentre the visible display
+ */
+ public void focusView()
+ {
+ sendChimeraCommand("focus", false);
+ }
+
+ /**
+ * Send a 'show' command for all atoms in the currently selected columns
+ *
+ * TODO: pull up to abstract structure viewer interface
+ *
+ * @param vp
+ */
+ public void highlightSelection(AlignmentViewPanel vp)
+ {
+ List<Integer> cols = vp.getAlignViewport().getColumnSelection()
+ .getSelected();
+ AlignmentI alignment = vp.getAlignment();
+ StructureSelectionManager sm = getSsm();
+ for (SequenceI seq : alignment.getSequences())
{
- for (String[] chainsForPdb : allNames)
+ /*
+ * convert selected columns into sequence positions
+ */
+ int[] positions = new int[cols.size()];
+ int i = 0;
+ for (Integer col : cols)
{
- if (chainsForPdb != null)
- {
- for (String chain : chainsForPdb)
- {
- if (chain != null && !names.contains(chain))
- {
- names.add(chain);
- }
- }
- }
+ positions[i++] = seq.findPosition(col);
}
+ sm.highlightStructure(this, seq, positions);
}
- return names;
}
/**
- * Send a 'focus' command to Chimera to recentre the visible display
+ * Constructs and send commands to Chimera to set attributes on residues for
+ * features visible in Jalview
+ *
+ * @param avp
*/
- public void focusView()
+ public void sendFeaturesToViewer(AlignmentViewPanel avp)
{
- sendChimeraCommand("focus", false);
+ // TODO refactor as required to pull up to an interface
+ AlignmentI alignment = avp.getAlignment();
+ FeatureRenderer fr = getFeatureRenderer(avp);
+
+ /*
+ * fr is null if feature display is turned off
+ */
+ if (fr == null)
+ {
+ return;
+ }
+
+ String[] files = getPdbFile();
+ if (files == null)
+ {
+ return;
+ }
+
+ StructureMappingcommandSet commandSet = ChimeraCommands
+ .getSetAttributeCommandsForFeatures(getSsm(), files,
+ getSequence(), fr, alignment);
+ String[] commands = commandSet.commands;
+ if (commands.length > 10)
+ {
+ sendCommandsByFile(commands);
+ }
+ else
+ {
+ for (String command : commands)
+ {
+ sendAsynchronousCommand(command, null);
+ }
+ }
+ }
+
+ /**
+ * Write commands to a temporary file, and send a command to Chimera to open
+ * the file as a commands script. For use when sending a large number of
+ * separate commands would overload the REST interface mechanism.
+ *
+ * @param commands
+ */
+ protected void sendCommandsByFile(String[] commands)
+ {
+ try
+ {
+ File tmp = File.createTempFile("chim", ".com");
+ tmp.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+ for (String command : commands)
+ {
+ out.println(command);
+ }
+ out.flush();
+ out.close();
+ String path = tmp.getAbsolutePath();
+ sendAsynchronousCommand("open cmd:" + path, null);
+ } catch (IOException e)
+ {
+ System.err
+ .println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Get Chimera residues which have the named attribute, find the mapped
+ * positions in the Jalview sequence(s), and set as sequence features
+ *
+ * @param attName
+ * @param alignmentPanel
+ */
+ public void copyStructureAttributesToFeatures(String attName,
+ AlignmentViewPanel alignmentPanel)
+ {
+ // todo pull up to AAStructureBindingModel (and interface?)
+
+ /*
+ * ask Chimera to list residues with the attribute, reporting its value
+ */
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+
+ String cmd = "list residues attr '" + attName + "'";
+ List<String> residues = sendChimeraCommand(cmd, true);
+
+ boolean featureAdded = createFeaturesForAttributes(attName, residues);
+ if (featureAdded)
+ {
+ alignmentPanel.getFeatureRenderer().featuresAdded();
+ }
+ }
+
+ /**
+ * 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>
+ *
+ * @param attName
+ * @param residues
+ * @return
+ */
+ protected boolean createFeaturesForAttributes(String attName,
+ List<String> residues)
+ {
+ boolean featureAdded = false;
+ String featureGroup = getViewerFeatureGroup();
+
+ for (String residue : residues)
+ {
+ AtomSpec spec = null;
+ String[] tokens = residue.split(" ");
+ if (tokens.length < 5)
+ {
+ continue;
+ }
+ 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))
+ {
+ continue;
+ }
+
+ try
+ {
+ spec = AtomSpec.fromChimeraAtomspec(atomSpec);
+ } 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)
+ */
+ SearchResults 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 featureAdded;
+ }
+
+ /**
+ * Answers the feature group name to apply to features created in Jalview from
+ * Chimera attributes
+ *
+ * @return
+ */
+ protected String getViewerFeatureGroup()
+ {
+ // todo pull up to interface
+ return CHIMERA_FEATURE_GROUP;
+ }
+
+
+ public Hashtable<String, String> getChainFile()
+ {
+ return chainFile;
+ }
+
+ public List<ChimeraModel> getChimeraModelByChain(String chain)
+ {
+ return chimeraMaps.get(chainFile.get(chain));
+ }
+
+ public int getModelNoForChain(String chain)
+ {
+ List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+ if (foundModels != null && !foundModels.isEmpty())
+ {
+ return foundModels.get(0).getModelNumber();
+ }
+ return -1;
}
}
git://source.jalview.org / jalview.git / blobdiff