package jalview.ext.rbvi.chimera;
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.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
+import jalview.io.DataSourceType;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import java.io.PrintWriter;
import java.net.BindException;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
+import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
{
public static final String CHIMERA_FEATURE_GROUP = "Chimera";
- private static final String CHIMERA_FEATURE_PREFIX = "chim_";
-
// 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 boolean loadingFinished = true;
- public String fileLoadingError;
-
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
*/
private long loadNotifiesHandled = 0;
+ private Thread chimeraMonitor;
+
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
}
return true;
} catch (Exception q)
* @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,
+ DataSourceType protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, protocol);
+ viewer = new ChimeraManager(new StructureManager(true));
+ }
+
+ /**
+ * Starts a thread that waits for the Chimera process to finish, so that we
+ * can then close the associated resources. This avoids leaving orphaned
+ * Chimera viewer panels in Jalview if the user closes Chimera.
+ */
+ protected void startChimeraProcessMonitor()
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
- viewer = new ChimeraManager(
- new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ final Process p = viewer.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();
}
/**
viewer.startListening(chimeraListener.getUri());
} catch (BindException e)
{
- System.err.println("Failed to start Chimera listener: "
- + e.getMessage());
+ System.err.println(
+ "Failed to start Chimera listener: " + e.getMessage());
}
}
/**
- * Construct a title string for the viewer window based on the data Jalview
- * knows about
- *
- * @param verbose
- * @return
- */
- public String getViewerTitle(boolean verbose)
- {
- return getViewerTitle(CHIMERA_FEATURE_GROUP, verbose);
- }
-
- /**
* Tells Chimera to display only the specified chains
*
* @param toshow
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);
}
*/
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
viewer.exitChimera();
}
viewer = null;
+ if (chimeraMonitor != null)
+ {
+ chimeraMonitor.interrupt();
+ }
releaseUIResources();
}
+ @Override
public void colourByChain()
{
colourBySequence = false;
* <li>all others - white</li>
* </ul>
*/
+ @Override
public void colourByCharge()
{
colourBySequence = false;
}
/**
- * Construct and send a command to align structures against a reference
- * structure, based on one or more sequence alignments
- *
- * @param _alignment
- * an array of alignments to process
- * @param _refStructure
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param _hiddenCols
- * an array of corresponding hidden columns for each alignment
+ * {@inheritDoc}
*/
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, HiddenColumns[] _hiddenCols)
{
StringBuilder allComs = new StringBuilder(128);
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (!waitForFileLoad(files))
{
- return;
+ return null;
}
refreshPdbEntries();
{
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
+ HiddenColumns hiddenCols = _hiddenCols[a];
if (refStructure >= files.length)
{
}
/*
- * 'matched' array will hold 'true' for visible alignment columns where
+ * 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to the PDB structure
*/
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
SuperposeData[] structures = new SuperposeData[files.length];
refStructure = candidateRefStructure;
}
- int nmatched = 0;
- for (boolean b : matched)
- {
- if (b)
- {
- nmatched++;
- }
- }
+ int nmatched = matched.cardinality();
if (nmatched < 4)
{
- // TODO: bail out here because superposition illdefined?
+ return MessageManager.formatMessage("label.insufficient_residues",
+ nmatched);
}
/*
int lpos = -1;
boolean run = false;
StringBuilder molsel = new StringBuilder();
- for (int r = 0; r < matched.length; r++)
+
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
{
- if (matched[r])
+ int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
+ if (lpos != pdbResNum - 1)
{
- int pdbResNum = structures[pdbfnum].pdbResNo[r];
- if (lpos != pdbResNum - 1)
+ /*
+ * discontiguous - append last residue now
+ */
+ if (lpos != -1)
{
- /*
- * discontiguous - append last residue now
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- molsel.append(chainCd);
- molsel.append(",");
- }
- run = false;
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ molsel.append(",");
}
- else
+ run = false;
+ }
+ else
+ {
+ /*
+ * extending a contiguous run
+ */
+ if (!run)
{
/*
- * extending a contiguous run
+ * start the range selection
*/
- if (!run)
- {
- /*
- * start the range selection
- */
- molsel.append(String.valueOf(lpos));
- molsel.append("-");
- }
- run = true;
+ molsel.append(String.valueOf(lpos));
+ molsel.append("-");
}
- lpos = pdbResNum;
+ run = true;
}
+ lpos = pdbResNum;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
/*
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
- System.out.println("Superimpose command(s):\n"
- + command.toString());
+ System.out.println(
+ "Superimpose command(s):\n" + command.toString());
}
allComs.append("~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString())
.append(";" + command.toString());
}
}
+
+ String error = null;
if (selectioncom.length() > 0)
{
// TODO: visually distinguish regions that were superposed
}
allComs.append("; ~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString()).append("; focus");
- sendChimeraCommand(allComs.toString(), false);
+ List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
+ true);
+ for (String reply : chimeraReplies)
+ {
+ if (reply.toLowerCase().contains("unequal numbers of atoms"))
+ {
+ error = reply;
+ }
+ }
}
-
+ return error;
}
/**
* to the Chimera command 'list models type molecule', see
* ChimeraManager.getModelList().
*/
- List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+ List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
boolean hasSubModels = maps != null && maps.size() > 1;
return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
/**
* Launch Chimera, unless an instance linked to this object is already
- * running. Returns true if chimera is successfully launched, or already
+ * running. Returns true if Chimera is successfully launched, or already
* running, else false.
*
* @return
*/
public boolean launchChimera()
{
- if (!viewer.isChimeraLaunched())
- {
- return viewer.launchChimera(StructureManager.getChimeraPaths());
- }
if (viewer.isChimeraLaunched())
{
return true;
}
- log("Failed to launch Chimera!");
- return false;
+
+ boolean launched = viewer
+ .launchChimera(StructureManager.getChimeraPaths());
+ if (launched)
+ {
+ startChimeraProcessMonitor();
+ }
+ else
+ {
+ log("Failed to launch Chimera!");
+ }
+ return launched;
}
/**
String progressMsg);
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
{
- if (!colourBySequence || !loadingFinished)
- {
- return;
- }
- if (getSsm() == null)
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
{
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
+ for (String command : cpdbbyseq.commands)
+ {
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
+ }
}
- AlignmentI alignment = alignmentv.getAlignment();
+ }
- StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr, alignment);
- for (String command : colourBySequenceCommands.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
+ /**
+ * @param files
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ @Override
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+ {
+ return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, viewPanel);
}
/**
// //////////////////////////
/**
- * 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 viewer'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++)
- {
- 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 -
// ////////////////////////////////
// /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
if (viewer == 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 chimeraMaps.keySet().toArray(
- modelFileNames = new String[chimeraMaps.size()]);
- }
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
+ }
/**
* Construct and send a command to highlight zero, one or more atoms. We do
* 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);
+ List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selection);
/*
* Broadcast the selection (which may be empty, if the user just cleared all
return loadNotifiesHandled;
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
- for (String res : residueSet)
+ for (String resName : residueSet)
{
- Color col = cs.findColour(res.charAt(0));
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
+ Color col = cs.findColour(res, 0, null, null, 0f);
command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
+ + col.getGreen() / normalise + "," + col.getBlue() / normalise
+ + " ::" + resName + ";");
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
*/
+ @Override
public void setBackgroundColour(Color col)
{
viewerCommandHistory(false);
double normalise = 255D;
final String command = "background solid " + col.getRed() / normalise
- + "," + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + ";";
+ + "," + col.getGreen() / normalise + ","
+ + col.getBlue() / normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
*
* @return
*/
+ @Override
public List<String> getChainNames()
{
- List<String> names = new ArrayList<String>();
- String[][] allNames = getChains();
- if (allNames != null)
- {
- for (String[] chainsForPdb : allNames)
- {
- if (chainsForPdb != null)
- {
- for (String chain : chainsForPdb)
- {
- if (chain != null && !names.contains(chain))
- {
- names.add(chain);
- }
- }
- }
- }
- }
- return names;
+ return chainNames;
}
/**
* features visible in Jalview
*
* @param avp
+ * @return
*/
- public void sendFeaturesToViewer(AlignmentViewPanel avp)
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
// 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();
+ String[] files = getStructureFiles();
if (files == null)
{
- return;
+ return 0;
}
StructureMappingcommandSet commandSet = ChimeraCommands
.getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), fr, alignment);
+ getSequence(), avp);
String[] commands = commandSet.commands;
if (commands.length > 10)
{
sendAsynchronousCommand(command, null);
}
}
+ return commands.length;
}
/**
sendAsynchronousCommand("open cmd:" + path, null);
} catch (IOException e)
{
- System.err
- .println("Sending commands to Chimera via file failed with "
- + e.getMessage());
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
}
}
String cmd = "list residues attr '" + attName + "'";
List<String> residues = sendChimeraCommand(cmd, true);
- /*
- * TODO check if Jalview already has this feature name, if so give it a
- * distinguishing prefix e.g. chim_
- */
- FeatureRenderer fr = alignmentPanel.getFeatureRenderer();
- // todo should getRenderOrder be in api.FeatureRenderer?
- // FIXME this is empty if feature display is turned off
- List<String> existingFeatures = ((jalview.gui.FeatureRenderer) fr)
- .getRenderOrder();
- if (existingFeatures.contains(attName))
+ boolean featureAdded = createFeaturesForAttributes(attName, residues);
+ if (featureAdded)
{
- // TODO check if feature of this name is in group Chimera
- // if so don't create a new feature name!
- // problem: needs a lookup of features for feature group
- attName = getStructureFeaturePrefix() + attName;
+ alignmentPanel.getFeatureRenderer().featuresAdded();
}
+ }
- /*
- * Expect 0, 1 or more reply lines of the format (chi2 is attName):
- * residue id #0:5.A chi2 -155.000836316 index 5
- * or
- * residue id #0:6.A chi3 None
- *
- * We assume here that attributes on structure do not naturally convert
- * to ranges on sequence, i.e. we just set one feature per mapped position.
- *
- * To conflate positions, would need to first build a map
- * Map<String value, Map<Sequence seq, List<Integer position>>>
- * and then traverse it to find feature ranges.
- */
+ /**
+ * 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();
spec.setPdbFile(pdbFile);
List<AtomSpec> atoms = Collections.singletonList(spec);
- SearchResults sr = getSsm()
+
+ /*
+ * 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 (Match m : sr.getResults())
+ for (SearchResultMatchI m : sr.getResults())
{
SequenceI seq = m.getSequence();
int start = m.getStart();
featureAdded |= seq.addSequenceFeature(sf);
}
}
- if (featureAdded)
- {
- fr.featuresAdded();
- }
- }
-
- /**
- * Answers a 'namespace' prefix to use for features created in Jalview from
- * attributes in the structure viewer
- *
- * @return
- */
- protected String getStructureFeaturePrefix()
- {
- // TODO pull up as abstract
- return CHIMERA_FEATURE_PREFIX;
+ return featureAdded;
}
/**
// 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