/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.Comparison;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
+ // Chimera clause to exclude alternate locations in atom selection
+ private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
+
+ private static final String COLOURING_CHIMERA = MessageManager
+ .getString("status.colouring_chimera");
private static final boolean debug = false;
private static final String ALPHACARBON = "CA";
- private StructureManager csm;
-
/*
* Object through which we talk to Chimera
*/
*/
private boolean loadingFinished = true;
- /*
- * state flag used to check if the Chimera viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
- private List<String> atomsPicked = new ArrayList<String>();
-
- private List<String> chainNames;
-
- private Map<String, String> chainFile;
-
public String fileLoadingError;
/*
{
super(ssm, pdbentry, sequenceIs, chains, protocol);
viewer = new ChimeraManager(
- csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
/**
}
/**
- * Constructor
- *
- * @param ssm
- * @param theViewer
- */
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- ChimeraManager theViewer)
- {
- super(ssm, null);
- viewer = theViewer;
- csm = viewer.getStructureManager();
- }
-
- /**
* Construct a title string for the viewer window based on the data Jalview
* knows about
*
}
/**
- * prepare the view for a given set of models/chains. chainList contains
- * strings of the form 'pdbfilename:Chaincode'
+ * Tells Chimera to display only the specified chains
*
* @param toshow
- * list of chains to make visible
*/
- public void centerViewer(List<String> toshow)
+ public void showChains(List<String> toshow)
{
+ /*
+ * Construct a chimera command like
+ *
+ * ~display #*;~ribbon #*;ribbon :.A,:.B
+ */
StringBuilder cmd = new StringBuilder(64);
- int mlength, p;
- for (String lbl : toshow)
+ boolean first = true;
+ for (String chain : toshow)
{
- mlength = 0;
- do
+ if (!first)
{
- 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)
- {
- cmd.setLength(cmd.length() - 4);
+ cmd.append(",");
+ }
+ cmd.append(":.").append(chain);
+ first = false;
}
- String cmdstring = cmd.toString();
- evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring
- + ";focus " + cmdstring, false);
+
+ /*
+ * could append ";focus" to this command to resize the display to fill the
+ * window, but it looks more helpful not to (easier to relate chains to the
+ * whole)
+ */
+ final String command = "~display #*; ~ribbon #*; ribbon "
+ + cmd.toString();
+ sendChimeraCommand(command, false);
}
/**
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);
+ sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
}
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions.
+ * Constructs and sends a Chimera command to colour by charge
+ * <ul>
+ * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
+ * <li>Lysine and Arginine (positive charge) blue</li>
+ * <li>Cysteine - yellow</li>
+ * <li>all others - white</li>
+ * </ul>
*/
- public void superposeStructures(AlignmentI alignment)
- {
- superposeStructures(alignment, -1, null);
- }
-
- /**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
- *
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
- */
- public void superposeStructures(AlignmentI alignment, int refStructure)
+ public void colourByCharge()
{
- superposeStructures(alignment, refStructure, null);
+ colourBySequence = false;
+ String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
*
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
- * @param hiddenCols
- * TODO
+ * @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
*/
- 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)
{
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
- StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd
+ StringBuilder allComs = new StringBuilder(128);
String[] files = getPdbFile();
- // check to see if we are still waiting for Chimera files
- long starttime = System.currentTimeMillis();
- boolean waiting = true;
- do
- {
- waiting = false;
- for (String file : files)
- {
- try
- {
- // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
- // every possible exception
- StructureMapping[] sm = getSsm().getMapping(file);
- if (sm == null || sm.length == 0)
- {
- waiting = true;
- }
- } catch (Exception x)
- {
- waiting = true;
- } catch (Error q)
- {
- waiting = true;
- }
- }
- // we wait around for a reasonable time before we give up
- } while (waiting
- && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
- if (waiting)
+
+ if (!waitForFileLoad(files))
{
- System.err
- .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures.");
return;
}
+
refreshPdbEntries();
- StringBuffer selectioncom = new StringBuffer();
+ StringBuilder selectioncom = new StringBuilder(256);
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 "
+ System.err.println("Ignoring invalid reference structure value "
+ refStructure);
refStructure = -1;
}
- if (refStructure < -1)
- {
- refStructure = -1;
- }
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns 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++)
{
-
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++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
- StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
- // RACE CONDITION - getMapping only returns Jmol loaded filenames once
- // Jmol callback has completed.
- if (mapping == null || mapping.length < 1)
- {
- throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data"));
- }
- int lastPos = -1;
- final int seqCountForPdbFile = getSequence()[pdbfnum].length;
- for (int s = 0; s < seqCountForPdbFile; s++)
+ structures[f] = new SuperposeData(alignment.getWidth());
+ }
+
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
+
+ int nmatched = 0;
+ for (boolean b : matched)
+ {
+ if (b)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI theSequence = getSequence()[pdbfnum][s];
- if (mapping[m].getSequence() == theSequence
- && (sp = alignment.findIndex(theSequence)) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- if (!matched[r])
- {
- continue;
- }
- matched[r] = false; // assume this is not a good site
- if (r >= asp.getLength())
- {
- continue;
- }
-
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- // no mapping to gaps in sequence
- continue;
- }
- int t = asp.findPosition(r); // sequence position
- int apos = mapping[m].getAtomNum(t);
- int pos = mapping[m].getPDBResNum(t);
-
- if (pos < 1 || pos == lastPos)
- {
- // can't align unmapped sequence
- continue;
- }
- matched[r] = true; // this is a good ite
- lastPos = pos;
- // just record this residue position
- commonrpositions[pdbfnum][r] = pos;
- }
- // create model selection suffix
- isel[pdbfnum] = "#" + pdbfnum;
- if (mapping[m].getChain() == null
- || mapping[m].getChain().trim().length() == 0)
- {
- targetC[pdbfnum] = "";
- }
- else
- {
- targetC[pdbfnum] = "." + mapping[m].getChain();
- }
- chainNames[pdbfnum] = mapping[m].getPdbId()
- + targetC[pdbfnum];
- atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON;
- // move on to next pdb file
- s = seqCountForPdbFile;
- break;
- }
- }
+ nmatched++;
}
}
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
-
+ /*
+ * Generate select statements to select regions to superimpose structures
+ */
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++)
{
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ String chainCd = "." + structures[pdbfnum].chain;
+ int lpos = -1;
+ boolean run = false;
+ StringBuilder molsel = new StringBuilder();
+ for (int r = 0; r < matched.length; r++)
{
- 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 (matched[r])
+ int pdbResNum = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNum - 1)
{
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append((run ? "" : ":") + lpos);
- molsel.append(chainCd);
- molsel.append(",");
- }
- }
- else
+ /*
+ * discontiguous - append last residue now
+ */
+ if (lpos != -1)
{
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(":" + lpos);
- molsel.append("-");
- }
- run = true;
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ molsel.append(",");
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ run = false;
}
- }
- // 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)
+ else
{
- selectioncom.append("| ");
+ /*
+ * extending a contiguous run
+ */
+ if (!run)
+ {
+ /*
+ * start the range selection
+ */
+ molsel.append(String.valueOf(lpos));
+ molsel.append("-");
+ }
+ run = true;
}
+ lpos = pdbResNum;
}
- else
+ }
+
+ /*
+ * and terminate final selection
+ */
+ if (lpos != -1)
+ {
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("#").append(String.valueOf(pdbfnum))
+ .append(":");
+ selectioncom.append(selcom[pdbfnum]);
+ selectioncom.append(" ");
+ if (pdbfnum < files.length - 1)
{
- selcom[pdbfnum] = null;
+ selectioncom.append("| ");
}
}
+ else
+ {
+ selcom[pdbfnum] = null;
+ }
}
+
StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
/*
* Form Chimera match command, from the 'new' structure to the
- * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons):
+ * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
*
- * match #1:1-91.B@CA #0:1-91.A@CA
+ * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
*
* @see
* https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
- command.append("match #" + pdbfnum /* +".1" */);
- // TODO: handle sub-models
+ command.append("match ").append(getModelSpec(pdbfnum)).append(":");
command.append(selcom[pdbfnum]);
- command.append("@" + atomSpec[pdbfnum]);
- command.append(" #" + refStructure /* +".1" */);
+ command.append("@").append(
+ structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
+ // JAL-1757 exclude alternate CA locations
+ command.append(NO_ALTLOCS);
+ command.append(" ").append(getModelSpec(refStructure)).append(":");
command.append(selcom[refStructure]);
- command.append("@" + atomSpec[refStructure]);
+ command.append("@").append(
+ structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
+ command.append(NO_ALTLOCS);
}
if (selectioncom.length() > 0)
{
System.out.println("Superimpose command(s):\n"
+ command.toString());
}
- allComs.append("~display all; chain @CA|P; ribbon "
- + selectioncom.toString() + ";"+command.toString());
- // selcom.append("; ribbons; ");
+ allComs.append("~display all; chain @CA|P; ribbon ")
+ .append(selectioncom.toString())
+ .append(";" + command.toString());
}
}
if (selectioncom.length() > 0)
- {// finally, mark all regions that were superposed.
+ {
+ // TODO: visually distinguish regions that were superposed
if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
{
selectioncom.setLength(selectioncom.length() - 1);
{
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 */);
+ allComs.append("; ~display all; chain @CA|P; ribbon ")
+ .append(selectioncom.toString()).append("; focus");
+ sendChimeraCommand(allComs.toString(), false);
+ }
+
+ }
+
+ /**
+ * 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 pdbfnum
+ * @return
+ */
+ protected String getModelSpec(int pdbfnum)
+ {
+ if (pdbfnum < 0 || pdbfnum >= getPdbCount())
+ {
+ return "";
}
-
+
+ /*
+ * 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(getPdbFile()[pdbfnum]);
+ boolean hasSubModels = maps != null && maps.size() > 1;
+ return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
- private void checkLaunched()
+ /**
+ * Launch Chimera, unless an instance linked to this object is already
+ * running. Returns true if chimera is successfully launched, or already
+ * running, else false.
+ *
+ * @return
+ */
+ public boolean launchChimera()
{
if (!viewer.isChimeraLaunched())
{
- viewer.launchChimera(StructureManager.getChimeraPaths());
+ return viewer.launchChimera(StructureManager.getChimeraPaths());
}
- if (!viewer.isChimeraLaunched())
+ if (viewer.isChimeraLaunched())
{
- log("Failed to launch Chimera!");
+ return true;
}
+ log("Failed to launch Chimera!");
+ return false;
}
/**
}
/**
- * Send a command to Chimera, launching it first if necessary, and optionally
- * log any responses.
+ * Send a command to Chimera, and optionally log any responses.
*
* @param command
* @param logResponse
*/
- public void evalStateCommand(final String command, boolean logResponse)
+ public void sendChimeraCommand(final String command, boolean logResponse)
{
+ if (viewer == null)
+ {
+ // ? thread running after viewer shut down
+ return;
+ }
viewerCommandHistory(false);
- checkLaunched();
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
- if (debug && logResponse)
+ if (logResponse && debug)
{
log("Response from command ('" + command + "') was:\n" + lastReply);
}
}
/**
+ * Send a Chimera command asynchronously in a new thread. If the progress
+ * message is not null, display this message while the command is executing.
+ *
+ * @param command
+ * @param progressMsg
+ */
+ protected abstract void sendAsynchronousCommand(String command,
+ String progressMsg);
+
+ /**
* colour any structures associated with sequences in the given alignment
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
{
for (String command : cpdbbyseq.commands)
{
- executeWhenReady(command);
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
}
protected void executeWhenReady(String command)
{
waitForChimera();
- evalStateCommand(command, false);
+ sendChimeraCommand(command, false);
waitForChimera();
}
{
while (viewer != null && viewer.isBusy())
{
- try {
+ try
+ {
Thread.sleep(15);
} catch (InterruptedException q)
- {}
+ {
+ }
}
}
-
-
// End StructureListener
// //////////////////////////
/**
* 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
+ * prior to matching the viewer's contents to the list of structure files
* Jalview knows about.
*/
public abstract void refreshPdbEntries();
// ////////////////////////////////
// /StructureListener
+ @Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight an atom.
+ * Construct and send a command to highlight zero, one or more atoms.
*
* <pre>
* Done by generating a command like (to 'highlight' position 44)
- * ~show #0:43.C;show #0:44.C
- * Note this removes the highlight from the previous position.
+ * show #0:44.C
* </pre>
*/
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
- if (cms != null)
+ if (atoms == null)
+ {
+ return;
+ }
+ StringBuilder atomSpecs = new StringBuilder();
+ boolean first = true;
+ for (AtomSpec atom : atoms)
{
- StringBuilder sb = new StringBuilder();
- sb.append(" #" + cms.get(0).getModelNumber());
- sb.append(":" + pdbResNum);
- if (!chain.equals(" "))
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+ String pdbfile = atom.getPdbFile();
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
+ if (cms != null && !cms.isEmpty())
{
- sb.append("." + chain);
+ /*
+ * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
+ * concatenate multiple 'show' commands
+ */
+ atomSpecs.append(first ? "" : ";show ");
+ first = false;
+ atomSpecs.append("#" + cms.get(0).getModelNumber());
+ atomSpecs.append(":" + pdbResNum);
+ if (!chain.equals(" "))
+ {
+ atomSpecs.append("." + chain);
+ }
}
- String atomSpec = sb.toString();
+ }
+ String atomSpec = atomSpecs.toString();
- StringBuilder command = new StringBuilder(32);
- if (lastMousedOverAtomSpec != null)
- {
- command.append("~show " + lastMousedOverAtomSpec + ";");
- }
- viewerCommandHistory(false);
+ /*
+ * Avoid repeated commands for the same residue
+ */
+ if (atomSpec.equals(lastMousedOverAtomSpec))
+ {
+ return;
+ }
+
+ StringBuilder command = new StringBuilder(32);
+ viewerCommandHistory(false);
+ if (atomSpec.length() > 0)
+ {
command.append("show ").append(atomSpec);
- String cmd = command.toString();
- if (cmd.length() > 0)
- {
- viewer.stopListening(chimeraListener.getUri());
- viewer.sendChimeraCommand(cmd, false);
- viewer.startListening(chimeraListener.getUri());
- }
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ viewer.sendChimeraCommand(command.toString(), false);
}
+ viewerCommandHistory(true);
+ this.lastMousedOverAtomSpec = atomSpec;
}
/**
{
continue; // malformed
}
-
+
int hashPos = atomSpec.indexOf("#");
String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
int dotPos = modelSubmodel.indexOf(".");
int modelId = 0;
- try {
+ try
+ {
modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
: modelSubmodel.substring(0, dotPos));
- } catch (NumberFormatException e) {
+ } catch (NumberFormatException e)
+ {
// ignore, default to model 0
}
-
+
String residueChain = atomSpec.substring(colonPos + 1);
dotPos = residueChain.indexOf(".");
int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
: residueChain.substring(0, dotPos));
-
+
String chainId = dotPos == -1 ? "" : residueChain
.substring(dotPos + 1);
-
+
/*
* Work out the pdbfilename from the model number
*/
/ normalise + " ::" + res + ";");
}
- evalStateCommand(command.toString(),false);
+ sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
viewerCommandHistory(true);
}
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
{
viewerCommandHistory(false);
double normalise = 255D;
- final String command = "background solid " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
+ final String command = "background solid " + col.getRed() / normalise
+ + "," + col.getGreen() / normalise + "," + col.getBlue()
/ normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
/**
- *
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
- */
- public String printMapping(String pdbfile)
- {
- return getSsm().printMapping(pdbfile);
- }
-
- /**
* Ask Chimera to save its session to the given file. Returns true if
* successful, else false.
*
*/
public boolean openSession(String filepath)
{
- evalStateCommand("open " + filepath, true);
+ sendChimeraCommand("open " + filepath, true);
// todo: test for failure - how?
return true;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
+ /**
+ * Returns a list of chains mapped in this viewer. Note this list is not
+ * currently scoped per structure.
+ *
+ * @return
+ */
+ public List<String> getChainNames()
{
- this.finishedInit = finishedInit;
+ 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;
}
- public List<String> getChainNames()
+ /**
+ * Send a 'focus' command to Chimera to recentre the visible display
+ */
+ public void focusView()
{
- return chainNames;
+ sendChimeraCommand("focus", false);
}
-
}
git://source.jalview.org / jalview.git / blobdiff