/*
- * 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.
*
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.httpserver.AbstractRequestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import java.awt.Color;
-import java.awt.event.ComponentEvent;
-import java.io.File;
+import java.net.BindException;
import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-public abstract class JalviewChimeraBinding extends
- SequenceStructureBindingModel implements StructureListener,
- SequenceStructureBinding, StructureSelectionManagerProvider
-
+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 PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
- private StructureManager csm;
-
+ /*
+ * Object through which we talk to Chimera
+ */
private ChimeraManager viewer;
- /**
+ /*
+ * Object which listens to Chimera notifications
+ */
+ private AbstractRequestHandler chimeraListener;
+
+ /*
* set if chimera state is being restored from some source - instructs binding
* not to apply default display style when structure set is updated for first
* time.
*/
private boolean loadingFromArchive = false;
- /**
- * second flag to indicate if the jmol viewer should ignore sequence colouring
+ /*
+ * flag to indicate if the Chimera viewer should ignore sequence colouring
* events from the structure manager because the GUI is still setting up
*/
private boolean loadingFinished = true;
- /**
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
- boolean allChainsSelected = false;
-
- /**
- * 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[]
- */
- 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>();
+ /*
+ * Map of ChimeraModel objects keyed by PDB full local file name
+ */
+ 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
*/
- int frameNo = 0;
+ private int frameNo = 0;
- String lastCommand;
+ private String lastCommand;
- String lastMessage;
+ String lastHighlightCommand;
- boolean loadedInline;
+ /*
+ * 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;
+ /**
+ * 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
+ */
public boolean openFile(PDBEntry pe)
{
String file = pe.getFile();
try
{
+ List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
List<ChimeraModel> oldList = viewer.getModelList();
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- List<ChimeraModel> newList = viewer.getModelList();
- if (oldList.size() < newList.size())
+ 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)
+ if (open.getModelName().equals(pe.getId()))
{
- oldList.remove(0);
- newList.remove(0);
+ alreadyOpen = true;
+ modelsToMap.add(open);
}
- chimmaps.put(file, newList);
+ }
+
+ /*
+ * If Chimera doesn't yet have this model, ask it to open it, and retrieve
+ * the model name(s) added by Chimera.
+ */
+ if (!alreadyOpen)
+ {
+ viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ List<ChimeraModel> newList = viewer.getModelList();
+ // JAL-1728 newList.removeAll(oldList) does not work
for (ChimeraModel cm : newList)
{
- while (mdlToFile.size() < 1 + cm.getModelNumber())
+ if (cm.getModelName().equals(pe.getId()))
{
- mdlToFile.add(new String(""));
+ modelsToMap.add(cm);
}
- mdlToFile.set(cm.getModelNumber(), file);
}
+ }
- 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 Jmol ;
- // pdbentry[pe].getFile(), protocol);
+ chimeraMaps.put(file, modelsToMap);
- if (ssm != null)
+ if (getSsm() != null)
+ {
+ getSsm().addStructureViewerListener(this);
+ // ssm.addSelectionListener(this);
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
{
- ssm.addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
+ fr.featuresAdded();
}
- return true;
+ refreshGUI();
}
+ 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
+ * Constructor
+ *
+ * @param ssm
+ * @param pdbentry
+ * @param sequenceIs
+ * @param chains
+ * @param protocol
*/
- public SequenceI[][] sequence;
-
- public StructureSelectionManager ssm;
-
- private List<String> lastReply;
-
public JalviewChimeraBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
{
- this.ssm = ssm;
- this.sequence = sequenceIs;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
- if (chains == null)
- {
- this.chains = new String[pdbentry.length][];
- }
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
viewer = new ChimeraManager(
- csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
- /*
- * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
- * "jalviewJmol", ap.av.applet .getDocumentBase(),
- * ap.av.applet.getCodeBase(), "", this);
- *
- * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
- */
+ new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- ChimeraManager viewer2)
+ /**
+ * Start a dedicated HttpServer to listen for Chimera notifications, and tell
+ * it to start listening
+ */
+ public void startChimeraListener()
{
- this.ssm = ssm;
- viewer = viewer2;
- csm = viewer.getStructureManager();
+ try
+ {
+ chimeraListener = new ChimeraListener(this);
+ viewer.startListening(chimeraListener.getUri());
+ } catch (BindException e)
+ {
+ System.err.println("Failed to start Chimera listener: "
+ + e.getMessage());
+ }
}
/**
*/
public String getViewerTitle(boolean verbose)
{
- 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());
-
- 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();
+ return getViewerTitle("Chimera", verbose);
}
/**
- * 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);
}
/**
- * Close down the Jalview viewer, and (optionally) the associate Chimera
- * window.
+ * Close down the Jalview viewer and listener, and (optionally) the associated
+ * Chimera window.
*/
public void closeViewer(boolean closeChimera)
{
- ssm.removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getPdbFile());
if (closeChimera)
{
viewer.exitChimera();
}
- // viewer.evalStringQuiet("zap");
- // viewer.setJmolStatusListener(null);
+ if (this.chimeraListener != null)
+ {
+ chimeraListener.shutdown();
+ chimeraListener = null;
+ }
lastCommand = null;
viewer = null;
+
releaseUIResources();
}
- /**
- * called by JalviewJmolbinding after closeViewer is called - release any
- * resources and references so they can be garbage collected.
- */
- protected abstract void releaseUIResources();
-
public void colourByChain()
{
colourBySequence = false;
- // TODO: colour by chain should colour each chain distinctly across all
- // visible models
- // TODO: http://issues.jalview.org/browse/JAL-628
- evalStateCommand("select *;color chain",false);
- }
-
- public void colourByCharge()
- {
- colourBySequence = false;
- evalStateCommand("colour *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow", false);
+ sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
}
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions.
- */
- public void superposeStructures(AlignmentI alignment)
- {
- superposeStructures(alignment, -1, null);
- }
-
- /**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
- *
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
+ * 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, 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 Jmol 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 = 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)
+
+ 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 = 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++)
+ 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++)
- {
- 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;
- }
- }
+ 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)
+ /*
+ * discontiguous - append last residue now
+ */
+ if (lpos != -1)
{
- nmatched++;
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ molsel.append(",");
}
- 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);
+ 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)
{
- // TODO remove debug output
- 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 (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 ")
+ .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 */);
+ if (debug)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ }
+ allComs.append("; ~display all; chain @CA|P; ribbon ")
+ .append(selectioncom.toString()).append("; focus");
+ sendChimeraCommand(allComs.toString(), false);
}
-
+
}
- private void checkLaunched()
+ /**
+ * 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 (!viewer.isChimeraLaunched())
+ if (pdbfnum < 0 || pdbfnum >= getPdbCount())
{
- viewer.launchChimera(csm.getChimeraPaths());
+ 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" : "");
+ }
+
+ /**
+ * 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())
{
- log("Failed to launch Chimera!");
+ return viewer.launchChimera(StructureManager.getChimeraPaths());
}
+ if (viewer.isChimeraLaunched())
+ {
+ return true;
+ }
+ log("Failed to launch Chimera!");
+ return false;
}
/**
* @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))
{
-// 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)
-// {
-// }
-// ;
+ List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ logResponse);
+ if (logResponse && debug)
+ {
+ log("Response from command ('" + command + "') was:\n" + lastReply);
+ }
}
viewerCommandHistory(true);
lastCommand = command;
}
/**
+ * 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.
{
return;
}
- if (ssm == null)
+ if (getSsm() == null)
{
return;
}
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands
- .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
- alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
- for (String cbyseq : cpdbbyseq.commands)
+ for (String command : cpdbbyseq.commands)
{
- waitForChimera();
- evalStateCommand(cbyseq, false);
- waitForChimera();
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
}
- private void waitForChimera()
+ /**
+ * @param files
+ * @param sr
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
{
- while (viewer.isBusy())
- {
- try {
- Thread.sleep(15);
- } catch (InterruptedException q)
- {}
- }
+ return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
- public boolean isColourBySequence()
+ /**
+ * @param command
+ */
+ protected void executeWhenReady(String command)
{
- return colourBySequence;
+ waitForChimera();
+ sendChimeraCommand(command, false);
+ waitForChimera();
}
- public void setColourBySequence(boolean colourBySequence)
+ private void waitForChimera()
{
- this.colourBySequence = colourBySequence;
+ while (viewer != null && viewer.isBusy())
+ {
+ try
+ {
+ Thread.sleep(15);
+ } catch (InterruptedException q)
+ {
+ }
+ }
}
// 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
/**
* 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)
// // 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()]);
}
/**
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();
- }
- }
-
- boolean debug = true;
-
- private void log(String message)
- {
- System.err.println("## Chimera log: " + message);
- }
-
- private void viewerCommandHistory(boolean enable)
- {
- log("(Not yet implemented) History "
- + ((debug || enable) ? "on" : "off"));
- }
-
- public 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)
+ /**
+ * 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)
{
- // 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)
- {
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
- {
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
- }
- }
- // handle insertion codes
- if (alocsep != -1)
+ if (atoms == null || atoms.size() == 0)
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, alocsep));
-
- }
- else
- {
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
+ return;
}
- String chainId;
- if (strInfo.indexOf(":") > -1)
- {
- chainId = strInfo.substring(strInfo.indexOf(":") + 1,
- strInfo.indexOf("."));
- }
- else
- {
- chainId = " ";
- }
+ StringBuilder cmd = new StringBuilder(128);
+ boolean first = true;
+ boolean found = false;
- String pdbfilename = modelFileNames[frameNo]; // default is first or current
- // model
- if (mdlSep > -1)
+ for (AtomSpec atom : atoms)
{
- if (chainSeparator1 == -1)
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+ String pdbfile = atom.getPdbFile();
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
+ if (cms != null && !cms.isEmpty())
{
- chainSeparator1 = strInfo.indexOf(".", mdlSep);
- }
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
- try
- {
- // 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)
+ {
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
+ .append(":");
+ }
+ else
{
- _mp--;
+ cmd.append(",");
}
- pdbfilename = modelFileNames[_mp];
- if (pdbfilename == null)
+ first = false;
+ cmd.append(pdbResNum);
+ if (!chain.equals(" "))
{
- // pdbfilename = new File(viewer.getModelFileName(mnumber))
- // .getAbsolutePath();
+ cmd.append(".").append(chain);
}
-
- } catch (Exception e)
- {
+ found = true;
}
- ;
}
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
- }
-
- lastMessage = strInfo;
- }
+ String command = cmd.toString();
- 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);
- }
- // rewrite these selections for chimera (DNA, RNA and protein)
- int chainSeparator = strInfo.indexOf(":");
- int p = 0;
- if (chainSeparator == -1)
- {
- chainSeparator = strInfo.indexOf(".");
- }
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
- String mdlString = "";
- if ((p = strInfo.indexOf(":")) > -1)
- {
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ return;
}
- if ((p = strInfo.indexOf("/")) > -1)
- {
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
- }
- picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
- + mdlString + "))";
- viewerCommandHistory(false);
-
- if (!atomsPicked.contains(picked))
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- viewer.select(picked);
- atomsPicked.add(picked);
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
}
- else
+ if (found)
{
- viewer.select("not " + picked);
- atomsPicked.remove(picked);
+ viewer.sendChimeraCommand(command, false);
}
- viewerCommandHistory(true);
- // TODO: in application this happens
- //
- // if (scriptWindow != null)
- // {
- // scriptWindow.sendConsoleMessage(strInfo);
- // scriptWindow.sendConsoleMessage("\n");
- // }
-
+ this.lastHighlightCommand = command;
}
- // 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
+ */
+ List<String> selection = viewer.getSelectedResidueSpecs();
- 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)
+ /*
+ * Parse model number, residue and chain for each selected position,
+ * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
+ */
+ List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
+ for (String atomSpec : selection)
{
- int oldm = 0;
- for (int i = 0; i < oldmodels.length; i++)
+ int colonPos = atomSpec.indexOf(":");
+ if (colonPos == -1)
{
- for (int n = 0; n < modelfilenames.length; n++)
- {
- if (modelfilenames[n] == oldmodels[i])
- {
- oldmodels[i] = null;
- break;
- }
- }
- if (oldmodels[i] != null)
- {
- oldm++;
- }
+ continue; // malformed
}
- if (oldm > 0)
+
+ int hashPos = atomSpec.indexOf("#");
+ String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
+ int dotPos = modelSubmodel.indexOf(".");
+ int modelId = 0;
+ try
+ {
+ modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
+ : modelSubmodel.substring(0, dotPos));
+ } catch (NumberFormatException e)
+ {
+ // ignore, default to model 0
+ }
+
+ String residueChain = atomSpec.substring(colonPos + 1);
+ dotPos = residueChain.indexOf(".");
+ int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
+ : residueChain.substring(0, dotPos));
+
+ String chainId = dotPos == -1 ? "" : residueChain
+ .substring(dotPos + 1);
+
+ /*
+ * Work out the pdbfilename from the model number
+ */
+ String pdbfilename = modelFileNames[frameNo];
+ findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
{
- String[] oldmfn = new String[oldm];
- oldm = 0;
- for (int i = 0; i < oldmodels.length; i++)
+ for (ChimeraModel cm : chimeraMaps.get(pdbfile))
{
- if (oldmodels[i] != null)
+ if (cm.getModelNumber() == modelId)
{
- oldmfn[oldm++] = oldmodels[i];
+ pdbfilename = pdbfile;
+ break findfileloop;
}
}
- // deregister the Jmol instance for these structures - we'll add
- // ourselves again at the end for the current structure set.
- ssm.removeStructureViewerListener(this, oldmfn);
}
+ atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
}
- // register ourselves as a listener and notify the gui that it needs to
- // update itself.
- ssm.addStructureViewerListener(this);
+ /*
+ * 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);
+ private void log(String message)
+ {
+ System.err.println("## Chimera log: " + message);
+ }
+
+ private void viewerCommandHistory(boolean enable)
+ {
+ // log("(Not yet implemented) History "
+ // + ((debug || enable) ? "on" : "off"));
+ }
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
}
public void setJalviewColourScheme(ColourSchemeI cs)
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();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- {
- continue;
- }
+ StringBuilder command = new StringBuilder(128);
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
- // TODO: need colour string function and res selection here
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
+ {
+ Color col = cs.findColour(res.charAt(0));
+ command.append("color " + col.getRed() / normalise + ","
+ + col.getGreen() / normalise + "," + col.getBlue()
+ / normalise + " ::" + res + ";");
}
- evalStateCommand(command.toString(),false);
+ sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
viewerCommandHistory(true);
}
- public void showHelp()
- {
- // chimera help
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
- }
-
- /**
- * open the URL somehow
- *
- * @param target
- */
- public abstract void showUrl(String url, String target);
-
/**
- * called when the binding thinks the UI needs to be refreshed after a Jmol
+ * 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 occured.
+ * error has occurred.
*/
public abstract void refreshGUI();
- public void componentResized(ComponentEvent e)
- {
-
- }
-
- public void componentMoved(ComponentEvent e)
- {
-
- }
-
- public void componentShown(ComponentEvent e)
- {
- }
-
- public void componentHidden(ComponentEvent e)
- {
- }
-
+ @Override
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
/**
*
- * @return true if Jmol is still restoring state or loading is still going on
- * (see setFinsihedLoadingFromArchive)
+ * @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;
}
- public void setBackgroundColour(java.awt.Color col)
+ /**
+ * Send the Chimera 'background solid <color>" command.
+ *
+ * @see https
+ * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
+ * .html
+ * @param col
+ */
+ public void setBackgroundColour(Color col)
{
viewerCommandHistory(false);
- // todo set background colour
- viewer.sendChimeraCommand(
- "background [" + col.getRed() + "," + col.getGreen() + ","
- + col.getBlue() + "];", false);
+ double normalise = 255D;
+ final String command = "background solid " + col.getRed() / normalise
+ + "," + col.getGreen() / normalise + "," + col.getBlue()
+ / normalise + ";";
+ viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
/**
- * add structures and any known sequence associations
+ * Ask Chimera to save its session to the given file. Returns true if
+ * successful, else false.
*
- * @returns the pdb entries added to the current set.
+ * @param filepath
+ * @return
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
+ public boolean saveSession(String filepath)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
- for (int i = 0; i < pdbentry.length; i++)
+ if (isChimeraRunning())
{
- v.add(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
- {
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
+ List<String> reply = viewer.sendChimeraCommand("save " + filepath,
+ true);
+ if (reply.contains("Session written"))
{
- rtn.add(new int[]
- { v.size(), i });
- v.add(pdbe[i]);
+ return true;
}
else
{
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
+ Cache.log
+ .error("Error saving Chimera session: " + reply.toString());
}
}
- 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++)
- {
- 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]]);
- }
- }
- else
- {
- pdbe = null;
- }
- return pdbe;
+ return false;
}
/**
- * Adds sequences to the pe'th pdbentry's sequence set.
+ * Ask Chimera to open a session file. Returns true if successful, else false.
+ * The filename must have a .py extension for this command to work.
*
- * @param pe
- * @param seq
+ * @param filepath
+ * @return
*/
- public void addSequence(int pe, SequenceI[] seq)
+ public boolean openSession(String filepath)
{
- addSequenceAndChain(pe, seq, null);
+ sendChimeraCommand("open " + filepath, true);
+ // todo: test for failure - how?
+ return true;
}
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ /**
+ * Returns a list of chains mapped in this viewer. Note this list is not
+ * currently scoped per structure.
+ *
+ * @return
+ */
+ public List<String> getChainNames()
{
- if (pe < 0 || pe >= pdbentry.length)
- {
- throw new Error(MessageManager.formatMessage(
- "error.implementation_error_no_pdbentry_from_index",
- new Object[]
- { Integer.valueOf(pe).toString() }));
- }
- final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
- if (chains == null)
+ List<String> names = new ArrayList<String>();
+ String[][] allNames = getChains();
+ if (allNames != null)
{
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
- {
- for (int i = 0; i < sequence[pe].length; i++)
+ for (String[] chainsForPdb : allNames)
{
- s.add(sequence[pe][i]);
- if (chains[pe] != null)
- {
- if (i < chains[pe].length)
- {
- c.add(chains[pe][i]);
- }
- else
- {
- c.add(nullChain);
- }
- }
- else
+ if (chainsForPdb != null)
{
- if (tchain != null && tchain.length > 0)
+ for (String chain : chainsForPdb)
{
- c.add(nullChain);
+ if (chain != null && !names.contains(chain))
+ {
+ names.add(chain);
+ }
}
}
}
}
- 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 names;
}
/**
- *
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
+ * Send a 'focus' command to Chimera to recentre the visible display
*/
- public String printMapping(String pdbfile)
+ public void focusView()
{
- return ssm.printMapping(pdbfile);
+ 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())
+ {
+ /*
+ * convert selected columns into sequence positions
+ */
+ int[] positions = new int[cols.size()];
+ int i = 0;
+ for (Integer col : cols)
+ {
+ positions[i++] = seq.findPosition(col);
+ }
+ sm.highlightStructure(this, seq, positions);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff