/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.rbvi.chimera;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
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 PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
/*
* 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;
/*
* 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;
public String fileLoadingError;
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
private Map> chimeraMaps = new LinkedHashMap>();
/*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
private int frameNo = 0;
private String lastCommand;
/*
* current set of model filenames loaded
*/
String[] modelFileNames = null;
String lastHighlightCommand;
/*
* 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 modelsToMap = new ArrayList();
List oldList = viewer.getModelList();
boolean alreadyOpen = false;
/*
* If Chimera already has this model, don't reopen it, but do remap it.
*/
for (ChimeraModel open : oldList)
{
if (open.getModelName().equals(pe.getId()))
{
alreadyOpen = true;
modelsToMap.add(open);
}
}
/*
* 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 newList = viewer.getModelList();
// JAL-1728 newList.removeAll(oldList) does not work
for (ChimeraModel cm : newList)
{
if (cm.getModelName().equals(pe.getId()))
{
modelsToMap.add(cm);
}
}
}
chimeraMaps.put(file, modelsToMap);
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
// ssm.addSelectionListener(this);
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
fr.featuresAdded();
}
refreshGUI();
}
return true;
} catch (Exception q)
{
log("Exception when trying to open model " + file + "\n"
+ q.toString());
q.printStackTrace();
}
return false;
}
/**
* Constructor
*
* @param ssm
* @param pdbentry
* @param sequenceIs
* @param chains
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
{
super(ssm, pdbentry, sequenceIs, chains, protocol);
viewer = new ChimeraManager(
new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
/**
* Start a dedicated HttpServer to listen for Chimera notifications, and tell
* it to start listening
*/
public void startChimeraListener()
{
try
{
chimeraListener = new ChimeraListener(this);
viewer.startListening(chimeraListener.getUri());
} catch (BindException e)
{
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", verbose);
}
/**
* Tells Chimera to display only the specified chains
*
* @param toshow
*/
public void showChains(List toshow)
{
/*
* Construct a chimera command like
*
* ~display #*;~ribbon #*;ribbon :.A,:.B
*/
StringBuilder cmd = new StringBuilder(64);
boolean first = true;
for (String chain : toshow)
{
if (!first)
{
cmd.append(",");
}
cmd.append(":.").append(chain);
first = 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 listener, and (optionally) the associated
* Chimera window.
*/
public void closeViewer(boolean closeChimera)
{
getSsm().removeStructureViewerListener(this, this.getPdbFile());
if (closeChimera)
{
viewer.exitChimera();
}
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
lastCommand = null;
viewer = null;
releaseUIResources();
}
public void colourByChain()
{
colourBySequence = false;
sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
}
/**
* Constructs and sends a Chimera command to colour by charge
*
* - Aspartic acid and Glutamic acid (negative charge) red
* - Lysine and Arginine (positive charge) blue
* - Cysteine - yellow
* - all others - white
*
*/
public void colourByCharge()
{
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);
}
/**
* 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
*/
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
StringBuilder allComs = new StringBuilder(128);
String[] files = getPdbFile();
if (!waitForFileLoad(files))
{
return;
}
refreshPdbEntries();
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 (refStructure >= files.length)
{
System.err.println("Ignoring invalid reference structure value "
+ refStructure);
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;
}
SuperposeData[] structures = new SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
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)
{
nmatched++;
}
}
if (nmatched < 4)
{
// TODO: bail out here because superposition illdefined?
}
/*
* Generate select statements to select regions to superimpose structures
*/
String[] selcom = new String[files.length];
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++)
{
if (matched[r])
{
int pdbResNum = structures[pdbfnum].pdbResNo[r];
if (lpos != pdbResNum - 1)
{
/*
* discontiguous - append last residue now
*/
if (lpos != -1)
{
molsel.append(String.valueOf(lpos));
molsel.append(chainCd);
molsel.append(",");
}
run = false;
}
else
{
/*
* extending a contiguous run
*/
if (!run)
{
/*
* start the range selection
*/
molsel.append(String.valueOf(lpos));
molsel.append("-");
}
run = true;
}
lpos = pdbResNum;
}
}
/*
* 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)
{
selectioncom.append("| ");
}
}
else
{
selcom[pdbfnum] = null;
}
}
StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
|| selcom[refStructure] == null)
{
continue;
}
if (command.length() > 0)
{
command.append(";");
}
/*
* Form Chimera match command, from the 'new' structure to the
* 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
*
* 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 ").append(getModelSpec(pdbfnum)).append(":");
command.append(selcom[pdbfnum]);
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("@").append(
structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
command.append(NO_ALTLOCS);
}
if (selectioncom.length() > 0)
{
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
System.out.println("Superimpose command(s):\n"
+ command.toString());
}
allComs.append("~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString())
.append(";" + command.toString());
}
}
if (selectioncom.length() > 0)
{
// TODO: visually distinguish regions that were superposed
if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
{
selectioncom.setLength(selectioncom.length() - 1);
}
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
}
allComs.append("; ~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString()).append("; focus");
sendChimeraCommand(allComs.toString(), false);
}
}
/**
* Helper method to construct model spec in Chimera format:
*
* - #0 (#1 etc) for a PDB file with no sub-models
* - #0.1 (#1.1 etc) for a PDB file with sub-models
*
* 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 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())
{
return viewer.launchChimera(StructureManager.getChimeraPaths());
}
if (viewer.isChimeraLaunched())
{
return true;
}
log("Failed to launch Chimera!");
return false;
}
/**
* Answers true if the Chimera process is still running, false if ended or not
* started.
*
* @return
*/
public boolean isChimeraRunning()
{
return viewer.isChimeraLaunched();
}
/**
* Send a command to Chimera, and optionally log any responses.
*
* @param command
* @param logResponse
*/
public void sendChimeraCommand(final String command, boolean logResponse)
{
if (viewer == null)
{
// ? thread running after viewer shut down
return;
}
viewerCommandHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
List 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.
*/
public void colourBySequence(boolean showFeatures,
jalview.api.AlignmentViewPanel alignmentv)
{
if (!colourBySequence || !loadingFinished)
{
return;
}
if (getSsm() == null)
{
return;
}
String[] files = getPdbFile();
SequenceRenderer sr = getSequenceRenderer(alignmentv);
FeatureRenderer fr = null;
if (showFeatures)
{
fr = getFeatureRenderer(alignmentv);
}
AlignmentI alignment = alignmentv.getAlignment();
for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
files, sr, fr, alignment))
{
for (String command : cpdbbyseq.commands)
{
sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
}
/**
* @param files
* @param sr
* @param fr
* @param alignment
* @return
*/
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
getSequence(), sr, fr, alignment);
}
/**
* @param command
*/
protected void executeWhenReady(String command)
{
waitForChimera();
sendChimeraCommand(command, false);
waitForChimera();
}
private void waitForChimera()
{
while (viewer != null && viewer.isBusy())
{
try
{
Thread.sleep(15);
} catch (InterruptedException q)
{
}
}
}
// End StructureListener
// //////////////////////////
/**
* 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 -
* use getPdbFile to get number of unique models.
*/
private int _modelFileNameMap[];
// ////////////////////////////////
// /StructureListener
@Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
{
return new String[0];
}
// if (modelFileNames == null)
// {
// Collection 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);
/**
* 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 atoms)
{
if (atoms == null || atoms.size() == 0)
{
return;
}
StringBuilder cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
for (AtomSpec atom : atoms)
{
int pdbResNum = atom.getPdbResNum();
String chain = atom.getChain();
String pdbfile = atom.getPdbFile();
List cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
if (first)
{
cmd.append("rlabel #").append(cms.get(0).getModelNumber())
.append(":");
}
else
{
cmd.append(",");
}
first = false;
cmd.append(pdbResNum);
if (!chain.equals(" "))
{
cmd.append(".").append(chain);
}
found = true;
}
}
String command = cmd.toString();
/*
* avoid repeated commands for the same residue
*/
if (command.equals(lastHighlightCommand))
{
return;
}
/*
* unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
}
if (found)
{
viewer.sendChimeraCommand(command, false);
}
this.lastHighlightCommand = command;
}
/**
* Query Chimera for its current selection, and highlight it on the alignment
*/
public void highlightChimeraSelection()
{
/*
* Ask Chimera for its current selection
*/
List selection = viewer.getSelectedResidueSpecs();
/*
* 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 atomSpecs = new ArrayList();
for (String atomSpec : selection)
{
int colonPos = atomSpec.indexOf(":");
if (colonPos == -1)
{
continue; // malformed
}
int hashPos = atomSpec.indexOf("#");
String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
int dotPos = modelSubmodel.indexOf(".");
int modelId = 0;
try
{
modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
: modelSubmodel.substring(0, dotPos));
} catch (NumberFormatException e)
{
// 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())
{
for (ChimeraModel cm : chimeraMaps.get(pdbfile))
{
if (cm.getModelNumber() == modelId)
{
pdbfilename = pdbfile;
break findfileloop;
}
}
}
atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
}
/*
* Broadcast the selection (which may be empty, if the user just cleared all
* selections)
*/
getSsm().mouseOverStructure(atomSpecs);
}
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)
{
colourBySequence = false;
if (cs == null)
{
return;
}
// Chimera expects RBG values in the range 0-1
final double normalise = 255D;
viewerCommandHistory(false);
StringBuilder command = new StringBuilder(128);
List 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 + ";");
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
viewerCommandHistory(true);
}
/**
* called when the binding thinks the UI needs to be refreshed after a Chimera
* state change. this could be because structures were loaded, or because an
* error has occurred.
*/
public abstract void refreshGUI();
@Override
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
}
/**
*
* @return true if Chimeral is still restoring state or loading is still going
* on (see setFinsihedLoadingFromArchive)
*/
@Override
public boolean isLoadingFromArchive()
{
return loadingFromArchive && !loadingFinished;
}
/**
* modify flag which controls if sequence colouring events are honoured by the
* binding. Should be true for normal operation
*
* @param finishedLoading
*/
@Override
public void setFinishedLoadingFromArchive(boolean finishedLoading)
{
loadingFinished = finishedLoading;
}
/**
* Send the Chimera 'background solid " command.
*
* @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
*/
public void setBackgroundColour(Color col)
{
viewerCommandHistory(false);
double normalise = 255D;
final String command = "background solid " + col.getRed() / normalise
+ "," + col.getGreen() / normalise + "," + col.getBlue()
/ normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
/**
* Ask Chimera to save its session to the given file. Returns true if
* successful, else false.
*
* @param filepath
* @return
*/
public boolean saveSession(String filepath)
{
if (isChimeraRunning())
{
List reply = viewer.sendChimeraCommand("save " + filepath,
true);
if (reply.contains("Session written"))
{
return true;
}
else
{
Cache.log
.error("Error saving Chimera session: " + reply.toString());
}
}
return false;
}
/**
* 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 filepath
* @return
*/
public boolean openSession(String filepath)
{
sendChimeraCommand("open " + filepath, true);
// todo: test for failure - how?
return true;
}
/**
* Returns a list of chains mapped in this viewer. Note this list is not
* currently scoped per structure.
*
* @return
*/
public List getChainNames()
{
List names = new ArrayList();
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;
}
/**
* Send a 'focus' command to Chimera to recentre the visible display
*/
public void focusView()
{
sendChimeraCommand("focus", false);
}
/**
* Send a 'show' command for all atoms in the currently selected columns
*
* TODO: pull up to abstract structure viewer interface
*
* @param vp
*/
public void highlightSelection(AlignmentViewPanel vp)
{
List 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);
}
}
}