package jalview.ext.rbvi.chimera;
import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
-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.ColorUtils;
import jalview.util.MessageManager;
-import java.awt.Color;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Collections;
-import java.util.Hashtable;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
// 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 List<String> chainNames = new ArrayList<>();
-
- private Hashtable<String, String> chainFile = new Hashtable<>();
-
/*
* Object through which we talk to Chimera
*/
- private ChimeraManager viewer;
+ private ChimeraManager chimeraManager;
/*
* Object which listens to Chimera notifications
try
{
List<ChimeraModel> modelsToMap = new ArrayList<>();
- List<ChimeraModel> oldList = viewer.getModelList();
+ List<ChimeraModel> oldList = chimeraManager.getModelList();
boolean alreadyOpen = false;
/*
*/
if (!alreadyOpen)
{
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- if (viewer.isChimeraX())
+ chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ if (chimeraManager.isChimeraX())
{
/*
* ChimeraX hack: force chimera model name to pdbId
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- sendChimeraCommand(command, false);
+ executeCommand(command, false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
* Chimera: query for actual models and find the one with
* matching model name - set in viewer.openModel()
*/
- List<ChimeraModel> newList = viewer.getModelList();
+ List<ChimeraModel> newList = chimeraManager.getModelList();
// JAL-1728 newList.removeAll(oldList) does not work
for (ChimeraModel cm : newList)
{
DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
- viewer = new ChimeraManager(new StructureManager(true));
+ chimeraManager = new ChimeraManager(new StructureManager(true));
String viewerType = Cache.getProperty(Preferences.STRUCTURE_DISPLAY);
- viewer.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
-
+ chimeraManager.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
+ setStructureCommands(new ChimeraCommands());
}
/**
*/
protected void startChimeraProcessMonitor()
{
- final Process p = viewer.getChimeraProcess();
+ final Process p = chimeraManager.getChimeraProcess();
chimeraMonitor = new Thread(new Runnable()
{
try
{
chimeraListener = new ChimeraListener(this);
- viewer.startListening(chimeraListener.getUri());
+ chimeraManager.startListening(chimeraListener.getUri());
} catch (BindException e)
{
System.err.println(
}
/**
- * Tells Chimera to display only the specified chains
- *
- * @param toshow
- */
- public void showChains(List<String> toshow)
- {
- /*
- * Construct a chimera command like
- *
- * ~display #*;~ribbon #*;ribbon :.A,:.B
- */
- StringBuilder cmd = new StringBuilder(64);
- boolean first = true;
- for (String chain : toshow)
- {
- int modelNumber = getModelNoForChain(chain);
- String showChainCmd = modelNumber == -1 ? ""
- : modelNumber + ":." + chain.split(":")[1];
- if (!first)
- {
- cmd.append(",");
- }
- cmd.append(showChainCmd);
- 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.
*/
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
- viewer.exitChimera();
+ chimeraManager.exitChimera();
}
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
- viewer = null;
+ chimeraManager = null;
if (chimeraMonitor != null)
{
releaseUIResources();
}
- @Override
- public void colourByChain()
- {
- colourBySequence = false;
- sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
- }
-
- /**
- * 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>
- */
- @Override
- public void colourByCharge()
- {
- colourBySequence = false;
- String command = viewer.isChimeraX()
- ? "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"
- : "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
-
/**
* {@inheritDoc}
*/
refreshPdbEntries();
StringBuilder selectioncom = new StringBuilder(256);
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
for (int a = 0; a < _alignment.length; a++)
{
int refStructure = _refStructure[a];
}
// allComs.append("; ~display all; chain @CA|P; ribbon ")
// .append(selectioncom.toString()).append("; focus");
- List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
+ List<String> chimeraReplies = executeCommand(allComs.toString(),
true);
for (String reply : chimeraReplies)
{
*/
public boolean launchChimera()
{
- if (viewer.isChimeraLaunched())
+ if (chimeraManager.isChimeraLaunched())
{
return true;
}
- boolean launched = viewer.launchChimera(
- StructureManager.getChimeraPaths(viewer.isChimeraX()));
+ boolean launched = chimeraManager.launchChimera(
+ StructureManager.getChimeraPaths(chimeraManager.isChimeraX()));
if (launched)
{
startChimeraProcessMonitor();
*/
public boolean isChimeraRunning()
{
- return viewer.isChimeraLaunched();
+ return chimeraManager.isChimeraLaunched();
}
/**
* @param command
* @param getResponse
*/
- public List<String> sendChimeraCommand(final String command,
+ @Override
+ public List<String> executeCommand(final String command,
boolean getResponse)
{
- if (viewer == null)
+ if (chimeraManager == null || command == null)
{
// ? thread running after viewer shut down
return null;
if (true /*lastCommand == null || !lastCommand.equals(command)*/)
{
// trim command or it may never find a match in the replyLog!!
- List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ List<String> lastReply = chimeraManager.sendChimeraCommand(command.trim(),
getResponse);
if (getResponse)
{
String progressMsg);
/**
- * Sends a set of colour commands to the structure viewer
- *
- * @param colourBySequenceCommands
- */
- @Override
- protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
- {
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
- {
- for (String command : cpdbbyseq.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
- }
- }
-
- /**
- * @param files
- * @param sr
- * @param viewPanel
- * @return
- */
- @Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
- {
- return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel, viewer.isChimeraX());
- }
-
- /**
* @param command
*/
protected void executeWhenReady(String command)
{
waitForChimera();
- sendChimeraCommand(command, false);
+ executeCommand(command, false);
waitForChimera();
}
private void waitForChimera()
{
- while (viewer != null && viewer.isBusy())
+ while (chimeraManager != null && chimeraManager.isBusy())
{
try
{
@Override
public synchronized String[] getStructureFiles()
{
- if (viewer == null)
+ if (chimeraManager == null)
{
return new String[0];
}
return;
}
- boolean forChimeraX = viewer.isChimeraX();
+ boolean forChimeraX = chimeraManager.isChimeraX();
StringBuilder cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
*/
if (lastHighlightCommand != null)
{
- viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
}
if (found)
{
- viewer.sendChimeraCommand(command, false);
+ chimeraManager.sendChimeraCommand(command, false);
}
this.lastHighlightCommand = command;
}
/*
* Ask Chimera for its current selection
*/
- List<String> selection = viewer.getSelectedResidueSpecs();
+ List<String> selection = chimeraManager.getSelectedResidueSpecs();
/*
* Parse model number, residue and chain for each selected position,
protected List<AtomSpec> convertStructureResiduesToAlignment(
List<String> structureSelection)
{
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
List<AtomSpec> atomSpecs = new ArrayList<>();
for (String atomSpec : structureSelection)
{
return loadNotifiesHandled;
}
- @Override
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- viewerCommandHistory(false);
- StringBuilder command = new StringBuilder(128);
-
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
-
- /*
- * concatenate colour commands, one per residue symbol
- * Chimera format: color colorCode ::VAL
- * ChimeraX format: color :VAL colourCode
- */
- boolean chimeraX = viewer.isChimeraX();
- for (String resName : residueSet)
- {
- char res = resName.length() == 3
- ? ResidueProperties.getSingleCharacterCode(resName)
- : resName.charAt(0);
- Color col = cs.findColour(res, 0, null, null, 0f);
- command.append("color ");
- String colorSpec = ColorUtils.toTkCode(col);
- if (chimeraX)
- {
- command.append(":").append(resName).append(" ").append(colorSpec);
- }
- else
- {
- command.append(colorSpec).append(" ::").append(resName);
- }
- command.append(";");
- }
-
- 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
}
/**
- * Send the Chimera 'background solid <color>" command.
- *
- * @see https
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
- * .html
- * @param col
- */
- @Override
- public void setBackgroundColour(Color col)
- {
- viewerCommandHistory(false);
- String command = "set bgColor " + ColorUtils.toTkCode(col);
- viewer.sendChimeraCommand(command, false);
- viewerCommandHistory(true);
- }
-
- /**
* Ask Chimera to save its session to the given file. Returns true if
* successful, else false.
*
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
*/
String command = isChimeraX() ? "save session " : "save ";
- List<String> reply = viewer.sendChimeraCommand(command + filepath,
+ List<String> reply = chimeraManager.sendChimeraCommand(command + filepath,
true);
if (reply.contains("Session written"))
{
* Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
*/
- sendChimeraCommand("open " + filepath, true);
+ executeCommand("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
- */
- @Override
- public List<String> getChainNames()
- {
- return chainNames;
- }
-
- /**
- * Send a 'focus' command to Chimera to recentre the visible display
- */
- public void focusView()
- {
- sendChimeraCommand(viewer.isChimeraX() ? "view" : "focus", false);
- }
-
- /**
* Send a 'show' command for all atoms in the currently selected columns
*
* TODO: pull up to abstract structure viewer interface
StructureMappingcommandSet commandSet = ChimeraCommands
.getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), avp, viewer.isChimeraX());
+ getSequence(), avp, chimeraManager.isChimeraX());
String[] commands = commandSet.commands;
if (commands.length > 10)
{
*/
protected void sendCommandsByFile(String[] commands)
{
- boolean toChimeraX = viewer.isChimeraX();
+ boolean toChimeraX = chimeraManager.isChimeraX();
try
{
File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
// fails for 'average.bfactor' (which is bad):
String cmd = "list residues attr '" + attName + "'";
- List<String> residues = sendChimeraCommand(cmd, true);
+ List<String> residues = executeCommand(cmd, true);
boolean featureAdded = createFeaturesForAttributes(attName, residues);
if (featureAdded)
{
boolean featureAdded = false;
String featureGroup = getViewerFeatureGroup();
- boolean chimeraX = viewer.isChimeraX();
+ boolean chimeraX = chimeraManager.isChimeraX();
for (String residue : residues)
{
return CHIMERA_FEATURE_GROUP;
}
- public Hashtable<String, String> getChainFile()
- {
- return chainFile;
- }
-
- public List<ChimeraModel> getChimeraModelByChain(String chain)
- {
- return chimeraMaps.get(chainFile.get(chain));
- }
-
- public int getModelNoForChain(String chain)
+ @Override
+ public int getModelNoForFile(String pdbFile)
{
- List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+ List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
if (foundModels != null && !foundModels.isEmpty())
{
return foundModels.get(0).getModelNumber();
*/
public List<String> getChimeraAttributes()
{
- List<String> atts = viewer.getAttrList();
+ List<String> atts = chimeraManager.getAttrList();
Iterator<String> it = atts.iterator();
while (it.hasNext())
{
public boolean isChimeraX()
{
- return viewer.isChimeraX();
+ return chimeraManager.isChimeraX();
}
}
git://source.jalview.org / jalview.git / blobdiff