/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.api.SequenceStructureBinding;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.SequenceStructureBindingModel;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.event.ComponentEvent;
import java.io.File;
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.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
SequenceStructureBindingModel implements StructureListener,
SequenceStructureBinding, StructureSelectionManagerProvider
{
private static final String PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
private StructureManager csm;
private ChimeraManager viewer;
/**
* 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 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 Chimera 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 atomsPicked = new ArrayList();
public List chainNames;
private Map 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> chimmaps = new LinkedHashMap>();
private List mdlToFile = new ArrayList();
/**
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
int frameNo = 0;
String lastCommand;
String lastMessage;
boolean loadedInline;
public boolean openFile(PDBEntry pe)
{
String file = pe.getFile();
try
{
List oldList = viewer.getModelList();
viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
List newList = viewer.getModelList();
if (oldList.size() < newList.size())
{
while (oldList.size() > 0)
{
oldList.remove(0);
newList.remove(0);
}
chimmaps.put(file, newList);
for (ChimeraModel cm : newList)
{
while (mdlToFile.size() < 1 + cm.getModelNumber())
{
mdlToFile.add(new String(""));
}
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 Chimera ;
// pdbentry[pe].getFile(), protocol);
if (ssm != null)
{
ssm.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;
}
/**
* 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
*/
public SequenceI[][] sequence;
public StructureSelectionManager ssm;
private List 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][];
}
viewer = new ChimeraManager(
csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
public JalviewChimeraBinding(StructureSelectionManager ssm,
ChimeraManager viewer2)
{
this.ssm = ssm;
viewer = viewer2;
csm = viewer.getStructureManager();
}
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
*
* @param verbose
* @return
*/
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();
}
/**
* prepare the view for a given set of models/chains. chainList contains
* strings of the form 'pdbfilename:Chaincode'
*
* @param toshow
* list of chains to make visible
*/
public void centerViewer(List toshow)
{
StringBuilder cmd = new StringBuilder(64);
int mlength, p;
for (String lbl : toshow)
{
mlength = 0;
do
{
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);
}
String cmdstring = cmd.toString();
evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring
+ ";focus " + cmdstring, false);
}
/**
* Close down the Jalview viewer, and (optionally) the associate Chimera
* window.
*/
public void closeViewer(boolean closeChimera)
{
ssm.removeStructureViewerListener(this, this.getPdbFile());
if (closeChimera)
{
viewer.exitChimera();
}
lastCommand = null;
viewer = null;
releaseUIResources();
}
/**
* called by JalviewChimerabinding after closeViewer is called - release any
* resources and references so they can be garbage collected.
*/
protected abstract void releaseUIResources();
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);
}
/**
* 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)
*/
public void superposeStructures(AlignmentI alignment, int refStructure)
{
superposeStructures(alignment, refStructure, 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)
* @param hiddenCols
* TODO
*/
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
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 = 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)
{
System.err
.println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures.");
return;
}
refreshPdbEntries();
StringBuffer selectioncom = new StringBuffer();
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 "
+ refStructure);
refStructure = -1;
}
if (refStructure < -1)
{
refStructure = -1;
}
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++)
{
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++)
{
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;
}
}
}
}
// TODO: consider bailing if nmatched less than 4 because superposition
// not
// well defined.
// TODO: refactor superposable position search (above) from jmol selection
// construction (below)
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++)
{
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 (pdbfnum == 0)
{
nmatched++;
}
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);
}
}
// 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)
{
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. (residues 1-91, chain B/A, alphacarbons):
*
* match #1:1-91.B@CA #0:1-91.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(selcom[pdbfnum]);
command.append("@" + atomSpec[pdbfnum]);
command.append(" #" + refStructure /* +".1" */);
command.append(selcom[refStructure]);
command.append("@" + atomSpec[refStructure]);
}
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 (selectioncom.length() > 0)
{// finally, mark all 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 */);
}
}
private void checkLaunched()
{
if (!viewer.isChimeraLaunched())
{
viewer.launchChimera(csm.getChimeraPaths());
}
if (!viewer.isChimeraLaunched())
{
log("Failed to launch Chimera!");
}
}
/**
* 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 evalStateCommand(final String command, boolean logResponse)
{
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)
// {
// }
// ;
}
viewerCommandHistory(true);
lastCommand = command;
}
/**
* 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 (ssm == 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 : ChimeraCommands
.getColourBySequenceCommand(ssm, files, sequence, sr, fr,
alignment))
{
for (String cbyseq : cpdbbyseq.commands)
{
waitForChimera();
evalStateCommand(cbyseq, false);
waitForChimera();
}
}
}
private void waitForChimera()
{
while (viewer != null && viewer.isBusy())
{
try {
Thread.sleep(15);
} catch (InterruptedException q)
{}
}
}
public boolean isColourBySequence()
{
return colourBySequence;
}
public void setColourBySequence(boolean colourBySequence)
{
this.colourBySequence = colourBySequence;
}
// 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
*
* @param alignment
*
* @return
*/
public abstract FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment);
/**
* 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
* 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
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 chimmaps.keySet().toArray(
modelFileNames = new String[chimmaps.size()]);
}
/**
* map from string to applet
*/
public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
}
/**
* returns the current sequenceRenderer that should be used to colour the
* structures
*
* @param alignment
*
* @return
*/
public abstract SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment);
/**
* Highlight the specified atom positions in the structure.
*
* @param atomIndex
* @param pdbResNum
* @param chain
* @param pdbfile
*/
@Override
public void highlightAtoms(List atoms)
{
for (AtomSpec atom : atoms)
{
int pdbResNum = atom.getPdbResNum();
String chain = atom.getChain();
List cms = chimmaps.get(atom.getPdbId());
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 = 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 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)
{
// 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)
{
pdbResNum = Integer.parseInt(strInfo.substring(
strInfo.indexOf("]") + 1, alocsep));
}
else
{
pdbResNum = Integer.parseInt(strInfo.substring(
strInfo.indexOf("]") + 1, chainSeparator));
}
String chainId;
if (strInfo.indexOf(":") > -1)
{
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
}
else
{
chainId = " ";
}
String pdbfilename = modelFileNames[frameNo]; // default is first or current
// model
if (mdlSep > -1)
{
if (chainSeparator1 == -1)
{
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])
{
_mp--;
}
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
// pdbfilename = new File(viewer.getModelFileName(mnumber))
// .getAbsolutePath();
}
} catch (Exception e)
{
}
;
}
if (lastMessage == null || !lastMessage.equals(strInfo))
{
ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
}
lastMessage = strInfo;
}
public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
{
/**
* this implements the toggle label behaviour copied from the original
* structure viewer, MCView
*/
if (strData != null)
{
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("."));
}
if ((p = strInfo.indexOf("/")) > -1)
{
mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
}
picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
+ mdlString + "))";
viewerCommandHistory(false);
if (!atomsPicked.contains(picked))
{
viewer.select(picked);
atomsPicked.add(picked);
}
else
{
viewer.select("not " + picked);
atomsPicked.remove(picked);
}
viewerCommandHistory(true);
// TODO: in application this happens
//
// if (scriptWindow != null)
// {
// scriptWindow.sendConsoleMessage(strInfo);
// scriptWindow.sendConsoleMessage("\n");
// }
}
// 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()
{
return loadNotifiesHandled;
}
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();
chainFile = new HashMap();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
int oldm = 0;
for (int i = 0; i < oldmodels.length; i++)
{
for (int n = 0; n < modelfilenames.length; n++)
{
if (modelfilenames[n] == oldmodels[i])
{
oldmodels[i] = null;
break;
}
}
if (oldmodels[i] != null)
{
oldm++;
}
}
if (oldm > 0)
{
String[] oldmfn = new String[oldm];
oldm = 0;
for (int i = 0; i < oldmodels.length; i++)
{
if (oldmodels[i] != null)
{
oldmfn[oldm++] = oldmodels[i];
}
}
// deregister the Jmol instance for these structures - we'll add
// ourselves again at the end for the current structure set.
ssm.removeStructureViewerListener(this, oldmfn);
}
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
ssm.addStructureViewerListener(this);
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
fr.featuresAdded();
}
refreshGUI();
loadNotifiesHandled++;
}
setLoadingFromArchive(false);
}
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
if (cs == null)
{
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();
StringBuilder command = new StringBuilder(128);
command.append("color white;");
while (en.hasMoreElements())
{
res = en.nextElement().toString();
index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
if (index > 20)
{
continue;
}
col = cs.findColour(ResidueProperties.aa[index].charAt(0));
command.append("color " + col.getRed() / normalise + ","
+ col.getGreen() / normalise + "," + col.getBlue()
/ normalise + " ::" + res + ";");
}
evalStateCommand(command.toString(),false);
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();
public void componentResized(ComponentEvent e)
{
}
public void componentMoved(ComponentEvent e)
{
}
public void componentShown(ComponentEvent e)
{
}
public void componentHidden(ComponentEvent e)
{
}
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
}
/**
*
* @return true if Chimeral is still restoring state or loading is still going
* on (see setFinsihedLoadingFromArchive)
*/
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
*/
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);
}
/**
* add structures and any known sequence associations
*
* @returns the pdb entries added to the current set.
*/
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
List v = new ArrayList();
List rtn = new ArrayList();
for (int i = 0; i < pdbentry.length; i++)
{
v.add(pdbentry[i]);
}
for (int i = 0; i < pdbe.length; i++)
{
int r = v.indexOf(pdbe[i]);
if (r == -1 || r >= pdbentry.length)
{
rtn.add(new int[]
{ v.size(), i });
v.add(pdbe[i]);
}
else
{
// just make sure the sequence/chain entries are all up to date
addSequenceAndChain(r, seq[i], chns[i]);
}
}
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;
}
/**
* Adds sequences to the pe'th pdbentry's sequence set.
*
* @param pe
* @param seq
*/
public void addSequence(int pe, SequenceI[] seq)
{
addSequenceAndChain(pe, seq, null);
}
private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
{
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 s = new ArrayList();
List c = new ArrayList();
if (chains == null)
{
chains = new String[pdbentry.length][];
}
if (sequence[pe] != null)
{
for (int i = 0; i < sequence[pe].length; i++)
{
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 (tchain != null && tchain.length > 0)
{
c.add(nullChain);
}
}
}
}
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;
}
}
/**
*
* @param pdbfile
* @return text report of alignment between pdbfile and any associated
* alignment sequences
*/
public String printMapping(String pdbfile)
{
return ssm.printMapping(pdbfile);
}
}