/*
* 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.jmol;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
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.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import javajs.awt.Dimension;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.script.T;
import org.jmol.viewer.JC;
import org.jmol.viewer.Viewer;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
/*
* state flag used to check if the Jmol viewer's paint method can be called
*/
private boolean finishedInit = false;
boolean allChainsSelected = false;
/*
* when true, try to search the associated datamodel for sequences that are
* associated with any unknown structures in the Jmol view.
*/
private boolean associateNewStructs = false;
Vector atomsPicked = new Vector();
public Vector chainNames;
Hashtable chainFile;
public String fileLoadingError;
/*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
int frameNo = 0;
// protected JmolGenericPopup jmolpopup; // not used - remove?
String lastCommand;
String lastMessage;
boolean loadedInline;
/**
* current set of model filenames loaded in the Jmol instance
*/
String[] modelFileNames = null;
StringBuffer resetLastRes = new StringBuffer();
public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
{
super(ssm, pdbentry, sequenceIs, chains, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
* ap.av.applet.getCodeBase(), "", this);
*
* jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
*/
}
public JalviewJmolBinding(StructureSelectionManager ssm,
SequenceI[][] seqs, Viewer theViewer)
{
super(ssm, seqs);
viewer = theViewer;
viewer.setJmolStatusListener(this);
viewer.addSelectionListener(this);
}
/**
* construct a title string for the viewer window based on the data jalview
* knows about
*
* @return
*/
public String getViewerTitle()
{
return getViewerTitle("Jmol", true);
}
/**
* prepare the view for a given set of models/chains. chainList contains
* strings of the form 'pdbfilename:Chaincode'
*
* @param chainList
* list of chains to make visible
*/
public void centerViewer(Vector chainList)
{
StringBuilder cmd = new StringBuilder(128);
int mlength, p;
for (String lbl : chainList)
{
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(":" + lbl.substring(mlength + 1) + " /"
+ (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
{
cmd.setLength(cmd.length() - 4);
}
evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
}
public void closeViewer()
{
viewer.acm.setModeMouse(JC.MOUSE_NONE);
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getPdbFile());
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
lastCommand = null;
viewer = null;
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");
}
public void colourByCharge()
{
colourBySequence = false;
evalStateCommand("select *;color white;select ASP,GLU;color red;"
+ "select LYS,ARG;color blue;select CYS;color yellow");
}
/**
* 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 });
}
/**
* 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)
{
String[] files = getPdbFile();
if (!waitForFileLoad(files))
{
return;
}
StringBuilder selectioncom = new StringBuilder(256);
// In principle - nSeconds specifies the speed of animation for each
// superposition - but is seems to behave weirdly, so we don't specify it.
String nSeconds = " ";
if (files.length > 10)
{
nSeconds = " 0.00001 ";
}
else
{
nSeconds = " " + (2.0 / files.length) + " ";
// if (nSeconds).substring(0,5)+" ";
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
nSeconds = " ";
// union of all aligned positions are collected together.
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;
}
/*
* '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;
}
String[] selcom = new String[files.length];
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
*/
{
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
String chainCd = ":" + structures[pdbfnum].chain;
int lpos = -1;
boolean run = false;
StringBuilder molsel = new StringBuilder();
molsel.append("{");
for (int r = 0; r < matched.length; r++)
{
if (matched[r])
{
int pdbResNo = structures[pdbfnum].pdbResNo[r];
if (lpos != pdbResNo - 1)
{
// discontinuity
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
molsel.append("|");
}
run = false;
}
else
{
// continuous run - and lpos >-1
if (!run)
{
// at the beginning, so add dash
molsel.append(lpos);
molsel.append("-");
}
run = true;
}
lpos = pdbResNo;
}
}
/*
* add final selection phrase
*/
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
molsel.append("}");
}
if (molsel.length() > 1)
{
selcom[pdbfnum] = molsel.toString();
selectioncom.append("((");
selectioncom.append(selcom[pdbfnum].substring(1,
selcom[pdbfnum].length() - 1));
selectioncom.append(" )& ");
selectioncom.append(pdbfnum + 1);
selectioncom.append(".1)");
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;
}
command.append("echo ");
command.append("\"Superposing (");
command.append(structures[pdbfnum].pdbId);
command.append(") against reference (");
command.append(structures[refStructure].pdbId);
command.append(")\";\ncompare " + nSeconds);
command.append("{");
command.append(Integer.toString(1 + pdbfnum));
command.append(".1} {");
command.append(Integer.toString(1 + refStructure));
// conformation=1 excludes alternate locations for CA (JAL-1757)
command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
// for (int s = 0; s < 2; s++)
// {
// command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
// }
command.append(selcom[pdbfnum]);
command.append(selcom[refStructure]);
command.append(" ROTATE TRANSLATE;\n");
}
if (selectioncom.length() > 0)
{
System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
System.out
.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
}
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());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
}
public void evalStateCommand(String command)
{
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
System.out.println(command);
viewer.evalStringQuiet(command + "\n");
}
jmolHistory(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(AlignmentViewPanel alignmentv)
{
boolean showFeatures = alignmentv.getAlignViewport()
.isShowSequenceFeatures();
if (!colourBySequence || !isLoadingFinished())
{
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 cbyseq : cpdbbyseq.commands)
{
executeWhenReady(cbyseq);
}
}
}
/**
* @param files
* @param sr
* @param fr
* @param alignment
* @return
*/
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
return JmolCommands
.getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
fr,
alignment);
}
/**
* @param command
*/
protected void executeWhenReady(String command)
{
evalStateCommand(command);
}
public void createImage(String file, String type, int quality)
{
System.out.println("JMOL CREATE IMAGE");
}
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
System.out.println("JMOL CREATE IMAGE");
return null;
}
public String eval(String strEval)
{
// System.out.println(strEval);
// "# 'eval' is implemented only for the applet.";
return null;
}
// 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;
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
int colour = viewer.ms.at[atomIndex]
.atomPropertyInt(T.color);
return new Color(colour);
}
/**
* 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
@Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
{
return new String[0];
}
if (modelFileNames == null)
{
String mset[] = new String[viewer.ms.mc];
_modelFileNameMap = new int[mset.length];
String m = viewer.ms.getModelFileName(0);
if (m != null)
{
mset[0] = m;
try
{
mset[0] = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet
System.err
.println("jmolBinding: Using local file string from Jmol: "
+ m);
}
if (mset[0].indexOf("/file:") != -1)
{
// applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
}
}
int j = 1;
for (int i = 1; i < mset.length; i++)
{
m = viewer.ms.getModelFileName(i);
mset[j] = m;
if (m != null)
{
try
{
mset[j] = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet, so keep raw handle
// System.err.println("jmolBinding: Using local file string from Jmol: "+m);
}
}
_modelFileNameMap[j] = i; // record the model index for the filename
// skip any additional models in the same file (NMR structures)
if ((mset[j] == null ? mset[j] != mset[j - 1]
: (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
{
j++;
}
}
modelFileNames = new String[j];
System.arraycopy(mset, 0, modelFileNames, 0, j);
}
return modelFileNames;
}
/**
* map from string to applet
*/
@Override
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);
// ///////////////////////////////
// JmolStatusListener
public void handlePopupMenu(int x, int y)
{
// jmolpopup.show(x, y);
// jmolpopup.jpiShow(x, y);
}
/**
* Highlight zero, one or more atoms on the structure
*/
@Override
public void highlightAtoms(List atoms)
{
if (atoms != null)
{
for (AtomSpec atom : atoms)
{
highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
atom.getChain(), atom.getPdbFile());
}
}
}
// jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
if (modelFileNames == null)
{
return;
}
// look up file model number for this pdbfile
int mdlNum = 0;
// may need to adjust for URLencoding here - we don't worry about that yet.
while (mdlNum < modelFileNames.length
&& !pdbfile.equals(modelFileNames[mdlNum]))
{
mdlNum++;
}
if (mdlNum == modelFileNames.length)
{
return;
}
jmolHistory(false);
// if (!pdbfile.equals(pdbentry.getFile()))
// return;
if (resetLastRes.length() > 0)
{
viewer.evalStringQuiet(resetLastRes.toString());
}
StringBuilder cmd = new StringBuilder(64);
cmd.append("select " + pdbResNum); // +modelNum
resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum); // +modelNum
cmd.append(":");
resetLastRes.append(":");
if (!chain.equals(" "))
{
cmd.append(chain);
resetLastRes.append(chain);
}
{
cmd.append(" /" + (mdlNum + 1));
resetLastRes.append("/" + (mdlNum + 1));
}
cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ " and not hetero; spacefill 0;");
cmd.append("spacefill 200;select none");
viewer.evalStringQuiet(cmd.toString());
jmolHistory(true);
}
boolean debug = true;
private void jmolHistory(boolean enable)
{
viewer.evalStringQuiet("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);
}
public void mouseOverStructure(int atomIndex, String strInfo)
{
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.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
} catch (Exception e)
{
}
;
}
if (lastMessage == null || !lastMessage.equals(strInfo))
{
getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
}
lastMessage = strInfo;
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
if (data != null)
{
System.err.println("Ignoring additional hover info: " + data
+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
/*
* { if (history != null && strStatus != null &&
* !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
* } }
*/
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);
}
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 + "))";
jmolHistory(false);
if (!atomsPicked.contains(picked))
{
viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
{
viewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
jmolHistory(true);
// TODO: in application this happens
//
// if (scriptWindow != null)
// {
// scriptWindow.sendConsoleMessage(strInfo);
// scriptWindow.sendConsoleMessage("\n");
// }
}
@Override
public void notifyCallback(CBK type, Object[] data)
{
try
{
switch (type)
{
case LOADSTRUCT:
notifyFileLoaded((String) data[1], (String) data[2],
(String) data[3], (String) data[4],
((Integer) data[5]).intValue());
break;
case PICK:
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
break;
case SCRIPT:
notifyScriptTermination((String) data[2],
((Integer) data[3]).intValue());
break;
case ECHO:
sendConsoleEcho((String) data[1]);
break;
case MESSAGE:
sendConsoleMessage((data == null) ? ((String) null)
: (String) data[1]);
break;
case ERROR:
// System.err.println("Ignoring error callback.");
break;
case SYNC:
case RESIZE:
refreshGUI();
break;
case MEASURE:
case CLICK:
default:
System.err.println("Unhandled callback " + type + " "
+ data[1].toString());
break;
}
} catch (Exception e)
{
System.err.println("Squashed Jmol callback handler error:");
e.printStackTrace();
}
}
@Override
public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
case ECHO:
case LOADSTRUCT:
case MEASURE:
case MESSAGE:
case PICK:
case SCRIPT:
case HOVER:
case ERROR:
return true;
default:
return false;
}
}
// incremented every time a load notification is successfully handled -
// lightweight mechanism for other threads to detect when they can start
// referrring 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 Vector();
chainFile = new Hashtable();
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.
getSsm().removeStructureViewerListener(this, oldmfn);
}
}
refreshPdbEntries();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
MCview.PDBfile pdb = null;
String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
// calculate essential attributes for the pdb data imported inline.
// prolly need to resolve modelnumber properly - for now just use our
// 'best guess'
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
if (fileName == null)
{
if (false)
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
pdbfile, AppletFormatAdapter.PASTE);
getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
matches = true;
foundEntry = true;
}
}
else
{
File fl = new File(getPdbEntry(pe).getFile());
matches = fl.equals(new File(fileName));
if (matches)
{
foundEntry = true;
// TODO: Jmol can in principle retrieve from CLASSLOADER but
// this
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
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 ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
fileName, protocol);
// pdbentry[pe].getFile(), protocol);
}
}
if (matches)
{
// add an entry for every chain in the model
for (int i = 0; i < pdb.chains.size(); i++)
{
String chid = new String(pdb.id + ":"
+ pdb.chains.elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.addElement(chid);
}
notifyLoaded = true;
}
}
if (!foundEntry && associateNewStructs)
{
// this is a foreign pdb file that jalview doesn't know about - add
// it to the dataset and try to find a home - either on a matching
// sequence or as a new sequence.
String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
"PDB");
// parse pdb file into a chain, etc.
// locate best match for pdb in associated views and add mapping to
// ssm
// if properly registered then
notifyLoaded = true;
}
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
// if (jmolpopup != null)
// {
// // potential for deadlock here:
// // jmolpopup.updateComputedMenus();
// }
if (!isLoadingFromArchive())
{
viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
getSsm().addStructureViewerListener(this);
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
fr.featuresAdded();
}
refreshGUI();
loadNotifiesHandled++;
}
setLoadingFromArchive(false);
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
public abstract void notifyScriptTermination(String strStatus,
int msWalltime);
/**
* display a message echoed from the jmol viewer
*
* @param strEcho
*/
public abstract void sendConsoleEcho(String strEcho); /*
* { showConsole(true);
*
* history.append("\n" +
* strEcho); }
*/
// /End JmolStatusListener
// /////////////////////////////
/**
* @param strStatus
* status message - usually the response received after a script
* executed
*/
public abstract void sendConsoleMessage(String strStatus);
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
System.err.println("Ignoring set-callback request to associate "
+ callbackType + " with function " + callbackFunction);
}
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
if (cs == null)
{
return;
}
jmolHistory(false);
StringBuilder command = new StringBuilder(128);
command.append("select *;color white;");
List residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
for (String res : residueSet)
{
Color col = cs.findColour(res.charAt(0));
command.append("select " + res + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
evalStateCommand(command.toString());
jmolHistory(true);
}
public void showHelp()
{
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
* state change. this could be because structures were loaded, or because an
* error has occured.
*/
public abstract void refreshGUI();
/**
* called to show or hide the associated console window container.
*
* @param show
*/
public abstract void showConsole(boolean show);
/**
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* in applet context)
* @param htmlName
* @param documentBase
* @param codeBase
* @param commandOptions
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions)
{
allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
codeBase, commandOptions, null, null);
}
/**
*
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* in applet context)
* @param htmlName
* @param documentBase
* @param codeBase
* @param commandOptions
* @param consolePanel
* - panel to contain Jmol console
* @param buttonsToShow
* - buttons to show on the console, in ordr
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
if (commandOptions == null)
{
commandOptions = "";
}
viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
viewer.setJmolStatusListener(this); // extends JmolCallbackListener
console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
}
}
protected abstract JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow);
protected org.jmol.api.JmolAppConsoleInterface console = null;
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
viewer.evalStringQuiet("background [" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
jmolHistory(true);
}
@Override
public Dimension resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
return null;
}
public boolean isFinishedInit()
{
return finishedInit;
}
public void setFinishedInit(boolean finishedInit)
{
this.finishedInit = finishedInit;
}
/**
*
*/
protected void closeConsole()
{
if (console != null)
{
try
{
console.setVisible(false);
} catch (Error e)
{
} catch (Exception x)
{
}
;
console = null;
}
}
/**
* ComponentListener method
*/
@Override
public void componentMoved(ComponentEvent e)
{
}
/**
* ComponentListener method
*/
@Override
public void componentResized(ComponentEvent e)
{
}
/**
* ComponentListener method
*/
@Override
public void componentShown(ComponentEvent e)
{
showConsole(true);
}
/**
* ComponentListener method
*/
@Override
public void componentHidden(ComponentEvent e)
{
showConsole(false);
}
}