*/
package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.assertTrue;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
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.ArrayList;
-import java.util.Collection;
import java.util.Enumeration;
import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
-
-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.constant.EnumCallback;
-import org.jmol.popup.JmolPopup;
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;
-import sun.rmi.runtime.Log;
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;
/**
* when true, try to search the associated datamodel for sequences that are
- * associated with any unknown structures in the Jmol view.
+ * associated with any unknown structures in the Chimera view.
*/
private boolean associateNewStructs = false;
- Vector atomsPicked = new Vector();
+ List<String> atomsPicked = new ArrayList<String>();
- public Vector chainNames;
+ public List<String> chainNames;
- Hashtable chainFile;
+ private Map<String, String> chainFile;
/**
- * array of target chains for seuqences - tied to pdbentry and sequence[]
+ * array of target chains for sequences - tied to pdbentry and sequence[]
*/
protected String[][] chains;
public String fileLoadingError;
- private Map<String, List<ChimeraModel>> chimmaps = new HashMap<String, List<ChimeraModel>>();
+ private Map<String, List<ChimeraModel>> chimmaps = new LinkedHashMap<String, List<ChimeraModel>>();
private List<String> mdlToFile = new ArrayList<String>();
try
{
List<ChimeraModel> oldList = viewer.getModelList();
- viewer.openModel(file, ModelType.PDB_MODEL);
+ viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
List<ChimeraModel> newList = viewer.getModelList();
if (oldList.size() < newList.size())
{
chimmaps.put(file, newList);
for (ChimeraModel cm : newList)
{
- while (mdlToFile.size()<1+cm.getModelNumber())
+ while (mdlToFile.size() < 1 + cm.getModelNumber())
{
mdlToFile.add(new String(""));
}
* prepare the view for a given set of models/chains. chainList contains
* strings of the form 'pdbfilename:Chaincode'
*
- * @param chainList
+ * @param toshow
* list of chains to make visible
*/
- public void centerViewer(Vector chainList)
+ public void centerViewer(List<String> toshow)
{
- StringBuffer cmd = new StringBuffer();
- String lbl;
+ StringBuilder cmd = new StringBuilder(64);
int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ for (String lbl : toshow)
{
mlength = 0;
- lbl = (String) chainList.elementAt(i);
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((String) chainFile.get(lbl)) + "."
+ cmd.append("#" + getModelNum(chainFile.get(lbl)) + "."
+ lbl.substring(mlength + 1) + " or ");
}
if (cmd.length() > 0)
+ {
cmd.setLength(cmd.length() - 4);
- evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus "
- + cmd);
+ }
+ String cmdstring = cmd.toString();
+ evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring
+ + ";focus " + cmdstring, false);
}
public void closeViewer()
// 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");
+ evalStateCommand("select *;color chain",false);
}
public void colourByCharge()
{
colourBySequence = false;
evalStateCommand("colour *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
+ + "select LYS,ARG;color blue;select CYS;color yellow", false);
}
/**
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 Jmol files
long starttime = System.currentTimeMillis();
if (waiting)
{
System.err
- .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+ .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures.");
return;
}
+ refreshPdbEntries();
StringBuffer selectioncom = new StringBuffer();
- // 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];
if (a > 0
&& selectioncom.length() > 0
&& !selectioncom.substring(selectioncom.length() - 1).equals(
- "|"))
+ " "))
{
- selectioncom.append("|");
+ selectioncom.append(" ");
}
// process this alignment
if (refStructure >= files.length)
{
refStructure = -1;
}
- StringBuffer command = new StringBuffer();
boolean matched[] = new boolean[alignment.getWidth()];
for (int m = 0; m < matched.length; m++)
int commonrpositions[][] = new int[files.length][alignment.getWidth()];
String isel[] = new String[files.length];
- // reference structure - all others are superposed in it
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]);
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
{
- throw new Error(
- "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data"));
}
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
commonrpositions[pdbfnum][r] = pos;
}
// create model selection suffix
- isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ isel[pdbfnum] = "#" + pdbfnum;
if (mapping[m].getChain() == null
|| mapping[m].getChain().trim().length() == 0)
{
}
else
{
- targetC[pdbfnum] = ":" + mapping[m].getChain();
+ 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;
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++)
int lpos = -1;
boolean run = false;
StringBuffer molsel = new StringBuffer();
- molsel.append("{");
for (int r = 0; r < matched.length; r++)
{
if (matched[r])
// discontinuity
if (lpos != -1)
{
- molsel.append(lpos);
+ molsel.append((run ? "" : ":") + lpos);
molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
+ molsel.append(",");
}
}
else
if (!run)
{
// at the beginning, so add dash
- molsel.append(lpos);
+ molsel.append(":" + lpos);
molsel.append("-");
}
run = true;
// add final selection phrase
if (lpos != -1)
{
- molsel.append(lpos);
+ molsel.append((run ? "" : ":") + lpos);
molsel.append(chainCd);
- molsel.append("}");
+ // 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)");
+ selectioncom.append("#" + pdbfnum);
+ selectioncom.append(selcom[pdbfnum]);
+ selectioncom.append(" ");
if (pdbfnum < files.length - 1)
{
- selectioncom.append("|");
+ selectioncom.append("| ");
}
}
else
}
}
}
+ StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
{
continue;
}
- command.append("echo ");
- command.append("\"Superposing (");
- command.append(chainNames[pdbfnum]);
- command.append(") against reference (");
- command.append(chainNames[refStructure]);
- command.append(")\";\ncompare " + nSeconds);
- command.append("{");
- command.append(1 + pdbfnum);
- command.append(".1} {");
- command.append(1 + refStructure);
- command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
-
- // form the matched pair strings
- String sep = "";
- for (int s = 0; s < 2; s++)
+ if (command.length() > 0)
{
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ command.append(";");
}
- command.append(" ROTATE TRANSLATE;\n");
+
+ /*
+ * 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());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
- // selcom.append("; ribbons; ");
System.out
.println("Superimpose command(s):\n" + command.toString());
-
- evalStateCommand(command.toString());
+ allComs.append("~display all; chain @CA|P; ribbon "
+ + selectioncom.toString() + ";"+command.toString());
+ // selcom.append("; ribbons; ");
}
}
if (selectioncom.length() > 0)
selectioncom.setLength(selectioncom.length() - 1);
}
System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
+ allComs.append("; ~display all; chain @CA|P; ribbon "
+ + selectioncom.toString() + "");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+ evalStateCommand(allComs.toString(), true /* false */);
}
+
}
private void checkLaunched()
}
}
- public void evalStateCommand(String command)
+ public void evalStateCommand(final String command, boolean resp)
{
viewerCommandHistory(false);
checkLaunched();
if (lastCommand == null || !lastCommand.equals(command))
{
-
- lastReply = viewer.sendChimeraCommand(command, true);
- if (debug)
- {
- log("Response from command ('" + command + "') was:\n" + lastReply);
- }
+// 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(), resp);
+ if (debug && resp)
+ {
+ log("Response from command ('" + command + "') was:\n"
+ + lastReply);
+ }
+// }
+// });
+ // TODO - use j7/8 thread management
+// try
+// {
+// t.join();
+// } catch (InterruptedException foo)
+// {
+// }
+// ;
}
viewerCommandHistory(true);
lastCommand = command;
jalview.api.AlignmentViewPanel alignmentv)
{
if (!colourBySequence || !loadingFinished)
+ {
return;
+ }
if (ssm == null)
{
return;
for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands
.getColourBySequenceCommand(ssm, files, sequence, sr, fr,
alignment))
+ {
for (String cbyseq : cpdbbyseq.commands)
{
- evalStateCommand(cbyseq);
+ waitForChimera();
+ evalStateCommand(cbyseq, false);
+ waitForChimera();
}
+ }
+ }
+
+ private void waitForChimera()
+ {
+ while (viewer.isBusy())
+ {
+ try {
+ Thread.sleep(15);
+ } catch (InterruptedException q)
+ {}
+ }
}
public boolean isColourBySequence()
this.colourBySequence = colourBySequence;
}
- 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
// //////////////////////////
String pdbfile)
{
if (getModelNum(pdbfile) < 0)
+ {
return null;
+ }
log("get model / residue colour attribute unimplemented");
return null;
}
for (int i = 0; i < mfn.length; i++)
{
if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
return i;
+ }
}
return -1;
}
{
return new String[0];
}
-// if (modelFileNames == null)
-// {
-// Collection<ChimeraModel> 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);
-// }
+ // if (modelFileNames == null)
+ // {
+ // Collection<ChimeraModel> 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()]);
int mdlNum = cms.get(0).getModelNumber();
viewerCommandHistory(false);
- viewer.stopListening();
+ // viewer.stopListening();
if (resetLastRes.length() > 0)
{
- viewer.sendChimeraCommand(resetLastRes.toString(), false);
+ eval.setLength(0);
+ eval.append(resetLastRes.toString() + ";");
}
- eval.setLength(0);
eval.append("display "); // +modelNum
resetLastRes.setLength(0);
resetLastRes.append("~display ");
{
eval.append(" #" + (mdlNum));
- resetLastRes.append("#" + (mdlNum));
+ resetLastRes.append(" #" + (mdlNum));
}
// complete select string
eval.append("." + chain);
resetLastRes.append("." + chain);
}
- eval.append(eval.toString());
-
- resetLastRes.append(resetLastRes.toString()
- );
-
+
viewer.sendChimeraCommand(eval.toString(), false);
viewerCommandHistory(true);
- viewer.startListening();
+ // viewer.startListening();
}
}
String chainId;
if (strInfo.indexOf(":") > -1)
+ {
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
+ }
else
{
chainId = " ";
;
}
if (lastMessage == null || !lastMessage.equals(strInfo))
+ {
ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ }
lastMessage = strInfo;
}
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)
{
if (!atomsPicked.contains(picked))
{
viewer.select(picked);
- atomsPicked.addElement(picked);
+ atomsPicked.add(picked);
}
else
{
viewer.select("not " + picked);
- atomsPicked.removeElement(picked);
+ atomsPicked.remove(picked);
}
viewerCommandHistory(true);
// TODO: in application this happens
// incremented every time a load notification is successfully handled -
// lightweight mechanism for other threads to detect when they can start
- // referrring to new structures.
+ // referring to new structures.
private long loadNotifiesHandled = 0;
public long getLoadNotifiesHandled()
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
- chainFile = new Hashtable();
+ chainNames = new ArrayList<String>();
+ chainFile = new HashMap<String, String>();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
// first check if we've lost any structures
colourBySequence = false;
if (cs == null)
+ {
return;
+ }
String res;
int index;
res = en.nextElement().toString();
index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
if (index > 20)
+ {
continue;
+ }
col = cs.findColour(ResidueProperties.aa[index].charAt(0));
// TODO: need colour string function and res selection here
+ col.getGreen() + "," + col.getBlue() + "];");
}
- evalStateCommand(command.toString());
+ evalStateCommand(command.toString(),false);
viewerCommandHistory(true);
}
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
- int pe = -1;
- Vector v = new Vector();
- Vector rtn = new Vector();
+ List<PDBEntry> v = new ArrayList<PDBEntry>();
+ List<int[]> rtn = new ArrayList<int[]>();
for (int i = 0; i < pdbentry.length; i++)
{
- v.addElement(pdbentry[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.addElement(new int[]
+ rtn.add(new int[]
{ v.size(), i });
- v.addElement(pdbe[i]);
+ v.add(pdbe[i]);
}
else
{
addSequenceAndChain(r, seq[i], chns[i]);
}
}
- pdbe = new PDBEntry[v.size()];
- v.copyInto(pdbe);
+ pdbe = v.toArray(new PDBEntry[v.size()]);
pdbentry = pdbe;
if (rtn.size() > 0)
{
- // expand the tied seuqence[] and string[] arrays
+ // 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);
pdbe = new PDBEntry[rtn.size()];
for (int r = 0; r < pdbe.length; r++)
{
- int[] stri = ((int[]) rtn.elementAt(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
return pdbe;
}
+ /**
+ * Adds sequences to the pe'th pdbentry's sequence set.
+ *
+ * @param pe
+ * @param seq
+ */
public void addSequence(int pe, SequenceI[] seq)
{
- // add sequences to the pe'th pdbentry's seuqence set.
addSequenceAndChain(pe, seq, null);
}
{
if (pe < 0 || pe >= pdbentry.length)
{
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_no_pdbentry_from_index",
+ new Object[]
+ { Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
- Vector s = new Vector();
- Vector c = new Vector();
+ List<SequenceI> s = new ArrayList<SequenceI>();
+ List<String> c = new ArrayList<String>();
if (chains == null)
{
chains = new String[pdbentry.length][];
{
for (int i = 0; i < sequence[pe].length; i++)
{
- s.addElement(sequence[pe][i]);
+ s.add(sequence[pe][i]);
if (chains[pe] != null)
{
if (i < chains[pe].length)
{
- c.addElement(chains[pe][i]);
+ c.add(chains[pe][i]);
}
else
{
- c.addElement(nullChain);
+ c.add(nullChain);
}
}
else
{
if (tchain != null && tchain.length > 0)
{
- c.addElement(nullChain);
+ c.add(nullChain);
}
}
}
{
if (!s.contains(seq[i]))
{
- s.addElement(seq[i]);
+ s.add(seq[i]);
if (tchain != null && i < tchain.length)
{
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+ c.add(tchain[i] == null ? nullChain : tchain[i]);
}
}
}
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
+ SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
sequence[pe] = tmp;
if (c.size() > 0)
{
- String[] tch = new String[c.size()];
- c.copyInto(tch);
+ String[] tch = c.toArray(new String[c.size()]);
for (int i = 0; i < tch.length; i++)
{
if (tch[i] == nullChain)
git://source.jalview.org / jalview.git / blobdiff