--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.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.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
+
+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.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 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 jmol 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 Jmol 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 Jmol view.
+ */
+ private boolean associateNewStructs = false;
+
+ Vector atomsPicked = new Vector();
+
+ public Vector chainNames;
+
+ Hashtable chainFile;
+
+ /**
+ * array of target chains for seuqences - tied to pdbentry and sequence[]
+ */
+ protected String[][] chains;
+
+ boolean colourBySequence = true;
+
+ StringBuffer eval = new StringBuffer();
+
+ public String fileLoadingError;
+
+ private Map<String, List<ChimeraModel>> chimmaps = new HashMap<String, List<ChimeraModel>>();
+
+ private List<String> mdlToFile = new ArrayList<String>();
+
+ /**
+ * 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<ChimeraModel> oldList = viewer.getModelList();
+ viewer.openModel(file, ModelType.PDB_MODEL);
+ List<ChimeraModel> 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 Jmol ;
+ // 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<String> 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));
+ /*
+ * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
+ * "jalviewJmol", ap.av.applet .getDocumentBase(),
+ * ap.av.applet.getCodeBase(), "", this);
+ *
+ * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", 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
+ *
+ * @return
+ */
+ public String getViewerTitle()
+ {
+ 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.
+ StringBuffer title = new StringBuffer("Chimera view for "
+ + sequence[0][0].getName() + ":" + pdbentry[0].getId());
+
+ 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 chainList
+ * list of chains to make visible
+ */
+ public void centerViewer(Vector chainList)
+ {
+ StringBuffer cmd = new StringBuffer();
+ String lbl;
+ int mlength, p;
+ for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ {
+ 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)) + "."
+ + lbl.substring(mlength + 1) + " or ");
+ }
+ if (cmd.length() > 0)
+ cmd.setLength(cmd.length() - 4);
+ evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus "
+ + cmd);
+ }
+
+ public void closeViewer()
+ {
+ ssm.removeStructureViewerListener(this, this.getPdbFile());
+ // and shut down Chimera
+ viewer.exitChimera();
+ // viewer.evalStringQuiet("zap");
+ // viewer.setJmolStatusListener(null);
+ lastCommand = null;
+ viewer = null;
+ releaseUIResources();
+ }
+
+ /**
+ * called by JalviewJmolbinding after closeViewer is called - release any
+ * resources and references so they can be garbage collected.
+ */
+ protected abstract void 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("colour *;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 });
+ }
+
+ public void superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
+ String[] files = getPdbFile();
+ // check to see if we are still waiting for Jmol 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: Jmol seems to be taking a long time to process all the structures.");
+ return;
+ }
+ 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];
+ 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;
+ }
+ StringBuffer command = new StringBuffer();
+
+ 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];
+ // reference structure - all others are superposed in it
+ String[] targetC = new String[files.length];
+ String[] chainNames = 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(
+ "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ }
+ 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 + 1) + ".1";
+ 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];
+ // 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;
+ // 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();
+ molsel.append("{");
+ 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(lpos);
+ molsel.append(chainCd);
+ // molsel.append("} {");
+ 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(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;
+ }
+ }
+ }
+ 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(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++)
+ {
+ command.append(selcom[(s == 0 ? pdbfnum : 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; ");
+ System.out
+ .println("Superimpose command(s):\n" + command.toString());
+
+ evalStateCommand(command.toString());
+ }
+ }
+ 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());
+ }
+ }
+
+ private void checkLaunched()
+ {
+ if (!viewer.isChimeraLaunched())
+ {
+ viewer.launchChimera(csm.getChimeraPaths());
+ }
+ if (!viewer.isChimeraLaunched())
+ {
+ log("Failed to launch Chimera!");
+ }
+ }
+
+ public void evalStateCommand(String command)
+ {
+ viewerCommandHistory(false);
+ checkLaunched();
+ if (lastCommand == null || !lastCommand.equals(command))
+ {
+
+ lastReply = viewer.sendChimeraCommand(command, true);
+ if (debug)
+ {
+ log("Response from command ('" + command + "') was:\n" + lastReply);
+ }
+ }
+ 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)
+ {
+ evalStateCommand(cbyseq);
+ }
+ }
+
+ public boolean isColourBySequence()
+ {
+ return colourBySequence;
+ }
+
+ public void setColourBySequence(boolean colourBySequence)
+ {
+ 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
+ // //////////////////////////
+
+ 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<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()]);
+ }
+
+ /**
+ * 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);
+
+ // jmol/ssm only
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ List<ChimeraModel> cms = chimmaps.get(pdbfile);
+ if (cms != null)
+ {
+ int mdlNum = cms.get(0).getModelNumber();
+
+ viewerCommandHistory(false);
+ viewer.stopListening();
+ if (resetLastRes.length() > 0)
+ {
+ viewer.sendChimeraCommand(resetLastRes.toString(), false);
+ }
+
+ eval.setLength(0);
+ 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);
+ }
+ eval.append(eval.toString());
+
+ resetLastRes.append(resetLastRes.toString()
+ );
+
+ viewer.sendChimeraCommand(eval.toString(), false);
+ viewerCommandHistory(true);
+ viewer.startListening();
+ }
+ }
+
+ boolean debug = true;
+
+ 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.addElement(picked);
+ }
+ else
+ {
+ viewer.select("not " + picked);
+ atomsPicked.removeElement(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
+ // 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.
+ 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;
+ viewerCommandHistory(false);
+ // TODO: Switch between nucleotide or aa selection expressions
+ Enumeration en = ResidueProperties.aa3Hash.keys();
+ StringBuffer command = new StringBuffer("select *;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));
+ // TODO: need colour string function and res selection here
+ command.append("select " + res + ";color[" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
+ }
+
+ evalStateCommand(command.toString());
+ viewerCommandHistory(true);
+ }
+
+ public void showHelp()
+ {
+ // chimera help
+ 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();
+
+ 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 Jmol 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;
+ }
+
+ public void setBackgroundColour(java.awt.Color col)
+ {
+ viewerCommandHistory(false);
+ // todo set background colour
+ viewer.sendChimeraCommand(
+ "background [" + col.getRed() + "," + col.getGreen() + ","
+ + col.getBlue() + "];", 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)
+ {
+ int pe = -1;
+ Vector v = new Vector();
+ Vector rtn = new Vector();
+ for (int i = 0; i < pdbentry.length; i++)
+ {
+ v.addElement(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[]
+ { v.size(), i });
+ v.addElement(pdbe[i]);
+ }
+ else
+ {
+ // just make sure the sequence/chain entries are all up to date
+ addSequenceAndChain(r, seq[i], chns[i]);
+ }
+ }
+ pdbe = new PDBEntry[v.size()];
+ v.copyInto(pdbe);
+ pdbentry = pdbe;
+ if (rtn.size() > 0)
+ {
+ // expand the tied seuqence[] 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 = ((int[]) rtn.elementAt(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;
+ }
+
+ public void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
+
+ private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ {
+ if (pe < 0 || pe >= pdbentry.length)
+ {
+ throw new Error(
+ "Implementation error - no corresponding pdbentry (for index "
+ + pe + ") to add sequences mappings to");
+ }
+ final String nullChain = "TheNullChain";
+ Vector s = new Vector();
+ Vector c = new Vector();
+ if (chains == null)
+ {
+ chains = new String[pdbentry.length][];
+ }
+ if (sequence[pe] != null)
+ {
+ for (int i = 0; i < sequence[pe].length; i++)
+ {
+ s.addElement(sequence[pe][i]);
+ if (chains[pe] != null)
+ {
+ if (i < chains[pe].length)
+ {
+ c.addElement(chains[pe][i]);
+ }
+ else
+ {
+ c.addElement(nullChain);
+ }
+ }
+ else
+ {
+ if (tchain != null && tchain.length > 0)
+ {
+ c.addElement(nullChain);
+ }
+ }
+ }
+ }
+ for (int i = 0; i < seq.length; i++)
+ {
+ if (!s.contains(seq[i]))
+ {
+ s.addElement(seq[i]);
+ if (tchain != null && i < tchain.length)
+ {
+ c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+ }
+ }
+ }
+ SequenceI[] tmp = new SequenceI[s.size()];
+ s.copyInto(tmp);
+ sequence[pe] = tmp;
+ if (c.size() > 0)
+ {
+ String[] tch = new String[c.size()];
+ c.copyInto(tch);
+ 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff