2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.jmol;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.HiddenColumns;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.SequenceI;
30 import jalview.gui.IProgressIndicator;
31 import jalview.io.DataSourceType;
32 import jalview.io.StructureFile;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.ResidueProperties;
35 import jalview.structure.AtomSpec;
36 import jalview.structure.StructureMappingcommandSet;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.structures.models.AAStructureBindingModel;
39 import jalview.util.MessageManager;
41 import java.awt.Color;
42 import java.awt.Container;
43 import java.awt.event.ComponentEvent;
44 import java.awt.event.ComponentListener;
47 import java.util.ArrayList;
48 import java.util.BitSet;
49 import java.util.Hashtable;
50 import java.util.List;
52 import java.util.StringTokenizer;
53 import java.util.Vector;
55 import org.jmol.adapter.smarter.SmarterJmolAdapter;
56 import org.jmol.api.JmolAppConsoleInterface;
57 import org.jmol.api.JmolSelectionListener;
58 import org.jmol.api.JmolStatusListener;
59 import org.jmol.api.JmolViewer;
60 import org.jmol.c.CBK;
61 import org.jmol.script.T;
62 import org.jmol.viewer.Viewer;
64 public abstract class JalviewJmolBinding extends AAStructureBindingModel
65 implements JmolStatusListener, JmolSelectionListener,
68 private String lastMessage;
70 boolean allChainsSelected = false;
73 * when true, try to search the associated datamodel for sequences that are
74 * associated with any unknown structures in the Jmol view.
76 private boolean associateNewStructs = false;
78 Vector<String> atomsPicked = new Vector<>();
80 private List<String> chainNames;
82 Hashtable<String, String> chainFile;
85 * the default or current model displayed if the model cannot be identified
86 * from the selection message
90 // protected JmolGenericPopup jmolpopup; // not used - remove?
96 StringBuffer resetLastRes = new StringBuffer();
100 public JalviewJmolBinding(StructureSelectionManager ssm,
101 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
102 DataSourceType protocol)
104 super(ssm, pdbentry, sequenceIs, protocol);
106 * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
107 * "jalviewJmol", ap.av.applet .getDocumentBase(),
108 * ap.av.applet.getCodeBase(), "", this);
110 * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
114 public JalviewJmolBinding(StructureSelectionManager ssm,
115 SequenceI[][] seqs, Viewer theViewer)
120 viewer.setJmolStatusListener(this);
121 viewer.addSelectionListener(this);
125 * construct a title string for the viewer window based on the data jalview
130 public String getViewerTitle()
132 return getViewerTitle("Jmol", true);
136 * prepare the view for a given set of models/chains. chainList contains
137 * strings of the form 'pdbfilename:Chaincode'
140 * list of chains to make visible
142 public void centerViewer(Vector<String> chainList)
144 StringBuilder cmd = new StringBuilder(128);
146 for (String lbl : chainList)
152 mlength = lbl.indexOf(":", p);
153 } while (p < mlength && mlength < (lbl.length() - 2));
154 // TODO: lookup each pdb id and recover proper model number for it.
155 cmd.append(":" + lbl.substring(mlength + 1) + " /"
156 + (1 + getModelNum(chainFile.get(lbl))) + " or ");
158 if (cmd.length() > 0)
160 cmd.setLength(cmd.length() - 4);
162 evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
165 public void closeViewer()
167 // remove listeners for all structures in viewer
168 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
175 releaseUIResources();
179 public void colourByChain()
181 colourBySequence = false;
182 // TODO: colour by chain should colour each chain distinctly across all
184 // TODO: http://issues.jalview.org/browse/JAL-628
185 evalStateCommand("select *;color chain");
189 public void colourByCharge()
191 colourBySequence = false;
192 evalStateCommand("select *;color white;select ASP,GLU;color red;"
193 + "select LYS,ARG;color blue;select CYS;color yellow");
197 * superpose the structures associated with sequences in the alignment
198 * according to their corresponding positions.
200 public void superposeStructures(AlignmentI alignment)
202 superposeStructures(alignment, -1, null);
206 * superpose the structures associated with sequences in the alignment
207 * according to their corresponding positions. ded)
209 * @param refStructure
210 * - select which pdb file to use as reference (default is -1 - the
211 * first structure in the alignment)
213 public void superposeStructures(AlignmentI alignment, int refStructure)
215 superposeStructures(alignment, refStructure, null);
219 * superpose the structures associated with sequences in the alignment
220 * according to their corresponding positions. ded)
222 * @param refStructure
223 * - select which pdb file to use as reference (default is -1 - the
224 * first structure in the alignment)
228 public void superposeStructures(AlignmentI alignment, int refStructure,
229 HiddenColumns hiddenCols)
231 superposeStructures(new AlignmentI[] { alignment },
233 { refStructure }, new HiddenColumns[] { hiddenCols });
240 public String superposeStructures(AlignmentI[] _alignment,
241 int[] _refStructure, HiddenColumns[] _hiddenCols)
243 while (viewer.isScriptExecuting())
248 } catch (InterruptedException i)
254 * get the distinct structure files modelled
255 * (a file with multiple chains may map to multiple sequences)
257 String[] files = getStructureFiles();
258 if (!waitForFileLoad(files))
263 StringBuilder selectioncom = new StringBuilder(256);
264 // In principle - nSeconds specifies the speed of animation for each
265 // superposition - but is seems to behave weirdly, so we don't specify it.
266 String nSeconds = " ";
267 if (files.length > 10)
269 nSeconds = " 0.005 ";
273 nSeconds = " " + (2.0 / files.length) + " ";
274 // if (nSeconds).substring(0,5)+" ";
277 // see JAL-1345 - should really automatically turn off the animation for
278 // large numbers of structures, but Jmol doesn't seem to allow that.
280 // union of all aligned positions are collected together.
281 for (int a = 0; a < _alignment.length; a++)
283 int refStructure = _refStructure[a];
284 AlignmentI alignment = _alignment[a];
285 HiddenColumns hiddenCols = _hiddenCols[a];
286 if (a > 0 && selectioncom.length() > 0 && !selectioncom
287 .substring(selectioncom.length() - 1).equals("|"))
289 selectioncom.append("|");
291 // process this alignment
292 if (refStructure >= files.length)
295 "Invalid reference structure value " + refStructure);
300 * 'matched' bit j will be set for visible alignment columns j where
301 * all sequences have a residue with a mapping to the PDB structure
303 BitSet matched = new BitSet();
304 for (int m = 0; m < alignment.getWidth(); m++)
306 if (hiddenCols == null || hiddenCols.isVisible(m))
312 SuperposeData[] structures = new SuperposeData[files.length];
313 for (int f = 0; f < files.length; f++)
315 structures[f] = new SuperposeData(alignment.getWidth());
319 * Calculate the superposable alignment columns ('matched'), and the
320 * corresponding structure residue positions (structures.pdbResNo)
322 int candidateRefStructure = findSuperposableResidues(alignment,
323 matched, structures);
324 if (refStructure < 0)
327 * If no reference structure was specified, pick the first one that has
328 * a mapping in the alignment
330 refStructure = candidateRefStructure;
333 String[] selcom = new String[files.length];
334 int nmatched = matched.cardinality();
337 return (MessageManager.formatMessage("label.insufficient_residues",
342 * generate select statements to select regions to superimpose structures
345 // TODO extract method to construct selection statements
346 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
348 String chainCd = ":" + structures[pdbfnum].chain;
351 StringBuilder molsel = new StringBuilder();
354 int nextColumnMatch = matched.nextSetBit(0);
355 while (nextColumnMatch != -1)
357 int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
358 if (lpos != pdbResNo - 1)
364 molsel.append(chainCd);
371 // continuous run - and lpos >-1
374 // at the beginning, so add dash
381 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
384 * add final selection phrase
389 molsel.append(chainCd);
392 if (molsel.length() > 1)
394 selcom[pdbfnum] = molsel.toString();
395 selectioncom.append("((");
396 selectioncom.append(selcom[pdbfnum].substring(1,
397 selcom[pdbfnum].length() - 1));
398 selectioncom.append(" )& ");
399 selectioncom.append(pdbfnum + 1);
400 selectioncom.append(".1)");
401 if (pdbfnum < files.length - 1)
403 selectioncom.append("|");
408 selcom[pdbfnum] = null;
412 StringBuilder command = new StringBuilder(256);
413 // command.append("set spinFps 10;\n");
415 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
417 if (pdbfnum == refStructure || selcom[pdbfnum] == null
418 || selcom[refStructure] == null)
422 command.append("echo ");
423 command.append("\"Superposing (");
424 command.append(structures[pdbfnum].pdbId);
425 command.append(") against reference (");
426 command.append(structures[refStructure].pdbId);
427 command.append(")\";\ncompare " + nSeconds);
429 command.append(Integer.toString(1 + pdbfnum));
430 command.append(".1} {");
431 command.append(Integer.toString(1 + refStructure));
432 // conformation=1 excludes alternate locations for CA (JAL-1757)
434 ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
436 // for (int s = 0; s < 2; s++)
438 // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
440 command.append(selcom[pdbfnum]);
441 command.append(selcom[refStructure]);
442 command.append(" ROTATE TRANSLATE;\n");
444 if (selectioncom.length() > 0)
446 // TODO is performing selectioncom redundant here? is done later on
447 // System.out.println("Select regions:\n" + selectioncom.toString());
448 evalStateCommand("select *; cartoons off; backbone; select ("
449 + selectioncom.toString() + "); cartoons; ");
450 // selcom.append("; ribbons; ");
451 String cmdString = command.toString();
452 // System.out.println("Superimpose command(s):\n" + cmdString);
454 evalStateCommand(cmdString);
457 if (selectioncom.length() > 0)
458 {// finally, mark all regions that were superposed.
459 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
461 selectioncom.setLength(selectioncom.length() - 1);
463 // System.out.println("Select regions:\n" + selectioncom.toString());
464 evalStateCommand("select *; cartoons off; backbone; select ("
465 + selectioncom.toString() + "); cartoons; ");
466 // evalStateCommand("select *; backbone; select "+selcom.toString()+";
467 // cartoons; center "+selcom.toString());
473 public void evalStateCommand(String command)
476 if (lastCommand == null || !lastCommand.equals(command))
478 jmolScript(command + "\n");
481 lastCommand = command;
484 Thread colourby = null;
487 * Sends a set of colour commands to the structure viewer
489 * @param colourBySequenceCommands
492 protected void colourBySequence(
493 final StructureMappingcommandSet[] colourBySequenceCommands)
495 if (colourby != null)
497 colourby.interrupt();
500 Thread colourby = new Thread(new Runnable()
505 for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
507 for (String cbyseq : cpdbbyseq.commands)
509 executeWhenReady(cbyseq);
515 this.colourby = colourby;
525 protected StructureMappingcommandSet[] getColourBySequenceCommands(
526 String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
528 return JmolCommands.getColourBySequenceCommand(getSsm(), files,
529 getSequence(), sr, viewPanel);
535 protected void executeWhenReady(String command)
537 evalStateCommand(command);
540 public void createImage(String file, String type, int quality)
542 System.out.println("JMOL CREATE IMAGE");
546 public String createImage(String fileName, String type,
547 Object textOrBytes, int quality)
549 System.out.println("JMOL CREATE IMAGE");
554 public String eval(String strEval)
556 // System.out.println(strEval);
557 // "# 'eval' is implemented only for the applet.";
561 // End StructureListener
562 // //////////////////////////
565 public float[][] functionXY(String functionName, int x, int y)
571 public float[][][] functionXYZ(String functionName, int nx, int ny,
574 // TODO Auto-generated method stub
578 public Color getColour(int atomIndex, int pdbResNum, String chain,
581 if (getModelNum(pdbfile) < 0)
585 // TODO: verify atomIndex is selecting correct model.
586 // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
587 int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
588 return new Color(colour);
592 * instruct the Jalview binding to update the pdbentries vector if necessary
593 * prior to matching the jmol view's contents to the list of structure files
594 * Jalview knows about.
596 public abstract void refreshPdbEntries();
598 private int getModelNum(String modelFileName)
600 String[] mfn = getStructureFiles();
605 for (int i = 0; i < mfn.length; i++)
607 if (mfn[i].equalsIgnoreCase(modelFileName))
616 * map between index of model filename returned from getPdbFile and the first
617 * index of models from this file in the viewer. Note - this is not trimmed -
618 * use getPdbFile to get number of unique models.
620 private int _modelFileNameMap[];
623 public synchronized String[] getStructureFiles()
625 List<String> mset = new ArrayList<>();
628 return new String[0];
631 if (modelFileNames == null)
633 int modelCount = viewer.ms.mc;
634 String filePath = null;
635 for (int i = 0; i < modelCount; ++i)
637 filePath = viewer.ms.getModelFileName(i);
638 if (!mset.contains(filePath))
643 modelFileNames = mset.toArray(new String[mset.size()]);
646 return modelFileNames;
650 * map from string to applet
653 public Map<String, Object> getRegistryInfo()
655 // TODO Auto-generated method stub
659 // ///////////////////////////////
660 // JmolStatusListener
662 public void handlePopupMenu(int x, int y)
664 // jmolpopup.show(x, y);
665 // jmolpopup.jpiShow(x, y);
669 * Highlight zero, one or more atoms on the structure
672 public void highlightAtoms(List<AtomSpec> atoms)
676 if (resetLastRes.length() > 0)
678 jmolScript(resetLastRes.toString());
679 resetLastRes.setLength(0);
681 for (AtomSpec atom : atoms)
683 highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
684 atom.getChain(), atom.getPdbFile());
690 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
693 if (modelFileNames == null)
698 // look up file model number for this pdbfile
700 // may need to adjust for URLencoding here - we don't worry about that yet.
701 while (mdlNum < modelFileNames.length
702 && !pdbfile.equals(modelFileNames[mdlNum]))
706 if (mdlNum == modelFileNames.length)
713 StringBuilder cmd = new StringBuilder(64);
714 cmd.append("select " + pdbResNum); // +modelNum
716 resetLastRes.append("select " + pdbResNum); // +modelNum
719 resetLastRes.append(":");
720 if (!chain.equals(" "))
723 resetLastRes.append(chain);
726 cmd.append(" /" + (mdlNum + 1));
727 resetLastRes.append("/" + (mdlNum + 1));
729 cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
731 resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
732 + " and not hetero; spacefill 0;");
734 cmd.append("spacefill 200;select none");
736 jmolScript(cmd.toString());
741 boolean debug = true;
743 private void jmolHistory(boolean enable)
745 jmolScript("History " + ((debug || enable) ? "on" : "off"));
748 public void loadInline(String string)
752 // viewer.loadInline(strModel, isAppend);
754 // construct fake fullPathName and fileName so we can identify the file
756 // Then, construct pass a reader for the string to Jmol.
757 // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
758 // fileName, null, reader, false, null, null, 0);
759 viewer.openStringInline(string);
762 protected void mouseOverStructure(int atomIndex, final String strInfo)
765 int alocsep = strInfo.indexOf("^");
766 int mdlSep = strInfo.indexOf("/");
767 int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
769 if (chainSeparator == -1)
771 chainSeparator = strInfo.indexOf(".");
772 if (mdlSep > -1 && mdlSep < chainSeparator)
774 chainSeparator1 = chainSeparator;
775 chainSeparator = mdlSep;
778 // handle insertion codes
781 pdbResNum = Integer.parseInt(
782 strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
787 pdbResNum = Integer.parseInt(
788 strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
792 if (strInfo.indexOf(":") > -1)
794 chainId = strInfo.substring(strInfo.indexOf(":") + 1,
795 strInfo.indexOf("."));
802 String pdbfilename = modelFileNames[frameNo]; // default is first or current
806 if (chainSeparator1 == -1)
808 chainSeparator1 = strInfo.indexOf(".", mdlSep);
810 String mdlId = (chainSeparator1 > -1)
811 ? strInfo.substring(mdlSep + 1, chainSeparator1)
812 : strInfo.substring(mdlSep + 1);
815 // recover PDB filename for the model hovered over.
816 int mnumber = Integer.valueOf(mdlId).intValue() - 1;
817 if (_modelFileNameMap != null)
819 int _mp = _modelFileNameMap.length - 1;
821 while (mnumber < _modelFileNameMap[_mp])
825 pdbfilename = modelFileNames[_mp];
829 if (mnumber >= 0 && mnumber < modelFileNames.length)
831 pdbfilename = modelFileNames[mnumber];
834 if (pdbfilename == null)
836 pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
840 } catch (Exception e)
846 * highlight position on alignment(s); if some text is returned,
847 * show this as a second line on the structure hover tooltip
849 String label = getSsm().mouseOverStructure(pdbResNum, chainId,
853 // change comma to pipe separator (newline token for Jmol)
854 label = label.replace(',', '|');
855 StringTokenizer toks = new StringTokenizer(strInfo, " ");
856 StringBuilder sb = new StringBuilder();
857 sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
858 .append(chainId).append("/1");
859 sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
860 .append(toks.nextToken());
861 sb.append("|").append(label).append("\"");
862 evalStateCommand(sb.toString());
866 public void notifyAtomHovered(int atomIndex, String strInfo, String data)
868 if (strInfo.equals(lastMessage))
872 lastMessage = strInfo;
875 System.err.println("Ignoring additional hover info: " + data
876 + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
878 mouseOverStructure(atomIndex, strInfo);
882 * { if (history != null && strStatus != null &&
883 * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
887 public void notifyAtomPicked(int atomIndex, String strInfo,
891 * this implements the toggle label behaviour copied from the original
892 * structure viewer, mc_view
896 System.err.println("Ignoring additional pick data string " + strData);
898 int chainSeparator = strInfo.indexOf(":");
900 if (chainSeparator == -1)
902 chainSeparator = strInfo.indexOf(".");
905 String picked = strInfo.substring(strInfo.indexOf("]") + 1,
907 String mdlString = "";
908 if ((p = strInfo.indexOf(":")) > -1)
910 picked += strInfo.substring(p, strInfo.indexOf("."));
913 if ((p = strInfo.indexOf("/")) > -1)
915 mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
917 picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
921 if (!atomsPicked.contains(picked))
923 jmolScript("select " + picked + ";label %n %r:%c");
924 atomsPicked.addElement(picked);
928 viewer.evalString("select " + picked + ";label off");
929 atomsPicked.removeElement(picked);
932 // TODO: in application this happens
934 // if (scriptWindow != null)
936 // scriptWindow.sendConsoleMessage(strInfo);
937 // scriptWindow.sendConsoleMessage("\n");
943 public void notifyCallback(CBK type, Object[] data)
950 notifyFileLoaded((String) data[1], (String) data[2],
951 (String) data[3], (String) data[4],
952 ((Integer) data[5]).intValue());
956 notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
958 // also highlight in alignment
959 // deliberate fall through
961 notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
965 notifyScriptTermination((String) data[2],
966 ((Integer) data[3]).intValue());
969 sendConsoleEcho((String) data[1]);
973 (data == null) ? ((String) null) : (String) data[1]);
976 // System.err.println("Ignoring error callback.");
987 "Unhandled callback " + type + " " + data[1].toString());
990 } catch (Exception e)
992 System.err.println("Squashed Jmol callback handler error:");
998 public boolean notifyEnabled(CBK callbackPick)
1000 switch (callbackPick)
1016 // incremented every time a load notification is successfully handled -
1017 // lightweight mechanism for other threads to detect when they can start
1018 // referrring to new structures.
1019 private long loadNotifiesHandled = 0;
1021 public long getLoadNotifiesHandled()
1023 return loadNotifiesHandled;
1026 public void notifyFileLoaded(String fullPathName, String fileName2,
1027 String modelName, String errorMsg, int modelParts)
1029 if (errorMsg != null)
1031 fileLoadingError = errorMsg;
1035 // TODO: deal sensibly with models loaded inLine:
1036 // modelName will be null, as will fullPathName.
1038 // the rest of this routine ignores the arguments, and simply interrogates
1039 // the Jmol view to find out what structures it contains, and adds them to
1040 // the structure selection manager.
1041 fileLoadingError = null;
1042 String[] oldmodels = modelFileNames;
1043 modelFileNames = null;
1044 chainNames = new ArrayList<>();
1045 chainFile = new Hashtable<>();
1046 boolean notifyLoaded = false;
1047 String[] modelfilenames = getStructureFiles();
1048 // first check if we've lost any structures
1049 if (oldmodels != null && oldmodels.length > 0)
1052 for (int i = 0; i < oldmodels.length; i++)
1054 for (int n = 0; n < modelfilenames.length; n++)
1056 if (modelfilenames[n] == oldmodels[i])
1058 oldmodels[i] = null;
1062 if (oldmodels[i] != null)
1069 String[] oldmfn = new String[oldm];
1071 for (int i = 0; i < oldmodels.length; i++)
1073 if (oldmodels[i] != null)
1075 oldmfn[oldm++] = oldmodels[i];
1078 // deregister the Jmol instance for these structures - we'll add
1079 // ourselves again at the end for the current structure set.
1080 getSsm().removeStructureViewerListener(this, oldmfn);
1083 refreshPdbEntries();
1084 for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
1086 String fileName = modelfilenames[modelnum];
1087 boolean foundEntry = false;
1088 StructureFile pdb = null;
1089 String pdbfile = null;
1090 // model was probably loaded inline - so check the pdb file hashcode
1093 // calculate essential attributes for the pdb data imported inline.
1094 // prolly need to resolve modelnumber properly - for now just use our
1096 pdbfile = viewer.getData(
1097 "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
1099 // search pdbentries and sequences to find correct pdbentry for this
1101 for (int pe = 0; pe < getPdbCount(); pe++)
1103 boolean matches = false;
1104 addSequence(pe, getSequence()[pe]);
1105 if (fileName == null)
1108 // see JAL-623 - need method of matching pasted data up
1110 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1111 pdbfile, DataSourceType.PASTE, getIProgressIndicator());
1112 getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
1119 File fl = new File(getPdbEntry(pe).getFile());
1120 matches = fl.equals(new File(fileName));
1124 // TODO: Jmol can in principle retrieve from CLASSLOADER but
1127 // to be tested. See mantis bug
1128 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
1129 DataSourceType protocol = DataSourceType.URL;
1134 protocol = DataSourceType.FILE;
1136 } catch (Exception e)
1141 // Explicitly map to the filename used by Jmol ;
1142 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1143 fileName, protocol, getIProgressIndicator());
1144 // pdbentry[pe].getFile(), protocol);
1150 // add an entry for every chain in the model
1151 for (int i = 0; i < pdb.getChains().size(); i++)
1153 String chid = new String(
1154 pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
1155 chainFile.put(chid, fileName);
1156 chainNames.add(chid);
1158 notifyLoaded = true;
1162 if (!foundEntry && associateNewStructs)
1164 // this is a foreign pdb file that jalview doesn't know about - add
1165 // it to the dataset and try to find a home - either on a matching
1166 // sequence or as a new sequence.
1167 String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
1169 // parse pdb file into a chain, etc.
1170 // locate best match for pdb in associated views and add mapping to
1172 // if properly registered then
1173 notifyLoaded = true;
1178 // so finally, update the jmol bits and pieces
1179 // if (jmolpopup != null)
1181 // // potential for deadlock here:
1182 // // jmolpopup.updateComputedMenus();
1184 if (!isLoadingFromArchive())
1187 "model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
1189 // register ourselves as a listener and notify the gui that it needs to
1191 getSsm().addStructureViewerListener(this);
1194 FeatureRenderer fr = getFeatureRenderer(null);
1200 loadNotifiesHandled++;
1202 setLoadingFromArchive(false);
1206 public List<String> getChainNames()
1211 protected IProgressIndicator getIProgressIndicator()
1216 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
1218 notifyAtomPicked(iatom, strMeasure, null);
1221 public abstract void notifyScriptTermination(String strStatus,
1225 * display a message echoed from the jmol viewer
1229 public abstract void sendConsoleEcho(String strEcho); /*
1230 * { showConsole(true);
1232 * history.append("\n" +
1236 // /End JmolStatusListener
1237 // /////////////////////////////
1241 * status message - usually the response received after a script
1244 public abstract void sendConsoleMessage(String strStatus);
1247 public void setCallbackFunction(String callbackType,
1248 String callbackFunction)
1250 System.err.println("Ignoring set-callback request to associate "
1251 + callbackType + " with function " + callbackFunction);
1256 public void setJalviewColourScheme(ColourSchemeI cs)
1258 colourBySequence = false;
1266 StringBuilder command = new StringBuilder(128);
1267 command.append("select *;color white;");
1268 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
1270 for (String resName : residueSet)
1272 char res = resName.length() == 3
1273 ? ResidueProperties.getSingleCharacterCode(resName)
1274 : resName.charAt(0);
1275 Color col = cs.findColour(res, 0, null, null, 0f);
1276 command.append("select " + resName + ";color[" + col.getRed() + ","
1277 + col.getGreen() + "," + col.getBlue() + "];");
1280 evalStateCommand(command.toString());
1284 public void showHelp()
1286 showUrl("http://wiki.jmol.org"
1287 // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
1292 * open the URL somehow
1296 public abstract void showUrl(String url, String target);
1299 * called when the binding thinks the UI needs to be refreshed after a Jmol
1300 * state change. this could be because structures were loaded, or because an
1301 * error has occured.
1303 public abstract void refreshGUI();
1306 * called to show or hide the associated console window container.
1310 public abstract void showConsole(boolean show);
1312 public static Viewer getJmolData(JmolParser jmolParser)
1314 return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
1315 "-x -o -n", jmolParser);
1322 * @param renderPanel
1324 * - when true will initialise jmol's file IO system (should be false
1325 * in applet context)
1327 * @param documentBase
1329 * @param commandOptions
1331 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1332 String htmlName, URL documentBase, URL codeBase,
1333 String commandOptions)
1335 allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
1336 codeBase, commandOptions, null, null);
1341 * @param renderPanel
1343 * - when true will initialise jmol's file IO system (should be false
1344 * in applet context)
1346 * @param documentBase
1348 * @param commandOptions
1349 * @param consolePanel
1350 * - panel to contain Jmol console
1351 * @param buttonsToShow
1352 * - buttons to show on the console, in order
1354 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1355 String htmlName, URL documentBase, URL codeBase,
1356 String commandOptions, final Container consolePanel,
1357 String buttonsToShow)
1360 System.err.println("Allocating Jmol Viewer: " + commandOptions);
1362 if (commandOptions == null)
1364 commandOptions = "";
1366 viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
1367 (jmolfileio ? new SmarterJmolAdapter() : null),
1368 htmlName + ((Object) this).toString(), documentBase, codeBase,
1369 commandOptions, this);
1371 viewer.setJmolStatusListener(this);
1373 // BH how about extending Jmol's status listener?
1377 console = createJmolConsole(consolePanel, buttonsToShow);
1378 } catch (Throwable e)
1380 System.err.println("Could not create Jmol application console. "
1382 e.printStackTrace();
1384 if (consolePanel != null)
1386 consolePanel.addComponentListener(this);
1392 protected abstract JmolAppConsoleInterface createJmolConsole(
1393 Container consolePanel, String buttonsToShow);
1395 // BH 2018 -- Jmol console is not working due to problems with styled
1398 protected org.jmol.api.JmolAppConsoleInterface console = null;
1401 public void setBackgroundColour(java.awt.Color col)
1404 jmolScript("background [" + col.getRed() + "," + col.getGreen() + ","
1405 + col.getBlue() + "];");
1409 private String jmolScript(String script)
1412 System.err.println(">>Jmol>> " + script);
1414 String s = viewer.scriptWait(script);
1416 System.err.println("<<Jmol<< " + s);
1422 public int[] resizeInnerPanel(String data)
1424 // Jalview doesn't honour resize panel requests
1431 protected void closeConsole()
1433 if (console != null)
1437 console.setVisible(false);
1440 } catch (Exception x)
1449 * ComponentListener method
1452 public void componentMoved(ComponentEvent e)
1457 * ComponentListener method
1460 public void componentResized(ComponentEvent e)
1465 * ComponentListener method
1468 public void componentShown(ComponentEvent e)
1474 * ComponentListener method
1477 public void componentHidden(ComponentEvent e)