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.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureRenderer;
26 import jalview.api.SequenceRenderer;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.IProgressIndicator;
32 import jalview.io.DataSourceType;
33 import jalview.io.StructureFile;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.ResidueProperties;
36 import jalview.structure.AtomSpec;
37 import jalview.structure.StructureMappingcommandSet;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.structures.models.AAStructureBindingModel;
40 import jalview.util.MessageManager;
42 import java.awt.Color;
43 import java.awt.Container;
44 import java.awt.event.ComponentEvent;
45 import java.awt.event.ComponentListener;
48 import java.util.ArrayList;
49 import java.util.BitSet;
50 import java.util.Hashtable;
51 import java.util.List;
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 boolean allChainsSelected = false;
71 * when true, try to search the associated datamodel for sequences that are
72 * associated with any unknown structures in the Jmol view.
74 private boolean associateNewStructs = false;
76 Vector<String> atomsPicked = new Vector<>();
78 private List<String> chainNames;
80 Hashtable<String, String> chainFile;
83 * the default or current model displayed if the model cannot be identified
84 * from the selection message
88 // 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());
172 releaseUIResources();
176 public void colourByChain()
178 colourBySequence = false;
179 // TODO: colour by chain should colour each chain distinctly across all
181 // TODO: http://issues.jalview.org/browse/JAL-628
182 evalStateCommand("select *;color chain");
186 public void colourByCharge()
188 colourBySequence = false;
189 evalStateCommand("select *;color white;select ASP,GLU;color red;"
190 + "select LYS,ARG;color blue;select CYS;color yellow");
194 * superpose the structures associated with sequences in the alignment
195 * according to their corresponding positions.
197 public void superposeStructures(AlignmentI alignment)
199 superposeStructures(alignment, -1, null);
203 * superpose the structures associated with sequences in the alignment
204 * according to their corresponding positions. ded)
206 * @param refStructure
207 * - select which pdb file to use as reference (default is -1 - the
208 * first structure in the alignment)
210 public void superposeStructures(AlignmentI alignment, int refStructure)
212 superposeStructures(alignment, refStructure, null);
216 * superpose the structures associated with sequences in the alignment
217 * according to their corresponding positions. ded)
219 * @param refStructure
220 * - select which pdb file to use as reference (default is -1 - the
221 * first structure in the alignment)
225 public void superposeStructures(AlignmentI alignment, int refStructure,
226 HiddenColumns hiddenCols)
228 superposeStructures(new AlignmentI[] { alignment },
230 { refStructure }, new HiddenColumns[] { hiddenCols });
237 public String superposeStructures(AlignmentI[] _alignment,
238 int[] _refStructure, HiddenColumns[] _hiddenCols)
240 while (viewer.isScriptExecuting())
245 } catch (InterruptedException i)
251 * get the distinct structure files modelled
252 * (a file with multiple chains may map to multiple sequences)
254 String[] files = getStructureFiles();
255 if (!waitForFileLoad(files))
260 StringBuilder selectioncom = new StringBuilder(256);
261 // In principle - nSeconds specifies the speed of animation for each
262 // superposition - but is seems to behave weirdly, so we don't specify it.
263 String nSeconds = " ";
264 if (files.length > 10)
266 nSeconds = " 0.005 ";
270 nSeconds = " " + (2.0 / files.length) + " ";
271 // if (nSeconds).substring(0,5)+" ";
274 // see JAL-1345 - should really automatically turn off the animation for
275 // large numbers of structures, but Jmol doesn't seem to allow that.
277 // union of all aligned positions are collected together.
278 for (int a = 0; a < _alignment.length; a++)
280 int refStructure = _refStructure[a];
281 AlignmentI alignment = _alignment[a];
282 HiddenColumns hiddenCols = _hiddenCols[a];
283 if (a > 0 && selectioncom.length() > 0 && !selectioncom
284 .substring(selectioncom.length() - 1).equals("|"))
286 selectioncom.append("|");
288 // process this alignment
289 if (refStructure >= files.length)
292 "Invalid reference structure value " + refStructure);
297 * 'matched' bit j will be set for visible alignment columns j where
298 * all sequences have a residue with a mapping to the PDB structure
300 BitSet matched = new BitSet();
301 for (int m = 0; m < alignment.getWidth(); m++)
303 if (hiddenCols == null || hiddenCols.isVisible(m))
309 SuperposeData[] structures = new SuperposeData[files.length];
310 for (int f = 0; f < files.length; f++)
312 structures[f] = new SuperposeData(alignment.getWidth());
316 * Calculate the superposable alignment columns ('matched'), and the
317 * corresponding structure residue positions (structures.pdbResNo)
319 int candidateRefStructure = findSuperposableResidues(alignment,
320 matched, structures);
321 if (refStructure < 0)
324 * If no reference structure was specified, pick the first one that has
325 * a mapping in the alignment
327 refStructure = candidateRefStructure;
330 String[] selcom = new String[files.length];
331 int nmatched = matched.cardinality();
334 return (MessageManager.formatMessage("label.insufficient_residues",
339 * generate select statements to select regions to superimpose structures
342 // TODO extract method to construct selection statements
343 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
345 String chainCd = ":" + structures[pdbfnum].chain;
348 StringBuilder molsel = new StringBuilder();
351 int nextColumnMatch = matched.nextSetBit(0);
352 while (nextColumnMatch != -1)
354 int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
355 if (lpos != pdbResNo - 1)
361 molsel.append(chainCd);
368 // continuous run - and lpos >-1
371 // at the beginning, so add dash
378 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
381 * add final selection phrase
386 molsel.append(chainCd);
389 if (molsel.length() > 1)
391 selcom[pdbfnum] = molsel.toString();
392 selectioncom.append("((");
393 selectioncom.append(selcom[pdbfnum].substring(1,
394 selcom[pdbfnum].length() - 1));
395 selectioncom.append(" )& ");
396 selectioncom.append(pdbfnum + 1);
397 selectioncom.append(".1)");
398 if (pdbfnum < files.length - 1)
400 selectioncom.append("|");
405 selcom[pdbfnum] = null;
409 StringBuilder command = new StringBuilder(256);
410 // command.append("set spinFps 10;\n");
412 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
414 if (pdbfnum == refStructure || selcom[pdbfnum] == null
415 || selcom[refStructure] == null)
419 command.append("echo ");
420 command.append("\"Superposing (");
421 command.append(structures[pdbfnum].pdbId);
422 command.append(") against reference (");
423 command.append(structures[refStructure].pdbId);
424 command.append(")\";\ncompare " + nSeconds);
426 command.append(Integer.toString(1 + pdbfnum));
427 command.append(".1} {");
428 command.append(Integer.toString(1 + refStructure));
429 // conformation=1 excludes alternate locations for CA (JAL-1757)
431 ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
433 // for (int s = 0; s < 2; s++)
435 // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
437 command.append(selcom[pdbfnum]);
438 command.append(selcom[refStructure]);
439 command.append(" ROTATE TRANSLATE;\n");
441 if (selectioncom.length() > 0)
443 // TODO is performing selectioncom redundant here? is done later on
444 // System.out.println("Select regions:\n" + selectioncom.toString());
445 evalStateCommand("select *; cartoons off; backbone; select ("
446 + selectioncom.toString() + "); cartoons; ");
447 // selcom.append("; ribbons; ");
448 String cmdString = command.toString();
449 // System.out.println("Superimpose command(s):\n" + cmdString);
451 evalStateCommand(cmdString);
454 if (selectioncom.length() > 0)
455 {// finally, mark all regions that were superposed.
456 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
458 selectioncom.setLength(selectioncom.length() - 1);
460 // System.out.println("Select regions:\n" + selectioncom.toString());
461 evalStateCommand("select *; cartoons off; backbone; select ("
462 + selectioncom.toString() + "); cartoons; ");
463 // evalStateCommand("select *; backbone; select "+selcom.toString()+";
464 // cartoons; center "+selcom.toString());
470 public void evalStateCommand(String command)
473 if (lastCommand == null || !lastCommand.equals(command))
475 viewer.evalStringQuiet(command + "\n");
478 lastCommand = command;
481 Thread colourby = null;
483 * Sends a set of colour commands to the structure viewer
485 * @param colourBySequenceCommands
488 protected void colourBySequence(
489 final StructureMappingcommandSet[] colourBySequenceCommands)
491 if (colourby != null)
493 colourby.interrupt();
496 colourby = new Thread(new Runnable()
501 for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
503 for (String cbyseq : cpdbbyseq.commands)
505 executeWhenReady(cbyseq);
520 protected StructureMappingcommandSet[] getColourBySequenceCommands(
521 String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
523 return JmolCommands.getColourBySequenceCommand(getSsm(), files,
524 getSequence(), sr, viewPanel);
530 protected void executeWhenReady(String command)
532 evalStateCommand(command);
535 public void createImage(String file, String type, int quality)
537 System.out.println("JMOL CREATE IMAGE");
541 public String createImage(String fileName, String type,
542 Object textOrBytes, int quality)
544 System.out.println("JMOL CREATE IMAGE");
549 public String eval(String strEval)
551 // System.out.println(strEval);
552 // "# 'eval' is implemented only for the applet.";
556 // End StructureListener
557 // //////////////////////////
560 public float[][] functionXY(String functionName, int x, int y)
566 public float[][][] functionXYZ(String functionName, int nx, int ny,
569 // TODO Auto-generated method stub
573 public Color getColour(int atomIndex, int pdbResNum, String chain,
576 if (getModelNum(pdbfile) < 0)
580 // TODO: verify atomIndex is selecting correct model.
581 // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
582 int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
583 return new Color(colour);
587 * instruct the Jalview binding to update the pdbentries vector if necessary
588 * prior to matching the jmol view's contents to the list of structure files
589 * Jalview knows about.
591 public abstract void refreshPdbEntries();
593 private int getModelNum(String modelFileName)
595 String[] mfn = getStructureFiles();
600 for (int i = 0; i < mfn.length; i++)
602 if (mfn[i].equalsIgnoreCase(modelFileName))
611 * map between index of model filename returned from getPdbFile and the first
612 * index of models from this file in the viewer. Note - this is not trimmed -
613 * use getPdbFile to get number of unique models.
615 private int _modelFileNameMap[];
618 public synchronized String[] getStructureFiles()
620 List<String> mset = new ArrayList<>();
623 return new String[0];
626 if (modelFileNames == null)
628 int modelCount = viewer.ms.mc;
629 String filePath = null;
630 for (int i = 0; i < modelCount; ++i)
632 filePath = viewer.ms.getModelFileName(i);
633 if (!mset.contains(filePath))
638 modelFileNames = mset.toArray(new String[mset.size()]);
641 return modelFileNames;
645 * map from string to applet
648 public Map<String, Object> getRegistryInfo()
650 // TODO Auto-generated method stub
654 // ///////////////////////////////
655 // JmolStatusListener
657 public void handlePopupMenu(int x, int y)
659 // jmolpopup.show(x, y);
660 // jmolpopup.jpiShow(x, y);
664 * Highlight zero, one or more atoms on the structure
667 public void highlightAtoms(List<AtomSpec> atoms)
671 if (resetLastRes.length() > 0)
673 viewer.evalStringQuiet(resetLastRes.toString());
674 resetLastRes.setLength(0);
676 for (AtomSpec atom : atoms)
678 highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
679 atom.getChain(), atom.getPdbFile());
685 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
688 if (modelFileNames == null)
693 // look up file model number for this pdbfile
695 // may need to adjust for URLencoding here - we don't worry about that yet.
696 while (mdlNum < modelFileNames.length
697 && !pdbfile.equals(modelFileNames[mdlNum]))
701 if (mdlNum == modelFileNames.length)
708 StringBuilder cmd = new StringBuilder(64);
709 cmd.append("select " + pdbResNum); // +modelNum
711 resetLastRes.append("select " + pdbResNum); // +modelNum
714 resetLastRes.append(":");
715 if (!chain.equals(" "))
718 resetLastRes.append(chain);
721 cmd.append(" /" + (mdlNum + 1));
722 resetLastRes.append("/" + (mdlNum + 1));
724 cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
726 resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
727 + " and not hetero; spacefill 0;");
729 cmd.append("spacefill 200;select none");
731 viewer.evalStringQuiet(cmd.toString());
736 boolean debug = true;
738 private void jmolHistory(boolean enable)
740 viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
743 public void loadInline(String string)
747 // viewer.loadInline(strModel, isAppend);
749 // construct fake fullPathName and fileName so we can identify the file
751 // Then, construct pass a reader for the string to Jmol.
752 // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
753 // fileName, null, reader, false, null, null, 0);
754 viewer.openStringInline(string);
757 public void mouseOverStructure(int atomIndex, String strInfo)
760 int alocsep = strInfo.indexOf("^");
761 int mdlSep = strInfo.indexOf("/");
762 int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
764 if (chainSeparator == -1)
766 chainSeparator = strInfo.indexOf(".");
767 if (mdlSep > -1 && mdlSep < chainSeparator)
769 chainSeparator1 = chainSeparator;
770 chainSeparator = mdlSep;
773 // handle insertion codes
776 pdbResNum = Integer.parseInt(
777 strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
782 pdbResNum = Integer.parseInt(
783 strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
787 if (strInfo.indexOf(":") > -1)
789 chainId = strInfo.substring(strInfo.indexOf(":") + 1,
790 strInfo.indexOf("."));
797 String pdbfilename = modelFileNames[frameNo]; // default is first or current
801 if (chainSeparator1 == -1)
803 chainSeparator1 = strInfo.indexOf(".", mdlSep);
805 String mdlId = (chainSeparator1 > -1)
806 ? strInfo.substring(mdlSep + 1, chainSeparator1)
807 : strInfo.substring(mdlSep + 1);
810 // recover PDB filename for the model hovered over.
811 int mnumber = Integer.valueOf(mdlId).intValue() - 1;
812 if (_modelFileNameMap != null)
814 int _mp = _modelFileNameMap.length - 1;
816 while (mnumber < _modelFileNameMap[_mp])
820 pdbfilename = modelFileNames[_mp];
824 if (mnumber >= 0 && mnumber < modelFileNames.length)
826 pdbfilename = modelFileNames[mnumber];
829 if (pdbfilename == null)
831 pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
835 } catch (Exception e)
840 if (lastMessage == null || !lastMessage.equals(strInfo))
842 getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
845 lastMessage = strInfo;
848 public void notifyAtomHovered(int atomIndex, String strInfo, String data)
852 System.err.println("Ignoring additional hover info: " + data
853 + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
855 mouseOverStructure(atomIndex, strInfo);
859 * { if (history != null && strStatus != null &&
860 * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
864 public void notifyAtomPicked(int atomIndex, String strInfo,
868 * this implements the toggle label behaviour copied from the original
869 * structure viewer, MCView
873 System.err.println("Ignoring additional pick data string " + strData);
875 int chainSeparator = strInfo.indexOf(":");
877 if (chainSeparator == -1)
879 chainSeparator = strInfo.indexOf(".");
882 String picked = strInfo.substring(strInfo.indexOf("]") + 1,
884 String mdlString = "";
885 if ((p = strInfo.indexOf(":")) > -1)
887 picked += strInfo.substring(p, strInfo.indexOf("."));
890 if ((p = strInfo.indexOf("/")) > -1)
892 mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
894 picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
898 if (!atomsPicked.contains(picked))
900 viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
901 atomsPicked.addElement(picked);
905 viewer.evalString("select " + picked + ";label off");
906 atomsPicked.removeElement(picked);
909 // TODO: in application this happens
911 // if (scriptWindow != null)
913 // scriptWindow.sendConsoleMessage(strInfo);
914 // scriptWindow.sendConsoleMessage("\n");
920 public void notifyCallback(CBK type, Object[] data)
927 notifyFileLoaded((String) data[1], (String) data[2],
928 (String) data[3], (String) data[4],
929 ((Integer) data[5]).intValue());
933 notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
935 // also highlight in alignment
936 // deliberate fall through
938 notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
942 notifyScriptTermination((String) data[2],
943 ((Integer) data[3]).intValue());
946 sendConsoleEcho((String) data[1]);
950 (data == null) ? ((String) null) : (String) data[1]);
953 // System.err.println("Ignoring error callback.");
964 "Unhandled callback " + type + " " + data[1].toString());
967 } catch (Exception e)
969 System.err.println("Squashed Jmol callback handler error:");
975 public boolean notifyEnabled(CBK callbackPick)
977 switch (callbackPick)
993 // incremented every time a load notification is successfully handled -
994 // lightweight mechanism for other threads to detect when they can start
995 // referrring to new structures.
996 private long loadNotifiesHandled = 0;
998 public long getLoadNotifiesHandled()
1000 return loadNotifiesHandled;
1003 public void notifyFileLoaded(String fullPathName, String fileName2,
1004 String modelName, String errorMsg, int modelParts)
1006 if (errorMsg != null)
1008 fileLoadingError = errorMsg;
1012 // TODO: deal sensibly with models loaded inLine:
1013 // modelName will be null, as will fullPathName.
1015 // the rest of this routine ignores the arguments, and simply interrogates
1016 // the Jmol view to find out what structures it contains, and adds them to
1017 // the structure selection manager.
1018 fileLoadingError = null;
1019 String[] oldmodels = modelFileNames;
1020 modelFileNames = null;
1021 chainNames = new ArrayList<>();
1022 chainFile = new Hashtable<>();
1023 boolean notifyLoaded = false;
1024 String[] modelfilenames = getStructureFiles();
1025 // first check if we've lost any structures
1026 if (oldmodels != null && oldmodels.length > 0)
1029 for (int i = 0; i < oldmodels.length; i++)
1031 for (int n = 0; n < modelfilenames.length; n++)
1033 if (modelfilenames[n] == oldmodels[i])
1035 oldmodels[i] = null;
1039 if (oldmodels[i] != null)
1046 String[] oldmfn = new String[oldm];
1048 for (int i = 0; i < oldmodels.length; i++)
1050 if (oldmodels[i] != null)
1052 oldmfn[oldm++] = oldmodels[i];
1055 // deregister the Jmol instance for these structures - we'll add
1056 // ourselves again at the end for the current structure set.
1057 getSsm().removeStructureViewerListener(this, oldmfn);
1060 refreshPdbEntries();
1061 for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
1063 String fileName = modelfilenames[modelnum];
1064 boolean foundEntry = false;
1065 StructureFile pdb = null;
1066 String pdbfile = null;
1067 // model was probably loaded inline - so check the pdb file hashcode
1070 // calculate essential attributes for the pdb data imported inline.
1071 // prolly need to resolve modelnumber properly - for now just use our
1073 pdbfile = viewer.getData(
1074 "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
1076 // search pdbentries and sequences to find correct pdbentry for this
1078 for (int pe = 0; pe < getPdbCount(); pe++)
1080 boolean matches = false;
1081 addSequence(pe, getSequence()[pe]);
1082 if (fileName == null)
1085 // see JAL-623 - need method of matching pasted data up
1087 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1088 pdbfile, DataSourceType.PASTE,
1089 getIProgressIndicator());
1090 getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
1097 File fl = new File(getPdbEntry(pe).getFile());
1098 matches = fl.equals(new File(fileName));
1102 // TODO: Jmol can in principle retrieve from CLASSLOADER but
1105 // to be tested. See mantis bug
1106 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
1107 DataSourceType protocol = DataSourceType.URL;
1112 protocol = DataSourceType.FILE;
1114 } catch (Exception e)
1119 // Explicitly map to the filename used by Jmol ;
1120 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1121 fileName, protocol, getIProgressIndicator());
1122 // pdbentry[pe].getFile(), protocol);
1128 // add an entry for every chain in the model
1129 for (int i = 0; i < pdb.getChains().size(); i++)
1131 String chid = new String(
1132 pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
1133 chainFile.put(chid, fileName);
1134 chainNames.add(chid);
1136 notifyLoaded = true;
1140 if (!foundEntry && associateNewStructs)
1142 // this is a foreign pdb file that jalview doesn't know about - add
1143 // it to the dataset and try to find a home - either on a matching
1144 // sequence or as a new sequence.
1145 String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
1147 // parse pdb file into a chain, etc.
1148 // locate best match for pdb in associated views and add mapping to
1150 // if properly registered then
1151 notifyLoaded = true;
1156 // so finally, update the jmol bits and pieces
1157 // if (jmolpopup != null)
1159 // // potential for deadlock here:
1160 // // jmolpopup.updateComputedMenus();
1162 if (!isLoadingFromArchive())
1164 viewer.evalStringQuiet(
1165 "model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
1167 // register ourselves as a listener and notify the gui that it needs to
1169 getSsm().addStructureViewerListener(this);
1172 FeatureRenderer fr = getFeatureRenderer(null);
1178 loadNotifiesHandled++;
1180 setLoadingFromArchive(false);
1184 public List<String> getChainNames()
1189 protected IProgressIndicator getIProgressIndicator()
1194 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
1196 notifyAtomPicked(iatom, strMeasure, null);
1199 public abstract void notifyScriptTermination(String strStatus,
1203 * display a message echoed from the jmol viewer
1207 public abstract void sendConsoleEcho(String strEcho); /*
1208 * { showConsole(true);
1210 * history.append("\n" +
1214 // /End JmolStatusListener
1215 // /////////////////////////////
1219 * status message - usually the response received after a script
1222 public abstract void sendConsoleMessage(String strStatus);
1225 public void setCallbackFunction(String callbackType,
1226 String callbackFunction)
1228 System.err.println("Ignoring set-callback request to associate "
1229 + callbackType + " with function " + callbackFunction);
1234 public void setJalviewColourScheme(ColourSchemeI cs)
1236 colourBySequence = false;
1244 StringBuilder command = new StringBuilder(128);
1245 command.append("select *;color white;");
1246 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
1248 for (String resName : residueSet)
1250 char res = resName.length() == 3
1251 ? ResidueProperties.getSingleCharacterCode(resName)
1252 : resName.charAt(0);
1253 Color col = cs.findColour(res, 0, null, null, 0f);
1254 command.append("select " + resName + ";color[" + col.getRed() + ","
1255 + col.getGreen() + "," + col.getBlue() + "];");
1258 evalStateCommand(command.toString());
1262 public void showHelp()
1264 showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
1268 * open the URL somehow
1272 public abstract void showUrl(String url, String target);
1275 * called when the binding thinks the UI needs to be refreshed after a Jmol
1276 * state change. this could be because structures were loaded, or because an
1277 * error has occured.
1279 public abstract void refreshGUI();
1282 * called to show or hide the associated console window container.
1286 public abstract void showConsole(boolean show);
1289 * @param renderPanel
1291 * - when true will initialise jmol's file IO system (should be false
1292 * in applet context)
1294 * @param documentBase
1296 * @param commandOptions
1298 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1299 String htmlName, URL documentBase, URL codeBase,
1300 String commandOptions)
1302 allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
1303 codeBase, commandOptions, null, null);
1308 * @param renderPanel
1310 * - when true will initialise jmol's file IO system (should be false
1311 * in applet context)
1313 * @param documentBase
1315 * @param commandOptions
1316 * @param consolePanel
1317 * - panel to contain Jmol console
1318 * @param buttonsToShow
1319 * - buttons to show on the console, in ordr
1321 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1322 String htmlName, URL documentBase, URL codeBase,
1323 String commandOptions, final Container consolePanel,
1324 String buttonsToShow)
1326 if (commandOptions == null)
1328 commandOptions = "";
1330 viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
1331 (jmolfileio ? new SmarterJmolAdapter() : null),
1332 htmlName + ((Object) this).toString(), documentBase, codeBase,
1333 commandOptions, this);
1335 viewer.setJmolStatusListener(this); // extends JmolCallbackListener
1337 console = createJmolConsole(consolePanel, buttonsToShow);
1338 if (consolePanel != null)
1340 consolePanel.addComponentListener(this);
1346 protected abstract JmolAppConsoleInterface createJmolConsole(
1347 Container consolePanel, String buttonsToShow);
1349 protected org.jmol.api.JmolAppConsoleInterface console = null;
1352 public void setBackgroundColour(java.awt.Color col)
1355 viewer.evalStringQuiet("background [" + col.getRed() + ","
1356 + col.getGreen() + "," + col.getBlue() + "];");
1361 public int[] resizeInnerPanel(String data)
1363 // Jalview doesn't honour resize panel requests
1370 protected void closeConsole()
1372 if (console != null)
1376 console.setVisible(false);
1379 } catch (Exception x)
1388 * ComponentListener method
1391 public void componentMoved(ComponentEvent e)
1396 * ComponentListener method
1399 public void componentResized(ComponentEvent e)
1404 * ComponentListener method
1407 public void componentShown(ComponentEvent e)
1413 * ComponentListener method
1416 public void componentHidden(ComponentEvent e)
1422 public void showStructures(AlignViewportI av)
1424 // TODO show Jmol structure optionally restricted to visible alignment