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.ColumnSelection;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.AppletFormatAdapter;
31 import jalview.schemes.ColourSchemeI;
32 import jalview.schemes.ResidueProperties;
33 import jalview.structure.AtomSpec;
34 import jalview.structure.StructureMappingcommandSet;
35 import jalview.structure.StructureSelectionManager;
36 import jalview.structures.models.AAStructureBindingModel;
38 import java.awt.Color;
39 import java.awt.Container;
40 import java.awt.event.ComponentEvent;
41 import java.awt.event.ComponentListener;
44 import java.security.AccessControlException;
45 import java.util.Hashtable;
46 import java.util.List;
48 import java.util.Vector;
50 import javajs.awt.Dimension;
52 import org.jmol.adapter.smarter.SmarterJmolAdapter;
53 import org.jmol.api.JmolAppConsoleInterface;
54 import org.jmol.api.JmolSelectionListener;
55 import org.jmol.api.JmolStatusListener;
56 import org.jmol.api.JmolViewer;
57 import org.jmol.c.CBK;
58 import org.jmol.script.T;
59 import org.jmol.viewer.JC;
60 import org.jmol.viewer.Viewer;
62 public abstract class JalviewJmolBinding extends AAStructureBindingModel
63 implements JmolStatusListener, JmolSelectionListener,
67 * state flag used to check if the Jmol viewer's paint method can be called
69 private boolean finishedInit = false;
71 boolean allChainsSelected = false;
74 * when true, try to search the associated datamodel for sequences that are
75 * associated with any unknown structures in the Jmol view.
77 private boolean associateNewStructs = false;
79 Vector<String> atomsPicked = new Vector<String>();
81 public Vector<String> chainNames;
83 Hashtable<String, String> chainFile;
85 public String fileLoadingError;
88 * the default or current model displayed if the model cannot be identified
89 * from the selection message
93 // protected JmolGenericPopup jmolpopup; // not used - remove?
102 * current set of model filenames loaded in the Jmol instance
104 String[] modelFileNames = null;
106 StringBuffer resetLastRes = new StringBuffer();
108 public Viewer viewer;
110 public JalviewJmolBinding(StructureSelectionManager ssm,
111 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
114 super(ssm, pdbentry, sequenceIs, chains, protocol);
116 * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
117 * "jalviewJmol", ap.av.applet .getDocumentBase(),
118 * ap.av.applet.getCodeBase(), "", this);
120 * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
124 public JalviewJmolBinding(StructureSelectionManager ssm,
125 SequenceI[][] seqs, Viewer theViewer)
130 viewer.setJmolStatusListener(this);
131 viewer.addSelectionListener(this);
135 * construct a title string for the viewer window based on the data jalview
140 public String getViewerTitle()
142 return getViewerTitle("Jmol", true);
146 * prepare the view for a given set of models/chains. chainList contains
147 * strings of the form 'pdbfilename:Chaincode'
150 * list of chains to make visible
152 public void centerViewer(Vector<String> chainList)
154 StringBuilder cmd = new StringBuilder(128);
156 for (String lbl : chainList)
162 mlength = lbl.indexOf(":", p);
163 } while (p < mlength && mlength < (lbl.length() - 2));
164 // TODO: lookup each pdb id and recover proper model number for it.
165 cmd.append(":" + lbl.substring(mlength + 1) + " /"
166 + (1 + getModelNum(chainFile.get(lbl))) + " or ");
168 if (cmd.length() > 0)
170 cmd.setLength(cmd.length() - 4);
172 evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
175 public void closeViewer()
177 viewer.acm.setModeMouse(JC.MOUSE_NONE);
178 // remove listeners for all structures in viewer
179 getSsm().removeStructureViewerListener(this, this.getPdbFile());
180 // and shut down jmol
181 viewer.evalStringQuiet("zap");
182 viewer.setJmolStatusListener(null);
185 releaseUIResources();
188 public void colourByChain()
190 colourBySequence = false;
191 // TODO: colour by chain should colour each chain distinctly across all
193 // TODO: http://issues.jalview.org/browse/JAL-628
194 evalStateCommand("select *;color chain");
197 public void colourByCharge()
199 colourBySequence = false;
200 evalStateCommand("select *;color white;select ASP,GLU;color red;"
201 + "select LYS,ARG;color blue;select CYS;color yellow");
205 * superpose the structures associated with sequences in the alignment
206 * according to their corresponding positions.
208 public void superposeStructures(AlignmentI alignment)
210 superposeStructures(alignment, -1, null);
214 * superpose the structures associated with sequences in the alignment
215 * according to their corresponding positions. ded)
217 * @param refStructure
218 * - select which pdb file to use as reference (default is -1 - the
219 * first structure in the alignment)
221 public void superposeStructures(AlignmentI alignment, int refStructure)
223 superposeStructures(alignment, refStructure, null);
227 * superpose the structures associated with sequences in the alignment
228 * according to their corresponding positions. ded)
230 * @param refStructure
231 * - select which pdb file to use as reference (default is -1 - the
232 * first structure in the alignment)
236 public void superposeStructures(AlignmentI alignment, int refStructure,
237 ColumnSelection hiddenCols)
239 superposeStructures(new AlignmentI[]
240 { alignment }, new int[]
241 { refStructure }, new ColumnSelection[]
246 * Construct and send a command to align structures against a reference
247 * structure, based on one or more sequence alignments
250 * an array of alignments to process
251 * @param _refStructure
252 * an array of corresponding reference structures (index into pdb
253 * file array); if a negative value is passed, the first PDB file
254 * mapped to an alignment sequence is used as the reference for
257 * an array of corresponding hidden columns for each alignment
259 public void superposeStructures(AlignmentI[] _alignment,
260 int[] _refStructure, ColumnSelection[] _hiddenCols)
262 String[] files = getPdbFile();
264 if (!waitForFileLoad(files))
269 StringBuilder selectioncom = new StringBuilder(256);
270 // In principle - nSeconds specifies the speed of animation for each
271 // superposition - but is seems to behave weirdly, so we don't specify it.
272 String nSeconds = " ";
273 if (files.length > 10)
275 nSeconds = " 0.00001 ";
279 nSeconds = " " + (2.0 / files.length) + " ";
280 // if (nSeconds).substring(0,5)+" ";
282 // see JAL-1345 - should really automatically turn off the animation for
283 // large numbers of structures, but Jmol doesn't seem to allow that.
285 // union of all aligned positions are collected together.
286 for (int a = 0; a < _alignment.length; a++)
288 int refStructure = _refStructure[a];
289 AlignmentI alignment = _alignment[a];
290 ColumnSelection hiddenCols = _hiddenCols[a];
292 && selectioncom.length() > 0
293 && !selectioncom.substring(selectioncom.length() - 1).equals(
296 selectioncom.append("|");
298 // process this alignment
299 if (refStructure >= files.length)
301 System.err.println("Invalid reference structure value "
307 * 'matched' array will hold 'true' for visible alignment columns where
308 * all sequences have a residue with a mapping to the PDB structure
310 boolean matched[] = new boolean[alignment.getWidth()];
311 for (int m = 0; m < matched.length; m++)
313 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
316 SuperposeData[] structures = new SuperposeData[files.length];
317 for (int f = 0; f < files.length; f++)
319 structures[f] = new SuperposeData(alignment.getWidth());
323 * Calculate the superposable alignment columns ('matched'), and the
324 * corresponding structure residue positions (structures.pdbResNo)
326 int candidateRefStructure = findSuperposableResidues(alignment,
327 matched, structures);
328 if (refStructure < 0)
331 * If no reference structure was specified, pick the first one that has
332 * a mapping in the alignment
334 refStructure = candidateRefStructure;
337 String[] selcom = new String[files.length];
339 for (boolean b : matched)
348 // TODO: bail out here because superposition illdefined?
352 * generate select statements to select regions to superimpose structures
355 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
357 String chainCd = ":" + structures[pdbfnum].chain;
360 StringBuilder molsel = new StringBuilder();
362 for (int r = 0; r < matched.length; r++)
366 int pdbResNo = structures[pdbfnum].pdbResNo[r];
367 if (lpos != pdbResNo - 1)
373 molsel.append(chainCd);
380 // continuous run - and lpos >-1
383 // at the beginning, so add dash
393 * add final selection phrase
398 molsel.append(chainCd);
401 if (molsel.length() > 1)
403 selcom[pdbfnum] = molsel.toString();
404 selectioncom.append("((");
405 selectioncom.append(selcom[pdbfnum].substring(1,
406 selcom[pdbfnum].length() - 1));
407 selectioncom.append(" )& ");
408 selectioncom.append(pdbfnum + 1);
409 selectioncom.append(".1)");
410 if (pdbfnum < files.length - 1)
412 selectioncom.append("|");
417 selcom[pdbfnum] = null;
421 StringBuilder command = new StringBuilder(256);
422 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
424 if (pdbfnum == refStructure || selcom[pdbfnum] == null
425 || selcom[refStructure] == null)
429 command.append("echo ");
430 command.append("\"Superposing (");
431 command.append(structures[pdbfnum].pdbId);
432 command.append(") against reference (");
433 command.append(structures[refStructure].pdbId);
434 command.append(")\";\ncompare " + nSeconds);
436 command.append(Integer.toString(1 + pdbfnum));
437 command.append(".1} {");
438 command.append(Integer.toString(1 + refStructure));
439 // conformation=1 excludes alternate locations for CA (JAL-1757)
440 command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
442 // for (int s = 0; s < 2; s++)
444 // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
446 command.append(selcom[pdbfnum]);
447 command.append(selcom[refStructure]);
448 command.append(" ROTATE TRANSLATE;\n");
450 if (selectioncom.length() > 0)
452 System.out.println("Select regions:\n" + selectioncom.toString());
453 evalStateCommand("select *; cartoons off; backbone; select ("
454 + selectioncom.toString() + "); cartoons; ");
455 // selcom.append("; ribbons; ");
456 String cmdString = command.toString();
458 .println("Superimpose command(s):\n" + cmdString);
460 evalStateCommand(cmdString);
463 if (selectioncom.length() > 0)
464 {// finally, mark all regions that were superposed.
465 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
467 selectioncom.setLength(selectioncom.length() - 1);
469 System.out.println("Select regions:\n" + selectioncom.toString());
470 evalStateCommand("select *; cartoons off; backbone; select ("
471 + selectioncom.toString() + "); cartoons; ");
472 // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
476 public void evalStateCommand(String command)
479 if (lastCommand == null || !lastCommand.equals(command))
481 viewer.evalStringQuiet(command + "\n");
484 lastCommand = command;
488 * colour any structures associated with sequences in the given alignment
489 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
490 * if colourBySequence is enabled.
492 public void colourBySequence(AlignmentViewPanel alignmentv)
494 boolean showFeatures = alignmentv.getAlignViewport()
495 .isShowSequenceFeatures();
496 if (!colourBySequence || !isLoadingFinished())
500 if (getSsm() == null)
504 String[] files = getPdbFile();
506 SequenceRenderer sr = getSequenceRenderer(alignmentv);
508 FeatureRenderer fr = null;
511 fr = getFeatureRenderer(alignmentv);
513 AlignmentI alignment = alignmentv.getAlignment();
515 for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
517 for (String cbyseq : cpdbbyseq.commands)
519 executeWhenReady(cbyseq);
531 protected StructureMappingcommandSet[] getColourBySequenceCommands(
532 String[] files, SequenceRenderer sr, FeatureRenderer fr,
533 AlignmentI alignment)
536 .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
544 protected void executeWhenReady(String command)
546 evalStateCommand(command);
549 public void createImage(String file, String type, int quality)
551 System.out.println("JMOL CREATE IMAGE");
554 public String createImage(String fileName, String type,
555 Object textOrBytes, int quality)
557 System.out.println("JMOL CREATE IMAGE");
561 public String eval(String strEval)
563 // System.out.println(strEval);
564 // "# 'eval' is implemented only for the applet.";
568 // End StructureListener
569 // //////////////////////////
571 public float[][] functionXY(String functionName, int x, int y)
576 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
578 // TODO Auto-generated method stub
582 public Color getColour(int atomIndex, int pdbResNum, String chain,
585 if (getModelNum(pdbfile) < 0)
589 // TODO: verify atomIndex is selecting correct model.
590 // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
591 int colour = viewer.ms.at[atomIndex]
592 .atomPropertyInt(T.color);
593 return new Color(colour);
597 * returns the current featureRenderer that should be used to colour the
604 public abstract FeatureRenderer getFeatureRenderer(
605 AlignmentViewPanel alignment);
608 * instruct the Jalview binding to update the pdbentries vector if necessary
609 * prior to matching the jmol view's contents to the list of structure files
610 * Jalview knows about.
612 public abstract void refreshPdbEntries();
614 private int getModelNum(String modelFileName)
616 String[] mfn = getPdbFile();
621 for (int i = 0; i < mfn.length; i++)
623 if (mfn[i].equalsIgnoreCase(modelFileName))
632 * map between index of model filename returned from getPdbFile and the first
633 * index of models from this file in the viewer. Note - this is not trimmed -
634 * use getPdbFile to get number of unique models.
636 private int _modelFileNameMap[];
638 // ////////////////////////////////
639 // /StructureListener
641 public synchronized String[] getPdbFile()
645 return new String[0];
647 if (modelFileNames == null)
649 String mset[] = new String[viewer.ms.mc];
650 _modelFileNameMap = new int[mset.length];
651 String m = viewer.ms.getModelFileName(0);
657 mset[0] = new File(m).getAbsolutePath();
658 } catch (AccessControlException x)
660 // usually not allowed to do this in applet
662 .println("jmolBinding: Using local file string from Jmol: "
665 if (mset[0].indexOf("/file:") != -1)
667 // applet path with docroot - discard as format won't match pdbfile
672 for (int i = 1; i < mset.length; i++)
674 m = viewer.ms.getModelFileName(i);
680 mset[j] = new File(m).getAbsolutePath();
681 } catch (AccessControlException x)
683 // usually not allowed to do this in applet, so keep raw handle
684 // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
687 _modelFileNameMap[j] = i; // record the model index for the filename
688 // skip any additional models in the same file (NMR structures)
689 if ((mset[j] == null ? mset[j] != mset[j - 1]
690 : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
695 modelFileNames = new String[j];
696 System.arraycopy(mset, 0, modelFileNames, 0, j);
698 return modelFileNames;
702 * map from string to applet
705 public Map<String, Object> getRegistryInfo()
707 // TODO Auto-generated method stub
712 * returns the current sequenceRenderer that should be used to colour the
719 public abstract SequenceRenderer getSequenceRenderer(
720 AlignmentViewPanel alignment);
722 // ///////////////////////////////
723 // JmolStatusListener
725 public void handlePopupMenu(int x, int y)
727 // jmolpopup.show(x, y);
728 // jmolpopup.jpiShow(x, y);
732 * Highlight zero, one or more atoms on the structure
735 public void highlightAtoms(List<AtomSpec> atoms)
739 for (AtomSpec atom : atoms)
741 highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
742 atom.getChain(), atom.getPdbFile());
748 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
751 if (modelFileNames == null)
756 // look up file model number for this pdbfile
758 // may need to adjust for URLencoding here - we don't worry about that yet.
759 while (mdlNum < modelFileNames.length
760 && !pdbfile.equals(modelFileNames[mdlNum]))
764 if (mdlNum == modelFileNames.length)
770 // if (!pdbfile.equals(pdbentry.getFile()))
772 if (resetLastRes.length() > 0)
774 viewer.evalStringQuiet(resetLastRes.toString());
777 StringBuilder cmd = new StringBuilder(64);
778 cmd.append("select " + pdbResNum); // +modelNum
780 resetLastRes.setLength(0);
781 resetLastRes.append("select " + pdbResNum); // +modelNum
784 resetLastRes.append(":");
785 if (!chain.equals(" "))
788 resetLastRes.append(chain);
791 cmd.append(" /" + (mdlNum + 1));
792 resetLastRes.append("/" + (mdlNum + 1));
794 cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
796 resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
797 + " and not hetero; spacefill 0;");
799 cmd.append("spacefill 200;select none");
801 viewer.evalStringQuiet(cmd.toString());
806 boolean debug = true;
808 private void jmolHistory(boolean enable)
810 viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
813 public void loadInline(String string)
817 // viewer.loadInline(strModel, isAppend);
819 // construct fake fullPathName and fileName so we can identify the file
821 // Then, construct pass a reader for the string to Jmol.
822 // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
823 // fileName, null, reader, false, null, null, 0);
824 viewer.openStringInline(string);
827 public void mouseOverStructure(int atomIndex, String strInfo)
830 int alocsep = strInfo.indexOf("^");
831 int mdlSep = strInfo.indexOf("/");
832 int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
834 if (chainSeparator == -1)
836 chainSeparator = strInfo.indexOf(".");
837 if (mdlSep > -1 && mdlSep < chainSeparator)
839 chainSeparator1 = chainSeparator;
840 chainSeparator = mdlSep;
843 // handle insertion codes
846 pdbResNum = Integer.parseInt(strInfo.substring(
847 strInfo.indexOf("]") + 1, alocsep));
852 pdbResNum = Integer.parseInt(strInfo.substring(
853 strInfo.indexOf("]") + 1, chainSeparator));
857 if (strInfo.indexOf(":") > -1)
859 chainId = strInfo.substring(strInfo.indexOf(":") + 1,
860 strInfo.indexOf("."));
867 String pdbfilename = modelFileNames[frameNo]; // default is first or current
871 if (chainSeparator1 == -1)
873 chainSeparator1 = strInfo.indexOf(".", mdlSep);
875 String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
876 chainSeparator1) : strInfo.substring(mdlSep + 1);
879 // recover PDB filename for the model hovered over.
880 int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
882 while (mnumber < _modelFileNameMap[_mp])
886 pdbfilename = modelFileNames[_mp];
887 if (pdbfilename == null)
889 pdbfilename = new File(
890 viewer.ms.getModelFileName(mnumber))
894 } catch (Exception e)
899 if (lastMessage == null || !lastMessage.equals(strInfo))
901 getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
904 lastMessage = strInfo;
907 public void notifyAtomHovered(int atomIndex, String strInfo, String data)
911 System.err.println("Ignoring additional hover info: " + data
912 + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
914 mouseOverStructure(atomIndex, strInfo);
918 * { if (history != null && strStatus != null &&
919 * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
923 public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
926 * this implements the toggle label behaviour copied from the original
927 * structure viewer, MCView
931 System.err.println("Ignoring additional pick data string " + strData);
933 int chainSeparator = strInfo.indexOf(":");
935 if (chainSeparator == -1)
937 chainSeparator = strInfo.indexOf(".");
940 String picked = strInfo.substring(strInfo.indexOf("]") + 1,
942 String mdlString = "";
943 if ((p = strInfo.indexOf(":")) > -1)
945 picked += strInfo.substring(p + 1, strInfo.indexOf("."));
948 if ((p = strInfo.indexOf("/")) > -1)
950 mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
952 picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
956 if (!atomsPicked.contains(picked))
958 viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
959 atomsPicked.addElement(picked);
963 viewer.evalString("select " + picked + ";label off");
964 atomsPicked.removeElement(picked);
967 // TODO: in application this happens
969 // if (scriptWindow != null)
971 // scriptWindow.sendConsoleMessage(strInfo);
972 // scriptWindow.sendConsoleMessage("\n");
978 public void notifyCallback(CBK type, Object[] data)
985 notifyFileLoaded((String) data[1], (String) data[2],
986 (String) data[3], (String) data[4],
987 ((Integer) data[5]).intValue());
991 notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
993 // also highlight in alignment
995 notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
999 notifyScriptTermination((String) data[2],
1000 ((Integer) data[3]).intValue());
1003 sendConsoleEcho((String) data[1]);
1006 sendConsoleMessage((data == null) ? ((String) null)
1007 : (String) data[1]);
1010 // System.err.println("Ignoring error callback.");
1020 System.err.println("Unhandled callback " + type + " "
1021 + data[1].toString());
1024 } catch (Exception e)
1026 System.err.println("Squashed Jmol callback handler error:");
1027 e.printStackTrace();
1032 public boolean notifyEnabled(CBK callbackPick)
1034 switch (callbackPick)
1050 // incremented every time a load notification is successfully handled -
1051 // lightweight mechanism for other threads to detect when they can start
1052 // referrring to new structures.
1053 private long loadNotifiesHandled = 0;
1055 public long getLoadNotifiesHandled()
1057 return loadNotifiesHandled;
1060 public void notifyFileLoaded(String fullPathName, String fileName2,
1061 String modelName, String errorMsg, int modelParts)
1063 if (errorMsg != null)
1065 fileLoadingError = errorMsg;
1069 // TODO: deal sensibly with models loaded inLine:
1070 // modelName will be null, as will fullPathName.
1072 // the rest of this routine ignores the arguments, and simply interrogates
1073 // the Jmol view to find out what structures it contains, and adds them to
1074 // the structure selection manager.
1075 fileLoadingError = null;
1076 String[] oldmodels = modelFileNames;
1077 modelFileNames = null;
1078 chainNames = new Vector<String>();
1079 chainFile = new Hashtable<String, String>();
1080 boolean notifyLoaded = false;
1081 String[] modelfilenames = getPdbFile();
1082 // first check if we've lost any structures
1083 if (oldmodels != null && oldmodels.length > 0)
1086 for (int i = 0; i < oldmodels.length; i++)
1088 for (int n = 0; n < modelfilenames.length; n++)
1090 if (modelfilenames[n] == oldmodels[i])
1092 oldmodels[i] = null;
1096 if (oldmodels[i] != null)
1103 String[] oldmfn = new String[oldm];
1105 for (int i = 0; i < oldmodels.length; i++)
1107 if (oldmodels[i] != null)
1109 oldmfn[oldm++] = oldmodels[i];
1112 // deregister the Jmol instance for these structures - we'll add
1113 // ourselves again at the end for the current structure set.
1114 getSsm().removeStructureViewerListener(this, oldmfn);
1117 refreshPdbEntries();
1118 for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
1120 String fileName = modelfilenames[modelnum];
1121 boolean foundEntry = false;
1122 MCview.PDBfile pdb = null;
1123 String pdbfile = null;
1124 // model was probably loaded inline - so check the pdb file hashcode
1127 // calculate essential attributes for the pdb data imported inline.
1128 // prolly need to resolve modelnumber properly - for now just use our
1130 pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
1133 // search pdbentries and sequences to find correct pdbentry for this
1135 for (int pe = 0; pe < getPdbCount(); pe++)
1137 boolean matches = false;
1138 if (fileName == null)
1141 // see JAL-623 - need method of matching pasted data up
1143 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1144 pdbfile, AppletFormatAdapter.PASTE);
1145 getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
1152 File fl = new File(getPdbEntry(pe).getFile());
1153 matches = fl.equals(new File(fileName));
1157 // TODO: Jmol can in principle retrieve from CLASSLOADER but
1160 // to be tested. See mantis bug
1161 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
1162 String protocol = AppletFormatAdapter.URL;
1167 protocol = AppletFormatAdapter.FILE;
1169 } catch (Exception e)
1174 // Explicitly map to the filename used by Jmol ;
1175 pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
1176 fileName, protocol);
1177 // pdbentry[pe].getFile(), protocol);
1183 // add an entry for every chain in the model
1184 for (int i = 0; i < pdb.chains.size(); i++)
1186 String chid = new String(pdb.id + ":"
1187 + pdb.chains.elementAt(i).id);
1188 chainFile.put(chid, fileName);
1189 chainNames.addElement(chid);
1191 notifyLoaded = true;
1195 if (!foundEntry && associateNewStructs)
1197 // this is a foreign pdb file that jalview doesn't know about - add
1198 // it to the dataset and try to find a home - either on a matching
1199 // sequence or as a new sequence.
1200 String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
1202 // parse pdb file into a chain, etc.
1203 // locate best match for pdb in associated views and add mapping to
1205 // if properly registered then
1206 notifyLoaded = true;
1211 // so finally, update the jmol bits and pieces
1212 // if (jmolpopup != null)
1214 // // potential for deadlock here:
1215 // // jmolpopup.updateComputedMenus();
1217 if (!isLoadingFromArchive())
1219 viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
1221 // register ourselves as a listener and notify the gui that it needs to
1223 getSsm().addStructureViewerListener(this);
1226 FeatureRenderer fr = getFeatureRenderer(null);
1232 loadNotifiesHandled++;
1234 setLoadingFromArchive(false);
1237 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
1239 notifyAtomPicked(iatom, strMeasure, null);
1242 public abstract void notifyScriptTermination(String strStatus,
1246 * display a message echoed from the jmol viewer
1250 public abstract void sendConsoleEcho(String strEcho); /*
1251 * { showConsole(true);
1253 * history.append("\n" +
1257 // /End JmolStatusListener
1258 // /////////////////////////////
1262 * status message - usually the response received after a script
1265 public abstract void sendConsoleMessage(String strStatus);
1267 public void setCallbackFunction(String callbackType,
1268 String callbackFunction)
1270 System.err.println("Ignoring set-callback request to associate "
1271 + callbackType + " with function " + callbackFunction);
1275 public void setJalviewColourScheme(ColourSchemeI cs)
1277 colourBySequence = false;
1285 StringBuilder command = new StringBuilder(128);
1286 command.append("select *;color white;");
1287 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
1289 for (String res : residueSet)
1291 Color col = cs.findColour(res.charAt(0));
1292 command.append("select " + res + ";color[" + col.getRed() + ","
1293 + col.getGreen() + "," + col.getBlue() + "];");
1296 evalStateCommand(command.toString());
1300 public void showHelp()
1302 showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
1306 * open the URL somehow
1310 public abstract void showUrl(String url, String target);
1313 * called when the binding thinks the UI needs to be refreshed after a Jmol
1314 * state change. this could be because structures were loaded, or because an
1315 * error has occured.
1317 public abstract void refreshGUI();
1320 * called to show or hide the associated console window container.
1324 public abstract void showConsole(boolean show);
1327 * @param renderPanel
1329 * - when true will initialise jmol's file IO system (should be false
1330 * in applet context)
1332 * @param documentBase
1334 * @param commandOptions
1336 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1337 String htmlName, URL documentBase, URL codeBase,
1338 String commandOptions)
1340 allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
1341 codeBase, commandOptions, null, null);
1346 * @param renderPanel
1348 * - when true will initialise jmol's file IO system (should be false
1349 * in applet context)
1351 * @param documentBase
1353 * @param commandOptions
1354 * @param consolePanel
1355 * - panel to contain Jmol console
1356 * @param buttonsToShow
1357 * - buttons to show on the console, in ordr
1359 public void allocateViewer(Container renderPanel, boolean jmolfileio,
1360 String htmlName, URL documentBase, URL codeBase,
1361 String commandOptions, final Container consolePanel,
1362 String buttonsToShow)
1364 if (commandOptions == null)
1366 commandOptions = "";
1368 viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
1369 (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
1370 + ((Object) this).toString(), documentBase, codeBase,
1371 commandOptions, this);
1373 viewer.setJmolStatusListener(this); // extends JmolCallbackListener
1375 console = createJmolConsole(consolePanel, buttonsToShow);
1376 if (consolePanel != null)
1378 consolePanel.addComponentListener(this);
1384 protected abstract JmolAppConsoleInterface createJmolConsole(
1385 Container consolePanel, String buttonsToShow);
1387 protected org.jmol.api.JmolAppConsoleInterface console = null;
1389 public void setBackgroundColour(java.awt.Color col)
1392 viewer.evalStringQuiet("background [" + col.getRed() + ","
1393 + col.getGreen() + "," + col.getBlue() + "];");
1398 public Dimension resizeInnerPanel(String data)
1400 // Jalview doesn't honour resize panel requests
1404 public boolean isFinishedInit()
1406 return finishedInit;
1409 public void setFinishedInit(boolean finishedInit)
1411 this.finishedInit = finishedInit;
1417 protected void closeConsole()
1419 if (console != null)
1423 console.setVisible(false);
1426 } catch (Exception x)
1435 * ComponentListener method
1438 public void componentMoved(ComponentEvent e)
1443 * ComponentListener method
1446 public void componentResized(ComponentEvent e)
1451 * ComponentListener method
1454 public void componentShown(ComponentEvent e)
1460 * ComponentListener method
1463 public void componentHidden(ComponentEvent e)