-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ext.jmol;\r
-\r
-import jalview.api.AlignmentViewPanel;\r
-import jalview.api.FeatureRenderer;\r
-import jalview.api.SequenceRenderer;\r
-import jalview.api.SequenceStructureBinding;\r
-import jalview.api.StructureSelectionManagerProvider;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.ColumnSelection;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.io.AppletFormatAdapter;\r
-import jalview.schemes.ColourSchemeI;\r
-import jalview.schemes.ResidueProperties;\r
-import jalview.structure.StructureListener;\r
-import jalview.structure.StructureMapping;\r
-import jalview.structure.StructureSelectionManager;\r
-\r
-import java.awt.Color;\r
-import java.awt.Container;\r
-import java.awt.event.ComponentEvent;\r
-import java.awt.event.ComponentListener;\r
-import java.io.File;\r
-import java.net.URL;\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Map;\r
-import java.util.Vector;\r
-\r
-import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
-import org.jmol.api.JmolAppConsoleInterface;\r
-import org.jmol.api.JmolSelectionListener;\r
-import org.jmol.api.JmolStatusListener;\r
-import org.jmol.api.JmolViewer;\r
-import org.jmol.constant.EnumCallback;\r
-import org.jmol.popup.JmolPopup;\r
-\r
-public abstract class JalviewJmolBinding implements StructureListener,\r
- JmolStatusListener, SequenceStructureBinding,\r
- JmolSelectionListener, ComponentListener, StructureSelectionManagerProvider\r
-\r
-{\r
- /**\r
- * set if Jmol state is being restored from some source - instructs binding\r
- * not to apply default display style when structure set is updated for first\r
- * time.\r
- */\r
- private boolean loadingFromArchive = false;\r
-\r
- /**\r
- * state flag used to check if the Jmol viewer's paint method can be called\r
- */\r
- private boolean finishedInit = false;\r
-\r
- public boolean isFinishedInit()\r
- {\r
- return finishedInit;\r
- }\r
-\r
- public void setFinishedInit(boolean finishedInit)\r
- {\r
- this.finishedInit = finishedInit;\r
- }\r
-\r
- boolean allChainsSelected = false;\r
-\r
- /**\r
- * when true, try to search the associated datamodel for sequences that are\r
- * associated with any unknown structures in the Jmol view.\r
- */\r
- private boolean associateNewStructs = false;\r
-\r
- Vector atomsPicked = new Vector();\r
-\r
- public Vector chainNames;\r
-\r
- Hashtable chainFile;\r
-\r
- /**\r
- * array of target chains for seuqences - tied to pdbentry and sequence[]\r
- */\r
- protected String[][] chains;\r
-\r
- boolean colourBySequence = true;\r
-\r
- StringBuffer eval = new StringBuffer();\r
-\r
- public String fileLoadingError;\r
-\r
- /**\r
- * the default or current model displayed if the model cannot be identified\r
- * from the selection message\r
- */\r
- int frameNo = 0;\r
-\r
- protected JmolPopup jmolpopup;\r
-\r
- String lastCommand;\r
-\r
- String lastMessage;\r
-\r
- boolean loadedInline;\r
-\r
- /**\r
- * current set of model filenames loaded in the Jmol instance\r
- */\r
- String[] modelFileNames = null;\r
-\r
- public PDBEntry[] pdbentry;\r
-\r
- /**\r
- * datasource protocol for access to PDBEntrylatest\r
- */\r
- String protocol = null;\r
-\r
- StringBuffer resetLastRes = new StringBuffer();\r
-\r
- /**\r
- * sequences mapped to each pdbentry\r
- */\r
- public SequenceI[][] sequence;\r
-\r
- public StructureSelectionManager ssm;\r
-\r
- public JmolViewer viewer;\r
-\r
- public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs,\r
- String[][] chains, String protocol)\r
- {\r
- this.ssm = ssm;\r
- this.sequence = sequenceIs;\r
- this.chains = chains;\r
- this.pdbentry = pdbentry;\r
- this.protocol = protocol;\r
- if (chains == null)\r
- {\r
- this.chains = new String[pdbentry.length][];\r
- }\r
- /*\r
- * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),\r
- * "jalviewJmol", ap.av.applet .getDocumentBase(),\r
- * ap.av.applet.getCodeBase(), "", this);\r
- * \r
- * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);\r
- */\r
- }\r
-\r
- public JalviewJmolBinding(StructureSelectionManager ssm, JmolViewer viewer2)\r
- {\r
- this.ssm = ssm;\r
- viewer = viewer2;\r
- viewer.setJmolStatusListener(this);\r
- viewer.addSelectionListener(this);\r
- }\r
-\r
- /**\r
- * construct a title string for the viewer window based on the data jalview\r
- * knows about\r
- * \r
- * @return\r
- */\r
- public String getViewerTitle()\r
- {\r
- if (sequence == null || pdbentry == null || sequence.length < 1\r
- || pdbentry.length < 1 || sequence[0].length < 1)\r
- {\r
- return ("Jalview Jmol Window");\r
- }\r
- // TODO: give a more informative title when multiple structures are\r
- // displayed.\r
- StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"\r
- + pdbentry[0].getId());\r
-\r
- if (pdbentry[0].getProperty() != null)\r
- {\r
- if (pdbentry[0].getProperty().get("method") != null)\r
- {\r
- title.append(" Method: ");\r
- title.append(pdbentry[0].getProperty().get("method"));\r
- }\r
- if (pdbentry[0].getProperty().get("chains") != null)\r
- {\r
- title.append(" Chain:");\r
- title.append(pdbentry[0].getProperty().get("chains"));\r
- }\r
- }\r
- return title.toString();\r
- }\r
-\r
- /**\r
- * prepare the view for a given set of models/chains. chainList contains\r
- * strings of the form 'pdbfilename:Chaincode'\r
- * \r
- * @param chainList\r
- * list of chains to make visible\r
- */\r
- public void centerViewer(Vector chainList)\r
- {\r
- StringBuffer cmd = new StringBuffer();\r
- String lbl;\r
- int mlength, p;\r
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)\r
- {\r
- mlength = 0;\r
- lbl = (String) chainList.elementAt(i);\r
- do\r
- {\r
- p = mlength;\r
- mlength = lbl.indexOf(":", p);\r
- } while (p < mlength && mlength < (lbl.length() - 2));\r
- // TODO: lookup each pdb id and recover proper model number for it.\r
- cmd.append(":" + lbl.substring(mlength + 1) + " /"\r
- + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");\r
- }\r
- if (cmd.length() > 0)\r
- cmd.setLength(cmd.length() - 4);\r
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);\r
- }\r
-\r
- public void closeViewer()\r
- {\r
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
- // remove listeners for all structures in viewer\r
- ssm.removeStructureViewerListener(this, this.getPdbFile());\r
- // and shut down jmol\r
- viewer.evalStringQuiet("zap");\r
- viewer.setJmolStatusListener(null);\r
- lastCommand = null;\r
- viewer = null;\r
- releaseUIResources();\r
- }\r
-\r
- /**\r
- * called by JalviewJmolbinding after closeViewer is called - release any\r
- * resources and references so they can be garbage collected.\r
- */\r
- protected abstract void releaseUIResources();\r
-\r
- public void colourByChain()\r
- {\r
- colourBySequence = false;\r
- // TODO: colour by chain should colour each chain distinctly across all\r
- // visible models\r
- // TODO: http://issues.jalview.org/browse/JAL-628\r
- evalStateCommand("select *;color chain");\r
- }\r
-\r
- public void colourByCharge()\r
- {\r
- colourBySequence = false;\r
- evalStateCommand("select *;color white;select ASP,GLU;color red;"\r
- + "select LYS,ARG;color blue;select CYS;color yellow");\r
- }\r
-\r
- /**\r
- * superpose the structures associated with sequences in the alignment\r
- * according to their corresponding positions.\r
- */\r
- public void superposeStructures(AlignmentI alignment)\r
- {\r
- superposeStructures(alignment, -1, null);\r
- }\r
-\r
- /**\r
- * superpose the structures associated with sequences in the alignment\r
- * according to their corresponding positions. ded)\r
- * \r
- * @param refStructure\r
- * - select which pdb file to use as reference (default is -1 - the\r
- * first structure in the alignment)\r
- */\r
- public void superposeStructures(AlignmentI alignment, int refStructure)\r
- {\r
- superposeStructures(alignment, refStructure, null);\r
- }\r
-\r
- /**\r
- * superpose the structures associated with sequences in the alignment\r
- * according to their corresponding positions. ded)\r
- * \r
- * @param refStructure\r
- * - select which pdb file to use as reference (default is -1 - the\r
- * first structure in the alignment)\r
- * @param hiddenCols\r
- * TODO\r
- */\r
- public void superposeStructures(AlignmentI alignment, int refStructure,\r
- ColumnSelection hiddenCols)\r
- {\r
- superposeStructures(new AlignmentI[]\r
- { alignment }, new int[]\r
- { refStructure }, new ColumnSelection[]\r
- { hiddenCols });\r
- }\r
-\r
- public void superposeStructures(AlignmentI[] _alignment,\r
- int[] _refStructure, ColumnSelection[] _hiddenCols)\r
- {\r
- String[] files = getPdbFile();\r
- StringBuffer selectioncom = new StringBuffer();\r
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);\r
- // union of all aligned positions are collected together.\r
- for (int a = 0; a < _alignment.length; a++)\r
- {\r
- int refStructure = _refStructure[a];\r
- AlignmentI alignment = _alignment[a];\r
- ColumnSelection hiddenCols = _hiddenCols[a];\r
- if (a > 0\r
- && selectioncom.length() > 0\r
- && !selectioncom.substring(selectioncom.length() - 1).equals(\r
- "|"))\r
- {\r
- selectioncom.append("|");\r
- }\r
- // process this alignment\r
- if (refStructure >= files.length)\r
- {\r
- System.err.println("Invalid reference structure value "\r
- + refStructure);\r
- refStructure = -1;\r
- }\r
- if (refStructure < -1)\r
- {\r
- refStructure = -1;\r
- }\r
- StringBuffer command = new StringBuffer();\r
-\r
- boolean matched[] = new boolean[alignment.getWidth()];\r
- for (int m = 0; m < matched.length; m++)\r
- {\r
-\r
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;\r
- }\r
-\r
- int commonrpositions[][] = new int[files.length][alignment.getWidth()];\r
- String isel[] = new String[files.length];\r
- // reference structure - all others are superposed in it\r
- String[] targetC = new String[files.length];\r
- String[] chainNames = new String[files.length];\r
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
- {\r
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
-\r
- if (mapping == null || mapping.length < 1)\r
- continue;\r
-\r
- int lastPos = -1;\r
- for (int s = 0; s < sequence[pdbfnum].length; s++)\r
- {\r
- for (int sp, m = 0; m < mapping.length; m++)\r
- {\r
- if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
- {\r
- if (refStructure == -1)\r
- {\r
- refStructure = pdbfnum;\r
- }\r
- SequenceI asp = alignment.getSequenceAt(sp);\r
- for (int r = 0; r < matched.length; r++)\r
- {\r
- if (!matched[r])\r
- {\r
- continue;\r
- }\r
- matched[r] = false; // assume this is not a good site\r
- if (r >= asp.getLength())\r
- {\r
- continue;\r
- }\r
-\r
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
- {\r
- // no mapping to gaps in sequence\r
- continue;\r
- }\r
- int t = asp.findPosition(r); // sequence position\r
- int apos = mapping[m].getAtomNum(t);\r
- int pos = mapping[m].getPDBResNum(t);\r
-\r
- if (pos < 1 || pos == lastPos)\r
- {\r
- // can't align unmapped sequence\r
- continue;\r
- }\r
- matched[r] = true; // this is a good ite\r
- lastPos = pos;\r
- // just record this residue position\r
- commonrpositions[pdbfnum][r] = pos;\r
- }\r
- // create model selection suffix\r
- isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";\r
- if (mapping[m].getChain() == null\r
- || mapping[m].getChain().trim().length() == 0)\r
- {\r
- targetC[pdbfnum] = "";\r
- }\r
- else\r
- {\r
- targetC[pdbfnum] = ":" + mapping[m].getChain();\r
- }\r
- chainNames[pdbfnum] = mapping[m].getPdbId()\r
- + targetC[pdbfnum];\r
- // move on to next pdb file\r
- s = sequence[pdbfnum].length;\r
- break;\r
- }\r
- }\r
- }\r
- }\r
- String[] selcom = new String[files.length];\r
- int nmatched = 0;\r
- // generate select statements to select regions to superimpose structures\r
- {\r
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
- {\r
- String chainCd = targetC[pdbfnum];\r
- int lpos = -1;\r
- boolean run = false;\r
- StringBuffer molsel = new StringBuffer();\r
- molsel.append("{");\r
- for (int r = 0; r < matched.length; r++)\r
- {\r
- if (matched[r])\r
- {\r
- if (pdbfnum == 0)\r
- {\r
- nmatched++;\r
- }\r
- if (lpos != commonrpositions[pdbfnum][r] - 1)\r
- {\r
- // discontinuity\r
- if (lpos != -1)\r
- {\r
- molsel.append(lpos);\r
- molsel.append(chainCd);\r
- // molsel.append("} {");\r
- molsel.append("|");\r
- }\r
- }\r
- else\r
- {\r
- // continuous run - and lpos >-1\r
- if (!run)\r
- {\r
- // at the beginning, so add dash\r
- molsel.append(lpos);\r
- molsel.append("-");\r
- }\r
- run = true;\r
- }\r
- lpos = commonrpositions[pdbfnum][r];\r
- // molsel.append(lpos);\r
- }\r
- }\r
- // add final selection phrase\r
- if (lpos != -1)\r
- {\r
- molsel.append(lpos);\r
- molsel.append(chainCd);\r
- molsel.append("}");\r
- }\r
- selcom[pdbfnum] = molsel.toString();\r
- selectioncom.append("((");\r
- selectioncom.append(selcom[pdbfnum].substring(1,\r
- selcom[pdbfnum].length() - 1));\r
- selectioncom.append(" )& ");\r
- selectioncom.append(pdbfnum + 1);\r
- selectioncom.append(".1)");\r
- if (pdbfnum < files.length - 1)\r
- {\r
- selectioncom.append("|");\r
- }\r
- }\r
- }\r
- // TODO: consider bailing if nmatched less than 4 because superposition\r
- // not\r
- // well defined.\r
- // TODO: refactor superposable position search (above) from jmol selection\r
- // construction (below)\r
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
- {\r
- if (pdbfnum == refStructure)\r
- {\r
- continue;\r
- }\r
- command.append("echo ");\r
- command.append("\"Superposing (");\r
- command.append(chainNames[pdbfnum]);\r
- command.append(") against reference (");\r
- command.append(chainNames[refStructure]);\r
- command.append(")\";\ncompare ");\r
- command.append("{");\r
- command.append(1 + pdbfnum);\r
- command.append(".1} {");\r
- command.append(1 + refStructure);\r
- command.append(".1} SUBSET {*.CA | *.P} ATOMS ");\r
-\r
- // form the matched pair strings\r
- String sep = "";\r
- for (int s = 0; s < 2; s++)\r
- {\r
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);\r
- }\r
- command.append(" ROTATE TRANSLATE;\n");\r
- }\r
- System.out.println("Select regions:\n" + selectioncom.toString());\r
- evalStateCommand("select *; cartoons off; backbone; select ("\r
- + selectioncom.toString() + "); cartoons; ");\r
- // selcom.append("; ribbons; ");\r
- System.out.println("Superimpose command(s):\n" + command.toString());\r
-\r
- evalStateCommand(command.toString());\r
- }\r
- if (selectioncom.length() > 0)\r
- {// finally, mark all regions that were superposed.\r
- if (selectioncom.substring(selectioncom.length() - 1).equals("|"))\r
- {\r
- selectioncom.setLength(selectioncom.length() - 1);\r
- }\r
- System.out.println("Select regions:\n" + selectioncom.toString());\r
- evalStateCommand("select *; cartoons off; backbone; select ("\r
- + selectioncom.toString() + "); cartoons; ");\r
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());\r
- }\r
- }\r
-\r
- public void evalStateCommand(String command)\r
- {\r
- jmolHistory(false);\r
- if (lastCommand == null || !lastCommand.equals(command))\r
- {\r
- viewer.evalStringQuiet(command + "\n");\r
- }\r
- jmolHistory(true);\r
- lastCommand = command;\r
- }\r
-\r
- /**\r
- * colour any structures associated with sequences in the given alignment\r
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only\r
- * if colourBySequence is enabled.\r
- */\r
- public void colourBySequence(boolean showFeatures,\r
- jalview.api.AlignmentViewPanel alignmentv)\r
- {\r
- if (!colourBySequence)\r
- return;\r
- if (ssm == null)\r
- {\r
- return;\r
- }\r
- String[] files = getPdbFile();\r
-\r
- SequenceRenderer sr = getSequenceRenderer(alignmentv);\r
-\r
- FeatureRenderer fr = null;\r
- if (showFeatures)\r
- {\r
- fr = getFeatureRenderer(alignmentv);\r
- }\r
- AlignmentI alignment = alignmentv.getAlignment();\r
-\r
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq: JmolCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment))\r
- for (String cbyseq : cpdbbyseq.commands) {\r
- evalStateCommand(cbyseq);\r
- }\r
- }\r
- \r
- public boolean isColourBySequence()\r
- {\r
- return colourBySequence;\r
- }\r
-\r
- public void setColourBySequence(boolean colourBySequence)\r
- {\r
- this.colourBySequence = colourBySequence;\r
- }\r
-\r
- public void createImage(String file, String type, int quality)\r
- {\r
- System.out.println("JMOL CREATE IMAGE");\r
- }\r
-\r
- public String createImage(String fileName, String type,\r
- Object textOrBytes, int quality)\r
- {\r
- System.out.println("JMOL CREATE IMAGE");\r
- return null;\r
- }\r
-\r
- public String eval(String strEval)\r
- {\r
- // System.out.println(strEval);\r
- // "# 'eval' is implemented only for the applet.";\r
- return null;\r
- }\r
-\r
- // End StructureListener\r
- // //////////////////////////\r
-\r
- public float[][] functionXY(String functionName, int x, int y)\r
- {\r
- return null;\r
- }\r
-\r
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- public Color getColour(int atomIndex, int pdbResNum, String chain,\r
- String pdbfile)\r
- {\r
- if (getModelNum(pdbfile) < 0)\r
- return null;\r
- // TODO: verify atomIndex is selecting correct model.\r
- return new Color(viewer.getAtomArgb(atomIndex));\r
- }\r
-\r
- /**\r
- * returns the current featureRenderer that should be used to colour the\r
- * structures\r
- * \r
- * @param alignment\r
- * \r
- * @return\r
- */\r
- public abstract FeatureRenderer getFeatureRenderer(\r
- AlignmentViewPanel alignment);\r
-\r
- /**\r
- * instruct the Jalview binding to update the pdbentries vector if necessary\r
- * prior to matching the jmol view's contents to the list of structure files\r
- * Jalview knows about.\r
- */\r
- public abstract void refreshPdbEntries();\r
-\r
- private int getModelNum(String modelFileName)\r
- {\r
- String[] mfn = getPdbFile();\r
- if (mfn == null)\r
- {\r
- return -1;\r
- }\r
- for (int i = 0; i < mfn.length; i++)\r
- {\r
- if (mfn[i].equalsIgnoreCase(modelFileName))\r
- return i;\r
- }\r
- return -1;\r
- }\r
-\r
- /**\r
- * map between index of model filename returned from getPdbFile and the first\r
- * index of models from this file in the viewer. Note - this is not trimmed -\r
- * use getPdbFile to get number of unique models.\r
- */\r
- private int _modelFileNameMap[];\r
-\r
- // ////////////////////////////////\r
- // /StructureListener\r
- public synchronized String[] getPdbFile()\r
- {\r
- if (viewer == null)\r
- {\r
- return new String[0];\r
- }\r
- if (modelFileNames == null)\r
- {\r
-\r
- String mset[] = new String[viewer.getModelCount()];\r
- _modelFileNameMap = new int[mset.length];\r
- int j = 1;\r
- mset[0] = viewer.getModelFileName(0);\r
- for (int i = 1; i < mset.length; i++)\r
- {\r
- mset[j] = viewer.getModelFileName(i);\r
- _modelFileNameMap[j] = i; // record the model index for the filename\r
- // skip any additional models in the same file (NMR structures)\r
- if ((mset[j] == null ? mset[j] != mset[j - 1]\r
- : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))\r
- {\r
- j++;\r
- }\r
- }\r
- modelFileNames = new String[j];\r
- System.arraycopy(mset, 0, modelFileNames, 0, j);\r
- }\r
- return modelFileNames;\r
- }\r
-\r
- /**\r
- * map from string to applet\r
- */\r
- public Map getRegistryInfo()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /**\r
- * returns the current sequenceRenderer that should be used to colour the\r
- * structures\r
- * \r
- * @param alignment\r
- * \r
- * @return\r
- */\r
- public abstract SequenceRenderer getSequenceRenderer(\r
- AlignmentViewPanel alignment);\r
-\r
- // ///////////////////////////////\r
- // JmolStatusListener\r
-\r
- public void handlePopupMenu(int x, int y)\r
- {\r
- jmolpopup.show(x, y);\r
- }\r
-\r
- // jmol/ssm only\r
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,\r
- String pdbfile)\r
- {\r
- if (modelFileNames == null)\r
- {\r
- return;\r
- }\r
-\r
- // look up file model number for this pdbfile\r
- int mdlNum = 0;\r
- String fn;\r
- // may need to adjust for URLencoding here - we don't worry about that yet.\r
- while (mdlNum < modelFileNames.length\r
- && !pdbfile.equals(modelFileNames[mdlNum]))\r
- {\r
- // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);\r
- mdlNum++;\r
- }\r
- if (mdlNum == modelFileNames.length)\r
- {\r
- return;\r
- }\r
-\r
- jmolHistory(false);\r
- // if (!pdbfile.equals(pdbentry.getFile()))\r
- // return;\r
- if (resetLastRes.length() > 0)\r
- {\r
- viewer.evalStringQuiet(resetLastRes.toString());\r
- }\r
-\r
- eval.setLength(0);\r
- eval.append("select " + pdbResNum); // +modelNum\r
-\r
- resetLastRes.setLength(0);\r
- resetLastRes.append("select " + pdbResNum); // +modelNum\r
-\r
- eval.append(":");\r
- resetLastRes.append(":");\r
- if (!chain.equals(" "))\r
- {\r
- eval.append(chain);\r
- resetLastRes.append(chain);\r
- }\r
- {\r
- eval.append(" /" + (mdlNum + 1));\r
- resetLastRes.append("/" + (mdlNum + 1));\r
- }\r
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");\r
-\r
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()\r
- + " and not hetero; spacefill 0;");\r
-\r
- eval.append("spacefill 200;select none");\r
-\r
- viewer.evalStringQuiet(eval.toString());\r
- jmolHistory(true);\r
-\r
- }\r
-\r
- boolean debug = true;\r
-\r
- private void jmolHistory(boolean enable)\r
- {\r
- viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));\r
- }\r
-\r
- public void loadInline(String string)\r
- {\r
- loadedInline = true;\r
- // TODO: re JAL-623\r
- // viewer.loadInline(strModel, isAppend);\r
- // could do this:\r
- // construct fake fullPathName and fileName so we can identify the file\r
- // later.\r
- // Then, construct pass a reader for the string to Jmol.\r
- // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,\r
- // fileName, null, reader, false, null, null, 0);\r
- viewer.openStringInline(string);\r
- }\r
-\r
- public void mouseOverStructure(int atomIndex, String strInfo)\r
- {\r
- int pdbResNum;\r
- int alocsep = strInfo.indexOf("^");\r
- int mdlSep = strInfo.indexOf("/");\r
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;\r
-\r
- if (chainSeparator == -1)\r
- {\r
- chainSeparator = strInfo.indexOf(".");\r
- if (mdlSep > -1 && mdlSep < chainSeparator)\r
- {\r
- chainSeparator1 = chainSeparator;\r
- chainSeparator = mdlSep;\r
- }\r
- }\r
- // handle insertion codes\r
- if (alocsep != -1)\r
- {\r
- pdbResNum = Integer.parseInt(strInfo.substring(\r
- strInfo.indexOf("]") + 1, alocsep));\r
-\r
- }\r
- else\r
- {\r
- pdbResNum = Integer.parseInt(strInfo.substring(\r
- strInfo.indexOf("]") + 1, chainSeparator));\r
- }\r
- String chainId;\r
-\r
- if (strInfo.indexOf(":") > -1)\r
- chainId = strInfo.substring(strInfo.indexOf(":") + 1,\r
- strInfo.indexOf("."));\r
- else\r
- {\r
- chainId = " ";\r
- }\r
-\r
- String pdbfilename = modelFileNames[frameNo]; // default is first or current\r
- // model\r
- if (mdlSep > -1)\r
- {\r
- if (chainSeparator1 == -1)\r
- {\r
- chainSeparator1 = strInfo.indexOf(".", mdlSep);\r
- }\r
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,\r
- chainSeparator1) : strInfo.substring(mdlSep + 1);\r
- try\r
- {\r
- // recover PDB filename for the model hovered over.\r
- pdbfilename = viewer\r
- .getModelFileName(new Integer(mdlId).intValue() - 1);\r
- } catch (Exception e)\r
- {\r
- }\r
- ;\r
- }\r
- if (lastMessage == null || !lastMessage.equals(strInfo))\r
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);\r
-\r
- lastMessage = strInfo;\r
- }\r
-\r
- public void notifyAtomHovered(int atomIndex, String strInfo, String data)\r
- {\r
- if (data != null)\r
- {\r
- System.err.println("Ignoring additional hover info: " + data\r
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");\r
- }\r
- mouseOverStructure(atomIndex, strInfo);\r
- }\r
-\r
- /*\r
- * { if (history != null && strStatus != null &&\r
- * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);\r
- * } }\r
- */\r
-\r
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)\r
- {\r
- /**\r
- * this implements the toggle label behaviour copied from the original\r
- * structure viewer, MCView\r
- */\r
- if (strData != null)\r
- {\r
- System.err.println("Ignoring additional pick data string " + strData);\r
- }\r
- int chainSeparator = strInfo.indexOf(":");\r
- int p = 0;\r
- if (chainSeparator == -1)\r
- chainSeparator = strInfo.indexOf(".");\r
-\r
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,\r
- chainSeparator);\r
- String mdlString = "";\r
- if ((p = strInfo.indexOf(":")) > -1)\r
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));\r
-\r
- if ((p = strInfo.indexOf("/")) > -1)\r
- {\r
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));\r
- }\r
- picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"\r
- + mdlString + "))";\r
- jmolHistory(false);\r
-\r
- if (!atomsPicked.contains(picked))\r
- {\r
- viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");\r
- atomsPicked.addElement(picked);\r
- }\r
- else\r
- {\r
- viewer.evalString("select " + picked + ";label off");\r
- atomsPicked.removeElement(picked);\r
- }\r
- jmolHistory(true);\r
- // TODO: in application this happens\r
- //\r
- // if (scriptWindow != null)\r
- // {\r
- // scriptWindow.sendConsoleMessage(strInfo);\r
- // scriptWindow.sendConsoleMessage("\n");\r
- // }\r
-\r
- }\r
-\r
- @Override\r
- public void notifyCallback(EnumCallback type, Object[] data)\r
- {\r
- try\r
- {\r
- switch (type)\r
- {\r
- case LOADSTRUCT:\r
- notifyFileLoaded((String) data[1], (String) data[2],\r
- (String) data[3], (String) data[4],\r
- ((Integer) data[5]).intValue());\r
-\r
- break;\r
- case PICK:\r
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],\r
- (String) data[0]);\r
- // also highlight in alignment\r
- case HOVER:\r
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],\r
- (String) data[0]);\r
- break;\r
- case SCRIPT:\r
- notifyScriptTermination((String) data[2],\r
- ((Integer) data[3]).intValue());\r
- break;\r
- case ECHO:\r
- sendConsoleEcho((String) data[1]);\r
- break;\r
- case MESSAGE:\r
- sendConsoleMessage((data == null) ? ((String) null)\r
- : (String) data[1]);\r
- break;\r
- case ERROR:\r
- // System.err.println("Ignoring error callback.");\r
- break;\r
- case SYNC:\r
- case RESIZE:\r
- refreshGUI();\r
- break;\r
- case MEASURE:\r
-\r
- case CLICK:\r
- default:\r
- System.err.println("Unhandled callback " + type + " "\r
- + data[1].toString());\r
- break;\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err.println("Squashed Jmol callback handler error:");\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- @Override\r
- public boolean notifyEnabled(EnumCallback callbackPick)\r
- {\r
- switch (callbackPick)\r
- {\r
- case ECHO:\r
- case LOADSTRUCT:\r
- case MEASURE:\r
- case MESSAGE:\r
- case PICK:\r
- case SCRIPT:\r
- case HOVER:\r
- case ERROR:\r
- return true;\r
- case RESIZE:\r
- case SYNC:\r
- case CLICK:\r
- case ANIMFRAME:\r
- case MINIMIZATION:\r
- }\r
- return false;\r
- }\r
-\r
- // incremented every time a load notification is successfully handled -\r
- // lightweight mechanism for other threads to detect when they can start\r
- // referrring to new structures.\r
- private long loadNotifiesHandled = 0;\r
-\r
- public long getLoadNotifiesHandled()\r
- {\r
- return loadNotifiesHandled;\r
- }\r
-\r
- public void notifyFileLoaded(String fullPathName, String fileName2,\r
- String modelName, String errorMsg, int modelParts)\r
- {\r
- if (errorMsg != null)\r
- {\r
- fileLoadingError = errorMsg;\r
- refreshGUI();\r
- return;\r
- }\r
- // TODO: deal sensibly with models loaded inLine:\r
- // modelName will be null, as will fullPathName.\r
-\r
- // the rest of this routine ignores the arguments, and simply interrogates\r
- // the Jmol view to find out what structures it contains, and adds them to\r
- // the structure selection manager.\r
- fileLoadingError = null;\r
- String[] oldmodels = modelFileNames;\r
- modelFileNames = null;\r
- chainNames = new Vector();\r
- chainFile = new Hashtable();\r
- boolean notifyLoaded = false;\r
- String[] modelfilenames = getPdbFile();\r
- // first check if we've lost any structures\r
- if (oldmodels != null && oldmodels.length > 0)\r
- {\r
- int oldm = 0;\r
- for (int i = 0; i < oldmodels.length; i++)\r
- {\r
- for (int n = 0; n < modelfilenames.length; n++)\r
- {\r
- if (modelfilenames[n] == oldmodels[i])\r
- {\r
- oldmodels[i] = null;\r
- break;\r
- }\r
- }\r
- if (oldmodels[i] != null)\r
- {\r
- oldm++;\r
- }\r
- }\r
- if (oldm > 0)\r
- {\r
- String[] oldmfn = new String[oldm];\r
- oldm = 0;\r
- for (int i = 0; i < oldmodels.length; i++)\r
- {\r
- if (oldmodels[i] != null)\r
- {\r
- oldmfn[oldm++] = oldmodels[i];\r
- }\r
- }\r
- // deregister the Jmol instance for these structures - we'll add\r
- // ourselves again at the end for the current structure set.\r
- ssm.removeStructureViewerListener(this, oldmfn);\r
- }\r
- }\r
- refreshPdbEntries();\r
- for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)\r
- {\r
- String fileName = modelfilenames[modelnum];\r
- boolean foundEntry = false;\r
- MCview.PDBfile pdb = null;\r
- String pdbfile = null, pdbfhash = null;\r
- // model was probably loaded inline - so check the pdb file hashcode\r
- if (loadedInline)\r
- {\r
- // calculate essential attributes for the pdb data imported inline.\r
- // prolly need to resolve modelnumber properly - for now just use our\r
- // 'best guess'\r
- pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])\r
- + ".0", "PDB");\r
- pdbfhash = "" + pdbfile.hashCode();\r
- }\r
- if (pdbentry != null)\r
- {\r
- // search pdbentries and sequences to find correct pdbentry for this\r
- // model\r
- for (int pe = 0; pe < pdbentry.length; pe++)\r
- {\r
- boolean matches = false;\r
- if (fileName == null)\r
- {\r
- if (false)\r
- // see JAL-623 - need method of matching pasted data up\r
- {\r
- pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,\r
- AppletFormatAdapter.PASTE);\r
- pdbentry[modelnum].setFile("INLINE" + pdb.id);\r
- matches = true;\r
- foundEntry = true;\r
- }\r
- }\r
- else\r
- {\r
- if (matches = pdbentry[pe].getFile().equals(fileName))\r
- {\r
- foundEntry = true;\r
- // TODO: Jmol can in principle retrieve from CLASSLOADER but\r
- // this\r
- // needs\r
- // to be tested. See mantis bug\r
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605\r
- String protocol = AppletFormatAdapter.URL;\r
- try\r
- {\r
- File fl = new java.io.File(pdbentry[pe].getFile());\r
- if (fl.exists())\r
- {\r
- protocol = AppletFormatAdapter.FILE;\r
- }\r
- } catch (Exception e)\r
- {\r
- } catch (Error e)\r
- {\r
- }\r
- ;\r
- pdb = ssm.setMapping(sequence[pe], chains[pe],\r
- pdbentry[pe].getFile(), protocol);\r
-\r
- }\r
- }\r
- if (matches)\r
- {\r
- // add an entry for every chain in the model\r
- for (int i = 0; i < pdb.chains.size(); i++)\r
- {\r
- String chid = new String(pdb.id + ":"\r
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);\r
- chainFile.put(chid, pdbentry[pe].getFile());\r
- chainNames.addElement(chid);\r
- }\r
- notifyLoaded = true;\r
- }\r
- }\r
- }\r
- if (!foundEntry && associateNewStructs)\r
- {\r
- // this is a foreign pdb file that jalview doesn't know about - add\r
- // it to the dataset and try to find a home - either on a matching\r
- // sequence or as a new sequence.\r
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",\r
- "PDB");\r
- // parse pdb file into a chain, etc.\r
- // locate best match for pdb in associated views and add mapping to\r
- // ssm\r
- // if properly registered then\r
- notifyLoaded = true;\r
-\r
- }\r
- }\r
- // FILE LOADED OK\r
- // so finally, update the jmol bits and pieces\r
- if (jmolpopup != null)\r
- {\r
- // potential for deadlock here:\r
- // jmolpopup.updateComputedMenus();\r
- }\r
- if (!isLoadingFromArchive())\r
- {\r
- viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");\r
- }\r
- // register ourselves as a listener and notify the gui that it needs to\r
- // update itself.\r
- ssm.addStructureViewerListener(this);\r
- if (notifyLoaded)\r
- {\r
- FeatureRenderer fr = getFeatureRenderer(null);\r
- if (fr != null)\r
- {\r
- fr.featuresAdded();\r
- }\r
- refreshGUI();\r
- loadNotifiesHandled++;\r
- }\r
- setLoadingFromArchive(false);\r
- }\r
-\r
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)\r
- {\r
- notifyAtomPicked(iatom, strMeasure, null);\r
- }\r
-\r
- public abstract void notifyScriptTermination(String strStatus,\r
- int msWalltime);\r
-\r
- /**\r
- * display a message echoed from the jmol viewer\r
- * \r
- * @param strEcho\r
- */\r
- public abstract void sendConsoleEcho(String strEcho); /*\r
- * { showConsole(true);\r
- * \r
- * history.append("\n" +\r
- * strEcho); }\r
- */\r
-\r
- // /End JmolStatusListener\r
- // /////////////////////////////\r
-\r
- /**\r
- * @param strStatus\r
- * status message - usually the response received after a script\r
- * executed\r
- */\r
- public abstract void sendConsoleMessage(String strStatus);\r
-\r
- public void setCallbackFunction(String callbackType,\r
- String callbackFunction)\r
- {\r
- System.err.println("Ignoring set-callback request to associate "\r
- + callbackType + " with function " + callbackFunction);\r
-\r
- }\r
-\r
- public void setJalviewColourScheme(ColourSchemeI cs)\r
- {\r
- colourBySequence = false;\r
-\r
- if (cs == null)\r
- return;\r
-\r
- String res;\r
- int index;\r
- Color col;\r
- jmolHistory(false);\r
- // TODO: Switch between nucleotide or aa selection expressions\r
- Enumeration en = ResidueProperties.aa3Hash.keys();\r
- StringBuffer command = new StringBuffer("select *;color white;");\r
- while (en.hasMoreElements())\r
- {\r
- res = en.nextElement().toString();\r
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();\r
- if (index > 20)\r
- continue;\r
-\r
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));\r
-\r
- command.append("select " + res + ";color[" + col.getRed() + ","\r
- + col.getGreen() + "," + col.getBlue() + "];");\r
- }\r
-\r
- evalStateCommand(command.toString());\r
- jmolHistory(true);\r
- }\r
-\r
- public void showHelp()\r
- {\r
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");\r
- }\r
-\r
- /**\r
- * open the URL somehow\r
- * \r
- * @param target\r
- */\r
- public abstract void showUrl(String url, String target);\r
-\r
- /**\r
- * called when the binding thinks the UI needs to be refreshed after a Jmol\r
- * state change. this could be because structures were loaded, or because an\r
- * error has occured.\r
- */\r
- public abstract void refreshGUI();\r
-\r
- /**\r
- * called to show or hide the associated console window container.\r
- * \r
- * @param show\r
- */\r
- public abstract void showConsole(boolean show);\r
-\r
- /**\r
- * @param renderPanel\r
- * @param jmolfileio\r
- * - when true will initialise jmol's file IO system (should be false\r
- * in applet context)\r
- * @param htmlName\r
- * @param documentBase\r
- * @param codeBase\r
- * @param commandOptions\r
- */\r
- public void allocateViewer(Container renderPanel, boolean jmolfileio,\r
- String htmlName, URL documentBase, URL codeBase,\r
- String commandOptions)\r
- {\r
- allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,\r
- codeBase, commandOptions, null, null);\r
- }\r
-\r
- /**\r
- * \r
- * @param renderPanel\r
- * @param jmolfileio\r
- * - when true will initialise jmol's file IO system (should be false\r
- * in applet context)\r
- * @param htmlName\r
- * @param documentBase\r
- * @param codeBase\r
- * @param commandOptions\r
- * @param consolePanel\r
- * - panel to contain Jmol console\r
- * @param buttonsToShow\r
- * - buttons to show on the console, in ordr\r
- */\r
- public void allocateViewer(Container renderPanel, boolean jmolfileio,\r
- String htmlName, URL documentBase, URL codeBase,\r
- String commandOptions, final Container consolePanel,\r
- String buttonsToShow)\r
- {\r
- if (commandOptions==null) {
- commandOptions="";
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.jmol;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.io.File;
+import java.net.URL;
+import java.security.AccessControlException;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import javajs.awt.Dimension;
+
+import org.jmol.adapter.smarter.SmarterJmolAdapter;
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolSelectionListener;
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.c.CBK;
+import org.jmol.script.T;
+import org.jmol.viewer.JC;
+import org.jmol.viewer.Viewer;
+
+public abstract class JalviewJmolBinding extends AAStructureBindingModel
+ implements JmolStatusListener, JmolSelectionListener,
+ ComponentListener
+{
+ boolean allChainsSelected = false;
+
+ /*
+ * when true, try to search the associated datamodel for sequences that are
+ * associated with any unknown structures in the Jmol view.
+ */
+ private boolean associateNewStructs = false;
+
+ Vector<String> atomsPicked = new Vector<String>();
+
+ public Vector<String> chainNames;
+
+ Hashtable<String, String> chainFile;
+
+ public String fileLoadingError;
+
+ /*
+ * the default or current model displayed if the model cannot be identified
+ * from the selection message
+ */
+ int frameNo = 0;
+
+ // protected JmolGenericPopup jmolpopup; // not used - remove?
+
+ String lastCommand;
+
+ String lastMessage;
+
+ boolean loadedInline;
+
+ /**
+ * current set of model filenames loaded in the Jmol instance
+ */
+ String[] modelFileNames = null;
+
+ StringBuffer resetLastRes = new StringBuffer();
+
+ public Viewer viewer;
+
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
+ /*
+ * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
+ * "jalviewJmol", ap.av.applet .getDocumentBase(),
+ * ap.av.applet.getCodeBase(), "", this);
+ *
+ * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+ */
+ }
+
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ SequenceI[][] seqs, Viewer theViewer)
+ {
+ super(ssm, seqs);
+
+ viewer = theViewer;
+ viewer.setJmolStatusListener(this);
+ viewer.addSelectionListener(this);
+ }
+
+ /**
+ * construct a title string for the viewer window based on the data jalview
+ * knows about
+ *
+ * @return
+ */
+ public String getViewerTitle()
+ {
+ return getViewerTitle("Jmol", true);
+ }
+
+ /**
+ * prepare the view for a given set of models/chains. chainList contains
+ * strings of the form 'pdbfilename:Chaincode'
+ *
+ * @param chainList
+ * list of chains to make visible
+ */
+ public void centerViewer(Vector<String> chainList)
+ {
+ StringBuilder cmd = new StringBuilder(128);
+ int mlength, p;
+ for (String lbl : chainList)
+ {
+ mlength = 0;
+ do
+ {
+ p = mlength;
+ mlength = lbl.indexOf(":", p);
+ } while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
+ cmd.append(":" + lbl.substring(mlength + 1) + " /"
+ + (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
- viewer = JmolViewer.allocateViewer(renderPanel,\r
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName\r
- + ((Object) this).toString(), documentBase, codeBase,\r
- commandOptions, this);\r
-\r
- console = createJmolConsole(viewer, consolePanel, buttonsToShow);\r
- if (consolePanel != null)\r
- {\r
- consolePanel.addComponentListener(this);\r
-\r
- }\r
-\r
- }\r
-\r
- protected abstract JmolAppConsoleInterface createJmolConsole(\r
- JmolViewer viewer2, Container consolePanel, String buttonsToShow);\r
-\r
- protected org.jmol.api.JmolAppConsoleInterface console = null;\r
-\r
- public void componentResized(ComponentEvent e)\r
- {\r
-\r
- }\r
-\r
- public void componentMoved(ComponentEvent e)\r
- {\r
-\r
- }\r
-\r
- public void componentShown(ComponentEvent e)\r
- {\r
- showConsole(true);\r
- }\r
-\r
- public void componentHidden(ComponentEvent e)\r
- {\r
- showConsole(false);\r
- }\r
-\r
- public void setLoadingFromArchive(boolean loadingFromArchive)\r
- {\r
- this.loadingFromArchive = loadingFromArchive;\r
- }\r
-\r
- public boolean isLoadingFromArchive()\r
- {\r
- return loadingFromArchive;\r
- }\r
-\r
- public void setBackgroundColour(java.awt.Color col)\r
- {\r
- jmolHistory(false);\r
- viewer.evalStringQuiet("background [" + col.getRed() + ","\r
- + col.getGreen() + "," + col.getBlue() + "];");\r
- jmolHistory(true);\r
- }\r
-\r
- /**\r
- * add structures and any known sequence associations\r
- * \r
- * @returns the pdb entries added to the current set.\r
- */\r
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,\r
- SequenceI[][] seq, String[][] chns)\r
- {\r
- int pe = -1;\r
- Vector v = new Vector();\r
- Vector rtn = new Vector();\r
- for (int i = 0; i < pdbentry.length; i++)\r
- {\r
- v.addElement(pdbentry[i]);\r
- }\r
- for (int i = 0; i < pdbe.length; i++)\r
- {\r
- int r = v.indexOf(pdbe[i]);\r
- if (r == -1 || r >= pdbentry.length)\r
- {\r
- rtn.addElement(new int[]\r
- { v.size(), i });\r
- v.addElement(pdbe[i]);\r
- }\r
- else\r
- {\r
- // just make sure the sequence/chain entries are all up to date\r
- addSequenceAndChain(r, seq[i], chns[i]);\r
- }\r
- }\r
- pdbe = new PDBEntry[v.size()];\r
- v.copyInto(pdbe);\r
- pdbentry = pdbe;\r
- if (rtn.size() > 0)\r
- {\r
- // expand the tied seuqence[] and string[] arrays\r
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];\r
- String[][] sch = new String[pdbentry.length][];\r
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);\r
- System.arraycopy(chains, 0, sch, 0, this.chains.length);\r
- sequence = sqs;\r
- chains = sch;\r
- pdbe = new PDBEntry[rtn.size()];\r
- for (int r = 0; r < pdbe.length; r++)\r
- {\r
- int[] stri = ((int[]) rtn.elementAt(r));\r
- // record the pdb file as a new addition\r
- pdbe[r] = pdbentry[stri[0]];\r
- // and add the new sequence/chain entries\r
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);\r
- }\r
- }\r
- else\r
- {\r
- pdbe = null;\r
- }\r
- return pdbe;\r
- }\r
-\r
- public void addSequence(int pe, SequenceI[] seq)\r
- {\r
- // add sequences to the pe'th pdbentry's seuqence set.\r
- addSequenceAndChain(pe, seq, null);\r
- }\r
-\r
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)\r
- {\r
- if (pe < 0 || pe >= pdbentry.length)\r
- {\r
- throw new Error(\r
- "Implementation error - no corresponding pdbentry (for index "\r
- + pe + ") to add sequences mappings to");\r
- }\r
- final String nullChain = "TheNullChain";\r
- Vector s = new Vector();\r
- Vector c = new Vector();\r
- if (chains == null)\r
- {\r
- chains = new String[pdbentry.length][];\r
- }\r
- if (sequence[pe] != null)\r
- {\r
- for (int i = 0; i < sequence[pe].length; i++)\r
- {\r
- s.addElement(sequence[pe][i]);\r
- if (chains[pe] != null)\r
- {\r
- if (i < chains[pe].length)\r
- {\r
- c.addElement(chains[pe][i]);\r
- }\r
- else\r
- {\r
- c.addElement(nullChain);\r
- }\r
- }\r
- else\r
- {\r
- if (tchain != null && tchain.length > 0)\r
- {\r
- c.addElement(nullChain);\r
- }\r
- }\r
- }\r
- }\r
- for (int i = 0; i < seq.length; i++)\r
- {\r
- if (!s.contains(seq[i]))\r
- {\r
- s.addElement(seq[i]);\r
- if (tchain != null && i < tchain.length)\r
- {\r
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);\r
- }\r
- }\r
- }\r
- SequenceI[] tmp = new SequenceI[s.size()];\r
- s.copyInto(tmp);\r
- sequence[pe] = tmp;\r
- if (c.size() > 0)\r
- {\r
- String[] tch = new String[c.size()];\r
- c.copyInto(tch);\r
- for (int i = 0; i < tch.length; i++)\r
- {\r
- if (tch[i] == nullChain)\r
- {\r
- tch[i] = null;\r
- }\r
- }\r
- chains[pe] = tch;\r
- }\r
- else\r
- {\r
- chains[pe] = null;\r
- }\r
- }\r
- /**\r
- * \r
- * @param pdbfile\r
- * @return text report of alignment between pdbfile and any associated alignment sequences\r
- */\r
- public String printMapping(String pdbfile)\r
- {\r
- return ssm.printMapping(pdbfile);\r
- }\r
- @Override\r
- public void resizeInnerPanel(String data)\r
- {\r
- // Jalview doesn't honour resize panel requests\r
- \r
- }\r
-}\r
+ if (cmd.length() > 0)
+ {
+ cmd.setLength(cmd.length() - 4);
+ }
+ evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
+ }
+
+ public void closeViewer()
+ {
+ viewer.acm.setModeMouse(JC.MOUSE_NONE);
+ // remove listeners for all structures in viewer
+ getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ // and shut down jmol
+ viewer.evalStringQuiet("zap");
+ viewer.setJmolStatusListener(null);
+ lastCommand = null;
+ viewer = null;
+ releaseUIResources();
+ }
+
+ public void colourByChain()
+ {
+ colourBySequence = false;
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
+ // TODO: http://issues.jalview.org/browse/JAL-628
+ evalStateCommand("select *;color chain");
+ }
+
+ public void colourByCharge()
+ {
+ colourBySequence = false;
+ evalStateCommand("select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions.
+ */
+ public void superposeStructures(AlignmentI alignment)
+ {
+ superposeStructures(alignment, -1, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure)
+ {
+ superposeStructures(alignment, refStructure, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ * @param hiddenCols
+ * TODO
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure,
+ ColumnSelection hiddenCols)
+ {
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
+ }
+
+ /**
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
+ *
+ * @param _alignment
+ * an array of alignments to process
+ * @param _refStructure
+ * an array of corresponding reference structures (index into pdb
+ * file array); if a negative value is passed, the first PDB file
+ * mapped to an alignment sequence is used as the reference for
+ * superposition
+ * @param _hiddenCols
+ * an array of corresponding hidden columns for each alignment
+ */
+ public void superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
+ {
+ }
+ ;
+ }
+ String[] files = getPdbFile();
+ if (!waitForFileLoad(files))
+ {
+ return;
+ }
+
+ StringBuilder selectioncom = new StringBuilder(256);
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
+ {
+ nSeconds = " 0.005 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ // nSeconds = " ";
+ // union of all aligned positions are collected together.
+ for (int a = 0; a < _alignment.length; a++)
+ {
+ int refStructure = _refStructure[a];
+ AlignmentI alignment = _alignment[a];
+ ColumnSelection hiddenCols = _hiddenCols[a];
+ if (a > 0
+ && selectioncom.length() > 0
+ && !selectioncom.substring(selectioncom.length() - 1).equals(
+ "|"))
+ {
+ selectioncom.append("|");
+ }
+ // process this alignment
+ if (refStructure >= files.length)
+ {
+ System.err.println("Invalid reference structure value "
+ + refStructure);
+ refStructure = -1;
+ }
+
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
+ boolean matched[] = new boolean[alignment.getWidth()];
+ for (int m = 0; m < matched.length; m++)
+ {
+ matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ }
+
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
+ {
+ structures[f] = new SuperposeData(alignment.getWidth());
+ }
+
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
+
+ String[] selcom = new String[files.length];
+ int nmatched = 0;
+ for (boolean b : matched)
+ {
+ if (b)
+ {
+ nmatched++;
+ }
+ }
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
+ {
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ String chainCd = ":" + structures[pdbfnum].chain;
+ int lpos = -1;
+ boolean run = false;
+ StringBuilder molsel = new StringBuilder();
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (matched[r])
+ {
+ int pdbResNo = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNo - 1)
+ {
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("|");
+ }
+ run = false;
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = pdbResNo;
+ }
+ }
+ /*
+ * add final selection phrase
+ */
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("((");
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum + 1);
+ selectioncom.append(".1)");
+ if (pdbfnum < files.length - 1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ else
+ {
+ selcom[pdbfnum] = null;
+ }
+ }
+ }
+ StringBuilder command = new StringBuilder(256);
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
+ {
+ continue;
+ }
+ command.append("echo ");
+ command.append("\"Superposing (");
+ command.append(structures[pdbfnum].pdbId);
+ command.append(") against reference (");
+ command.append(structures[refStructure].pdbId);
+ command.append(")\";\ncompare " + nSeconds);
+ command.append("{");
+ command.append(Integer.toString(1 + pdbfnum));
+ command.append(".1} {");
+ command.append(Integer.toString(1 + refStructure));
+ // conformation=1 excludes alternate locations for CA (JAL-1757)
+ command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
+
+ // for (int s = 0; s < 2; s++)
+ // {
+ // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ // }
+ command.append(selcom[pdbfnum]);
+ command.append(selcom[refStructure]);
+ command.append(" ROTATE TRANSLATE;\n");
+ }
+ if (selectioncom.length() > 0)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // selcom.append("; ribbons; ");
+ String cmdString = command.toString();
+ System.out.println("Superimpose command(s):\n" + cmdString);
+
+ evalStateCommand(cmdString);
+ }
+ }
+ if (selectioncom.length() > 0)
+ {// finally, mark all regions that were superposed.
+ if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+ {
+ selectioncom.setLength(selectioncom.length() - 1);
+ }
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+ }
+ }
+
+ public void evalStateCommand(String command)
+ {
+ jmolHistory(false);
+ if (lastCommand == null || !lastCommand.equals(command))
+ {
+ viewer.evalStringQuiet(command + "\n");
+ }
+ jmolHistory(true);
+ lastCommand = command;
+ }
+
+ /**
+ * colour any structures associated with sequences in the given alignment
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+ * if colourBySequence is enabled.
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv)
+ {
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (!colourBySequence || !isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ FeatureRenderer fr = null;
+ if (showFeatures)
+ {
+ fr = getFeatureRenderer(alignmentv);
+ }
+ AlignmentI alignment = alignmentv.getAlignment();
+
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
+ {
+ for (String cbyseq : cpdbbyseq.commands)
+ {
+ executeWhenReady(cbyseq);
+ }
+ }
+ }
+
+ /**
+ * @param files
+ * @param sr
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
+ {
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
+ }
+
+ /**
+ * @param command
+ */
+ protected void executeWhenReady(String command)
+ {
+ evalStateCommand(command);
+ }
+
+ public void createImage(String file, String type, int quality)
+ {
+ System.out.println("JMOL CREATE IMAGE");
+ }
+
+ public String createImage(String fileName, String type,
+ Object textOrBytes, int quality)
+ {
+ System.out.println("JMOL CREATE IMAGE");
+ return null;
+ }
+
+ public String eval(String strEval)
+ {
+ // System.out.println(strEval);
+ // "# 'eval' is implemented only for the applet.";
+ return null;
+ }
+
+ // End StructureListener
+ // //////////////////////////
+
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ return null;
+ }
+
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public Color getColour(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ if (getModelNum(pdbfile) < 0)
+ {
+ return null;
+ }
+ // TODO: verify atomIndex is selecting correct model.
+ // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
+ return new Color(colour);
+ }
+
+ /**
+ * returns the current featureRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
+
+ /**
+ * instruct the Jalview binding to update the pdbentries vector if necessary
+ * prior to matching the jmol view's contents to the list of structure files
+ * Jalview knows about.
+ */
+ public abstract void refreshPdbEntries();
+
+ private int getModelNum(String modelFileName)
+ {
+ String[] mfn = getPdbFile();
+ if (mfn == null)
+ {
+ return -1;
+ }
+ for (int i = 0; i < mfn.length; i++)
+ {
+ if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ /**
+ * map between index of model filename returned from getPdbFile and the first
+ * index of models from this file in the viewer. Note - this is not trimmed -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
+ // ////////////////////////////////
+ // /StructureListener
+ @Override
+ public synchronized String[] getPdbFile()
+ {
+ if (viewer == null)
+ {
+ return new String[0];
+ }
+ if (modelFileNames == null)
+ {
+ String mset[] = new String[viewer.ms.mc];
+ _modelFileNameMap = new int[mset.length];
+ String m = viewer.ms.getModelFileName(0);
+ if (m != null)
+ {
+ mset[0] = m;
+ try
+ {
+ mset[0] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet
+ System.err
+ .println("jmolBinding: Using local file string from Jmol: "
+ + m);
+ }
+ if (mset[0].indexOf("/file:") != -1)
+ {
+ // applet path with docroot - discard as format won't match pdbfile
+ mset[0] = m;
+ }
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
+ }
+ int j = 1;
+ for (int i = 1; i < mset.length; i++)
+ {
+ m = viewer.ms.getModelFileName(i);
+ mset[j] = m;
+ if (m != null)
+ {
+ try
+ {
+ mset[j] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ }
+ }
+ _modelFileNameMap[j] = i; // record the model index for the filename
+ // skip any additional models in the same file (NMR structures)
+ if ((mset[j] == null ? mset[j] != mset[j - 1]
+ : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+ {
+ j++;
+ }
+ }
+ modelFileNames = new String[j];
+ System.arraycopy(mset, 0, modelFileNames, 0, j);
+ }
+ return modelFileNames;
+ }
+
+ /**
+ * map from string to applet
+ */
+ @Override
+ public Map<String, Object> getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
+
+ // ///////////////////////////////
+ // JmolStatusListener
+
+ public void handlePopupMenu(int x, int y)
+ {
+ // jmolpopup.show(x, y);
+ // jmolpopup.jpiShow(x, y);
+ }
+
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ if (atoms != null)
+ {
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
+ }
+
+ // jmol/ssm only
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ if (modelFileNames == null)
+ {
+ return;
+ }
+
+ // look up file model number for this pdbfile
+ int mdlNum = 0;
+ // may need to adjust for URLencoding here - we don't worry about that yet.
+ while (mdlNum < modelFileNames.length
+ && !pdbfile.equals(modelFileNames[mdlNum]))
+ {
+ mdlNum++;
+ }
+ if (mdlNum == modelFileNames.length)
+ {
+ return;
+ }
+
+ jmolHistory(false);
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return;
+ if (resetLastRes.length() > 0)
+ {
+ viewer.evalStringQuiet(resetLastRes.toString());
+ }
+
+ StringBuilder cmd = new StringBuilder(64);
+ cmd.append("select " + pdbResNum); // +modelNum
+
+ resetLastRes.setLength(0);
+ resetLastRes.append("select " + pdbResNum); // +modelNum
+
+ cmd.append(":");
+ resetLastRes.append(":");
+ if (!chain.equals(" "))
+ {
+ cmd.append(chain);
+ resetLastRes.append(chain);
+ }
+ {
+ cmd.append(" /" + (mdlNum + 1));
+ resetLastRes.append("/" + (mdlNum + 1));
+ }
+ cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
+
+ resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ + " and not hetero; spacefill 0;");
+
+ cmd.append("spacefill 200;select none");
+
+ viewer.evalStringQuiet(cmd.toString());
+ jmolHistory(true);
+
+ }
+
+ boolean debug = true;
+
+ private void jmolHistory(boolean enable)
+ {
+ viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+ }
+
+ public void loadInline(String string)
+ {
+ loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
+ viewer.openStringInline(string);
+ }
+
+ public void mouseOverStructure(int atomIndex, String strInfo)
+ {
+ int pdbResNum;
+ int alocsep = strInfo.indexOf("^");
+ int mdlSep = strInfo.indexOf("/");
+ int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
+
+ if (chainSeparator == -1)
+ {
+ chainSeparator = strInfo.indexOf(".");
+ if (mdlSep > -1 && mdlSep < chainSeparator)
+ {
+ chainSeparator1 = chainSeparator;
+ chainSeparator = mdlSep;
+ }
+ }
+ // handle insertion codes
+ if (alocsep != -1)
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, alocsep));
+
+ }
+ else
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, chainSeparator));
+ }
+ String chainId;
+
+ if (strInfo.indexOf(":") > -1)
+ {
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+ strInfo.indexOf("."));
+ }
+ else
+ {
+ chainId = " ";
+ }
+
+ String pdbfilename = modelFileNames[frameNo]; // default is first or current
+ // model
+ if (mdlSep > -1)
+ {
+ if (chainSeparator1 == -1)
+ {
+ chainSeparator1 = strInfo.indexOf(".", mdlSep);
+ }
+ String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
+ chainSeparator1) : strInfo.substring(mdlSep + 1);
+ try
+ {
+ // recover PDB filename for the model hovered over.
+ int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
+ .intValue() - 1;
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
+ if (pdbfilename == null)
+ {
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+ .getAbsolutePath();
+ }
+
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (lastMessage == null || !lastMessage.equals(strInfo))
+ {
+ getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ }
+
+ lastMessage = strInfo;
+ }
+
+ public void notifyAtomHovered(int atomIndex, String strInfo, String data)
+ {
+ if (data != null)
+ {
+ System.err.println("Ignoring additional hover info: " + data
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ }
+ mouseOverStructure(atomIndex, strInfo);
+ }
+
+ /*
+ * { if (history != null && strStatus != null &&
+ * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
+ * } }
+ */
+
+ public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ {
+ /**
+ * this implements the toggle label behaviour copied from the original
+ * structure viewer, MCView
+ */
+ if (strData != null)
+ {
+ System.err.println("Ignoring additional pick data string " + strData);
+ }
+ int chainSeparator = strInfo.indexOf(":");
+ int p = 0;
+ if (chainSeparator == -1)
+ {
+ chainSeparator = strInfo.indexOf(".");
+ }
+
+ String picked = strInfo.substring(strInfo.indexOf("]") + 1,
+ chainSeparator);
+ String mdlString = "";
+ if ((p = strInfo.indexOf(":")) > -1)
+ {
+ picked += strInfo.substring(p, strInfo.indexOf("."));
+ }
+
+ if ((p = strInfo.indexOf("/")) > -1)
+ {
+ mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
+ }
+ picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
+ + mdlString + "))";
+ jmolHistory(false);
+
+ if (!atomsPicked.contains(picked))
+ {
+ viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+ atomsPicked.addElement(picked);
+ }
+ else
+ {
+ viewer.evalString("select " + picked + ";label off");
+ atomsPicked.removeElement(picked);
+ }
+ jmolHistory(true);
+ // TODO: in application this happens
+ //
+ // if (scriptWindow != null)
+ // {
+ // scriptWindow.sendConsoleMessage(strInfo);
+ // scriptWindow.sendConsoleMessage("\n");
+ // }
+
+ }
+
+ @Override
+ public void notifyCallback(CBK type, Object[] data)
+ {
+ try
+ {
+ switch (type)
+ {
+ case LOADSTRUCT:
+ notifyFileLoaded((String) data[1], (String) data[2],
+ (String) data[3], (String) data[4],
+ ((Integer) data[5]).intValue());
+
+ break;
+ case PICK:
+ notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ // also highlight in alignment
+ case HOVER:
+ notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case ECHO:
+ sendConsoleEcho((String) data[1]);
+ break;
+ case MESSAGE:
+ sendConsoleMessage((data == null) ? ((String) null)
+ : (String) data[1]);
+ break;
+ case ERROR:
+ // System.err.println("Ignoring error callback.");
+ break;
+ case SYNC:
+ case RESIZE:
+ refreshGUI();
+ break;
+ case MEASURE:
+
+ case CLICK:
+ default:
+ System.err.println("Unhandled callback " + type + " "
+ + data[1].toString());
+ break;
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Squashed Jmol callback handler error:");
+ e.printStackTrace();
+ }
+ }
+
+ @Override
+ public boolean notifyEnabled(CBK callbackPick)
+ {
+ switch (callbackPick)
+ {
+ case ECHO:
+ case LOADSTRUCT:
+ case MEASURE:
+ case MESSAGE:
+ case PICK:
+ case SCRIPT:
+ case HOVER:
+ case ERROR:
+ return true;
+ default:
+ return false;
+ }
+ }
+
+ // incremented every time a load notification is successfully handled -
+ // lightweight mechanism for other threads to detect when they can start
+ // referrring to new structures.
+ private long loadNotifiesHandled = 0;
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
+ }
+
+ public void notifyFileLoaded(String fullPathName, String fileName2,
+ String modelName, String errorMsg, int modelParts)
+ {
+ if (errorMsg != null)
+ {
+ fileLoadingError = errorMsg;
+ refreshGUI();
+ return;
+ }
+ // TODO: deal sensibly with models loaded inLine:
+ // modelName will be null, as will fullPathName.
+
+ // the rest of this routine ignores the arguments, and simply interrogates
+ // the Jmol view to find out what structures it contains, and adds them to
+ // the structure selection manager.
+ fileLoadingError = null;
+ String[] oldmodels = modelFileNames;
+ modelFileNames = null;
+ chainNames = new Vector<String>();
+ chainFile = new Hashtable<String, String>();
+ boolean notifyLoaded = false;
+ String[] modelfilenames = getPdbFile();
+ // first check if we've lost any structures
+ if (oldmodels != null && oldmodels.length > 0)
+ {
+ int oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ for (int n = 0; n < modelfilenames.length; n++)
+ {
+ if (modelfilenames[n] == oldmodels[i])
+ {
+ oldmodels[i] = null;
+ break;
+ }
+ }
+ if (oldmodels[i] != null)
+ {
+ oldm++;
+ }
+ }
+ if (oldm > 0)
+ {
+ String[] oldmfn = new String[oldm];
+ oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ if (oldmodels[i] != null)
+ {
+ oldmfn[oldm++] = oldmodels[i];
+ }
+ }
+ // deregister the Jmol instance for these structures - we'll add
+ // ourselves again at the end for the current structure set.
+ getSsm().removeStructureViewerListener(this, oldmfn);
+ }
+ }
+ refreshPdbEntries();
+ for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
+ {
+ String fileName = modelfilenames[modelnum];
+ boolean foundEntry = false;
+ MCview.PDBfile pdb = null;
+ String pdbfile = null;
+ // model was probably loaded inline - so check the pdb file hashcode
+ if (loadedInline)
+ {
+ // calculate essential attributes for the pdb data imported inline.
+ // prolly need to resolve modelnumber properly - for now just use our
+ // 'best guess'
+ pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ + ".0", "PDB");
+ }
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < getPdbCount(); pe++)
+ {
+ boolean matches = false;
+ if (fileName == null)
+ {
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
+ {
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ pdbfile, AppletFormatAdapter.PASTE);
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+ matches = true;
+ foundEntry = true;
+ }
+ }
+ else
+ {
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
+ {
+ foundEntry = true;
+ // TODO: Jmol can in principle retrieve from CLASSLOADER but
+ // this
+ // needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ String protocol = AppletFormatAdapter.URL;
+ try
+ {
+ if (fl.exists())
+ {
+ protocol = AppletFormatAdapter.FILE;
+ }
+ } catch (Exception e)
+ {
+ } catch (Error e)
+ {
+ }
+ // Explicitly map to the filename used by Jmol ;
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ fileName, protocol);
+ // pdbentry[pe].getFile(), protocol);
+
+ }
+ }
+ if (matches)
+ {
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+ String chid = new String(pdb.id + ":"
+ + pdb.chains.elementAt(i).id);
+ chainFile.put(chid, fileName);
+ chainNames.addElement(chid);
+ }
+ notifyLoaded = true;
+ }
+ }
+
+ if (!foundEntry && associateNewStructs)
+ {
+ // this is a foreign pdb file that jalview doesn't know about - add
+ // it to the dataset and try to find a home - either on a matching
+ // sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ // if properly registered then
+ notifyLoaded = true;
+
+ }
+ }
+ // FILE LOADED OK
+ // so finally, update the jmol bits and pieces
+ // if (jmolpopup != null)
+ // {
+ // // potential for deadlock here:
+ // // jmolpopup.updateComputedMenus();
+ // }
+ if (!isLoadingFromArchive())
+ {
+ viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ }
+ // register ourselves as a listener and notify the gui that it needs to
+ // update itself.
+ getSsm().addStructureViewerListener(this);
+ if (notifyLoaded)
+ {
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+ refreshGUI();
+ loadNotifiesHandled++;
+ }
+ setLoadingFromArchive(false);
+ }
+
+ public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
+ {
+ notifyAtomPicked(iatom, strMeasure, null);
+ }
+
+ public abstract void notifyScriptTermination(String strStatus,
+ int msWalltime);
+
+ /**
+ * display a message echoed from the jmol viewer
+ *
+ * @param strEcho
+ */
+ public abstract void sendConsoleEcho(String strEcho); /*
+ * { showConsole(true);
+ *
+ * history.append("\n" +
+ * strEcho); }
+ */
+
+ // /End JmolStatusListener
+ // /////////////////////////////
+
+ /**
+ * @param strStatus
+ * status message - usually the response received after a script
+ * executed
+ */
+ public abstract void sendConsoleMessage(String strStatus);
+
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ System.err.println("Ignoring set-callback request to associate "
+ + callbackType + " with function " + callbackFunction);
+
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ colourBySequence = false;
+
+ if (cs == null)
+ {
+ return;
+ }
+
+ jmolHistory(false);
+ StringBuilder command = new StringBuilder(128);
+ command.append("select *;color white;");
+ List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
+ {
+ Color col = cs.findColour(res.charAt(0));
+ command.append("select " + res + ";color[" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
+ }
+
+ evalStateCommand(command.toString());
+ jmolHistory(true);
+ }
+
+ public void showHelp()
+ {
+ showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ }
+
+ /**
+ * open the URL somehow
+ *
+ * @param target
+ */
+ public abstract void showUrl(String url, String target);
+
+ /**
+ * called when the binding thinks the UI needs to be refreshed after a Jmol
+ * state change. this could be because structures were loaded, or because an
+ * error has occured.
+ */
+ public abstract void refreshGUI();
+
+ /**
+ * called to show or hide the associated console window container.
+ *
+ * @param show
+ */
+ public abstract void showConsole(boolean show);
+
+ /**
+ * @param renderPanel
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
+ * @param htmlName
+ * @param documentBase
+ * @param codeBase
+ * @param commandOptions
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
+ {
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
+ }
+
+ /**
+ *
+ * @param renderPanel
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
+ * @param htmlName
+ * @param documentBase
+ * @param codeBase
+ * @param commandOptions
+ * @param consolePanel
+ * - panel to contain Jmol console
+ * @param buttonsToShow
+ * - buttons to show on the console, in ordr
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
+ {
+ if (commandOptions == null)
+ {
+ commandOptions = "";
+ }
+ viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
+ commandOptions, this);
+
+ viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
+ }
+
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow);
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+ public void setBackgroundColour(java.awt.Color col)
+ {
+ jmolHistory(false);
+ viewer.evalStringQuiet("background [" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
+ jmolHistory(true);
+ }
+
+ @Override
+ public Dimension resizeInnerPanel(String data)
+ {
+ // Jalview doesn't honour resize panel requests
+ return null;
+ }
+
+ /**
+ *
+ */
+ protected void closeConsole()
+ {
+ if (console != null)
+ {
+ try
+ {
+ console.setVisible(false);
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
+ }
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentMoved(ComponentEvent e)
+ {
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentResized(ComponentEvent e)
+ {
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff