--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 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.varna;\r
+\r
+import java.io.File;\r
+import java.net.URL;\r
+import java.util.*;\r
+import java.applet.Applet;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.JPanel;\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.*;\r
+import jalview.structure.*;\r
+import jalview.io.*;\r
+\r
+import org.jmol.api.*;\r
+import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
+\r
+import org.jmol.popup.*;\r
+import org.jmol.viewer.JmolConstants;\r
+import org.jmol.viewer.Viewer;\r
+\r
+import jalview.schemes.*;\r
+\r
+public abstract class JalviewVarnaBinding 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 JalviewVarnaBinding(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 JalviewVarnaBinding(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 (String cbyseq : VarnaCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment)) {\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
+ public void notifyCallback(int type, Object[] data)\r
+ {\r
+ try\r
+ {\r
+ switch (type)\r
+ {\r
+ case JmolConstants.CALLBACK_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 JmolConstants.CALLBACK_PICK:\r
+ notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],\r
+ (String) data[0]);\r
+ // also highlight in alignment\r
+ case JmolConstants.CALLBACK_HOVER:\r
+ notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],\r
+ (String) data[0]);\r
+ break;\r
+ case JmolConstants.CALLBACK_SCRIPT:\r
+ notifyScriptTermination((String) data[2],\r
+ ((Integer) data[3]).intValue());\r
+ break;\r
+ case JmolConstants.CALLBACK_ECHO:\r
+ sendConsoleEcho((String) data[1]);\r
+ break;\r
+ case JmolConstants.CALLBACK_MESSAGE:\r
+ sendConsoleMessage((data == null) ? ((String) null)\r
+ : (String) data[1]);\r
+ break;\r
+ case JmolConstants.CALLBACK_ERROR:\r
+ // System.err.println("Ignoring error callback.");\r
+ break;\r
+ case JmolConstants.CALLBACK_SYNC:\r
+ case JmolConstants.CALLBACK_RESIZE:\r
+ refreshGUI();\r
+ break;\r
+ case JmolConstants.CALLBACK_MEASURE:\r
+\r
+ case JmolConstants.CALLBACK_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
+ public boolean notifyEnabled(int callbackPick)\r
+ {\r
+ switch (callbackPick)\r
+ {\r
+ case JmolConstants.CALLBACK_ECHO:\r
+ case JmolConstants.CALLBACK_LOADSTRUCT:\r
+ case JmolConstants.CALLBACK_MEASURE:\r
+ case JmolConstants.CALLBACK_MESSAGE:\r
+ case JmolConstants.CALLBACK_PICK:\r
+ case JmolConstants.CALLBACK_SCRIPT:\r
+ case JmolConstants.CALLBACK_HOVER:\r
+ case JmolConstants.CALLBACK_ERROR:\r
+ return true;\r
+ case JmolConstants.CALLBACK_RESIZE:\r
+ case JmolConstants.CALLBACK_SYNC:\r
+ case JmolConstants.CALLBACK_CLICK:\r
+ case JmolConstants.CALLBACK_ANIMFRAME:\r
+ case JmolConstants.CALLBACK_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
+ pdbentry[pe].setId(pdb.id);\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="";
+ }
+ 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
+\r
+}\r
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+import java.awt.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import java.awt.event.*;
+import java.io.*;
+
+import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.structure.*;
+import jalview.datamodel.PDBEntry;
+import jalview.io.*;
+import jalview.schemes.*;
+
+public class AppVarna extends GStructureViewer implements Runnable,
+ SequenceStructureBinding, ViewSetProvider
+
+{
+ AppJmolBinding jmb;
+
+ JPanel scriptWindow;
+
+ JSplitPane splitPane;
+
+ RenderPanel renderPanel;
+
+ AlignmentPanel ap;
+
+ Vector atomsPicked = new Vector();
+
+ private boolean addingStructures = false;
+
+ /**
+ *
+ * @param file
+ * @param id
+ * @param seq
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+ */
+ public AppVarna(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds)
+ {
+ this(file, id, seq, ap, loadStatus, bounds, null);
+ }
+
+ /**
+ * @deprecated
+ */
+ public AppVarna(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,
+ String viewid)
+ {
+ this(new String[]
+ { file }, new String[]
+ { id }, new SequenceI[][]
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
+ }
+
+ ViewSelectionMenu seqColourBy;
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppVarna(String[] files, String[] ids, SequenceI[][] seqs,
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol,
+ String loadStatus, Rectangle bounds, String viewid)
+ {
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ PDBEntry pdbentry = new PDBEntry();
+ pdbentry.setFile(files[i]);
+ pdbentry.setId(ids[i]);
+ pdbentrys[i] = pdbentry;
+ }
+ // / TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ jmolColour.setSelected(true);
+ }
+ if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ jmolColour.setSelected(false);
+ }
+ this.setBounds(bounds);
+ initMenus();
+ viewId = viewid;
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+ // bounds.width,bounds.height);
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+
+ }
+
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith==null)
+ {
+ _colourwith=new Vector<AlignmentPanel>();
+ }
+ if (_alignwith==null)
+ {
+ _alignwith=new Vector<AlignmentPanel>();
+ }
+
+ seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the jmol display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText("Align structures using "
+ + _alignwith.size() + " linked alignment views");
+ }
+ });
+ handler.itemStateChanged(null);
+ jmolActionMenu.add(alpanels);
+ jmolActionMenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+ }
+ IProgressIndicator progressBar = null;
+
+ public AppVarna(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap)
+ {
+ progressBar = ap.alignFrame;
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
+ String alreadyMapped = jmb.ssm.alreadyMappedToFile(
+ pdbentry.getId());
+
+ if (alreadyMapped != null)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ pdbentry.getId() + " is already displayed."
+ + "\nDo you want to re-use this viewer ?",
+ "Map Sequences to Visible Window: " + pdbentry.getId(),
+ JOptionPane.YES_NO_OPTION);
+
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jmb.ssm.setMapping(seq, chains, alreadyMapped,
+ AppletFormatAdapter.FILE);
+ if (ap.seqPanel.seqCanvas.fr != null)
+ {
+ ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppVarna)
+ {
+ AppVarna topJmol = ((AppVarna) frames[i]);
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
+ {
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topJmol.jmb.addSequence(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ topJmol.buildJmolActionMenu();
+ break;
+ }
+ }
+ }
+ }
+
+ return;
+ }
+ }
+ // /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size() > 0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ AppVarna topJmol = (AppVarna) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "Do you want to add " + pdbentry.getId()
+ + " to the view called\n'" + topJmol.getTitle()
+ + "'\n", "Align to existing structure view",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
+
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+
+ if (pdbentry.getFile() != null)
+ {
+ initJmol("load \"" + pdbentry.getFile() + "\"");
+ }
+ else
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+ }
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+
+ }
+
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
+ {
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
+ {
+ t = new AlignmentPanel[list.length + panels.length];
+ System.arraycopy(list, 0, t, 0, list.length);
+ System.arraycopy(panels, 0, t, list.length, panels.length);
+ list = t;
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * list of alignment panels to use for superposition
+ */
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /**
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ /**
+ * set the primary alignmentPanel reference and add another alignPanel to the
+ * list of ones to use for colouring and aligning
+ *
+ * @param nap
+ */
+ public void addAlignmentPanel(AlignmentPanel nap)
+ {
+ if (ap == null)
+ {
+ ap = nap;
+ }
+ if (!_aps.contains(nap.av.getSequenceSetId()))
+ {
+ _aps.add(nap.av.getSequenceSetId());
+ }
+ }
+
+ /**
+ * remove any references held to the given alignment panel
+ *
+ * @param nap
+ */
+ public void removeAlignmentPanel(AlignmentPanel nap)
+ {
+ try
+ {
+ _alignwith.remove(nap);
+ _colourwith.remove(nap);
+ if (ap == nap)
+ {
+ ap = null;
+ for (AlignmentPanel aps : getAllAlignmentPanels())
+ {
+ if (aps != nap)
+ {
+ ap = aps;
+ break;
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ }
+ if (ap != null)
+ {
+ buildJmolActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _alignwith.remove(nap);
+ }
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+ {
+ useAlignmentPanelForColourbyseq(nap);
+ jmb.setColourBySequence(enableColourBySeq);
+ seqColour.setSelected(enableColourBySeq);
+ jmolColour.setSelected(!enableColourBySeq);
+ }
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param alignFrame
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+ final String[] chains, final boolean b,
+ final IProgressIndicator alignFrame)
+ {
+ if (pdbentry.getFile() == null)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
+
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = b;
+ progressBar = alignFrame; // visual indication happens on caller frame.
+ (worker = new Thread(this)).start();
+ return;
+ }
+
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols = new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppVarna)
+ {
+ AppVarna topJmol = ((AppVarna) frames[i]);
+ if (topJmol.isLinkedWith(ap2))
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
+ }
+
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
+ }
+ ;
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
+ jmb.newJmolPopup(true, "Jmol", true);
+ if (command==null)
+ {
+ command="";
+ }
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
+ }
+
+ void setChainMenuItems(Vector chains)
+ {
+ chainMenu.removeAll();
+ if (chains == null)
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem("All");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (int c = 0; c < chains.size(); c++)
+ {
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ centerViewer();
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
+ void centerViewer()
+ {
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.addElement(item.getText());
+ }
+ }
+ }
+ jmb.centerViewer(toshow);
+ }
+
+ void closeViewer()
+ {
+ jmb.closeViewer();
+ ap = null;
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
+ }
+
+ /**
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
+ public void run()
+ {
+ _started = true;
+ String pdbid = "";
+ // todo - record which pdbids were successfuly imported.
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
+ try
+ {
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ {
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.pdbentry[pi].getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Finished.", hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
+ .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+ files.append(" \"" + file + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
+ else
+ {
+ if (curfiles != null && curfiles.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < curfiles.length; c++)
+ {
+ if (curfiles[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.append(" \"" + file + "\"");
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "The following pdb entries could not be retrieved from the PDB:\n"
+ + errormsgs.toString()
+ + "\nPlease try downloading them manually.",
+ "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
+ }
+ if (files.length() > 0)
+ {
+ if (!addingStructures)
+ {
+
+ try
+ {
+ initJmol("load FILES " + files.toString());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(files.toString());
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ cmd = null;
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ // need to wait around until script has finished
+ while (lastnotify >= jmb.getLoadNotifiesHandled())
+ ;
+ {
+ try
+ {
+ Thread.sleep(35);
+ } catch (Exception e)
+ {
+ }
+ }
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+ }
+ }
+ _started = false;
+ worker = null;
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save PDB File");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ BufferedReader in = new BufferedReader(new FileReader(
+ jmb.getPdbFile()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(jmb.printMapping(
+ jmb.pdbentry[pdbe].getFile()));
+ cap.appendText("\n");
+ }
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+ 550, 600);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.PNG);
+ }
+
+ void makePDBImage(int type)
+ {
+ int width = getWidth();
+ int height = getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Make PNG image from view", width, height, null, null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
+ }
+
+ if (im.getGraphics() != null)
+ {
+ Rectangle rect = new Rectangle(width, height);
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ im.writeImage();
+ }
+ }
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (jmolColour.isSelected()) {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+ jmb.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size()==0 && ap!=null) {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
+ }
+ }
+
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ jmb.colourByChain();
+ }
+
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
+ {
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
+ {
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
+ }
+
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ {
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ }
+
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
+ {
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
+ }
+
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
+ {
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
+ }
+
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
+ {
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
+ }
+
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
+ {
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
+ }
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
+ public void userColour_actionPerformed(ActionEvent actionEvent)
+ {
+ userColour.setSelected(true);
+ new UserDefinedColours(this, null);
+ }
+
+ public void backGround_actionPerformed(ActionEvent actionEvent)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ "Select Background Colour", null);
+ if (col != null)
+ {
+ jmb.setBackgroundColour(col);
+ }
+ }
+
+ public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void showConsole(boolean showConsole)
+ {
+
+ if (showConsole)
+ {
+ if (splitPane == null)
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ splitPane.setTopComponent(renderPanel);
+ splitPane.setBottomComponent(scriptWindow);
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
+ }
+
+ }
+ else
+ {
+ if (splitPane != null)
+ {
+ splitPane.setVisible(false);
+ }
+
+ splitPane = null;
+
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
+
+ validate();
+ }
+
+ class RenderPanel extends JPanel
+ {
+ final Dimension currentSize = new Dimension();
+
+ final Rectangle rectClip = new Rectangle();
+
+ public void paintComponent(Graphics g)
+ {
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
+
+ if (jmb.fileLoadingError != null)
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Error loading file...", 20, currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
+ {
+ sb.append(jmb.pdbentry[e].getId());
+ if (e < jmb.pdbentry.length - 1)
+ {
+ sb.append(",");
+ }
+
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
+ }
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ }
+ else
+ {
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ }
+ }
+ }
+
+ String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
+ }
+ return viewId;
+ }
+
+ public void updateTitleAndMenus()
+ {
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ jmolActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildJmolActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+
+ }
+
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
+ {
+ return _aps.contains(ap2.av.getSequenceSetId());
+ }
+
+ public boolean isUsedforaligment(AlignmentPanel ap2)
+ {
+
+ return (_alignwith != null) && _alignwith.contains(ap2);
+ }
+
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
+ {
+ return (_colourwith != null) && _colourwith.contains(ap2);
+ }
+
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+
+}
git://source.jalview.org / jalview.git / commitdiff