-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.ext.jmol;
-
-import java.io.File;
-import java.net.URL;
-import java.util.*;
-import java.applet.Applet;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-import jalview.schemes.*;
-
-public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
-
-{
- /**
- * set if Jmol state is being restored from some source - instructs binding
- * not to apply default display style when structure set is updated for first
- * time.
- */
- private boolean loadingFromArchive = false;
-
- /**
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
- 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 atomsPicked = new Vector();
-
- public Vector chainNames;
-
- /**
- * array of target chains for seuqences - tied to pdbentry and sequence[]
- */
- protected String[][] chains;
-
- boolean colourBySequence = true;
-
- StringBuffer eval = new StringBuffer();
-
- public String fileLoadingError;
-
- /**
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- int frameNo = 0;
-
- protected JmolPopup jmolpopup;
-
- String lastCommand;
-
- String lastMessage;
-
- boolean loadedInline;
-
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
- public PDBEntry[] pdbentry;
-
- /**
- * datasource protocol for access to PDBEntry
- */
- String protocol = null;
-
- StringBuffer resetLastRes = new StringBuffer();
-
- /**
- * sequences mapped to each pdbentry
- */
- public SequenceI[][] sequence;
-
- StructureSelectionManager ssm;
-
- public JmolViewer viewer;
-
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String[][] chains, String protocol)
- {
- this.sequence = sequenceIs;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
- if (chains == null)
- {
- this.chains = new String[pdbentry.length][];
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 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 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
+ 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
+ // 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, new SmarterJmolAdapter(),
- * "jalviewJmol", ap.av.applet .getDocumentBase(),
- * ap.av.applet.getCodeBase(), "", this);
- *
- * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
- */
- }
-
- public JalviewJmolBinding(JmolViewer viewer2)
- {
- viewer = viewer2;
- 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()
- {
- if (sequence == null || pdbentry == null || sequence.length < 1
- || pdbentry.length < 1 || sequence[0].length < 1)
- {
- return ("Jalview Jmol Window");
- }
- // TODO: give a more informative title when multiple structures are
- // displayed.
- StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
- + pdbentry[0].getId());
-
- if (pdbentry[0].getProperty() != null)
- {
- if (pdbentry[0].getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry[0].getProperty().get("method"));
- }
- if (pdbentry[0].getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry[0].getProperty().get("chains"));
- }
- }
- return title.toString();
- }
-
- /**
- * 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 chainList)
- {
- StringBuffer cmd = new StringBuffer();
- String lbl;
- int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
- {
- mlength = 0;
- lbl = (String) chainList.elementAt(i);
- do
- {
- p = mlength;
- mlength = lbl.indexOf(":", p);
- } while (p < mlength && mlength < (lbl.length() - 2));
- cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
- }
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
- }
-
- public void closeViewer()
- {
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- // remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- lastCommand = null;
- viewer = null;
- }
-
- 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)
- {
- String[] files = getPdbFile();
- if (refStructure >= files.length)
- {
- System.err.println("Invalid reference structure value "
- + refStructure);
- refStructure = -1;
- }
- if (refStructure < -1)
- {
- refStructure = -1;
- }
- StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
- {
-
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
- }
-
- int commonrpositions[][] = new int[files.length][alignment.getWidth()];
- String isel[] = new String[files.length];
- // reference structure - all others are superposed in it
- String[] targetC = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- if (!matched[r])
- {
- continue;
- }
- matched[r] = false; // assume this is not a good site
- if (r >= asp.getLength())
- {
- continue;
- }
-
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- // no mapping to gaps in sequence
- continue;
- }
- int t = asp.findPosition(r); // sequence position
- int apos = mapping[m].getAtomNum(t);
- int pos = mapping[m].getPDBResNum(t);
-
- if (pos < 1 || pos == lastPos)
- {
- // can't align unmapped sequence
- continue;
- }
- matched[r] = true; // this is a good ite
- lastPos = pos;
- // just record this residue position
- commonrpositions[pdbfnum][r] = pos;
- }
- // create model selection suffix
- isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
- if (mapping[m].getChain() == null
- || mapping[m].getChain().trim().length() == 0)
- {
- targetC[pdbfnum] = "";
- }
- else
- {
- targetC[pdbfnum] = ":" + mapping[m].getChain();
- }
- // move on to next pdb file
- s = sequence[pdbfnum].length;
- break;
- }
- }
- }
- }
- String[] selcom = new String[files.length];
- // generate select statements to select regions to superimpose structures
- {
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- String chainCd = targetC[pdbfnum];
- int lpos = -1;
- boolean run = false;
- StringBuffer molsel = new StringBuffer();
- molsel.append("{");
- for (int r = 0; r < matched.length; r++)
- {
- if (matched[r])
- {
-
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
- }
- }
- else
- {
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
- }
- run = true;
- }
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
- }
- }
- // add final selection phrase
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- molsel.append("}");
- }
- 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("|");
- }
- }
- }
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- if (pdbfnum == refStructure)
- {
- continue;
- }
- command.append("compare ");
- command.append("{");
- command.append(1 + pdbfnum);
- command.append(".1} {");
- command.append(1 + refStructure);
- command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
-
- // form the matched pair strings
- String sep = "";
- for (int s = 0; s < 2; s++)
- {
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
- }
- command.append(" ROTATE TRANSLATE;\n");
- }
- System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
- // selcom.append("; ribbons; ");
- System.out.println("Superimpose command(s):\n" + command.toString());
-
- evalStateCommand(command.toString());
-
- // 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(boolean showFeatures, AlignmentI alignment)
- {
- if (!colourBySequence)
- return;
- if (ssm == null)
- {
- return;
- }
- String[] files = getPdbFile();
- SequenceRenderer sr = getSequenceRenderer();
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer();
- }
-
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
- }
- }
- evalStateCommand(command.toString());
- }
-
- public boolean isColourBySequence()
- {
- return colourBySequence;
- }
-
- public void setColourBySequence(boolean colourBySequence)
- {
- this.colourBySequence = colourBySequence;
- }
-
- StringBuffer condenseCommand(String command, int pos)
- {
-
- StringBuffer sb = new StringBuffer(command.substring(0,
- command.lastIndexOf("select") + 7));
-
- command = command.substring(sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- 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));
- }
-
- /**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer();
-
- /**
- * 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
- public synchronized String[] getPdbFile()
- {
- if (modelFileNames == null)
- {
-
- String mset[] = new String[viewer.getModelCount()];
- _modelFileNameMap = new int[mset.length];
- int j = 1;
- mset[0] = viewer.getModelFileName(0);
- for (int i = 1; i < mset.length; i++)
- {
- mset[j] = viewer.getModelFileName(i);
- _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
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer();
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- // 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;
- String fn;
- // may need to adjust for URLencoding here - we don't worry about that yet.
- while (mdlNum < modelFileNames.length
- && !pdbfile.equals(modelFileNames[mdlNum]))
- {
- // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
- mdlNum++;
- }
- if (mdlNum == modelFileNames.length)
- {
- return;
- }
-
- jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
-
- eval.append(":");
- resetLastRes.append(":");
- if (!chain.equals(" "))
- {
- eval.append(chain);
- resetLastRes.append(chain);
- }
- {
- eval.append(" /" + (mdlNum + 1));
- resetLastRes.append("/" + (mdlNum + 1));
- }
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.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 mdlSep = strInfo.indexOf("/");
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
- if (chainSeparator == -1)
- {
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
- {
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
- }
- }
- 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.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
- } catch (Exception e)
- {
- }
- ;
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.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 + 1, 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");
- // }
-
- }
-
- public void notifyCallback(int type, Object[] data)
- {
- try
- {
- switch (type)
- {
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4],
- ((Integer) data[5]).intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2],
- ((Integer) data[3]).intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String) data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
- break;
- case JmolConstants.CALLBACK_ERROR:
- // System.err.println("Ignoring error callback.");
- break;
- case JmolConstants.CALLBACK_SYNC:
- case JmolConstants.CALLBACK_RESIZE:
- refreshGUI();
- break;
- case JmolConstants.CALLBACK_MEASURE:
-
- case JmolConstants.CALLBACK_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();
- }
- }
-
- public boolean notifyEnabled(int callbackPick)
- {
- switch (callbackPick)
- {
- case JmolConstants.CALLBACK_ECHO:
- case JmolConstants.CALLBACK_LOADSTRUCT:
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_MESSAGE:
- case JmolConstants.CALLBACK_PICK:
- case JmolConstants.CALLBACK_SCRIPT:
- case JmolConstants.CALLBACK_HOVER:
- case JmolConstants.CALLBACK_ERROR:
- return true;
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
- case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
- case JmolConstants.CALLBACK_MINIMIZATION:
- }
- return false;
- }
-
- 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();
- boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
- // 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.
- ssm.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, pdbfhash = 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");
- pdbfhash = "" + pdbfile.hashCode();
- }
- if (pdbentry != null)
- {
- // search pdbentries and sequences to find correct pdbentry for this
- // model
- for (int pe = 0; pe < pdbentry.length; pe++)
- {
- boolean matches = false;
- if (fileName == null)
- {
- if (false)
- // see JAL-623 - need method of matching pasted data up
- {
- pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
- AppletFormatAdapter.PASTE);
- pdbentry[modelnum].setFile("INLINE" + pdb.id);
- matches = true;
- foundEntry = true;
- }
- }
- else
- {
- if (matches = pdbentry[pe].getFile().equals(fileName))
- {
- 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
- {
- File fl = new java.io.File(pdbentry[pe].getFile());
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
- {
- }
- ;
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), protocol);
-
-
- }
- }
- if (matches)
- {
- pdbentry[pe].setId(pdb.id);
- // add an entry for every chain in the model
- for (int i = 0; i < pdb.chains.size(); i++)
- {
- chainNames.addElement(new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
- }
- 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 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
- }
- setLoadingFromArchive(false);
- // register ourselves as a listener and notify the gui that it needs to
- // update itself.
- ssm.addStructureViewerListener(this);
- if (notifyLoaded)
- {
- FeatureRenderer fr = getFeatureRenderer();
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
- }
- }
-
- 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;
-
- String res;
- int index;
- Color col;
- jmolHistory(false);
- // TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].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();
-
- /**
- * @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(Component renderPanel, boolean jmolfileio,
- String htmlName, URL documentBase, URL codeBase,
- String commandOptions)
- {
- viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
- commandOptions, this);
- }
-
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
- }
-
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive;
- }
-
- public void setBackgroundColour(java.awt.Color col)
- {
- jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- jmolHistory(true);
- }
-
- /**
- * add structures and any known sequence associations
- *
- * @returns the pdb entries added to the current set.
- */
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
- {
- int pe = -1;
- Vector v = new Vector();
- Vector rtn = new Vector();
- for (int i = 0; i < pdbentry.length; i++)
- {
- v.addElement(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
- {
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
- {
- rtn.addElement(new int[]
- { v.size(), i });
- v.addElement(pdbe[i]);
- }
- else
- {
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
- }
- }
- pdbe = new PDBEntry[v.size()];
- v.copyInto(pdbe);
- pdbentry = pdbe;
- if (rtn.size() > 0)
- {
- // expand the tied seuqence[] and string[] arrays
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];
- String[][] sch = new String[pdbentry.length][];
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);
- System.arraycopy(chains, 0, sch, 0, this.chains.length);
- sequence = sqs;
- chains = sch;
- pdbe = new PDBEntry[rtn.size()];
- for (int r = 0; r < pdbe.length; r++)
- {
- int[] stri = ((int[]) rtn.elementAt(r));
- // record the pdb file as a new addition
- pdbe[r] = pdbentry[stri[0]];
- // and add the new sequence/chain entries
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
- }
- }
- else
- {
- pdbe = null;
- }
- return pdbe;
- }
-
- public void addSequence(int pe, SequenceI[] seq)
- {
- // add sequences to the pe'th pdbentry's seuqence set.
- addSequenceAndChain(pe, seq, null);
- }
-
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
- {
- if (pe < 0 || pe >= pdbentry.length)
- {
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
- }
- final String nullChain = "TheNullChain";
- Vector s = new Vector();
- Vector c = new Vector();
- if (chains == null)
- {
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
- {
- for (int i = 0; i < sequence[pe].length; i++)
- {
- s.addElement(sequence[pe][i]);
- if (chains[pe] != null)
- {
- if (i < chains[pe].length)
- {
- c.addElement(chains[pe][i]);
- }
- else
- {
- c.addElement(nullChain);
- }
- }
- else
- {
- if (tchain != null && tchain.length > 0)
- {
- c.addElement(nullChain);
- }
- }
- }
- }
- for (int i = 0; i < seq.length; i++)
- {
- if (!s.contains(seq[i]))
- {
- s.addElement(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
- }
- }
- }
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
- sequence[pe] = tmp;
- if (c.size() > 0)
- {
- String[] tch = new String[c.size()];
- c.copyInto(tch);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
- chains[pe] = tch;
- }
- else
- {
- chains[pe] = null;
- }
- }
-}
+ 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
git://source.jalview.org / jalview.git / blobdiff