--- /dev/null
+/*
+ * 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.util.*;
+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
+
+{
+
+ 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();
+
+ private Vector chainNames;
+
+ String[] chains;
+
+ boolean colourBySequence = true;
+
+ StringBuffer eval = new StringBuffer();
+
+ String fileLoadingError;
+
+ /**
+ * the default or current model displayed if the model cannot be identified
+ * from the selection message
+ */
+ int frameNo = 0;
+
+ JmolPopup jmolpopup;
+
+ String lastCommand;
+
+ String lastMessage;
+
+ boolean loadedInline;
+
+ /**
+ * current set of model filenames loaded in the Jmol instance
+ */
+ String[] modelFileNames = null;
+
+ PDBEntry[] pdbentry;
+
+ /**
+ * datasource protocol for access to PDBEntry
+ */
+ String protocol = null;
+
+ StringBuffer resetLastRes = new StringBuffer();
+
+ SequenceI[] sequence;
+
+ StructureSelectionManager ssm;
+
+ JmolViewer viewer;
+
+ public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
+ String[] chains, String protocol)
+ {
+ /*
+ * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
+ * "jalviewJmol", ap.av.applet .getDocumentBase(),
+ * ap.av.applet.getCodeBase(), "", this);
+ *
+ * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+ */
+ }
+
+ /**
+ * prepare the view for a given set of models/chains. chainList contains
+ * strings of the form 'pdbfilename:Chaincode'
+ *
+ * @param chainList
+ * list of chains to make visible
+ */
+ 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);
+
+ jmolHistory(false);
+ viewer
+ .evalString("select *;restrict " + cmd + ";cartoon;center "
+ + cmd);
+ jmolHistory(true);
+ }
+
+ 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);
+
+ viewer = null;
+ }
+
+ public void colourByChain()
+ {
+ jmolHistory(false);
+ colourBySequence = false;
+ viewer.evalStringQuiet("select *;color chain");
+ jmolHistory(true);
+ }
+
+ public void colourByCharge()
+ {
+ jmolHistory(false);
+ colourBySequence = false;
+ viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+ jmolHistory(true);
+ }
+
+ /**
+ * 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;
+ 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.length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[s]
+ && (sp = alignment.findIndex(sequence[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[s], r);
+
+ if (showFeatures)
+ col = fr.findFeatureColour(col, sequence[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;
+ }
+ }
+ }
+ }
+
+ jmolHistory(false);
+ if (lastCommand == null || !lastCommand.equals(command.toString()))
+ {
+ viewer.evalStringQuiet(command.toString());
+ }
+ jmolHistory(true);
+ lastCommand = command.toString();
+ }
+
+ 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)
+ {
+ }
+
+ public String createImage(String fileName, String type,
+ Object textOrBytes, int quality)
+ {
+ // TODO Auto-generated method stub
+ 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
+ */
+ abstract FeatureRenderer getFeatureRenderer();
+
+ 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;
+ }
+
+ // ////////////////////////////////
+ // /StructureListener
+ public String[] getPdbFile()
+ {
+ if (modelFileNames == null)
+ {
+ String mset[] = new String[viewer.getModelCount()];
+ for (int i = 0; i < mset.length; i++)
+ {
+ mset[i] = viewer.getModelFileName(i);
+ }
+ modelFileNames = mset;
+ }
+ return modelFileNames;
+ }
+
+ public Hashtable getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @return
+ */
+ 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);
+
+ }
+
+ private void jmolHistory(boolean enable)
+ {
+ viewer.setBooleanProperty("history", enable);
+ }
+
+ public void loadInline(String string)
+ {
+ loadedInline = true;
+ 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);
+ }
+ 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);
+
+ }
+
+ 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_MEASURE:
+ case JmolConstants.CALLBACK_CLICK:
+ default:
+ System.err.println("Unhandled callback " + type + " " + data);
+ 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_CLICK:
+ case JmolConstants.CALLBACK_ANIMFRAME:
+ case JmolConstants.CALLBACK_MINIMIZATION:
+ case JmolConstants.CALLBACK_RESIZE:
+ case JmolConstants.CALLBACK_SYNC:
+ }
+ return false;
+ }
+
+ public void notifyFileLoaded(String fullPathName, String fileName2,
+ String modelName, String errorMsg, int modelParts)
+ {
+ if (errorMsg != null)
+ {
+ fileLoadingError = errorMsg;
+ updateUI();
+ return;
+ }
+ fileLoadingError = null;
+ modelFileNames = null;
+ chainNames = new Vector();
+ boolean notifyLoaded = false;
+ String[] modelfilenames = getPdbFile();
+ ssm = StructureSelectionManager.getStructureSelectionManager();
+ for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
+ {
+ String fileName = modelfilenames[modelnum];
+ if (fileName != null)
+ {
+ // search pdbentries and sequences to find correct pdbentry and
+ // sequence[] pair for this filename
+ if (pdbentry != null)
+ {
+ boolean foundEntry = false;
+ for (int pe = 0; pe < pdbentry.length; pe++)
+ {
+ if (pdbentry[pe].getFile().equals(fileName))
+ {
+ foundEntry = true;
+ MCview.PDBfile pdb;
+ if (loadedInline)
+ {
+ // TODO: replace with getData ?
+ pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
+ .getFile(), AppletFormatAdapter.PASTE);
+ pdbentry[pe].setFile("INLINE" + pdb.id);
+ }
+ else
+ {
+ // 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
+
+ pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
+ .getFile(), AppletFormatAdapter.URL);
+
+ }
+
+ pdbentry[pe].setId(pdb.id);
+
+ 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
+ jmolpopup.updateComputedMenus();
+ viewer
+ .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ // register ourselves as a listener and notify the gui that it needs to
+ // update itself.
+ ssm.addStructureViewerListener(this);
+ if (notifyLoaded)
+ {
+ updateUI();
+ }
+
+ }
+
+ public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
+ {
+ notifyAtomPicked(iatom, strMeasure, null);
+ }
+
+ public 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);
+
+ 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() + "];");
+ }
+
+ viewer.evalStringQuiet(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.
+ */
+ abstract void updateUI();
+
+}
git://source.jalview.org / jalview.git / commitdiff