--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.IOException;
+import java.util.Map;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.constant.EnumStructure;
+import org.jmol.modelset.Chain;
+import org.jmol.modelset.Group;
+import org.jmol.modelset.Model;
+import org.jmol.modelset.ModelSet;
+import org.jmol.modelset.Polymer;
+import org.jmol.modelsetbio.BioPolymer;
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolApp;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+
+/**
+ * Import and process PDB files with Jmol
+ *
+ * @author jprocter
+ *
+ */
+public class PDBFileWithJmol extends AlignFile implements
+ JmolStatusListener
+{
+
+ JmolApp jmolApp = null;
+
+ Viewer viewer = null;
+
+ public PDBFileWithJmol(String inFile, String type)
+ throws ExceptionUnmatchedClosingParentheses, IOException,
+ ExceptionFileFormatOrSyntax, ParserConfigurationException,
+ SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
+ InterruptedException
+ {
+ super(inFile, type);
+ }
+
+ public PDBFileWithJmol()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * create a headless jmol instance for dataprocessing
+ *
+ * @return
+ */
+ private Viewer getJmolData()
+ {
+ if (viewer == null)
+ { // note that -o -n -x are all implied
+ jmolApp = new JmolApp();
+ jmolApp.isDataOnly = true;
+ jmolApp.haveConsole = false;
+ jmolApp.haveDisplay = false;
+ jmolApp.exitUponCompletion = true;
+ try
+ {
+ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
+ null, jmolApp.commandOptions, this);
+ viewer.setScreenDimension(jmolApp.startupWidth,
+ jmolApp.startupHeight);
+ jmolApp.startViewer(viewer, null);
+ } catch (ClassCastException x)
+ {
+ throw new Error(
+ "Jmol version "
+ + JmolViewer.getJmolVersion()
+ + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ x);
+ }
+ }
+ return viewer;
+ }
+
+ private void waitForScript(Viewer jmd)
+ {
+ while (jmd.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(50);
+
+ } catch (InterruptedException x)
+ {
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException, ExceptionFileFormatOrSyntax,
+ ParserConfigurationException, SAXException,
+ ExceptionPermissionDenied, ExceptionLoadingFailed,
+ InterruptedException, ExceptionUnmatchedClosingParentheses
+ {
+ Viewer jmd = getJmolData();
+ jmd.openReader(getDataName(), getDataName(), getReader());
+ waitForScript(jmd);
+ if (jmd.getModelCount() > 0)
+ {
+ ModelSet ms = jmd.getModelSet();
+ String structs = ms.calculateStructures(null, true, false, true);
+ // System.out.println("Structs\n"+structs);
+ for (Model model : ms.getModels())
+ {
+ for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
+ {
+ Polymer bp = model.getBioPolymer(_bp);
+ if (bp instanceof BioPolymer)
+ {
+ BioPolymer biopoly = (BioPolymer) bp;
+ char _lastChainId = 0;
+ int[] groups = biopoly.getLeadAtomIndices();
+ Group[] bpgrp = biopoly.getGroups();
+ char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
+ int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
+ do
+ {
+ if (groupc >= groups.length
+ || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
+ {
+ if (len > 0)
+ {
+ char newseq[] = new char[len];
+ System.arraycopy(seq, 0, newseq, 0, len);
+ Annotation asecstr[] = new Annotation[len];
+ for (int p = 0; p < len; p++)
+ {
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
+ {
+ asecstr[p] = new Annotation("" + secstr[p], null,
+ secstrcode[p], Float.NaN);
+ }
+ }
+ SequenceI sq = new Sequence("" + getDataName() + "|"
+ + model.getModelTitle() + "|" + _lastChainId,
+ newseq, firstrnum, lastrnum);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setFile(getDataName());
+ pdbe.setId(getDataName());
+ sq.addPDBId(pdbe);
+ seqs.add(sq);
+ if (!(biopoly.isDna() || biopoly.isRna()))
+ {
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure",
+ "Secondary Structure from PDB File", asecstr);
+ sq.addAlignmentAnnotation(ann);
+ annotations.add(ann);
+ }
+ }
+ len = 0;
+ firstrnum = 1;
+ lastrnum = 0;
+ }
+ if (groupc < groups.length)
+ {
+ if (len == 0)
+ {
+ firstrnum = bpgrp[groupc].getResno();
+ _lastChainId = bpgrp[groupc].getChainID();
+ }
+ else
+ {
+ lastrnum = bpgrp[groupc].getResno();
+ }
+ seq[len] = bpgrp[groupc].getGroup1();
+ switch (bpgrp[groupc].getProteinStructureSubType())
+ {
+ case HELIX_310:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = '3';
+ }
+ case HELIX_ALPHA:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ case HELIX_PI:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'P';
+ }
+ case HELIX:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ secstrcode[len] = 'H';
+ break;
+ case SHEET:
+ secstr[len] = 'E';
+ secstrcode[len] = 'E';
+ break;
+ default:
+ secstr[len] = 0;
+ secstrcode[len] = 0;
+ }
+ len++;
+ }
+ } while (groupc++ < groups.length);
+
+ }
+ }
+ }
+
+ /*
+ * lastScriptTermination = -9465; String dsspOut =
+ * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
+ * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
+ * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
+ */
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /*
+ * @Override public void notifyCallback(EnumCallback type, Object[] data) {
+ * try { switch (type) { case ERROR: case SCRIPT:
+ * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
+ * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
+ * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
+ * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
+ * data[5]).intValue());
+ *
+ * break; 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 void notifyCallback(EnumCallback type, Object[] data)
+ {
+ String strInfo = (data == null || data[1] == null ? null : data[1]
+ .toString());
+ switch (type)
+ {
+ case ECHO:
+ sendConsoleEcho(strInfo);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case MEASURE:
+ String mystatus = (String) data[3];
+ if (mystatus.indexOf("Picked") >= 0
+ || mystatus.indexOf("Sequence") >= 0) // picking mode
+ sendConsoleMessage(strInfo);
+ else if (mystatus.indexOf("Completed") >= 0)
+ sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
+ strInfo.length() - 1));
+ break;
+ case MESSAGE:
+ sendConsoleMessage(data == null ? null : strInfo);
+ break;
+ case PICK:
+ sendConsoleMessage(strInfo);
+ break;
+ default:
+ break;
+ }
+ }
+
+ private void notifyFileLoaded(String string, String string2,
+ String string3, String string4, int intValue)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ String lastConsoleEcho = "";
+
+ private void sendConsoleEcho(String string)
+ {
+ lastConsoleEcho += string;
+ lastConsoleEcho += "\n";
+ }
+
+ String lastConsoleMessage = "";
+
+ private void sendConsoleMessage(String string)
+ {
+ lastConsoleMessage += string;
+ lastConsoleMessage += "\n";
+ }
+
+ int lastScriptTermination = -1;
+
+ String lastScriptMessage = "";
+
+ private void notifyScriptTermination(String string, int intValue)
+ {
+ lastScriptMessage += string;
+ lastScriptMessage += "\n";
+ lastScriptTermination = intValue;
+ }
+
+ @Override
+ public boolean notifyEnabled(EnumCallback callbackPick)
+ {
+ switch (callbackPick)
+ {
+ case MESSAGE:
+ case SCRIPT:
+ case ECHO:
+ case LOADSTRUCT:
+ case ERROR:
+ return true;
+ case MEASURE:
+ case PICK:
+ case HOVER:
+ case RESIZE:
+ case SYNC:
+ case CLICK:
+ case ANIMFRAME:
+ case MINIMIZATION:
+ }
+ return false;
+ }
+
+ @Override
+ public String eval(String strEval)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String createImage(String fileName, String type,
+ Object text_or_bytes, int quality)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Map<String, Object> getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void showUrl(String url)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff