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Jmol: an open-source Java viewer for chemical structures in 3D
There is a newer version: 14.31.10
/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2017-04-14 13:25:20 -0500 (Fri, 14 Apr 2017) $
 * $Revision: 21519 $
 *
 * Copyright (C) 2003-2005  Miguel, Jmol Development Team
 *
 * Contact: [email protected]
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library 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
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.jmol.viewer;

import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
import java.util.Hashtable;
import java.util.Map;

import javajs.api.BytePoster;
import javajs.api.GenericFileInterface;
import javajs.util.AU;
import javajs.util.BArray;
import javajs.util.Base64;
import javajs.util.CompoundDocument;
import javajs.util.DataReader;
import javajs.util.LimitedLineReader;
import javajs.util.Lst;
import javajs.util.OC;
import javajs.util.PT;
import javajs.util.Rdr;
import javajs.util.SB;

import org.jmol.adapter.readers.spartan.SpartanUtil;
import org.jmol.api.Interface;
import org.jmol.api.JmolDomReaderInterface;
import org.jmol.api.JmolFilesReaderInterface;
import org.jmol.io.FileReader;
import org.jmol.io.JmolUtil;
import org.jmol.script.SV;
import org.jmol.script.T;
import org.jmol.util.Logger;
import org.jmol.viewer.Viewer.ACCESS;


public class FileManager implements BytePoster {

  public static String SIMULATION_PROTOCOL = "http://SIMULATION/";

  public Viewer vwr;


  FileManager(Viewer vwr) {
    this.vwr = vwr;
    clear();
  }

  private SpartanUtil spartanDoc;
  
  /**
   * An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
   * @return a SpartanUtil
   */
  public SpartanUtil spartanUtil() {
    return (spartanDoc == null ? spartanDoc = ((SpartanUtil) Interface.getInterface("org.jmol.adapter.readers.spartan.SpartanUtil", vwr, "fm getSpartanUtil()")).set(this) : spartanDoc);  
  }
  
  JmolUtil jzu;
 
  public JmolUtil getJzu() {
    return (jzu == null ? jzu = (JmolUtil) Interface.getOption("io.JmolUtil", vwr, "file") : jzu);
  }

  void clear() {
    // from zap
    setFileInfo(new String[] { vwr.getZapName() });
    spardirCache = null;   
  }

  private void setLoadState(Map htParams) {
    if (vwr.getPreserveState()) {
      htParams.put("loadState", vwr.g.getLoadState(htParams));
    }
  }

  private String pathForAllFiles = ""; // leave private because of setPathForAllFiles
  
  public String getPathForAllFiles() {
    return pathForAllFiles;
  }
  
  String setPathForAllFiles(String value) {
    if (value.length() > 0 && !value.endsWith("/") && !value.endsWith("|"))
        value += "/";
    return pathForAllFiles = value;
  }

  private String nameAsGiven = JC.ZAP_TITLE, fullPathName, lastFullPathName, lastNameAsGiven = JC.ZAP_TITLE, fileName;

  /**
   * Set fullPathName, fileName, and nameAsGiven
   * 
   * @param fileInfo if null, replace fullPathName and nameAsGiven with last version of such
   * 
   * 
   */
  public void setFileInfo(String[] fileInfo) {
    if (fileInfo == null) {
      fullPathName = lastFullPathName;
      nameAsGiven = lastNameAsGiven;
      return;
    }
    // used by ScriptEvaluator dataFrame and load methods to temporarily save the state here
    fullPathName = fileInfo[0];
    fileName = fileInfo[Math.min(1,  fileInfo.length - 1)];
    nameAsGiven = fileInfo[Math.min(2, fileInfo.length - 1)];
    if (!nameAsGiven.equals(JC.ZAP_TITLE)) {
      lastNameAsGiven = nameAsGiven;
      lastFullPathName = fullPathName;
    }
  }

  public String[] getFileInfo() {
    // used by ScriptEvaluator dataFrame method
    return new String[] { fullPathName, fileName, nameAsGiven };
  }

  public String getFullPathName(boolean orPrevious) {
    String f =(fullPathName != null ? fullPathName : nameAsGiven);
    return (!orPrevious || !f.equals(JC.ZAP_TITLE) ? f : lastFullPathName != null ? lastFullPathName : lastNameAsGiven);
  }

  public String getFileName() {
    return fileName != null ? fileName : nameAsGiven;
  }

  // for applet proxy
  private URL appletDocumentBaseURL = null;
  private String appletProxy;

  String getAppletDocumentBase() {
    return (appletDocumentBaseURL == null ? "" : appletDocumentBaseURL.toString());
  }

  void setAppletContext(String documentBase) {
    try {
      System.out.println("setting document base to \"" + documentBase + "\"");      
      appletDocumentBaseURL = (documentBase.length() == 0 ? null : new URL((URL) null, documentBase, null));
    } catch (MalformedURLException e) {
      System.out.println("error setting document base to " + documentBase);
    }
  }

  void setAppletProxy(String appletProxy) {
    this.appletProxy = (appletProxy == null || appletProxy.length() == 0 ? null
        : appletProxy);
  }


  /////////////// createAtomSetCollectionFromXXX methods /////////////////

  // where XXX = File, Files, String, Strings, ArrayData, DOM, Reader

  /*
   * note -- createAtomSetCollectionFromXXX methods
   * were "openXXX" before refactoring 11/29/2008 -- BH
   * 
   * The problem was that while they did open the file, they
   * (mostly) also closed them, and this was confusing.
   * 
   * The term "clientFile" was replaced by "atomSetCollection"
   * here because that's what it is --- an AtomSetCollection,
   * not a file. The file is closed at this point. What is
   * returned is the atomSetCollection object.
   * 
   * One could say this is just semantics, but there were
   * subtle bugs here, where readers were not always being 
   * closed explicitly. In the process of identifying Out of
   * Memory Errors, I felt it was necessary to clarify all this.
   * 
   * Apologies to those who feel the original clientFile notation
   * was more generalizable or understandable. 
   * 
   */
  Object createAtomSetCollectionFromFile(String name,
                                         Map htParams,
                                         boolean isAppend) {
    if (htParams.get("atomDataOnly") == null)
      setLoadState(htParams);
    String name0 = name;
    name = vwr.resolveDatabaseFormat(name);
    if (!name0.equals(name) && name0.indexOf("/") < 0 
        && Viewer.hasDatabasePrefix(name0)) {
      htParams.put("dbName", name0);
    }
    int pt = name.indexOf("::");
    String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
    String fileType = (pt >= 0 ? name.substring(0, pt) : null);
    Logger.info("\nFileManager.getAtomSetCollectionFromFile(" + nameAsGiven
        + ")" + (name.equals(nameAsGiven) ? "" : " //" + name));
    String[] names = getClassifiedName(nameAsGiven, true);
    if (names.length == 1)
      return names[0];
    String fullPathName = names[0];
    String fileName = names[1];
    htParams.put("fullPathName", (fileType == null ? "" : fileType + "::")
        + FileManager.fixDOSName(fullPathName));
    if (vwr.getBoolean(T.messagestylechime) && vwr.getBoolean(T.debugscript))
      vwr.getChimeMessenger().update(fullPathName);
    FileReader fileReader = new FileReader(vwr, fileName, fullPathName, nameAsGiven,
        fileType, null, htParams, isAppend);
    fileReader.run();
    return fileReader.getAtomSetCollection();
  }

  Object createAtomSetCollectionFromFiles(String[] fileNames,
                                          Map htParams,
                                          boolean isAppend) {
    setLoadState(htParams);
    String[] fullPathNames = new String[fileNames.length];
    String[] namesAsGiven = new String[fileNames.length];
    String[] fileTypes = new String[fileNames.length];
    for (int i = 0; i < fileNames.length; i++) {
      int pt = fileNames[i].indexOf("::");
      String nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2)
          : fileNames[i]);
      
      System.out.println(i + " FM " + nameAsGiven);
      String fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
      String[] names = getClassifiedName(nameAsGiven, true);
      if (names.length == 1)
        return names[0];
      fullPathNames[i] = names[0];
      fileNames[i] = fixDOSName(names[0]);
      fileTypes[i] = fileType;
      namesAsGiven[i] = nameAsGiven;
    }
    htParams.put("fullPathNames", fullPathNames);
    htParams.put("fileTypes", fileTypes);
    JmolFilesReaderInterface filesReader = newFilesReader(fullPathNames, namesAsGiven,
        fileTypes, null, htParams, isAppend);
    filesReader.run();
    return filesReader.getAtomSetCollection();
  }

  Object createAtomSetCollectionFromString(String strModel,
                                           Map htParams,
                                           boolean isAppend) {
    setLoadState(htParams);
    boolean isAddH = (strModel.indexOf(JC.ADD_HYDROGEN_TITLE) >= 0);
    String[] fnames = (isAddH ? getFileInfo() : null);
    FileReader fileReader = new FileReader(vwr, "string", null, null, null,
        Rdr.getBR(strModel), htParams, isAppend);
    fileReader.run();
    if (fnames != null)
      setFileInfo(fnames);
    if (!isAppend && !(fileReader.getAtomSetCollection() instanceof String)) {
// zap is unnecessary  - it was done already in FileReader, and it 
// inappropriately clears the PDB chain name map
//      vwr.zap(false, true, false);
      setFileInfo(new String[] { strModel == JC.MODELKIT_ZAP_STRING ? JC.MODELKIT_ZAP_TITLE
          : "string"});
    }
    return fileReader.getAtomSetCollection();
  }

  Object createAtomSeCollectionFromStrings(String[] arrayModels,
                                           SB loadScript,
                                           Map htParams,
                                           boolean isAppend) {
    if (!htParams.containsKey("isData")) {
      String oldSep = "\"" + vwr.getDataSeparator() + "\"";
      String tag = "\"" + (isAppend ? "append" : "model") + " inline\"";
      SB sb = new SB();
      sb.append("set dataSeparator \"~~~next file~~~\";\ndata ").append(tag);
      for (int i = 0; i < arrayModels.length; i++) {
        if (i > 0)
          sb.append("~~~next file~~~");
        sb.append(arrayModels[i]);
      }
      sb.append("end ").append(tag).append(";set dataSeparator ")
          .append(oldSep);
      loadScript.appendSB(sb);
    }
    setLoadState(htParams);
    Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");
    String[] fullPathNames = new String[arrayModels.length];
    DataReader[] readers = new DataReader[arrayModels.length];
    for (int i = 0; i < arrayModels.length; i++) {
      fullPathNames[i] = "string[" + i + "]";
      readers[i] = newDataReader(vwr, arrayModels[i]);
    }
    JmolFilesReaderInterface filesReader = newFilesReader(fullPathNames, fullPathNames,
        null, readers, htParams, isAppend);
    filesReader.run();
    return filesReader.getAtomSetCollection();
  }

  Object createAtomSeCollectionFromArrayData(Lst