Java Logger.error方法代码示例

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
public void run() {

  try {

    while (console.checking) {
      try {
        Thread.sleep(100); //wait for command checker
      } catch (Exception e) {
        break; //-- interrupt? 
      }
    }

    executeCommand(strCommand);
  } catch (Exception ie) {
    Logger.error("execution command interrupted!", ie);
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
/**
 * a general-use method to evaluate a "SET" type expression.
 * 
 * @param viewer
 * @param expr
 * @return an object of one of the following types: Boolean, Integer, Float,
 *         String, Point3f, BitSet
 */

public static Object evaluateExpression(Viewer viewer, Object expr) {
  // Text.formatText for MESSAGE and ECHO
  ScriptEvaluator e = new ScriptEvaluator(viewer);
  try {
    if (expr instanceof String) {
      if (e.compileScript(null, EXPRESSION_KEY + " = " + expr, false)) {
        e.contextVariables = viewer.getContextVariables();
        e.setStatement(0);
        return e.parameterExpressionString(2, 0);
      }
    } else if (expr instanceof Token[]) {
      e.contextVariables = viewer.getContextVariables();
      return e.atomExpression((Token[]) expr, 0, 0, true, false, true, false);
    }
  } catch (Exception ex) {
    Logger.error("Error evaluating: " + expr + "\n" + ex);
  }
  return "ERROR";
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
public void run() {
  long startTime = System.currentTimeMillis();
  long lastRepaintTime = startTime;
  
  //should save the atom coordinates
  if (!startMinimization())
      return;
  try {
    do {
      long currentTime = System.currentTimeMillis();
      int elapsed = (int) (currentTime - lastRepaintTime);
      int sleepTime = 33 - elapsed;
      if (sleepTime > 0)
        Thread.sleep(sleepTime);
      lastRepaintTime = currentTime = System.currentTimeMillis();
      if (!stepMinimization())
        endMinimization();            
      elapsed = (int) (currentTime - startTime);
    } while (minimizationOn && !isInterrupted());
  } catch (Exception e) {
    if (minimizationOn)
      Logger.error(e.getMessage());
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
/**
 * a largely untested reader of the DOM - where in a browser there
 * is model actually in XML format already present on the page.
 * -- Egon Willighagen
 * 
 * @param DOMNode
 * @param htParams 
 * @return an AtomSetCollection or a String error
 * @throws Exception
 */
static Object DOMResolve(Object DOMNode, Map<String, Object> htParams) throws Exception {
  String className = null;
  Class<?> atomSetCollectionReaderClass;
  AtomSetCollectionReader atomSetCollectionReader; 
  String atomSetCollectionReaderName = getXmlType((JSObject) DOMNode);
  if (Logger.debugging) {
    Logger.debug("The Resolver thinks " + atomSetCollectionReaderName);
  }
  htParams.put("readerName", atomSetCollectionReaderName);
  try {
    className = classBase + "xml.XmlReader";
    atomSetCollectionReaderClass = Class.forName(className);
    atomSetCollectionReader = (AtomSetCollectionReader) atomSetCollectionReaderClass.newInstance();
    return atomSetCollectionReader;
  } catch (Exception e) {
    String err = "File reader was not found:" + className;
    Logger.error(err, e);
    return err;
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void addBundles(String type, String la_co_va, String la_co, String la) {
  try {
      String className = "org.jmol.translation." + type + ".";
      if (la_co_va != null)
        addBundle(className, la_co_va);
      if (la_co != null)
        addBundle(className, la_co);
      if (la != null)
        addBundle(className, la);
  } catch (Exception exception) {
    Logger.error("Some exception occurred!", exception);
    translationResources = null;
    translationResourcesCount = 0;
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
void readAtomicOrbitalOrder() throws Exception {
  /*
   [AO_ORDER]
   DOrbitals XX YY ZZ XY XZ YZ
   FOrbitals XXX YYY ZZZ XXY XXZ YYX YYZ ZZX ZZY XYZ
   */
  
  while (getLine()) {
    String[] tokens = getTokens();
    if (tokens.length == 0)
      continue;
    String data = line.substring(9).trim().toLowerCase();
    boolean isOK = false;
    switch(tokens.length - 1) {
    case 3:
    case 4:
      isOK = true;
      break;
    case 5:
      isOK = (tokens[0].equals("DOrbitals") && getDFMap(data, JmolAdapter.SHELL_D_SPHERICAL, DS_LIST, 99));
      break;
    case 6:
      isOK = (tokens[0].equals("DOrbitals") && getDFMap(data, JmolAdapter.SHELL_D_CARTESIAN, DC_LIST, 2));
      break;
    case 7:
      isOK = (tokens[0].equals("FOrbitals") && getDFMap(data, JmolAdapter.SHELL_F_SPHERICAL, FS_LIST, 99));
      break;
    case 10:
      isOK = (tokens[0].equals("FOrbitals") && getDFMap(data, JmolAdapter.SHELL_F_CARTESIAN, FC_LIST, 3));
      break;
    }      
    if (!isOK) {
      Logger.error("atomic orbital order is unrecognized -- skipping reading of MOs due to line: " + line);
      orbitals = null;
    }
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
void readPsiMolecularOrbitals() throws Exception {
  
  //TODO: This reader will fail for G orbitals
  //TODO: No way to check order
  
  Map<String, Object>[] mos = ArrayUtil.createArrayOfHashtable(5);
  List<String>[] data = ArrayUtil.createArrayOfArrayList(5);
  int nThisLine = 0;
  while (readLine() != null && line.toUpperCase().indexOf("DENS") < 0) {
    String[] tokens = getTokens();
    int ptData = (line.charAt(5) == ' ' ? 2 : 4);
    if (line.indexOf("                    ") == 0) {
      addMOData(nThisLine, data, mos);
      nThisLine = tokens.length;
      tokens = getTokens(readLine());
      for (int i = 0; i < nThisLine; i++) {
        mos[i] = new Hashtable<String, Object>();
        data[i] = new ArrayList<String>();
        mos[i].put("symmetry", tokens[i]);
      }
      tokens = getStrings(readLine().substring(21), nThisLine, 10);
      for (int i = 0; i < nThisLine; i++) {
        mos[i].put("energy", new Float(tokens[i]));
      }
      continue;
    }
    try {
      for (int i = 0; i < nThisLine; i++) {
        data[i].add(tokens[i + ptData]);
      }
    } catch (Exception e) {
      Logger.error("Error reading Psi3 file molecular orbitals at line: "
          + line);
      break;
    }
  }
  addMOData(nThisLine, data, mos);
  moData.put("mos", orbitals);
  setMOData(moData);
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void setProperty(int tok, Dipole dipole, int iValue, float fValue) {
  switch (tok) {
  case Token.on:
    dipole.visible = true;
    return;
  case Token.off:
    dipole.visible = false;       
    return;
  case Token.delete:
    deleteDipole(dipole);
    return;
  case Token.wireframe:
    dipole.mad = tempDipole.mad = (short) iValue;
    return;
  case Token.axes:
    dipole.offsetAngstroms = fValue;
    return;
  case Token.percent:
    dipole.offsetAngstroms = fValue * dipole.dipoleValue;
    return;
  case Token.sidechain:
    dipole.offsetSide = fValue;
    return;
  case Token.cross:
    dipole.noCross = (iValue == 0);
    return;
  case Token.color:
    dipole.colix = colix;
    return;
  case Token.translucent:
    dipole.setTranslucent(iValue == 1, translucentLevel);
    return;
  }
  Logger.error("Unkown dipole property! " + Token.nameOf(tok));
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
protected BitSet getVoxelBitSet(int nPoints) throws Exception {
  if (bsVoxelBitSet != null)
    return bsVoxelBitSet;
  BitSet bs = new BitSet();
  int bsVoxelPtr = 0;
  if (surfaceDataCount <= 0)
    return bs; //unnecessary -- probably a plane or color density
  int nThisValue = 0;
  while (bsVoxelPtr < nPoints) {
    nThisValue = parseInt();
    if (nThisValue == Integer.MIN_VALUE) {
      readLine();
      // note -- does not allow for empty lines;
      // must be a continuous block of numbers.
      if (line == null || (nThisValue = parseInt(line)) == Integer.MIN_VALUE) {
        if (!endOfData)
          Logger.error("end of file in JvxlReader?" + " line=" + line);
        endOfData = true;
        nThisValue = 10000;
        //throw new NullPointerException();
      }
    } 
    thisInside = !thisInside;
    ++jvxlNSurfaceInts;
    if (thisInside)
      bs.set(bsVoxelPtr, bsVoxelPtr + nThisValue);
    bsVoxelPtr += nThisValue;
  }
  return bs;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
String dialogAsk(String type, String fileName) {
  inputFileName = fileName;
  dialogType = type;
  //System.out.println("Jvm12 thread: " + Thread.currentThread().getName());
  try {
    SwingUtilities.invokeAndWait(new Runnable() {
      public void run() {
        if (dialogType.equals("load")) {
          outputFileName = newDialog(false).getOpenFileNameFromDialog(
              viewer.getAppletContext(), viewer, inputFileName, null, null, false);
          return;
        }
        JmolDialogInterface sd = newDialog(false);
        if (dialogType.equals("save")) {
          outputFileName = sd.getSaveFileNameFromDialog(viewer,
              inputFileName, null);
          return;
        }
        if (dialogType.startsWith("saveImage")) {
          outputFileName = sd.getImageFileNameFromDialog(viewer,
              inputFileName, imageType, imageChoices, imageExtensions,
              qualityJPG, qualityPNG);
          qualityJPG = sd.getQuality("JPG");
          qualityPNG = sd.getQuality("PNG");
          String sType = sd.getType();
          if (sType != null)
            imageType = sType;
          int iQuality = sd.getQuality(sType);
          if (iQuality >= 0)
            imageQuality = iQuality;
          return;
        }
        outputFileName = null;
      }
    });
  } catch (Exception e) {
    Logger.error(e.getMessage());
  }
  return outputFileName;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void render1(Graphics g, Image img, int x, int y) {
  if (g != null && img != null) {
    try {
      g.drawImage(img, x, y, null);
    } catch (NullPointerException npe) {
      Logger.error("Sun!! ... fix graphics your bugs!");
    }
  }
  g3d.releaseScreenImage();
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
public OutputStream getOutputStream(String localName, String[] fullPath) {
  Object ret = createImage(localName, "OutputStream", null,
      Integer.MIN_VALUE, 0, 0, fullPath);
  if (ret instanceof String) {
    Logger.error((String) ret);
    return null;
  }
  return (OutputStream) ret;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
public ForceField getForceField() {
  if (pFF == null) {
    try {
      String className = getClass().getName();
      className = className.substring(0, className.lastIndexOf(".")) 
      + ".forcefield.ForceField" + ff;
      Logger.info( "minimize: using " + className);
      pFF = (ForceField) Class.forName(className).newInstance();
    } catch (Exception e) {
      Logger.error(e.getMessage());
    }
  }
  //Logger.info("minimize: forcefield = " + pFF);
  return pFF;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
public boolean importData(JComponent c, Transferable t) {
  if (sourceIndices == null || !canImport(c, t.getTransferDataFlavors())) {
    return false;
  }
  JList target = null;
  List<?> alist = null;
  try {
    target = (JList) c;
    if (hasLocalArrayListFlavor(t.getTransferDataFlavors())) {
      alist = (List<?>) t.getTransferData(localArrayListFlavor);
    } else if (hasSerialArrayListFlavor(t.getTransferDataFlavors())) {
      alist = (List<?>) t.getTransferData(serialArrayListFlavor);
    } else {
      return false;
    }
  } catch (UnsupportedFlavorException ufe) {
    Logger.error("importData: unsupported data flavor");
    return false;
  } catch (IOException ioe) {
    Logger.error("importData: I/O exception");
    return false;
  }

  // At this point we use the same code to retrieve the data
  // locally or serially.

  // We'll drop at the current selected index.
  int targetIndex = target.getSelectedIndex();

  // Prevent the user from dropping data back on itself.
  // For example, if the user is moving items #4,#5,#6 and #7 and
  // attempts to insert the items after item #5, this would
  // be problematic when removing the original items.
  // This is interpreted as dropping the same data on itself
  // and has no effect.
  if (source.equals(target)) {
    // System.out.print("checking indices index TO: " + targetIndex + "
    // FROM:");
    // for (int i = 0; i < sourceIndices.length;i++)
    // System.out.print(" "+sourceIndices[i]);
    // System.out.println("");
    if (targetIndex >= sourceIndices[0]
        && targetIndex <= sourceIndices[sourceIndices.length - 1]) {
      // System.out.println("setting indices null : " + targetIndex + " " +
      // sourceIndices[0] + " " + sourceIndices[sourceIndices.length - 1]);
      sourceIndices = null;
      return true;
    }
  }

  DefaultListModel listModel = (DefaultListModel) target.getModel();
  int max = listModel.getSize();
  if (targetIndex < 0) {
    targetIndex = max;
  } else {
    if (sourceIndices[0] < targetIndex)
      targetIndex++;
    if (targetIndex > max) {
      targetIndex = max;
    }
  }
  addIndex = targetIndex;
  addCount = alist.size();
  for (int i = 0; i < alist.size(); i++) {
    listModel.add(targetIndex++, objectOf(listModel, alist.get(i)));
  }
  return true;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void readMolecularOrbitals() throws Exception {
  if (shells == null)
    return;
  Map<String, Object>[] mos = ArrayUtil.createArrayOfHashtable(5);
  List<String>[] data = ArrayUtil.createArrayOfArrayList(5);
  int nThisLine = 0;
  while (readLine() != null
      && line.toUpperCase().indexOf("DENS") < 0) {
    String[] tokens;
    if (line.indexOf("                    ") == 0) {
      addMOData(nThisLine, data, mos);
      tokens = getTokens(readLine());
      nThisLine = tokens.length;
      for (int i = 0; i < nThisLine; i++) {
        mos[i] = new Hashtable<String, Object>();
        data[i] = new ArrayList<String>();
        String sym = tokens[i];
        mos[i].put("symmetry", sym);
        if (sym.indexOf("--O") >= 0)
          mos[i].put("occupancy", new Float(2));
        else if (sym.indexOf("--V") >= 0)
          mos[i].put("occupancy", new Float(0));
      }
      line = readLine().substring(21);
      tokens = getTokens();
      if (tokens.length != nThisLine)
        tokens = getStrings(line, nThisLine, 10);
      for (int i = 0; i < nThisLine; i++)
        mos[i].put("energy", new Float(tokens[i]));
      continue;
    } else if (line.length() < 21 || (line.charAt(11) != ' ' 
                                      && ! Character.isDigit(line.charAt(11)) 
                                      ) ) {
      continue;
    }
    try {
      String type = line.substring(13, 18).trim();
      if (!isQuantumBasisSupported(type.charAt(0)) && "XYZ".indexOf(type.charAt(0)) >= 0)
        type = (type.length() == 2 ? "D" : "F") + type;
      if (!isQuantumBasisSupported(type.charAt(0)))
        continue;
      tokens = getStrings(line.substring(21), nThisLine, 10);
      for (int i = 0; i < nThisLine; i++)
        data[i].add(tokens[i]);
    } catch (Exception e) {
      Logger.error("Error reading Gaussian file Molecular Orbitals at line: "
          + line);
      break;
    }
  }
  addMOData(nThisLine, data, mos);
  setMOData(false); // perhaps in the future we might change this to TRUE
}