Java Logger.debugging方法代码示例

import org.jmol.util.Logger; //导入方法依赖的package包/类
/**
 * after the vectors intinfo and floatinfo are completed, we
 * 
 * @param doScale
 * @param doSort TODO
 */
protected final void setSlaters(boolean doScale, boolean doSort) {
  if (slaterArray == null) {
    int nSlaters = slaters.size();
    slaterArray = new SlaterData[nSlaters];
    for (int i = 0; i < slaterArray.length; i++) 
      slaterArray[i] = slaters.get(i);
  }
  if (doScale)
    for (int i = 0; i < slaterArray.length; i++) {
      SlaterData sd = slaterArray[i];
      sd.coef *= scaleSlater(sd.x, sd.y, sd.z, sd.r, sd.zeta);
      if (Logger.debugging) {
        Logger.debug("SlaterReader " + i + ": " + sd.iAtom + " " + sd.x + " " + sd.y +  " " + sd.z + " " + sd.r + " " + sd.zeta + " " + sd.coef);
      }
    }
  if (doSort) {
    Arrays.sort(slaterArray, new SlaterSorter());
    int[] pointers = new int[slaterArray.length];      
    for (int i = 0; i < slaterArray.length; i++)
      pointers[i] = slaterArray[i].index;
    sortOrbitalCoefficients(pointers);
  }
  moData.put("slaters", slaterArray);
  atomSetCollection.setAtomSetAuxiliaryInfo("moData", moData);
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
void popContext(boolean isFlowCommand, boolean statementOnly) {
  if (thisContext == null)
    return;
  if (thisContext.scriptLevel > 0)
    scriptLevel = thisContext.scriptLevel - 1;
  // we must save (and thus NOT restore) the current statement
  // business when doing push/pop for commands like FOR and WHILE
  ScriptContext scTemp = (isFlowCommand ? getScriptContext() : null);
  restoreScriptContext(thisContext, true, isFlowCommand, statementOnly);
  restoreScriptContext(scTemp, true, false, true);
  if (Logger.debugging || isCmdLine_c_or_C_Option)
    Logger.info("--<<-------------".substring(0, Math.max(17, scriptLevel + 5))
        + scriptLevel + " " + filename + " "
        + (thisContext == null ? "" : "" + thisContext.token) + " "
        + thisContext);
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private String getString(String string) {
  if (!doTranslate || translationResourcesCount == 0)
    return string;
  for (int bundle = 0; bundle < translationResourcesCount; bundle++) {
    try {
      String trans = translationResources[bundle].getString(string);
      return trans;
    } catch (MissingResourceException e) {
      // Normal
    }
  }
  if (Logger.debugging) {
    Logger.info("No trans, using default: " + string);
  }
  return string;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private boolean getCachedLine() {
  slopeKey = new Float(slope);
  if (!lineCache.containsKey(slopeKey))
    return false;
  lineBits = lineCache.get(slopeKey);
  nFound++;
  if (nFound == 1000000)
    if (Logger.debugging) {
      Logger.debug("nCached/nFound lines: " + nCached + " " + nFound);
    }
  return true;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name,
                                float[] notionalUnitCell) {
  spaceGroup = SpaceGroup.createSpaceGroup(desiredSpaceGroupIndex, name,
      notionalUnitCell);
  if (spaceGroup != null && Logger.debugging)
    Logger.debug("using generated space group " + spaceGroup.dumpInfo(null));
  return spaceGroup != null;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private Point4f hklParameter(int i) throws ScriptException {
  if (!isSyntaxCheck && viewer.getCurrentUnitCell() == null)
    error(ERROR_noUnitCell);
  Point3f pt = (Point3f) getPointOrPlane(i, false, true, false, true, 3, 3);
  Point4f p = getHklPlane(pt);
  if (p == null)
    error(ERROR_badMillerIndices);
  if (!isSyntaxCheck && Logger.debugging)
    Logger.info("defined plane: " + p);
  return p;
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
/**
 * 
 * @return TRUE if data, even if ''; FALSE if '.' or  '?' or eof.
 * 
 * @throws Exception
 */
private boolean getData() throws Exception {
  key = tokenizer.getTokenPeeked();
  data = tokenizer.getNextToken();
  if (Logger.debugging)
    Logger.debug(key  + " " + data);
  if (data == null) {
    Logger.warn("CIF ERROR ? end of file; data missing: " + key);
    return false;
  }
  return (data.length() == 0 || data.charAt(0) != '\0');
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
protected void initializeBspf() {
  if (bspf == null) {
    if (showRebondTimes && Logger.debugging)
      Logger.startTimer();
    bspf = new Bspf(3);
    /*      if (MIX_BSPT_ORDER) {
     Logger.debug("mixing bspt order");
     int stride = 3;
     int step = (atomCount + stride - 1) / stride;
     for (int i = 0; i < step; ++i)
     for (int j = 0; j < stride; ++j) {
     int k = i * stride + j;
     if (k >= atomCount)
     continue;
     Atom atom = atoms[k];
     bspf.addTuple(atom.modelIndex, atom);
     }
     } else {
     */
    Logger.debug("sequential bspt order");
    for (int i = atomCount; --i >= 0;) {
      // important that we go backward here, because we are going to 
      // use System.arrayCopy to expand the array ONCE only
      Atom atom = atoms[i];
      bspf.addTuple(models[atom.modelIndex].trajectoryBaseIndex, atom);
    }
    //      }
    if (showRebondTimes && Logger.debugging) {
      Logger.checkTimer("Time to build bspf");
      bspf.stats();
      //        bspf.dump();
    }
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void removeBinding(Iterator<String> e, String key) {
  if (Logger.debugging)
    Logger.debug("removing binding " + key);
  if (e == null)
    bindings.remove(key); 
  else
    e.remove();
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
synchronized private static void cleanRegistry() {
  AppletWrapper app = null;
  boolean closed = true;
  for (Map.Entry<String, Applet> entry : htRegistry.entrySet()) {
    String theApplet = entry.getKey();
    try {
      app = (AppletWrapper) (entry.getValue());
      JSObject theWindow = JSObject.getWindow(app);
      //System.out.print("checking " + app + " window : ");
      closed = ((Boolean) theWindow.getMember("closed")).booleanValue();
      //System.out.println(closed);
      if (closed || theWindow.hashCode() == 0) {
        //error trap
      }
      if (Logger.debugging)
        Logger.debug("Preserving registered applet " + theApplet
            + " window: " + theWindow.hashCode());
    } catch (Exception e) {
      closed = true;
    }
    if (closed) {
      if (Logger.debugging)
        Logger.debug("Dereferencing closed window applet " + theApplet);
      htRegistry.remove(theApplet);
      app.destroy();
    }
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private void readAtoms(int atomCount0, boolean doAddAtoms) throws Exception {
  for (int i = 0; i < modelAtomCount; i++) {
    String tokens[] = getTokens(readLine());
    Atom atom = (doAddAtoms ? r.atomSetCollection.addNewAtom()
        : r.atomSetCollection.getAtom(atomCount0 - modelAtomCount + i));
    atom.elementSymbol = AtomSetCollectionReader
        .getElementSymbol(parseInt(tokens[0]));
    r.setAtomCoord(atom, parseFloat(tokens[1]) * AtomSetCollectionReader.ANGSTROMS_PER_BOHR, 
        parseFloat(tokens[2]) * AtomSetCollectionReader.ANGSTROMS_PER_BOHR, 
        parseFloat(tokens[3]) * AtomSetCollectionReader.ANGSTROMS_PER_BOHR);
  }
  if (doAddAtoms && Logger.debugging) {
    Logger.debug(atomCount + " atoms read");
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
public void assignPotentials(Atom[] atoms, float[] potentials,
                             BitSet bsAromatic, BitSet bsCarbonyl,
                             BitSet bsIgnore, String data) {
  getAtomicPotentials(data, "atomicLipophilicity.txt");
  for (int i = 0; i < atoms.length; i++) {
    float f = Math.abs(atoms[i].getFormalCharge());
    if (f == 0) {
      if (bsIgnore != null && bsIgnore.get(i)) {
        f = Float.NaN;
      } else {
        f = getTabulatedPotential(atoms[i]);
        if (Float.isNaN(f))
          switch (atoms[i].getElementNumber()) {
          case 6:
            f = (bsAromatic.get(i) ? 0.31f : bsCarbonyl.get(i) ? -0.54f
                : 0.45f);
            break;
          case 7:
            f = (bsAromatic.get(i) ? -0.6f : bsCarbonyl.get(i) ? -0.44f
                : -1.0f);
            break;
          case 8:
            f = (bsCarbonyl.get(i) ? -0.9f : -0.17f);
            break;
          default:
            f = Float.NaN;
          }
      }
    }
    if (Logger.debugging)
      Logger.info(atoms[i].getInfo() + " " + f);
    potentials[i] = f;
  }
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
@Override
protected void finalizeReader() throws Exception {
  super.finalizeReader();
  if (nOrbitals > 0)
    setMOs("eV");
  if (Logger.debugging)
    Logger.debug(orbitals.size() + " molecular orbitals read");
}
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
private boolean readMolecularOrbitalVectors() throws Exception {

    if (shells == null)
      return true;
    Map<String, Object>[] mos = null;
    List<String>[] data = null;
    int moCount = 0;
    int iListed = 0;
    int ptOffset = -1;
    int fieldSize = 0;
    int nThisLine = 0;
    discardLines(5);
    boolean isBeta = false;
    boolean betaOnly = !filterMO();
    while (readLine() != null) {
      if (parseInt(line) != iListed + 1) {
        if (line.indexOf("beta") < 0)
          break;
        alphaBeta = "beta ";
        if (!filterMO())
          break;
        isBeta = true;
        iListed = 0;
        readLine();
        continue;
      }
      
      readLine();
      String[] tokens = getTokens();
      if (Logger.debugging) {
        Logger.debug(tokens.length + " --- " + line);
      }
      nThisLine = tokens.length;
      ptOffset = 6;
      fieldSize = 12;
      mos = ArrayUtil.createArrayOfHashtable(nThisLine);
      data = ArrayUtil.createArrayOfArrayList(nThisLine);
      for (int i = 0; i < nThisLine; i++) {
        mos[i] = new Hashtable<String, Object>();
        data[i] = new ArrayList<String>();
      }

      while (readLine() != null && line.length() > 0)
        for (int i = 0, pt = ptOffset; i < nThisLine; i++, pt += fieldSize)
          data[i].add(line.substring(pt, pt + fieldSize).trim());

      for (int iMo = 0; iMo < nThisLine; iMo++) {
        float[] coefs = new float[data[iMo].size()];
        int iCoeff = 0;
        while (iCoeff < coefs.length) {
          coefs[iCoeff] = parseFloat(data[iMo].get(iCoeff));
          iCoeff++;
        }
        mos[iMo].put("coefficients", coefs);
        mos[iMo].put("type", alphaBeta + " "            + (++iListed));
        ++moCount;
        Map<String, Object> mo = (moInfo == null ? null : moInfo.get(Integer
            .valueOf(isBeta ? -iListed : iListed)));
        if (mo != null)
          mos[iMo].putAll(mo);
        if (!betaOnly || isBeta)
          setMO(mos[iMo]);
      }
      line = "";
    }
    energyUnits = "a.u.";
    setMOData(false);
    return true;
  }
 

import org.jmol.util.Logger; //导入方法依赖的package包/类
public void setDebugging() {
  debugScript = viewer.getDebugScript();
  logMessages = (debugScript && Logger.debugging);
}