Esempio n. 1
0
  /**
   * When this class is loaded, preload the cache with a few items which we think will often be
   * needed. This can avoid the necessity of running a belief network context in simple problems.
   */
  static {
    System.err.println("PiHelperLoader.static: preload the helper cache.");

    helper_cache = new Hashtable();
    Vector seq = new Vector();

    seq.addElement(riso.distributions.ConditionalDiscrete.class);
    seq.addElement(riso.distributions.Discrete.class);

    helper_cache.put(
        new HelperCacheKey("pi", seq),
        riso.distributions.computes_pi.ConditionalDiscrete_Discrete.class);

    seq = new Vector();
    seq.addElement(riso.distributions.Discrete.class);

    helper_cache.put(
        new HelperCacheKey("lambda", seq), riso.distributions.computes_lambda.Discrete.class);

    seq = new Vector();
    seq.addElement(riso.distributions.AbstractDistribution.class);
    seq.addElement(riso.distributions.AbstractDistribution.class);

    helper_cache.put(
        new HelperCacheKey("pi_message", seq),
        riso.distributions.computes_pi_message.AbstractDistribution_AbstractDistribution.class);

    seq = new Vector();
    seq.addElement(riso.distributions.ConditionalDiscrete.class);
    seq.addElement(riso.distributions.Discrete.class);
    seq.addElement(riso.distributions.Discrete.class);

    helper_cache.put(
        new HelperCacheKey("lambda_message", seq),
        riso.distributions.computes_lambda_message.ConditionalDiscrete_Discrete_Discrete.class);

    seq = new Vector();
    seq.addElement(riso.distributions.ConditionalDiscrete.class);
    seq.addElement(riso.distributions.Discrete.class);

    helper_cache.put(
        new HelperCacheKey("lambda_message", seq),
        riso.distributions.computes_lambda_message.ConditionalDiscrete_Discrete_.class);

    seq = new Vector();
    seq.addElement(riso.distributions.Discrete.class);
    seq.addElement(riso.distributions.Discrete.class);

    helper_cache.put(
        new HelperCacheKey("posterior", seq),
        riso.distributions.computes_posterior.Discrete_Discrete.class);

    System.err.println("PiHelperLoader.static: helper_cache.size(): " + helper_cache.size());
  }
Esempio n. 2
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 public Vector getAssociatedLevelLists() {
   Vector levelLists = new Vector();
   Vector endPts = CollectionHelper.makeVector("Keyword");
   Hashtable keywordParents =
       oncotcap.Oncotcap.getDataSource()
           .getParentTree(
               "Keyword", endPts, CollectionHelper.makeVector(this), TreeDisplayModePanel.ROOT);
   // Take each of the parents and get the associated level lists
   if (keywordParents.size() <= 0) return levelLists;
   Hashtable levelListsHashtable =
       oncotcap.Oncotcap.getDataSource()
           .getInstanceTree(
               "EnumLevelList",
               new Vector(),
               makeLevelListFilter(keywordParents),
               TreeDisplayModePanel.ROOT);
   for (Enumeration e = keywordParents.keys(); e.hasMoreElements(); ) {
     System.out.println("Keyword.getAssociatedLevelLists: " + e.nextElement());
   }
   // Collect all the level lists from the hashtable
   Vector selectedItems = CollectionHelper.makeVector(keyword);
   for (Enumeration e = levelListsHashtable.keys(); e.hasMoreElements(); ) {
     Object obj = e.nextElement();
     if (obj instanceof EnumLevelList) {
       levelLists.addElement(obj);
     }
   }
   return levelLists;
 }
Esempio n. 3
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  public static PiHelper load_pi_helper(
      PiHelper pi_helper_cache, ConditionalDistribution pxu, Distribution[] pi_messages)
      throws Exception {
    if (pi_messages.length == 0) return new TrivialPiHelper();

    Vector seq = new Vector();
    seq.addElement(pxu.getClass());
    for (int i = 0; i < pi_messages.length; i++) seq.addElement(pi_messages[i].getClass());

    if (pi_helper_cache != null
        && MatchClassPattern.matches(pi_helper_cache.description(), seq, new int[1], new int[1]))
      return pi_helper_cache;

    Class c = find_helper_class(seq, "pi");
    return (PiHelper) c.newInstance();
  }
Esempio n. 4
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 public void addWelcomeFile(String s) {
   // user specified at least one user welcome file, remove the system
   // files
   if (s == null) return;
   s = s.trim();
   if (s.length() == 0) return;
   if (expectUserWelcomeFiles) {
     removeWelcomeFiles();
     expectUserWelcomeFiles = false;
   }
   welcomeFiles.addElement(s);
 }
Esempio n. 5
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 private Vector getChildren(Keyword keyword, Vector allKids) {
   allKids.addElement(keyword);
   // 			System.out.println("Addtoallkids " + keyword + "  " + allKids );
   Vector children = keyword.getChildren();
   if (children != null) {
     Iterator i = children.iterator();
     while (i.hasNext()) {
       Keyword child = (Keyword) i.next();
       getChildren(child, allKids);
     }
   }
   return allKids;
 }
  public static Vector getClassFieldsValues(Object classFile) {
    Vector ret = new Vector();
    try {
      Field[] fields = classFile.getClass().getDeclaredFields();

      for (int loop = 0; loop < fields.length; loop++) {
        ret.addElement(fields[loop].getInt(classFile));
      }

    } catch (Exception d) {
      d.printStackTrace();
      Miscellaneous.exit();
    }
    return ret;
  }
Esempio n. 7
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  public Class[] getClassesFromClass(Class c) {
    Vector cList = new Vector();
    Class cTemp;
    Class[] aList;

    cTemp = c;
    while ((cTemp = cTemp.getSuperclass()) != null) {
      cList.addElement(cTemp);
    }

    aList = new Class[cList.size()];
    for (int i = 0; i < cList.size(); i++) {
      aList[i] = (Class) cList.elementAt(i);
    }
    return aList;
  }
Esempio n. 8
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  public static Vector extractKeywordFromText(String text) {
    // see if there are any existing keywords represented
    // in this text
    // Get all keywords

    Vector extractedKeywords = new Vector();
    Iterator keywords = allKeywords.iterator();
    while (keywords.hasNext()) {
      Keyword keyword = (Keyword) keywords.next();
      if (text != null
          && keyword.toString() != null
          && text.toLowerCase().indexOf(keyword.toString().toLowerCase()) > -1) {
        extractedKeywords.addElement(keyword);
      }
    }
    return extractedKeywords;
  }
Esempio n. 9
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 String[] openUrlAsList(String address) {
   Vector v = new Vector();
   try {
     URL url = new URL(address);
     InputStream in = url.openStream();
     BufferedReader br = new BufferedReader(new InputStreamReader(in));
     String line;
     while (true) {
       line = br.readLine();
       if (line == null) break;
       if (!line.equals("")) v.addElement(line);
     }
     br.close();
   } catch (Exception e) {
   }
   String[] lines = new String[v.size()];
   v.copyInto((String[]) lines);
   return lines;
 }
Esempio n. 10
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 /**
  * Virtual host support - this context will be part of a virtual host with the specified name. You
  * should set all the aliases. XXX Not implemented
  */
 public void addHostAlias(String alias) {
   vhostAliases.addElement(alias);
 }
Esempio n. 11
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 private void init() {
   initGetterMap();
   initSetterMap();
   allKeywords.addElement(this);
   initPopupMenu();
 }
Esempio n. 12
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  /**
   * Sets the TabularData to the AaplicationTable
   *
   * @param data The TabularData to be set to the AaplicationTable
   */
  public void setAlarmTable(TabularData data) throws Exception {
    AgentException ae = null;

    for (Enumeration e = data.enumerate(); e.hasMoreElements(); ) {
      Object[] index = (Object[]) e.nextElement();
      CompositeData comp = data.getRow(index);

      if (table != null)
        entry =
            (AlarmEntry)
                Utilities.getEntryFromCompositeData(table, comp, indexNames, instrClassName);
      else if (vec != null)
        entry =
            (AlarmEntry) Utilities.getEntryFromCompositeData(vec, comp, indexNames, instrClassName);

      if (comp.getOperationType().equals(CompositeData.CREATED)) { // create new entry

        if (entry != null)
          throw new AgentException("Row already exist", CommonUtils.ROWCREATIONFAILED); // no i18n
        entry = new AlarmEntry();

        if (table != null) table.put(index, entry);
        else if (vec != null) vec.addElement(entry);
        for (Enumeration ce = comp.enumerate(); ce.hasMoreElements(); ) {
          String key = (String) ce.nextElement();
          try {
            Utilities.setField(entry, instrClassName, key, comp.getDataItem(key));
          } catch (AgentException aexp) {
            ae = aexp;
          }
        }
      } else if (comp.getOperationType().equals(CompositeData.DELETED)) {

        if (table != null) {
          for (Enumeration en = table.keys(); en.hasMoreElements(); ) {
            Object keyObject = en.nextElement();
            if (entry.equals(table.get(keyObject))) table.remove(keyObject);
          }
        } else if (vec != null)
          if (!vec.removeElement(entry))
            throw new AgentException("Invalid Index", CommonUtils.INVALIDINDEX); // no i18n
        data.deleteRow(index);
      } else if (comp.getOperationType().equals(CompositeData.MODIFIED)) {

        for (Enumeration ce = comp.enumerate(); ce.hasMoreElements(); ) {
          String key = (String) ce.nextElement();
          if (!comp.isModified(key)) continue;
          try {

            Utilities.setField(entry, instrClassName, key, comp.getDataItem(key));
          } catch (AgentException aexp) {
            ae = aexp;
          }
        }
      }

      comp.setOperationType(CompositeData.NOCHANGES);
    }

    if (ae != null) throw ae;
  }
Esempio n. 13
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  /**
   * This method returns a <tt>Class</tt> for a helper which can handle the list of distributions
   * specified by <tt>seq1</tt>. We maintain a cache of recently-loaded helpers, so check the cache
   * before going to the trouble of searching for a helper. The cache is blown away every
   * <tt>HELPER_CACHE_REFRESH</tt> seconds.
   *
   * <p>If we can't find a helper in the cache, we must search through the list of available helpers
   * to find an appropriate one. First try to find helper using class sequence as specified by
   * <tt>seq</tt>. Whether or not that succeeds, promote any <tt>Gaussian</tt> in the sequence to
   * <tt>MixGaussians</tt>, and try again. If we get a better match on the second try, return the
   * helper thus found.
   */
  public static Class find_helper_class(Vector seq1, String helper_type)
      throws ClassNotFoundException {
    // Let's see if an appropriate helper is in the cache.
    // If the cache is too old, empty it and search for the helper anew.

    if (System.currentTimeMillis() - cache_timestamp > HELPER_CACHE_REFRESH) {
      helper_cache = new Hashtable();
      cache_timestamp = System.currentTimeMillis();
      // Go on and search for appropriate helper.
    } else {
      HelperCacheKey key = new HelperCacheKey(helper_type, seq1);
      Class helper_class = (Class) helper_cache.get(key);
      if (helper_class != null) {
        if (Global.debug > -1)
          System.err.println(
              "PiHelperLoader.find_helper_class: found helper class: "
                  + helper_class
                  + "; no need to search.");
        return helper_class;
      }
      // else no luck; we have to search for helper.
    }

    // Well, we didn't find a helper in the cache, so let's go to work.
    if (Global.debug > -1)
      System.err.println(
          "PiHelperLoader.find_helper_class: DID NOT FIND HELPER CLASS; NOW SEARCH.");

    Class c1 = null, c2 = null;
    ClassNotFoundException cnfe1 = null, cnfe2 = null;
    int[] class_score1 = new int[1], count_score1 = new int[1];
    int[] class_score2 = new int[1], count_score2 = new int[1];

    try {
      c1 = find_helper_class1(seq1, helper_type, class_score1, count_score1);
    } catch (ClassNotFoundException e) {
      cnfe1 = e;
    } // hang on, we may need to re-throw later.

    Class gaussian_class = Class.forName("riso.distributions.Gaussian");
    MixGaussians mog = new MixGaussians(1, 1);

    Vector seq2 = new Vector(seq1.size());
    for (int i = 0; i < seq1.size(); i++)
      if (gaussian_class.isAssignableFrom((Class) seq1.elementAt(i)))
        seq2.addElement(mog.getClass());
      else seq2.addElement(seq1.elementAt(i));

    try {
      c2 = find_helper_class1(seq2, helper_type, class_score2, count_score2);
    } catch (ClassNotFoundException e) {
      cnfe2 = e;
    }

    if (cnfe1 == null && cnfe2 == null) {
      // Both matched; see which one fits better.
      // Break ties in favor of the helper for non-promoted messages.

      if (class_score1[0] >= class_score2[0]
          || (class_score1[0] == class_score2[0] && count_score1[0] >= count_score2[0])) {
        if (Global.debug > 1)
          System.err.println(
              "\taccept helper " + c1 + " for non-promoted classes instead of " + c2);
        if (Global.debug > 1)
          System.err.println(
              "\t\t"
                  + class_score1[0]
                  + ", "
                  + class_score2[0]
                  + "; "
                  + count_score1[0]
                  + ", "
                  + count_score2[0]);
        helper_cache.put(new HelperCacheKey(helper_type, seq1), c1);
        return c1;
      } else {
        if (Global.debug > 1)
          System.err.println("\taccept helper " + c2 + " for promoted classes instead of " + c1);
        if (Global.debug > 1)
          System.err.println(
              "\t\t"
                  + class_score1[0]
                  + ", "
                  + class_score2[0]
                  + "; "
                  + count_score1[0]
                  + ", "
                  + count_score2[0]);
        helper_cache.put(new HelperCacheKey(helper_type, seq1), c2);
        return c2;
      }
    } else if (cnfe1 == null && cnfe2 != null) {
      // Only the first try matched, return it.
      helper_cache.put(new HelperCacheKey(helper_type, seq1), c1);
      return c1;
    } else if (cnfe1 != null && cnfe2 == null) {
      // Only the second try matched, return it.
      helper_cache.put(new HelperCacheKey(helper_type, seq1), c2);
      return c2;
    } else {
      // Neither try matched. Re-throw the exception generated by the first try.
      throw cnfe1;
    }
  }
Esempio n. 14
0
  /**
   * Reads XML element(s) into an indexed bean property by first locating the XML element(s)
   * corresponding to this property.
   *
   * @param ob The bean whose property is being set
   * @param desc The property that will be set
   * @param nodes The list of XML items that may contain the property
   * @throws IOException If there is an error reading the document
   */
  public void readIndexedProperty(
      Object ob, IndexedPropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
      throws IOException {
    // Create a vector to hold the property values
    Vector v = new Vector();

    int numAttrs = attrs.getLength();

    for (int i = 0; i < numAttrs; i++) {
      // See if this attribute matches the property name
      if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
        // Get the property value
        Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());

        if (obValue != null) {
          // Add the value to the list of values to be set
          v.addElement(obValue);
        }
      }
    }

    int numNodes = nodes.getLength();

    for (int i = 0; i < numNodes; i++) {
      Node node = nodes.item(i);

      // Skip non-element nodes
      if (!(node instanceof Element)) continue;

      Element element = (Element) node;

      // See if this element tag matches the property name
      if (namesMatch(desc.getName(), element.getTagName())) {
        // Get the property value
        Object obValue = getObjectValue(desc, element);

        if (obValue != null) {
          // Add the value to the list of values to be set
          v.addElement(obValue);
        }
      }
    }

    // Get the method used to set the property value
    Method setter = desc.getWriteMethod();

    // If this property has no setter, don't write it
    if (setter == null) return;

    // Create a new array of property values
    Object propArray = Array.newInstance(desc.getPropertyType().getComponentType(), v.size());

    // Copy the vector into the array
    v.copyInto((Object[]) propArray);

    try {
      // Store the array of property values
      setter.invoke(ob, new Object[] {propArray});
    } catch (InvocationTargetException exc) {
      throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
    } catch (IllegalAccessException exc) {
      throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
    }
  }
Esempio n. 15
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  /**
   * Reads an XML element into a bean property by first locating the XML element corresponding to
   * this property.
   *
   * @param ob The bean whose property is being set
   * @param desc The property that will be set
   * @param nodes The list of XML items that may contain the property
   * @throws IOException If there is an error reading the document
   */
  public void readProperty(Object ob, PropertyDescriptor desc, NodeList nodes, NamedNodeMap attrs)
      throws IOException {
    int numAttrs = attrs.getLength();

    for (int i = 0; i < numAttrs; i++) {
      // See if the attribute name matches the property name
      if (namesMatch(desc.getName(), attrs.item(i).getNodeName())) {
        // Get the method used to set this property
        Method setter = desc.getWriteMethod();

        // If this object has no setter, don't bother writing it
        if (setter == null) continue;

        // Get the value of the property
        Object obValue = getObjectValue(desc, attrs.item(i).getNodeValue());
        if (obValue != null) {
          try {
            // Set the property value
            setter.invoke(ob, new Object[] {obValue});
          } catch (InvocationTargetException exc) {
            throw new IOException(
                "Error setting property " + desc.getName() + ": " + exc.toString());
          } catch (IllegalAccessException exc) {
            throw new IOException(
                "Error setting property " + desc.getName() + ": " + exc.toString());
          }
        }

        return;
      }
    }

    int numNodes = nodes.getLength();

    Vector arrayBuild = null;

    for (int i = 0; i < numNodes; i++) {
      Node node = nodes.item(i);

      // If this node isn't an element, skip it
      if (!(node instanceof Element)) continue;

      Element element = (Element) node;

      // See if the tag name matches the property name
      if (namesMatch(desc.getName(), element.getTagName())) {
        // Get the method used to set this property
        Method setter = desc.getWriteMethod();

        // If this object has no setter, don't bother writing it
        if (setter == null) continue;

        // Get the value of the property
        Object obValue = getObjectValue(desc, element);

        // 070201 MAW: Modified from change submitted by Steve Poulson
        if (setter.getParameterTypes()[0].isArray()) {
          if (arrayBuild == null) {
            arrayBuild = new Vector();
          }
          arrayBuild.addElement(obValue);

          // 070201 MAW: Go ahead and read through the rest of the nodes in case
          //             another one matches the array. This has the effect of skipping
          //             over the "return" statement down below
          continue;
        }

        if (obValue != null) {
          try {
            // Set the property value
            setter.invoke(ob, new Object[] {obValue});
          } catch (InvocationTargetException exc) {
            throw new IOException(
                "Error setting property " + desc.getName() + ": " + exc.toString());
          } catch (IllegalAccessException exc) {
            throw new IOException(
                "Error setting property " + desc.getName() + ": " + exc.toString());
          }
        }
        return;
      }
    }

    // If we build a vector of array members, convert the vector into
    // an array and save it in the property
    if (arrayBuild != null) {
      // Get the method used to set this property
      Method setter = desc.getWriteMethod();

      if (setter == null) return;

      Object[] obValues = (Object[]) Array.newInstance(desc.getPropertyType(), arrayBuild.size());

      arrayBuild.copyInto(obValues);

      try {
        setter.invoke(ob, new Object[] {obValues});
      } catch (InvocationTargetException exc) {
        throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
      } catch (IllegalAccessException exc) {
        throw new IOException("Error setting property " + desc.getName() + ": " + exc.toString());
      }

      return;
    }
  }
 public void bundleChanged(BundleEvent evt) {
   if (evt.getType() == BundleEvent.STARTED || evt.getType() == BundleEvent.STOPPED) {
     events.addElement(evt);
   }
 }
Esempio n. 17
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  /**
   * Parse the section file and fill in the Dbase.
   *
   * @return Success code
   */
  public void parse() throws Exception {
    JOAParameter tempProperties[] = new JOAParameter[100];
    FileInputStream in = null;
    DataInputStream inData = null;
    short inShort = 0;
    long bytesRead = 0;
    long bytesInFile = mFile.length();
    short[] sarray = new short[1];
    int mTotalStns = 0;

    EPSProgressDialog mProgress = new EPSProgressDialog(new Frame(), mProgressStr, Color.blue);
    mProgress.setVisible(true);

    // Get an epic key database specific to JOA
    EPIC_Key_DB mEpicKeyDB = new EPIC_Key_DB("joa_epic.key");

    // Get an epic key database specific to JOA
    EPIC_Key_DB mOrigEpicKeyDB = new EPIC_Key_DB("epic.key");

    // create a vector for temporary storage of the dbases
    Vector dBases = new Vector(100);

    try {
      in = new FileInputStream(mFile);
      BufferedInputStream bis = new BufferedInputStream(in, 1000000);
      inData = new DataInputStream(bis);

      // read version
      short vers = inData.readShort();
      bytesRead += 2;

      if (vers < 2) {
        FileImportException fiex = new FileImportException();
        String errStr = "Invalid version for a JOA binary file";
        fiex.setErrorType(errStr);
        throw fiex;
      }

      // read number of bytes in file description string
      inShort = inData.readShort();
      bytesRead += 2;

      // read the file description String
      byte buf[] = new byte[inShort];
      inData.read(buf, 0, inShort);
      String fileDescrip = new String(buf);
      bytesRead += inShort;

      // create a new open file object
      JOADataFile of = new JOADataFile(fileDescrip);

      // read the number of sections
      int numSections = inData.readShort();
      bytesRead += 2;

      // read each section
      JOASection sech;
      int ord = 0;
      for (int s = 0; s < numSections; s++) {
        mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));

        // read the section header
        inShort = inData.readShort();
        bytesRead += 2;
        byte buf1[] = new byte[inShort];
        inData.read(buf1, 0, inShort);
        String sectionDescrip = new String(buf1);
        bytesRead += inShort;

        // read the ship code
        byte bufsc[] = new byte[2];
        bufsc[0] = inData.readByte();
        bufsc[1] = inData.readByte();
        String shipCode = new String(bufsc);
        bytesRead += 2;

        // read num casts
        int numCasts = inData.readShort();
        bytesRead += 2;

        // read num parameters
        int numVars = inData.readShort();
        bytesRead += 2;

        // quality code
        int qcStd = 1;
        if (vers == 4) {
          qcStd = inData.readShort();
          bytesRead += 2;
        }

        // create a new section
        of.mNumSections++;
        sech = new JOASection(of.mNumSections, sectionDescrip, shipCode, numCasts, numVars);

        if (vers == 2) {
          // read the properties
          byte bufv[] = new byte[4];
          for (int p = 0; p < numVars; p++) {
            // parameter name
            inData.read(bufv, 0, 4);
            String tempVar = new String(bufv);
            bytesRead += 4;

            // units
            inShort = inData.readShort();
            bytesRead += 2;

            String units = null;
            if (inShort > 0) {
              byte buf11[] = new byte[inShort];
              inData.read(buf11, 0, inShort);
              units = new String(buf11);
              bytesRead += inShort;
            }

            // convert varnames to UC
            tempVar.toUpperCase();

            // create new property
            tempProperties[p] = new JOAParameter(tempVar, units);

            // add this property to the section property list
            if (tempProperties[p].mUnits == null) {
              tempProperties[p].mUnits =
                  EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
            }

            if (tempProperties[p].mUnits == null) {
              tempProperties[p].mUnits = new String("na");
            }
            tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;

            // read the actual scale
            int actScale = inData.readShort();
            bytesRead += 2;

            if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
            else tempProperties[p].mActScale = 1.0;

            // read the actual origin
            int actOrigin = inData.readShort();
            tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;

            // read reverse y
            int reverseY = inData.readShort();
            bytesRead += 2;

            if (reverseY == 0) tempProperties[p].mReverseY = false;
            else tempProperties[p].mReverseY = true;

            tempProperties[p].mWasCalculated = false;
          }
        } else {
          // read the properties
          String tempVar = null;
          for (int p = 0; p < numVars; p++) {
            // length of parameter name
            inShort = inData.readShort();
            bytesRead += 2;

            // parameter name
            if (inShort > 0) {
              byte buf13[] = new byte[inShort];
              inData.read(buf13, 0, inShort);
              tempVar = new String(buf13);
              bytesRead += inShort;
            }

            // units
            inShort = inData.readShort();
            bytesRead += 2;

            String units = null;
            if (inShort > 0) {
              byte buf11[] = new byte[inShort];
              inData.read(buf11, 0, inShort);
              units = new String(buf11);
              bytesRead += inShort;
            }

            // convert varnames to UC
            tempVar = tempVar.toUpperCase();

            // create new property
            tempProperties[p] = new JOAParameter(tempVar, units);

            // add this property to the section property list
            if (tempProperties[p].mUnits == null) {
              tempProperties[p].mUnits =
                  EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
            }

            if (tempProperties[p].mUnits == null) {
              tempProperties[p].mUnits = new String("na");
            }
            tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;

            // read the actual scale
            int actScale = inData.readShort();
            bytesRead += 2;
            if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
            else tempProperties[p].mActScale = 1.0;

            // read the actual origin
            int actOrigin = inData.readShort();
            tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;

            // read reverse y
            int reverseY = inData.readShort();
            bytesRead += 2;
            if (reverseY == 0) tempProperties[p].mReverseY = false;
            else tempProperties[p].mReverseY = true;

            tempProperties[p].mWasCalculated = false;
          }
        }

        // read the cast headers
        for (int c = 0; c < numCasts; c++) {
          // read station number
          inShort = inData.readShort();
          bytesRead += 2;
          byte bufx[] = new byte[inShort];
          inData.read(bufx, 0, inShort);
          String stnNum = new String(bufx);
          bytesRead += inShort;

          // read cast number
          int castNum = inData.readShort();
          bytesRead += 2;

          double myLat = 0.0;
          double myLon = 0.0;
          if (vers == 2) {
            // read latitude/lon
            int lat = inData.readInt();
            bytesRead += 4;

            int lon = inData.readInt();
            bytesRead += 4;

            myLat = lat * 0.001;
            myLon = lon * 0.001;
          } else if (vers > 2) {
            // read latitude/lon
            myLat = inData.readDouble();
            bytesRead += 8;

            myLon = inData.readDouble();
            bytesRead += 4;
          }

          // read number of bottles
          int numBottles = inData.readShort();
          bytesRead += 2;

          // read the date
          int year = inData.readInt();
          bytesRead += 4;
          int month = inData.readInt();
          bytesRead += 4;
          int day = inData.readInt();
          bytesRead += 4;
          int hour = inData.readInt();
          bytesRead += 4;
          double min = inData.readDouble();
          bytesRead += 8;

          // read bottom
          int bottomdbar = inData.readInt();

          // read station quality
          int stnQual = inData.readShort();
          bytesRead += 2;

          ord++;
          JOAStation sh =
              new JOAStation(
                  ord,
                  shipCode,
                  stnNum,
                  castNum,
                  myLat,
                  myLon,
                  numBottles,
                  year,
                  month,
                  day,
                  hour,
                  min,
                  bottomdbar,
                  stnQual);
          sech.mStations.addElement(sh);
          sh.setType("JOA BOTTLE");

          // make a DBase object
          Dbase db = new Dbase();

          // add the global attributes
          db.addEPSAttribute(
              "CRUISE", EPCHAR, sech.mSectionDescription.length(), sech.mSectionDescription);
          db.addEPSAttribute("CAST", EPCHAR, sh.mStnNum.length(), sh.mStnNum);
          sarray[0] = (short) sh.mBottomDepthInDBARS;
          db.addEPSAttribute("WATER_DEPTH", EPSHORT, 1, sarray);
          db.addEPSAttribute("DATA_ORIGIN", EPCHAR, sech.mShipCode.length(), sech.mShipCode);
          String dType = sh.getType();
          if (dType == null) dType = "UNKN";
          db.addEPSAttribute("DATA_TYPE", EPCHAR, dType.length(), dType);
          sarray[0] = (short) stnQual;
          db.addEPSAttribute("STN_QUALITY", EPSHORT, 1, sarray);
          db.setDataType("JOA BOTTLE");

          // add to temporary collection
          dBases.addElement(db);
        }

        int start = mTotalStns;
        int end = sech.mStations.size() + mTotalStns;
        for (int sc = start; sc < end; sc++) {
          mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));

          // get a dBase
          Dbase db = (Dbase) dBases.elementAt(sc);

          // get a station
          JOAStation sh = (JOAStation) sech.mStations.elementAt(sc - start);

          // create an array of arrays to store the data
          double[][] va = new double[sech.mNumVars][sh.mNumBottles];
          int[][] qc = new int[sech.mNumVars][sh.mNumBottles];
          short[] bqc = new short[sh.mNumBottles];
          int presPos = 0;

          // read the bottles
          for (int b = 0; b < sh.mNumBottles; b++) {
            // read the bottle quality code
            bqc[b] = inData.readShort();
            bytesRead += 2;

            for (int v = 0; v < sech.mNumVars; v++) {
              // store the position of the PRES variable
              if (tempProperties[v].mVarLabel.equals("PRES")) presPos = v;

              // get the measured parameter
              double dVarVal = EPSConstants.MISSINGVALUE;
              try {
                dVarVal = inData.readDouble();
              } catch (IOException e) {
                FileImportException fiex = new FileImportException();
                String errStr =
                    "Error reading the parameter data. "
                        + "\n"
                        + "Bottle #"
                        + b
                        + " Parameter #"
                        + v;
                fiex.setErrorType(errStr);
                throw fiex;
              }
              bytesRead += 8;

              // store the value in the multidimensional array
              va[v][b] = dVarVal;

              // get the quality flag
              short flag = (short) EPSConstants.MISSINGVALUE;

              try {
                flag = inData.readShort();
              } catch (IOException e) {
                FileImportException fiex = new FileImportException();
                String errStr =
                    "Error reading the parameter quality code. "
                        + "\n"
                        + "Bottle #"
                        + b
                        + " Parameter #"
                        + v;
                fiex.setErrorType(errStr);
                throw fiex;
              }
              bytesRead += 2;
              qc[v][b] = flag;
            } // for v
          } // for b

          // add the bottle quality codes as an attribute
          db.addEPSAttribute("BOTTLE_QUALITY_CODES", EPSHORT, sh.mNumBottles, bqc);

          // create the axes time = 0, depth = 1, lat = 2, lon = 3
          Axis timeAxis = new Axis();
          Axis zAxis = new Axis();
          Axis latAxis = new Axis();
          Axis lonAxis = new Axis();

          // time axis
          timeAxis.setName("time");
          timeAxis.setTime(true);
          timeAxis.setUnlimited(false);
          timeAxis.setAxisType(EPTAXIS);
          timeAxis.setLen(1);

          int hour = 0;
          if (sh.mHour != EPSConstants.MISSINGVALUE) hour = sh.mHour;

          double mins = 0;
          if (sh.mMinute != EPSConstants.MISSINGVALUE) mins = sh.mMinute;

          // make the time axis units
          String date = "days since ";
          int min = (int) mins;
          double fmin = mins - min;
          int secs = (int) (fmin * 60.0);
          double fsec = (fmin * 60.0) - secs;
          int msec = (int) (fsec * 1000.0);
          String fs = String.valueOf(fsec);
          fs = fs.substring(fs.indexOf(".") + 1, fs.length()).trim();
          int f = 0;
          if (fs != null && fs.length() > 0) f = Integer.valueOf(fs).intValue();

          // sprintf(time_string,"%04d-%02d-%02d %02d:%02d:%02d.%03d",yr,mon,day,hr,min,sec,f);
          String frmt =
              new String(
                  "{0,number,####}-{1,number,00}-{2,number,00} {3,number,00}:{4,number,00}:{5,number,00}.{6,number,000}");
          MessageFormat msgf = new MessageFormat(frmt);

          Object[] objs = {
            new Integer(sh.mYear),
            new Integer(sh.mMonth),
            new Integer(sh.mDay),
            new Integer(hour),
            new Integer(min),
            new Integer(secs),
            new Integer(f)
          };
          StringBuffer out = new StringBuffer();
          msgf.format(objs, out, null);
          String time_string = new String(out);
          date = date + time_string;
          timeAxis.addAttribute(0, "units", EPCHAR, date.length(), date);
          timeAxis.setUnits(date);
          GeoDate gd = null;
          try {
            gd = new GeoDate(sh.mMonth, sh.mDay, sh.mYear, hour, min, secs, msec);
            GeoDate[] ta = {gd};
            MultiArray tma = new ArrayMultiArray(ta);

            timeAxis.setData(tma);
            db.setAxis(timeAxis);
          } catch (Exception ex) {
            GeoDate[] ta = {new GeoDate()};
            MultiArray tma = new ArrayMultiArray(ta);

            timeAxis.setData(tma);
            db.setAxis(timeAxis);
          }

          // add the time axes variable
          EPSVariable var = new EPSVariable();
          var.setOname("time");
          var.setDtype(EPDOUBLE);
          var.setVclass(Double.TYPE);
          var.addAttribute(0, "units", EPCHAR, date.length(), date);
          var.setUnits(date);
          double[] vta = {0.0};
          MultiArray vtma = new ArrayMultiArray(vta);
          try {
            var.setData(vtma);
          } catch (Exception ex) {
          }
          db.addEPSVariable(var);

          // z axis
          zAxis.setName("depth");
          zAxis.setTime(false);
          zAxis.setUnlimited(false);
          zAxis.setLen(sh.mNumBottles);
          zAxis.setAxisType(EPZAXIS);
          zAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
          zAxis.addAttribute(1, "units", EPCHAR, 4, "dbar");
          zAxis.setUnits("dbar");
          zAxis.setFrmt("f10.1");
          // zAxis.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 1;
          zAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          double[] za = new double[sh.mNumBottles];
          for (int b = 0; b < sh.mNumBottles; b++) {
            za[b] = va[presPos][b];
          }
          MultiArray zma = new ArrayMultiArray(za);
          zAxis.setData(zma);
          db.setAxis(zAxis);

          // add the z axes variables
          var = new EPSVariable();
          var.setOname("depth");
          var.setDtype(EPDOUBLE);
          var.setVclass(Double.TYPE);
          var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
          var.addAttribute(1, "units", EPCHAR, 4, "dbar");
          var.setUnits("dbar");
          var.setFrmt("f10.1");
          // var.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 1;
          var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          MultiArray zvma = new ArrayMultiArray(za);
          try {
            var.setData(zvma);
          } catch (Exception ex) {
          }
          db.addEPSVariable(var);

          // lat axis
          latAxis.setName("latitude");
          latAxis.setTime(false);
          latAxis.setUnlimited(false);
          latAxis.setLen(1);
          latAxis.setAxisType(EPYAXIS);
          latAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
          latAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
          latAxis.setUnits("degrees");
          latAxis.setFrmt("f10.4");
          // latAxis.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 500;
          latAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          double lat = sh.mLat;
          double[] la = {lat};
          MultiArray lma = new ArrayMultiArray(la);
          latAxis.setData(lma);
          db.setAxis(latAxis);

          // add the y axes variable
          var = new EPSVariable();
          var.setOname("latitude");
          var.setDtype(EPDOUBLE);
          var.setVclass(Double.TYPE);
          var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
          var.addAttribute(1, "units", EPCHAR, 7, "degrees");
          var.setUnits("degrees");
          var.setFrmt("f10.4");
          // var.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 500;
          var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          MultiArray yvma = new ArrayMultiArray(la);
          try {
            var.setData(yvma);
          } catch (Exception ex) {
          }
          db.addEPSVariable(var);

          // lon axis
          lonAxis.setName("longitude");
          lonAxis.setTime(false);
          lonAxis.setUnlimited(false);
          lonAxis.setLen(1);
          lonAxis.setAxisType(EPXAXIS);
          lonAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
          lonAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
          lonAxis.setUnits("degrees");
          lonAxis.setFrmt("f10.4");
          // lonAxis.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 502;
          lonAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          double lon = sh.mLon;
          double[] lla = {lon};
          lma = new ArrayMultiArray(lla);
          lonAxis.setData(lma);
          db.setAxis(lonAxis);

          // add the x axes variable
          var = new EPSVariable();
          var.setOname("longitude");
          var.setDtype(EPDOUBLE);
          var.setVclass(Double.TYPE);
          var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
          var.addAttribute(1, "units", EPCHAR, 7, "degrees");
          var.setUnits("degrees");
          var.setFrmt("f10.4");
          // var.addAttribute(2, "type", EPCHAR, 0, "");
          sarray[0] = 502;
          var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
          MultiArray xvma = new ArrayMultiArray(lla);
          try {
            var.setData(xvma);
          } catch (Exception ex) {
          }

          db.addEPSVariable(var);

          // add the measured variables
          for (int v = 0; v < sech.mNumVars; v++) {
            // if (presPos == v)
            //	continue;

            // create an array of measured EPSVariables for this database
            EPSVariable epsVar = new EPSVariable();

            // initialize the new EPSVariables
            // look this variable up in JOA EPIC_Key. find matching entry in original EPIC Key
            String oname = tempProperties[v].mVarLabel;
            String sname = null;
            String lname = null;
            String gname = null;
            String units = null;
            String ffrmt = null;
            int keyID = -99;
            int type = -99;
            try {
              keyID = mEpicKeyDB.findKey(tempProperties[v].mVarLabel);
              Key key = mOrigEpicKeyDB.findKey(keyID);
              gname = key.getGname();
              sname = key.getSname();
              lname = key.getLname();
              units = key.getUnits();
              ffrmt = key.getFrmt();
              type = key.getType();
            } catch (Exception e) {
              lname = tempProperties[v].mVarLabel;
              gname = tempProperties[v].mVarLabel;
              sname = tempProperties[v].mVarLabel;
              units = tempProperties[v].mUnits;
            }

            // make a new variable
            epsVar = new EPSVariable();

            epsVar.setOname(oname);
            epsVar.setSname(sname);
            epsVar.setLname(lname);
            epsVar.setGname(gname);
            epsVar.setDtype(EPDOUBLE);
            epsVar.setVclass(Double.TYPE);
            int numAttributes = 0;
            if (ffrmt != null) {
              epsVar.addAttribute(numAttributes++, "FORTRAN_format", EPCHAR, ffrmt.length(), ffrmt);
              epsVar.setFrmt(ffrmt);
            }
            if (units != null && units.length() > 0) {
              epsVar.addAttribute(numAttributes++, "units", EPCHAR, units.length(), units);
              epsVar.setUnits(units);
            }
            if (keyID >= 0) {
              sarray[0] = (short) type;
              // epsVar.addAttribute(numAttributes++, "type", EPSHORT, 1, sarray);
            }
            if (keyID >= 0) {
              sarray[0] = (short) keyID;
              epsVar.addAttribute(numAttributes++, "epic_code", EPSHORT, 1, sarray);
            }

            // add the quality code attribute
            String qcVar = oname + "_QC";
            epsVar.addAttribute(numAttributes++, "OBS_QC_VARIABLE", EPCHAR, qcVar.length(), qcVar);

            // connect variable to axis
            epsVar.setDimorder(0, 0);
            epsVar.setDimorder(1, 1);
            epsVar.setDimorder(2, 2);
            epsVar.setDimorder(3, 3);
            epsVar.setT(timeAxis);
            epsVar.setZ(zAxis);
            epsVar.setY(latAxis);
            epsVar.setX(lonAxis);

            // set the data
            // create storage for the measured variables
            double[][][][] vaa = new double[1][sh.mNumBottles][1][1];
            for (int b = 0; b < sh.mNumBottles; b++) {
              vaa[0][b][0][0] = va[v][b];
            }
            MultiArray mdma = new ArrayMultiArray(vaa);
            try {
              epsVar.setData(mdma);
            } catch (Exception ex) {
              System.out.println("throwing");
            }

            // add the variable to the database
            db.addEPSVariable(epsVar);

            // create the quality code variable
            epsVar = new EPSVariable();
            epsVar.setOname(oname + "_QC");
            epsVar.setSname(sname + "_QC");
            epsVar.setLname(sname + "_QC");
            epsVar.setGname(sname + "_QC");
            epsVar.setDtype(EPSHORT);
            epsVar.setVclass(Short.TYPE);

            // connect variable to axis
            epsVar.setDimorder(0, 0);
            epsVar.setDimorder(1, 1);
            epsVar.setDimorder(2, 2);
            epsVar.setDimorder(3, 3);
            epsVar.setT(timeAxis);
            epsVar.setZ(zAxis);
            epsVar.setY(latAxis);
            epsVar.setX(lonAxis);

            // set the data
            // create storage for the qc variables
            short[][][][] qcaa = new short[1][sh.mNumBottles][1][1];
            for (int b = 0; b < sh.mNumBottles; b++) {
              qcaa[0][b][0][0] = (short) qc[v][b];
            }
            MultiArray qcma = new ArrayMultiArray(qcaa);
            try {
              epsVar.setData(qcma);
            } catch (Exception ex) {
              System.out.println("throwing");
            }

            // add the qc variable to the database
            db.addEPSVariable(epsVar);
          } // for v
        }
        mTotalStns += numCasts;
      } // for sc

      // read the file comments
      StringBuffer sb = null;
      while (true) {
        try {
          // read continuation line
          inShort = inData.readShort();
          bytesRead += 2;

          if (inShort == 1) {
            // read number of bytes in file description string
            inShort = inData.readShort();
            bytesRead += 2;

            // read the file description String
            byte buf2[] = new byte[inShort];
            inData.read(buf2, 0, inShort);
            String commentLine = new String(buf2);
            bytesRead += inShort;

            if (sb == null) sb = new StringBuffer(commentLine);
            else sb.append(commentLine);
          }
        } catch (IOException e) {
          break;
        }
      } // while true

      if (sb != null) {
        // make attributes for the comments
        mOwnerDBase.setDataComment(new String(sb));
      }

      // make a sub database in the dbase
      mOwnerDBase.createSubEntries(mTotalStns, mFile.getName());
      for (int d = 0; d < mTotalStns; d++) {
        Dbase db = (Dbase) dBases.elementAt(d);
        mOwnerDBase.addSubEntry(db);
      }
      mProgress.setPercentComplete(100.0);
      mProgress.setVisible(false);
      mProgress.dispose();
      in.close();
    } catch (IOException e) {
      mProgress.setVisible(false);
      mProgress.dispose();
      throw e;
    }
  }
 public void addHPubReqCompleteListener(HPubReqCompleteListener listenerToAdd) {
   listenerList.addElement(listenerToAdd);
 }
Esempio n. 19
0
 public Collection getConnectedNodes() {
   Vector connectedNodes = new Vector();
   connectedNodes.addElement(Keyword.class);
   return connectedNodes;
 }