/**
* 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());
}
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;
}
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();
}
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);
}
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;
}
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;
}
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;
}
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;
}
/**
* 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);
}
private void init() {
initGetterMap();
initSetterMap();
allKeywords.addElement(this);
initPopupMenu();
}
/**
* 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;
}
/**
* 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;
}
}
/**
* 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());
}
}
/**
* 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);
}
}
/**
* 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);
}
public Collection getConnectedNodes() {
Vector connectedNodes = new Vector();
connectedNodes.addElement(Keyword.class);
return connectedNodes;
}
