A C D E F G I M N O P Q R S T U V W X

A

addSenderIP(String) - Method in class unitloader.ProtocolQuery

Method to add a senderIP element to the header of the protocol.

C

callBack - Variable in class unitloader.UnitRequest

callBack - Variable in class unitloader.PosterThread

callBackHandler(int, Response) - Method in class unitloader.UnitRequest

Method to handle callbacks from threads is used to return results from threads to this object.

callThreads() - Method in class unitloader.UnitRequest

Start a PosterThread for every provider in the ProviderList.

cgiScriptPath - Variable in class unitloader.Response

cgiScriptPath - Variable in class unitloader.PosterThread

cgiScriptPath - Variable in class unitloader.Provider

characters(char[], int, int) - Method in class unitloader.XmlExtractor

Comp - class unitloader.Comp.

Title: the Comp class representing comparison operations.

Comp(String, String) - Constructor for class unitloader.Comp

Overloaded constructor to be used to create "isNull" and "isNotNull" operations.

Comp(String, String, List, boolean) - Constructor for class unitloader.Comp

Overloaded class constructor to be used to create 'in' like comparisons.

Comp(String, String, String, boolean) - Constructor for class unitloader.Comp

Overloaded constructor to be used to create 'equals', 'not equals', 'lower than', 'lower than or equals', 'greater than' and 'greater than or equals', and like comparisons.

composeQuery(int, int, Element, boolean) - Method in class unitloader.ProtocolQuery

content - Variable in class unitloader.Response

content - Variable in class unitloader.ResponseMail

contProcessing(List) - Method in class unitrequestor.ReqScan

Implementation of the contProcessing method which is called once all threads returned.

contProcessing(List) - Method in class unitrequestor.ReqSearch

Implementation of the contProcessing method which is called once all threads returned.

contProcessing(List) - Method in class unitrequestor.ReqCapabilities

Implementation of the contProcessing method which is called once all threads returned.

contProcessing(List) - Method in class unitrequestor.ReqScanInterface

This example implementation of contProcessing does some logging only.

contProcessing(List) - Method in class unitrequestor.ReqSearchInterface

Implementation of the contProcessing method doing some logging and sending back the resultset as an email if an email adress is given.

contProcessing(List) - Method in interface unitloader.IUnitRequest

This method has to be implemented in order to provide a callbackhandler used to perform tasks once all query threads are completed (e.g.

createEmailContent(List) - Static method in class unitloader.StaticStuff

Create an email message string containing the list of reponses from a BioCASE request.

createProviderList() - Method in class unitrequestor.ReqScan

createProviderList() - Method in class unitrequestor.ReqSearch

createProviderList() - Method in class unitrequestor.ReqCapabilities

createQuery() - Static method in class unitrequestor.ReqSearch

createQuery(Comp) - Method in class unitloader.ProtocolQuery

createQuery(QBool) - Method in class unitloader.ProtocolQuery

createQuery0() - Static method in class unitrequestor.ReqSearch

createQuery2() - Static method in class unitrequestor.ReqSearch

createQuery3() - Static method in class unitrequestor.ReqSearch

createQuery4() - Static method in class unitrequestor.ReqSearch

createSingleProvider() - Method in class unitrequestor.ReqScan

createSingleProvider() - Method in class unitrequestor.ReqSearch

createSingleProvider() - Method in class unitrequestor.ReqCapabilities

D

debugTimer(String) - Static method in class unitloader.StaticStuff

Print the current time (seconds) on the screen used for debugging timeout interrupts.

destination - Variable in class unitloader.Response

destination - Variable in class unitloader.XmlExtractor

diagnostics - Variable in class unitloader.Response

diagnostics - Variable in class unitloader.XmlExtractor

docStr - Variable in class unitloader.XmlExtractor

E

elem - Variable in class unitloader.Comp

emailAdr - Variable in class unitrequestor.ReqSearchInterface

endElement(String, String, String) - Method in class unitloader.XmlExtractor

take some action when we reach the end of selected elements.

everybodyFinished() - Method in class unitloader.UnitRequest

F

failures2Log(List) - Static method in class unitloader.StaticStuff

Write for every failed or timeouted response within the given result list a message into an automatically generated log file.

filterSet - Variable in class unitloader.ProtocolQuery

first - Variable in class unitloader.QBool

fromAddr - Variable in class unitloader.ResponseMail

G

getApplicationHome() - Static method in class unitloader.StaticStuff

Return the home directory where this application will find its configuration files including the unitloader subdirectory.

getCGIScriptPath() - Method in class unitloader.Response

Return path to the cgi script this response belongs to.

getCGIScriptPath() - Method in class unitloader.PosterThread

Accessor for cgiScriptPath.

getCGIScriptPath() - Method in class unitloader.Provider

Accessor for cgiScriptPath.

getContent() - Method in class unitloader.Response

Return xml document containing the real data.

getDateAndTime() - Static method in class unitloader.StaticStuff

Return a date time string as it is required for a protocol compliant request.

getDestination() - Method in class unitloader.Response

Return the intended destination of this document.

getDestination() - Method in class unitloader.XmlExtractor

Accessor for destination.

getDiagnostics() - Method in class unitloader.Response

Return the diagnostic message created by the provider software.

getDiagnostics() - Method in class unitloader.XmlExtractor

Accessor for diagnostics.

getDocStr() - Method in class unitloader.XmlExtractor

Accessor for docStr.

getElem() - Method in class unitloader.Comp

Return the element name.

getFailureMessage() - Method in class unitloader.XmlExtractor

Accessor for falureMessage.

getFailureState() - Method in class unitloader.XmlExtractor

Accessor for failureState.

getFirst() - Method in class unitloader.QBool

Returns the first operand of this object.

getId() - Method in class unitloader.PosterThread

Accessor for id.

getIntermediate() - Method in class unitrequestor.ReqScanInterface

Example method waiting a few seconds and returning intermediate results.

getIntermediate() - Method in class unitrequestor.ReqSearchInterface

Method to access an intermediate resultset waiting a few seconds and returning what has been returned.

getLogFileName() - Static method in class unitloader.StaticStuff

getMessage() - Method in class unitloader.Response

Return a message giving more details for the given status.

getNumResponse() - Method in class unitloader.UnitRequest

Accessor for numResponse used for retrieving the number of responses already contained in the resultlist.

getOp() - Method in class unitloader.Comp

Return the name of the opereation represented with this object.

getOp() - Method in class unitloader.QBool

Returns the name of the boolean operation represented with this object.

getParam(String) - Static method in class unitloader.StaticStuff

Read the given parameter from configuration.xml.

getProtocolQuery() - Method in class unitloader.Response

Return protocol query string this response belongs to.

getProtocolRequestDoc() - Method in class unitloader.ProtocolQuery

Accessor to get the entire BioCASE request XML document as it has been composed.

getProtocolRequestString() - Method in class unitloader.ProtocolQuery

getProvSoftware() - Method in class unitloader.Response

Return the software used by the provider module as free text string (intended) for human consumption.

getQueryConcept(String) - Static method in class unitloader.StaticStuff

Read (x)path query concept from file specified within configuration.xml.

getQueryConceptType(String) - Static method in class unitloader.StaticStuff

Read type information for the given query concept short name from queryconcept file defined in configuration.xml.

getRecordCount() - Method in class unitloader.Response

Return number of records contained in this response and -1 if no valid value is vailable for this.

getRecordCountValue() - Method in class unitloader.XmlExtractor

Accessor for recordCount.

getRecordDropped() - Method in class unitloader.Response

Return the number of database records which could not be converted to xml.

getRecordDroppedValue() - Method in class unitloader.XmlExtractor

Accessor for recordDropped.

getRecordStart() - Method in class unitloader.Response

Return number if the first record and -1 if no valid value is available for this.

getRecordStartValue() - Method in class unitloader.XmlExtractor

Accessor for recordStart.

getResultList() - Method in class unitloader.UnitRequest

Accessor for the ResultList.

getSecond() - Method in class unitloader.QBool

Returns the second operand of this object.

getSendTime() - Method in class unitloader.Response

Return the time this response has been produced by the provider (ISO).

getSendTime() - Method in class unitloader.XmlExtractor

Accessor for sendTime.

getSoftware() - Method in class unitloader.XmlExtractor

Accessor for software.

getSource() - Method in class unitloader.Response

Return the provider url.

getSource() - Method in class unitloader.XmlExtractor

Accessor for source.

getStatus() - Method in class unitloader.Response

Return status of the response to let the client know whether this query failed or has been timeouted.

getTimeNeeded() - Method in class unitloader.Response

Return time in (milliseconds) since the threadpool has been created.

getTotalSearchHits() - Method in class unitloader.Response

Return total number of search hits and -1 if no valid value is available for this.

getTotalSearchHitsValue() - Method in class unitloader.XmlExtractor

Accessor for totalSearchHits.

getType() - Method in class unitloader.Response

Return the type of request this reponse belongs to (search, capabilities, or scan).

getType() - Method in class unitloader.XmlExtractor

Accessor for type.

getURL() - Method in class unitloader.Response

Return url this response belongs to.

getUrlStr() - Method in class unitloader.PosterThread

Accessor for urlStr.

getUrlString() - Method in class unitloader.Provider

Accessor for urlString.

getValue() - Method in class unitloader.Comp

Return values the element is compared to.

go() - Method in class unitrequestor.ReqScan

Example method dumping some intermediate results to the screen.

go() - Method in class unitrequestor.ReqSearch

Example method dumping some intermediate results to the screen.

go() - Method in class unitrequestor.ReqCapabilities

Example method dumping some intermediate results to the screen.

I

iAmNumber - Variable in class unitloader.PosterThread

incontents - Variable in class unitloader.XmlExtractor

isEmailAdr(String) - Static method in class unitloader.StaticStuff

Method to identify valid email addresses.

isQBool(int) - Method in class unitloader.QBool

Check whether the given child (argument) specified with the parameter of this method is a boolean operation.

IUnitRequest - interface unitloader.IUnitRequest.

Title: the IUnitRequest interface.

M

mailHost - Variable in class unitloader.ResponseMail

matchOpType(String, String) - Static method in class unitloader.StaticStuff

Check whether the given operator (short name) can be applied to the given type (at present "alphanumeric" or "numeric").

message - Variable in class unitloader.Response

N

ns - Variable in class unitloader.XmlExtractor

ns - Variable in class unitloader.PosterThread

numResponse - Variable in class unitloader.UnitRequest

O

okResp - Variable in class unitrequestor.ReqSearchInterface

op - Variable in class unitloader.Comp

op - Variable in class unitloader.QBool

P

PosterThread - class unitloader.PosterThread.

Title: The PosterThread class.

PosterThread(int, String, String, String, int, boolean, UnitRequest) - Constructor for class unitloader.PosterThread

Constructor for a PosterThread object used to post queries to BioCASE providers.

pQuery - Variable in class unitloader.UnitRequest

ProtocolException - exception unitloader.ProtocolException.

Title: Protocol exception class

ProtocolException() - Constructor for class unitloader.ProtocolException

ProtocolException(String) - Constructor for class unitloader.ProtocolException

protocolNs - Variable in class unitloader.ProtocolQuery

protocolQuery - Variable in class unitloader.Response

ProtocolQuery - class unitloader.ProtocolQuery.

Title: The ProtocolQuery class used to create BioCASE queries ("search", "capablities", and "scan").

ProtocolQuery(String) - Constructor for class unitloader.ProtocolQuery

Constructor creates the root element for a protocol query, declares the namespaces to be used, and constructs the header for a valid BioCASE request.

Provider - class unitloader.Provider.

Title: the provider class

Provider(String, String) - Constructor for class unitloader.Provider

Constructor setting the url and script path where the query has to go.

providerLst - Variable in class unitloader.UnitRequest

providers - Variable in class unitrequestor.ReqScan

providers - Variable in class unitrequestor.ReqSearch

providers - Variable in class unitrequestor.ReqCapabilities

providers - Variable in class unitrequestor.ReqScanInterface

providers - Variable in class unitrequestor.ReqSearchInterface

provSoftware - Variable in class unitloader.Response

Q

QBool - class unitloader.QBool.

Title: the QBool class representing booelan operations.

QBool(String, Comp) - Constructor for class unitloader.QBool

Overloaded constructor for the one and only usefull unary boolean operator (not).

QBool(String, Comp, Comp) - Constructor for class unitloader.QBool

Overloaded constructor for binary boolean operators (or, and, nor, nand).

QBool(String, Comp, QBool) - Constructor for class unitloader.QBool

Overloaded constructor for binary boolean operators (or, and, nor, nand).

QBool(String, QBool) - Constructor for class unitloader.QBool

Overloaded constructor for unary boolean operators (not).

QBool(String, QBool, Comp) - Constructor for class unitloader.QBool

Overloaded constructor for binary boolean operators (or, and, nor, nand).

QBool(String, QBool, QBool) - Constructor for class unitloader.QBool

Overloaded constructor for binary boolean operators (or, and, nor, nand).

QBool(String, String, List) - Constructor for class unitloader.QBool

Overloaded constructor for nested QBools containing multiple comparisons with the same concept and comparison operator.

R

rawResponse2Screen() - Method in class unitloader.Response

Print this response to the screen even if it represents erroneous content (may be used for debugging purposes).

recordCount - Variable in class unitloader.Response

recordCount - Variable in class unitloader.XmlExtractor

recordDropped - Variable in class unitloader.Response

recordDropped - Variable in class unitloader.XmlExtractor

recordStart - Variable in class unitloader.Response

recordStart - Variable in class unitloader.XmlExtractor

replaceInvalidChar(String) - Method in class unitloader.XmlExtractor

Replace invalid xml character.

report(SAXException) - Method in class unitloader.XmlExtractor

report an exception

ReqCapabilities - class unitrequestor.ReqCapabilities.

Title: Example implementation of IUnitRequest (package unitloader)

ReqCapabilities() - Constructor for class unitrequestor.ReqCapabilities

Constructor creating a capability request.

ReqScan - class unitrequestor.ReqScan.

Title: Example implementation of IUnitRequest (package unitloader)

ReqScan() - Constructor for class unitrequestor.ReqScan

Constructor creating a scan request.

ReqScanInterface - class unitrequestor.ReqScanInterface.

Title: Example implementation of IUnitRequest (package unitloader)

ReqScanInterface(ArrayList, String, int, int) - Constructor for class unitrequestor.ReqScanInterface

Constructor creating a scan request.

ReqSearch - class unitrequestor.ReqSearch.

Title: Example implementation of IUnitRequest (package unitloader)

ReqSearch() - Constructor for class unitrequestor.ReqSearch

Constructor creating a search request.

ReqSearchInterface - class unitrequestor.ReqSearchInterface.

Title: Implementation of the IUnitRequest (package unitloader)

ReqSearchInterface(ArrayList, String, int, int, int) - Constructor for class unitrequestor.ReqSearchInterface

Overloaded constructor creating a search request (no email parameter)

ReqSearchInterface(ArrayList, String, String, int, int, int) - Constructor for class unitrequestor.ReqSearchInterface

Overloaded constructor creating a search request (including email parameter)

request - Variable in class unitrequestor.ReqScan

request - Variable in class unitrequestor.ReqSearch

request - Variable in class unitrequestor.ReqCapabilities

request - Variable in class unitrequestor.ReqScanInterface

request - Variable in class unitrequestor.ReqSearchInterface

requestComplete() - Method in class unitloader.ProtocolQuery

Check whether this request is complete.

requestType - Variable in class unitloader.ProtocolQuery

Response - class unitloader.Response.

Title: the Response class

Response(String, String, String, String, int, int, int, int, String, String, String, String, String, String, String, String) - Constructor for class unitloader.Response

Constructor for creating a response object.

response2HTML() - Method in class unitloader.Response

Create some useless (html) representing a response which may be used for debugging purposes when using the package with a web interface system.

response2Log(List) - Static method in class unitloader.StaticStuff

Write for every response within the given result list a message into an automatically generated log file.

response2Screen() - Method in class unitloader.Response

Print this response to the screen (no nice xml output).

ResponseMail - class unitloader.ResponseMail.

Title: the ResponseMail class to send back reponse sets as an email.

ResponseMail(String, String) - Constructor for class unitloader.ResponseMail

Overloaded constructor for ReponseMail object.

ResponseMail(String, String, String, String, String) - Constructor for class unitloader.ResponseMail

Overloaded constructor for ResponseMail object.

resultList - Variable in class unitloader.UnitRequest

results2Screen(List) - Static method in class unitloader.StaticStuff

Write a list of response objects to the screen.

root - Variable in class unitloader.ProtocolQuery

run() - Method in class unitloader.PosterThread

Run the query and call the callback handler to transfer the resulting xml document as a string.

S

second - Variable in class unitloader.QBool

sendMail() - Method in class unitloader.ResponseMail

Send the email.

sendTime - Variable in class unitloader.Response

sendTime - Variable in class unitloader.XmlExtractor

setContent(String) - Method in class unitloader.Response

Set xml document containing the real data.

setDestination(String) - Method in class unitloader.Response

Set the intended destination url for this response.

setDiagnostics(String) - Method in class unitloader.Response

Set the diagnostics message created by the provider software.

setFromAddr(String) - Method in class unitloader.ResponseMail

Set the email address used as tzhe sender.

setMailHost(String) - Method in class unitloader.ResponseMail

Set the mailHost.

setProtocolQuery(String) - Method in class unitloader.Response

Set the protocool query this response belongs to.

setProvSoftware(String) - Method in class unitloader.Response

Set software used by provider wrapper to produce the result.

setQuery(Comp, boolean) - Method in class unitloader.ProtocolQuery

Overloaded method to set the query part of a search request for comparison queries.

setQuery(int, int, Comp, boolean) - Method in class unitloader.ProtocolQuery

Overloaded method to set the query part of a search request for comparison operations.

setQuery(int, int, QBool, boolean) - Method in class unitloader.ProtocolQuery

Overloaded method to set the query part of a search request for boolean queries.

setQuery(QBool, boolean) - Method in class unitloader.ProtocolQuery

Overloaded method to set the query part of a search request for boolean queries.

setRecordCount(int) - Method in class unitloader.Response

Set the number of records contained in this response.

setRecordDropped(int) - Method in class unitloader.Response

Set the number of database records which could not be converted into xml.

setRecordStart(int) - Method in class unitloader.Response

Set the number of the first record returned.

setScanFilter(String) - Method in class unitloader.ProtocolQuery

Method to set the body of a scan request.

setSendTime(String) - Method in class unitloader.Response

Set the time when this resonse has been sent by the provider.

setSource(String) - Method in class unitloader.Response

Set the provider url.

setSubject(String) - Method in class unitloader.ResponseMail

Set the subject line for this email.

setTimeNeeded(int) - Method in class unitloader.Response

Set the time needed to create this response object.

setTotalSearchHits(int) - Method in class unitloader.Response

Set the total number of search hits (not necessarily contained in this recordset).

setType(String) - Method in class unitloader.Response

Set the type of request (scan, search, capabilities) this response belongs to.

software - Variable in class unitloader.XmlExtractor

source - Variable in class unitloader.Response

source - Variable in class unitloader.XmlExtractor

startElement(String, String, String, Attributes) - Method in class unitloader.XmlExtractor

Extract a xml file at the beginning of each new element, erase any text and get some start elements information.

StaticStuff - class unitloader.StaticStuff.

Title: Some static functions

StaticStuff() - Constructor for class unitloader.StaticStuff

status - Variable in class unitloader.Response

statusFlag - Variable in class unitloader.UnitRequest

subject - Variable in class unitloader.ResponseMail

T

t0 - Variable in class unitloader.UnitRequest

textBuffer - Variable in class unitloader.XmlExtractor

theQuery - Variable in class unitloader.PosterThread

threadPool - Variable in class unitloader.UnitRequest

timeNeeded - Variable in class unitloader.Response

timeNeeded() - Method in class unitloader.UnitRequest

timeOfTheDay() - Static method in class unitloader.StaticStuff

timeout - Variable in class unitrequestor.ReqScan

timeout - Variable in class unitrequestor.ReqSearch

timeout - Variable in class unitrequestor.ReqCapabilities

timeout - Variable in class unitrequestor.ReqScanInterface

timeout - Variable in class unitrequestor.ReqSearchInterface

timeout - Variable in class unitloader.UnitRequest

timeout - Variable in class unitloader.PosterThread

toAddr - Variable in class unitloader.ResponseMail

totalSearchHits - Variable in class unitloader.Response

totalSearchHits - Variable in class unitloader.XmlExtractor

type - Variable in class unitloader.Response

type - Variable in class unitloader.XmlExtractor

U

unitloader - package unitloader

UnitRequest - class unitloader.UnitRequest.

Title: the UnitRequest class.

UnitRequest(List, String, int, IUnitRequest) - Constructor for class unitloader.UnitRequest

Constructor for a UnitRequest.

unitrequestor - package unitrequestor

url - Variable in class unitloader.Response

url - Variable in class unitloader.PosterThread

url2cgiPath(String) - Static method in class unitloader.StaticStuff

Extract the file part (path to the file or cgi script) of the given url string.

url2hostAndPort(String) - Static method in class unitloader.StaticStuff

Extract the host and port part of the given url string.

urlStr - Variable in class unitloader.PosterThread

urlString - Variable in class unitloader.Provider

V

validation - Variable in class unitloader.PosterThread

value - Variable in class unitloader.Comp

W

wait - Variable in class unitrequestor.ReqScanInterface

wait - Variable in class unitrequestor.ReqSearchInterface

X

XmlExtractor - class unitloader.XmlExtractor.

Title: the XmlExtractor class

XmlExtractor() - Constructor for class unitloader.XmlExtractor

Constructor

xmlHeader - Variable in class unitloader.XmlExtractor

xsiNs - Variable in class unitloader.ProtocolQuery

A C D E F G I M N O P Q R S T U V W X