Uses of Interface
org.embl.ebi.escience.scuflworkers.java.LocalWorker

Packages that use LocalWorker

net.sourceforge.taverna.scuflworkers
net.sourceforge.taverna.scuflworkers.biojava	Provides BioJava-based LocalWorkers capable of sequence transcription, translation, and file parsing.
net.sourceforge.taverna.scuflworkers.image
net.sourceforge.taverna.scuflworkers.io	Provides LocalWorkers capable of reading and writing different types of files.
net.sourceforge.taverna.scuflworkers.jdbc	Provides LocalWorkers capable of executing SQL PreparedStatements.
net.sourceforge.taverna.scuflworkers.ncbi	Provides LocalWorkers capable of querying data from the NCBI databases.
net.sourceforge.taverna.scuflworkers.ui	Provides LocalWorkers capable of getting input from a user, or providing feedback to a user.
net.sourceforge.taverna.scuflworkers.xml
org.biomoby.client.taverna.plugin
org.embl.ebi.escience.scuflworkers.java

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers

Constructors in net.sourceforge.taverna.scuflworkers with parameters of type LocalWorker

LocalWorkerTest(LocalWorker worker, boolean allOutputsRequired, boolean allInputsRequired)
Constructor

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.biojava

Classes in net.sourceforge.taverna.scuflworkers.biojava that implement LocalWorker

class	BlastParserWorker This processor parses BLAST results and returns an XML document containing the results.
class	EMBLParserWorker This processor parses an EMBL-based file and outputs the results in Agave XML format.
class	FastaWorker This processor reads a FASTA file and returns the results as XML.
class	FileFormatIDWorker This class Last edited by $Author: sowen70 $
class	GenBankParserWorker This class parses genbank files and outputs the results in Agave XML format.
class	ReverseCompWorker This processor takes a raw DNA sequence and returns the reverse complement of the sequence.
class	SwissProtParserWorker This processor parses a SwissProt file and outputs the results in Agave XML format.
class	TranscribeWorker This processor takes a DNA sequence and transcribes it into an RNA sequence.
class	TranslateWorker This class translates a DNA sequence into a protein sequence.

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.image

Classes in net.sourceforge.taverna.scuflworkers.image that implement LocalWorker

class	RotateImageWorker This class Last edited by $Author: sowen70 $
class	ScaleImageWorker This class Last edited by $Author: sowen70 $

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.io

Classes in net.sourceforge.taverna.scuflworkers.io that implement LocalWorker

class	ConcatenateFileListWorker This processor concatenates a series of text files and saves the results into the output file.
class	DataRangeColumnTask This class allows the user to extract a single column of data from a data array produced by either an ExcelFileReader or by a DelimitedFileReader.
class	DataRangeTask This class extracts a range of values from a two dimension data array Last edited by $Author: alaninmcr $
class	DelimitedFileReader This file reads a delimited text file.
class	EnvVariableWorker This processor exposes the Java environment variables as an XML document.
class	ExcelFileReader This class reads an Excel spreadsheet and creates an ArrayList of ArrayLists containing string data.
class	FileListByExtTask This processor gets a list of files on a local directory.
class	FileListByRegexTask This processor lists the files in a given subdirectory using a regular expression.
class	ImageReader This processor reads an image file and places it in the output hash map.
class	ImageWriter This processor writes images out to a file.
class	JTidyWorker This processor tidies up bad HTML and converts it into valid XHTML.
class	LocalCommand This processor executes a commandline and returns the response as a String.
class	PostWorker This class POSTs a collection of parameter names/values and returns the resulting document.
class	RegexFileWorker This processor reads the text from a file, and replaces all instances of the oldText with instances of the new text.
class	TextFileReader This processor reads text from a file specified by the "fileurl" attribute.
class	TextFileWriter This processor writes the "filecontents" out to the the url specified in the "outputFile" parameter.
class	VelocityFileWriter This class merges an input map of objects with a Velocity template and outputs the results to an output file.

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.jdbc

Classes in net.sourceforge.taverna.scuflworkers.jdbc that implement LocalWorker

class	SQLQueryWorker This processor executes SQL prepared statements, and returns the results as an array of arrays.
class	SQLUpdateWorker This processor is used to execute SQL update/insert statements.

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.ncbi

Classes in net.sourceforge.taverna.scuflworkers.ncbi that implement LocalWorker

class	AbstractEFetchWorker This class provides the basis for all NCBI EFetch Tasks.
class	AbstractNCBIWorker This class provides basic common functionality needed by all NCBIWorkers.
class	EFetchWorker This class provides a wrapper for the NCBI EFetch Utilities.
class	EntrezGeneWorker This processor is responsible for fetching an Entrez Gene record in XML format.
class	EntrezProteinWorker This processor fetches an Entrez Protein record from NCBI.
class	HomoloGeneWorker This class fetches HomoloGene data from NCBI.
class	INSDSeqXMLWorker
class	LocusLinkWorker This class is designed to fetch locuslink data from the NCBI database as XML.
class	NucleotideFastaWorker This processor fetches a nucleotide sequence in FASTA format.
class	NucleotideGBSeqWorker This processor returns a GB Seq formatted record.
class	NucleotideINSDSeqXMLWorker This processor returns a INSD formatted nucleotide record
class	NucleotideTinySeqXMLWorker This processor fetches a nucleotide sequence from NCBI and returns the results in the TinySeqXML format.
class	NucleotideXMLWorker This class fetches Nucleotide XML documents.
class	OMIMWorker This processor fetches an OMIM record from the NCBI database in XML format.
class	ProteinFastaWorker This processor fetches a protein sequence in FASTA format.
class	ProteinGBSeqWorker This class fetches protein data in GBSeq XML format.
class	ProteinINSDSeqXMLWorker This processor fetches an INSD formatted protein record
class	ProteinTinySeqXMLWorker This processor fetches a protein in TinySeqXML format.
class	PubMedEFetchWorker This class is used to fetch pubmed articles in XML form.
class	PubMedESearchWorker This processor searches for articles in PubMed and returns their IDs in XML format.
class	PubMedSearchWorker This class downloads PubMed records in XML format.
class	SNPWorker This processor fetches SNP records.

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.ui

Classes in net.sourceforge.taverna.scuflworkers.ui that implement LocalWorker

class	AskWorker This processor creates a Dialog with a text box for user input.
class	ChooseWorker This processor allows the user to select an option from a list of radio buttons.
class	SelectFileWorker This processor allows the user to select a file.
class	SelectWorker This processor displays a dialog with a select box of options.
class	TellWorker This processor displays a message to the user.
class	WarnWorker This processor displays a warning message to the user.

Uses of LocalWorker in net.sourceforge.taverna.scuflworkers.xml

Classes in net.sourceforge.taverna.scuflworkers.xml that implement LocalWorker

class	XPathTextWorker This worker applies an arbitrary XPath expression to an XML document, and returns a nodelist containing the nodes that match the XPath expression.
class	XPathWorker This worker applies an arbitrary XPath expression to an XML document, and returns a nodelist containing the nodes that match the XPath expression.
class	XQueryWorker This class allows the user to create XQuery's against an XML document.
class	XSLTWorker This processor transforms an input XML document into an output document.

Uses of LocalWorker in org.biomoby.client.taverna.plugin

Classes in org.biomoby.client.taverna.plugin that implement LocalWorker

class	CreateMobyCollection A local processor to construct a biomoby data packet from either an ID or a string content
class	CreateMobyData A local processor to construct a biomoby data packet from either an ID or a string content
class	CreateMobySimple A local processor to construct a biomoby data packet from either an ID or a string content
class	ExtractMobyData A local processor to extract simple data types from biomoby data packets.

Uses of LocalWorker in org.embl.ebi.escience.scuflworkers.java

Subinterfaces of LocalWorker in org.embl.ebi.escience.scuflworkers.java

interface

LocalWorkerWithPorts Interface that defines LocalWorker's that need to generate their own InputPorts and OutputPorts.

Classes in org.embl.ebi.escience.scuflworkers.java that implement LocalWorker

class	ByteArrayToString Constructs a new String from the supplied byte[]
class	DecodeBase64 Decode base64 string into byte[]
class	EchoList Echo the input list to the output list, does no actual processing at all.
class	EmitLotsOfStrings Spit out a list of 40 strings
class	EncodeBase64 Encode byte[] data into base64 string
class	ExtractImageLinks Extract a list of all image links in the supplied html document
class	FailIfFalse A processor which fails if the test input matches the string 'false'
class	FailIfTrue A processor which fails if the test input matches the string 'true'
class	FilterStringList Filter a list of Strings, only passing through those that match the supplied regular expression.
class	FlattenList Consume a list of lists and emit a list containing the given level of flattening of the input.
class	GetLSID Outputs "replacelsid:input" which should be substituted for the input's lsid by the ProcessorTask.
class	PadNumber Pad a numeral with leading zeroes to take it up to a specified length, which defaults to seven.
class	ReadFilesFromDirectory Consumes a directory name and an optional file suffix and returns a list of strings/bytes representing the contents of those files.
class	RegularExpressionStringList Apply a regular expression to a string, returning a group that matches if there is a match.
class	SendEmail Send an email from a workflow
class	SliceList Return a sublist of a list.
class	SplitByRegex Split an input string into a list of strings using the given regular expression to determine the delimiter.
class	StringConcat Returns the result of appending firststring to secondstring
class	StringListMerge Consumes a string list and optional seperator character and emits a string formed from the concatenation of all items in the list with the seperator (default newline) interposed between them.
class	StringSetDifference Returns the items that are different between two sets or lists of string types where elements only exist in the output if they occur in either input, but not both.
class	StringSetIntersection Returns the intersection of two sets or lists of string types where elements only exist in the output if they occur in both inputs.
class	StringSetUnion Provide the union of two lists of strings, the result being a string list containing all strings that occur in either of the input lists.
class	StringStripDuplicates Consumes a string list and emits the string list with duplicate entries removed.
class	TestAlwaysFailingProcessor A processor that always fails instantly, useful for testing the reliability functions that we're putting in.
class	TestSometimesFails Processor which fails every four invocations.
class	WebImageFetcher Fetch a single image from URL
class	WebPageFetcher Fetch a single web page from URL
class	XMLInputSplitter A LocalWorker that takes a given input port for a complex type, and splits it to a single level generating an array of simple type inputs.
class	XMLOutputSplitter A LocalWorker that facilitates in extracting information from the inner elements of an XML output from a SOAP based service that returns a complex type.

Methods in org.embl.ebi.escience.scuflworkers.java that return LocalWorker

LocalWorker

LocalServiceProcessor.getWorker()

Methods in org.embl.ebi.escience.scuflworkers.java that return types with arguments of type LocalWorker

java.util.List<LocalWorker>

LocalWorkerRegistry.getLocalWorkers()

Constructors in org.embl.ebi.escience.scuflworkers.java with parameters of type LocalWorker

LocalServiceProcessor(ScuflModel model, java.lang.String name, LocalWorker worker)