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)