A C D E F G H I L M N P R S T U V

A

addCrossReference(SPTRCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

addCrossReferences(SPTRCrossReference[]) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

addReaction(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

addSynonym(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

AN - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

ApplicationResources - Class in uk.ac.ebi.intenz.tools.sib

ApplicationResources provides various property resources required to run the applications.
The application will not run unless their is a file called application.properties.

C

CA - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

CC - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

CC_LineFormatter - Class in uk.ac.ebi.intenz.tools.sib.writer

Handles the special needs regarding the format of the CC line.

CC_LineFormatter() - Constructor for class uk.ac.ebi.intenz.tools.sib.writer.CC_LineFormatter

CF - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

compare(File, File) - Static method in class uk.ac.ebi.intenz.tools.sib.comparator.FlatFileComparator

compareEntries(String, String) - Static method in class uk.ac.ebi.intenz.tools.sib.comparator.FlatFileComparator

Compares two entries by checking their data line by line.

copyAbsorptionInstance(Absorption) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyAnnotationInstance(Annotation) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyAuthorInstance(Author) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyBookInstance(Book) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyCluSTrEntry(CluSTrEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyElectronicArticleInstance(ElectronicArticle) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyEnzymeEntryInstance(EnzymeEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyFeatureInstance(Feature) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyFeatureLocationInstance(FeatureLocation) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyGeneInstance(Gene) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyGOEvidence(GOEvidence) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyGOProteinData(GOProteinData) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyGOStructure(GOStructure) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyGOTerm(GOTerm) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyIntegr8GeneInstance(Gene) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyIntegr8GeneInstance(Gene) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyIntegr8SPTREntryInstance(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyInterProCrossReferenceInstance(InterProCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyInterProEntry(InterProEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyInterProProteinData(InterProProteinData) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyInterProStructure(InterProStructure) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyIsoformInstance(Isoform) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyJournalArticleInstance(JournalArticle) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyKineticParameterInstance(KineticParameter) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyMassSpectrometryRangeInstance(MassSpectrometryRange) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyMaximumVelocityInstance(MaximumVelocity) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyMichaelisConstantInstance(MichaelisConstant) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyPatentInstance(Patent) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyPredictiveInstance(PredictiveInstance) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyProteomeEntryInstance(ProteomeEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyPythiaEntryInstance(PythiaEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySignaturDBHit(SignatureDBHit) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySignatureDBEntry(SignatureDBEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySPINSubmissionInstance(SPINSubmission) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySPTRCommentInstance(SPTRComment) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySPTRCrossReference(SPTRCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySPTRCrossReferenceInstance(SPTRCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySPTREntryInstance(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copySubmissionInstance(Submission) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyThesisInstance(Thesis) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyUniParcCrossReference(UniParcCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyUniParcCrossReferenceMetaData(UniParcCrossReferenceMetaData) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyUniParcEntry(UniParcEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyUnpublishedObservationsInstance(UnpublishedObservations) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

copyUnpublishedResultsInstance(UnpublishedResults) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

create(String, LineType) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.LineWrapperFactory

Returns a LineWrapper implementation which will be chosen according to the needs of the text to be wrapped.

createXrefHyperlinks(String) - Static method in class uk.ac.ebi.intenz.tools.sib.helper.FFWriterHelper

Deprecated.

Create hyperlinks for all cross-references (xrefs) in a flat file.

D

DE - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

DE_MODIFIED_ENTRIES - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

EC numbers of entries which have been transferred more than once, or to more than one entry, or deleted but actually transferred, and whose DE line must be changed to match the enzyme.dat entry.

DefaultLineFormatter - Class in uk.ac.ebi.intenz.tools.sib.writer

Provides a default implementation which can be applied to all line types.

DefaultLineFormatter() - Constructor for class uk.ac.ebi.intenz.tools.sib.writer.DefaultLineFormatter

DI - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

DR - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

E

EnzymeCrossReference - Class in uk.ac.ebi.intenz.tools.sib.sptr_enzyme

This class implements the SPTRCrossReference interface.

EnzymeCrossReference(String) - Constructor for class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Creates an EnzymeCrossReference instance to the given database.

EnzymeCrossReferenceException - Exception in uk.ac.ebi.intenz.tools.sib.sptr_enzyme

This exception is thrown when cross references are created with wrong values (for example database names).

EnzymeCrossReferenceException(String) - Constructor for exception uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReferenceException

EnzymeCrossReferenceException(Exception) - Constructor for exception uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReferenceException

EnzymeCrossReferenceException(String, Exception) - Constructor for exception uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReferenceException

EnzymeEntryImpl - Class in uk.ac.ebi.intenz.tools.sib.sptr_enzyme

This class is a simple implementation of the EnzymeEntry interface.

EnzymeEntryImpl() - Constructor for class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

EnzymeEntryValidationException - Exception in uk.ac.ebi.intenz.tools.sib.exceptions

This exception is used to indicate an error in the syntax of an ENZYME entry.

EnzymeEntryValidationException(String) - Constructor for exception uk.ac.ebi.intenz.tools.sib.exceptions.EnzymeEntryValidationException

EnzymeEntryValidator - Class in uk.ac.ebi.intenz.tools.sib.validator

This class provides a method to validate ENZYME entries.

EnzymeEntryValidator() - Constructor for class uk.ac.ebi.intenz.tools.sib.validator.EnzymeEntryValidator

EnzymeFlatFileComparatorApp - Class in uk.ac.ebi.intenz.tools.sib

This class provides methods for exporting enzyme data into the ENZYME flat file format.

EnzymeFlatFileComparatorApp() - Constructor for class uk.ac.ebi.intenz.tools.sib.EnzymeFlatFileComparatorApp

EnzymeFlatFileWriteException - Exception in uk.ac.ebi.intenz.tools.sib.writer

This exception is thrown whenever an error occurs during the creation of the ENZYME flat file.

EnzymeFlatFileWriteException(Exception) - Constructor for exception uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriteException

Stores the (lower-level) exception this exception should wrap.

EnzymeFlatFileWriteException(String, Exception) - Constructor for exception uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriteException

Stores the exception message and the (lower-level) exception this exception should wrap.

EnzymeFlatFileWriteException(String) - Constructor for exception uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriteException

Stores the exception message.

EnzymeFlatFileWriter - Class in uk.ac.ebi.intenz.tools.sib.writer

This utility class provides methods for exporting enzyme data into the ENZYME flat file format.

EnzymeFlatFileWriterApp - Class in uk.ac.ebi.intenz.tools.sib

This class provides methods for exporting enzyme data into the ENZYME flat file format.

EnzymeFlatFileWriterApp() - Constructor for class uk.ac.ebi.intenz.tools.sib.EnzymeFlatFileWriterApp

EnzymeHelper - Class in uk.ac.ebi.intenz.tools.sib.helper

Deprecated.

Use the new class uk.ac.ebi.intenz.webapp.helper.SibEntryHelper

EnzymeHelper() - Constructor for class uk.ac.ebi.intenz.tools.sib.helper.EnzymeHelper

Deprecated.

EnzymeXrefFactory - Class in uk.ac.ebi.intenz.tools.sib.sptr_enzyme

This class is a simple extension of the abstract Factory, which allows to create EnzymeCrossReference instances only.

EnzymeXrefFactory() - Constructor for class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

export(EnzymeEntryImpl) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

Gives single enzyme view (used in webapp tools).

export(Collection, String, File) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

Exports the given collection of enzymes into the ENZYME flat file format using the given file.

export(EnzymeEntryImpl, Writer) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

export(Collection, String, String, String) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

Exports the given collection of enzymes into the ENZYME flat file format using the given directory and file name to create the file.

F

FFWriterHelper - Class in uk.ac.ebi.intenz.tools.sib.helper

Deprecated.

this is a view-tier task, use the IntEnzUtilities class instead (public webapp)

FFWriterHelper() - Constructor for class uk.ac.ebi.intenz.tools.sib.helper.FFWriterHelper

Deprecated.

findPosition(String, int) - Method in interface uk.ac.ebi.intenz.tools.sib.writer.LineWrapper

Returns the next position in the line where the wrapping should be performed.

FlatFileComparator - Class in uk.ac.ebi.intenz.tools.sib.comparator

This class compares two ENZYME.dat flat file formats.

FlatFileComparator() - Constructor for class uk.ac.ebi.intenz.tools.sib.comparator.FlatFileComparator

formatLines(String, LineType) - Method in class uk.ac.ebi.intenz.tools.sib.writer.CC_LineFormatter

Formats the CC lines according to the format described in the class description.

formatLines(String, LineType) - Method in class uk.ac.ebi.intenz.tools.sib.writer.DefaultLineFormatter

Formats the text by adding the line headers and wrapping the content using LineWrapper implementations.

formatLines(String, LineType) - Method in interface uk.ac.ebi.intenz.tools.sib.writer.LineFormatter

This method takes care of proper formatting of the line(s) corresponding one line type as described in the class description.

G

getAccessionNumber() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Returns the accession number of this EnzymeCrossReference.

getCofactors() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getComment() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getCommentSentences(String) - Method in class uk.ac.ebi.intenz.tools.sib.writer.CC_LineFormatter

Breaks the comment text into individual sentences.

getCommonName() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getCrossReferences() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getDatabaseName() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Returns the name of the database this EnzymeCrossReference refers to.

getDbConfig() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getDbPassword() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getDbUrl() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getDbUserName() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getEC() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getExportFlatFileName() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getId() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getInputFlatFileName() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

Singleton method to create a single instance of the application resources.
The system will exit if the application resources is unable to be created.

getPropertyValue(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Returns the value of the property.

getReactions() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

getSibEnzymeEntry(EnzymeEntry, SpecialCharacters, EncodingType, boolean) - Static method in class uk.ac.ebi.intenz.tools.sib.helper.EnzymeHelper

Deprecated.

Use uk.ac.ebi.intenz.webapp.helper.SibEntryHelper

getSibEnzymeEntry(EnzymeEntry, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.tools.sib.helper.SibEntryHelper

getSpecialCharactersFileName() - Method in class uk.ac.ebi.intenz.tools.sib.ApplicationResources

getSynonyms() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

H

hasProperty(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Indicates if a cross reference property is set.

I

ID - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

insertLineBreaks(String, LineType) - Static method in class uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter

Inserts line breaks for the given line type if the given text is longer than 78 characters.

isTransferredOrDeleted() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

L

LINE_TYPES - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

An unmodifiable list of all line types.

LineFormatter - Interface in uk.ac.ebi.intenz.tools.sib.writer

This interface provides a method to format lines according to the rules of the enzyme.dat file.

LineType - Class in uk.ac.ebi.intenz.tools.sib.writer

Represents an enumeration of all ENZYME line types.

LINEWIDTH - Static variable in interface uk.ac.ebi.intenz.tools.sib.writer.LineFormatter

Defines the maximum line width within the flat file.

LineWrapper - Interface in uk.ac.ebi.intenz.tools.sib.writer

Defines a method to retrieve the next line wrapping position.

LineWrapperFactory - Class in uk.ac.ebi.intenz.tools.sib.writer

This class provides a factory method to retrieve the adequate LineWrapper implementation.

LineWrapperFactory() - Constructor for class uk.ac.ebi.intenz.tools.sib.writer.LineWrapperFactory

M

main(String[]) - Static method in class uk.ac.ebi.intenz.tools.sib.EnzymeFlatFileComparatorApp

Compares the content of two ENZYME flat files.

main(String[]) - Static method in class uk.ac.ebi.intenz.tools.sib.EnzymeFlatFileWriterApp

Exports all IntEnz entries containing only data valid for the ENZYME database.

MIM - Static variable in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Constant for database cross reference to MIM Disease Database.

N

newAbsorptionInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newAnnotationInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newAuthorInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newBookInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newClusterMember(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newCluSTrEntry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newElectronicArticleInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newEnzymeCrossReference(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

Returns a new instance of an EnzymeCrossReference.

newEnzymeEntryInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newFeatureInstance(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newFeatureLocationInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newGeneInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newGOEvidence() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newGOProteinData(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newGOStructure() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newGOTerm() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newIntegr8GeneInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newIntegr8SPTREntryInstance(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newIntegr8SPTREntryInstance(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newInterProCrossReferenceInstance(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newInterProEntry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newInterProProteinData(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newInterProStructure(InterProEntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newIsoformInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newJournalArticleInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newKineticParameterInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newMassSpectrometryRangeInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newMaximumVelocityInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newMichaelisConstantInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newPatentInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newPredictiveInstance(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newProteomeEntryInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newPythiaEntryInstance(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSignatureDBEntry(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSignatureDBHit() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPINSubmissionInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPTRCommentInstance(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPTRCrossReference(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPTRCrossReferenceInstance(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPTREntryInstance(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSPTREntryInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newSubmissionInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newThesisInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniParcCrossReference(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniParcCrossReferenceMetaData() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniParcEntry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniParcEntry(SPTREntry, String, UniParcCrossReferenceMetaData) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef100Entry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef100Entry(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef50Entry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef50Entry(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef90Entry() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUniRef90Entry(SPTREntry) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUnpublishedObservationsInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

newUnpublishedResultsInstance() - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeXrefFactory

P

PR - Static variable in class uk.ac.ebi.intenz.tools.sib.writer.LineType

PROSITE - Static variable in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Constant for database cross reference to PROSITE.

R

removeCrossReference(SPTRCrossReference) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

removeReaction(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

removeSynonym(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

S

setAccessionNumber(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Sets the accession number of this EnzymeCrossReference.

setCofactors(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setComment(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setCommonName(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setCrossReferences(SPTRCrossReference[]) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setEC(String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setId(int) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setPropertyValue(int, String) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Sets a property and value of this EnzymeCrossReference.

setReactions(String[]) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setSynonyms(String[]) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

setTransferredOrDeleted(boolean) - Method in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeEntryImpl

SibEntryHelper - Class in uk.ac.ebi.intenz.tools.sib.helper

This class ...

SibEntryHelper() - Constructor for class uk.ac.ebi.intenz.tools.sib.helper.SibEntryHelper

SWISSPROT - Static variable in class uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

Constant for database cross reference to SwissProt.

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toString() - Method in class uk.ac.ebi.intenz.tools.sib.writer.LineType

Returns the line type code.

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uk.ac.ebi.intenz.tools.sib - package uk.ac.ebi.intenz.tools.sib

This package contains a class which allows to execute the flat file writer from the command line.
In addition a comparator is available which can be used to check a generated flat file with a given one.

uk.ac.ebi.intenz.tools.sib.comparator - package uk.ac.ebi.intenz.tools.sib.comparator

uk.ac.ebi.intenz.tools.sib.exceptions - package uk.ac.ebi.intenz.tools.sib.exceptions

uk.ac.ebi.intenz.tools.sib.helper - package uk.ac.ebi.intenz.tools.sib.helper

uk.ac.ebi.intenz.tools.sib.sptr_enzyme - package uk.ac.ebi.intenz.tools.sib.sptr_enzyme

This package contains SPTR classes which implement SPTR interfaces.

uk.ac.ebi.intenz.tools.sib.validator - package uk.ac.ebi.intenz.tools.sib.validator

uk.ac.ebi.intenz.tools.sib.writer - package uk.ac.ebi.intenz.tools.sib.writer

This package contains classes for writing the enzyme.dat flat file.

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validate(String) - Static method in class uk.ac.ebi.intenz.tools.sib.validator.EnzymeEntryValidator

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