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

A

AA - class de.zimek.proteinfeatures.groups.AA.

AA() - Constructor for class de.zimek.proteinfeatures.groups.AA

AAComposition - class de.zimek.proteinfeatures.attributeAssigner.composition.AAComposition.

AAComposition() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.composition.AAComposition

AADistribution - class de.zimek.proteinfeatures.attributeAssigner.distribution.AADistribution.

AADistribution() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.distribution.AADistribution

AAINDEX_PACKAGE - Static variable in class de.zimek.proteinfeatures.ArffFileCreator

The name of the package for aaindex assigners.

AAIndex - interface de.zimek.proteinfeatures.aaindex.AAIndex.

Specification for any AAIndex.

AATransition - class de.zimek.proteinfeatures.attributeAssigner.transition.AATransition.

AATransition() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.transition.AATransition

AMINOACIDS - Static variable in interface de.zimek.proteinfeatures.protein.ProteinConstants

ARCHITECTURE - Static variable in class de.zimek.proteinfeatures.protein.CathID

ATTRIBUTE_MARK - Static variable in interface de.zimek.proteinfeatures.attributeAssigner.ArffAttributeAssigner

Mark for an attribute-description in an arff-file.

ATTRIBUTE_PROPERTY - Static variable in class de.zimek.proteinfeatures.ArffFileCreator

The property-name for attributes.

AbstractArffRealAttributeAssigner - class de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner.

AbstractArffRealAttributeAssigner() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner

AbstractGroup - class de.zimek.proteinfeatures.groups.AbstractGroup.

AbstractGroup() - Constructor for class de.zimek.proteinfeatures.groups.AbstractGroup

AbstractGroupAssigner - class de.zimek.proteinfeatures.attributeAssigner.AbstractGroupAssigner.

AbstractGroupAssigner() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.AbstractGroupAssigner

AbstractGroupCompositionAssigner - class de.zimek.proteinfeatures.attributeAssigner.composition.AbstractGroupCompositionAssigner.

AbstractGroupCompositionAssigner() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.composition.AbstractGroupCompositionAssigner

AbstractGroupDistributionAssigner - class de.zimek.proteinfeatures.attributeAssigner.distribution.AbstractGroupDistributionAssigner.

AbstractGroupDistributionAssigner() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.distribution.AbstractGroupDistributionAssigner

AbstractGroupTransitionAssigner - class de.zimek.proteinfeatures.attributeAssigner.AbstractGroupTransitionAssigner.

AbstractGroupTransitionAssigner() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.AbstractGroupTransitionAssigner

AbstractParser - class de.zimek.proteinfeatures.parser.AbstractParser.

AbstractParser() - Constructor for class de.zimek.proteinfeatures.parser.AbstractParser

ArffAttributeAssigner - interface de.zimek.proteinfeatures.attributeAssigner.ArffAttributeAssigner.

ArffFileCreator - class de.zimek.proteinfeatures.ArffFileCreator.

Main class for creating protein features in arff format.

ArffFileCreator(Properties) - Constructor for class de.zimek.proteinfeatures.ArffFileCreator

Initializes the ArffFileCreator according to the settings in the given properties.

Arffizer - class de.zimek.ding.Arffizer.

This class simply transforms the protein attribute lists as provided by Ding and Dubchak to arff format, using minimum support of 7 for each class.

Arffizer() - Constructor for class de.zimek.ding.Arffizer

AstralDBParser - class de.zimek.proteinfeatures.parser.AstralDBParser.

AstralDBParser() - Constructor for class de.zimek.proteinfeatures.parser.AstralDBParser

AutoCorrelationFunction - class de.zimek.proteinfeatures.attributeAssigner.AutoCorrelationFunction.

Provides the AutoCorrelationFunction for an AAIndex and a set m.

AutoCorrelationFunction() - Constructor for class de.zimek.proteinfeatures.attributeAssigner.AutoCorrelationFunction

Default constructor constructs no aaIndex.

aaIndex - Variable in class de.zimek.proteinfeatures.attributeAssigner.AutoCorrelationFunction

aaIndexFor(char) - Method in interface de.zimek.proteinfeatures.aaindex.AAIndex

Returns the amino-acid-index for a given amino-acid according to the actual implemented AAIndex.

aaIndexFor(char) - Method in class de.zimek.proteinfeatures.aaindex.OobatakeOoi

Returns the aaindex for the given amino acid according to Oobatake-Ooi.

architecture - Variable in class de.zimek.proteinfeatures.protein.CathID

arffAttributeAssigner - Variable in class de.zimek.proteinfeatures.ArffFileCreator

The ArffAttributeAssigners that are to create features.

as - Variable in class de.zimek.proteinfeatures.protein.Protein

astralID - Variable in class de.zimek.proteinfeatures.protein.Protein

astralIDs(InputStream) - Static method in class de.zimek.ding.DomainToAstralMapper

attributeName - Variable in class de.zimek.proteinfeatures.attributeAssigner.dingAttributes.DingAttribute

attributeNamePrefix - Variable in class de.zimek.proteinfeatures.groups.AbstractGroup

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner

Returns the attributes according to the actual attribute-assigner.

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.AbstractGroupTransitionAssigner

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.AutoCorrelationFunction

Returns a list of attributes of length m according to the currently set AAIndex.

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.MotifAssigner

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.ProteinLength

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.composition.AbstractGroupCompositionAssigner

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.dingAttributes.DingAttribute

attributes(Protein) - Method in class de.zimek.proteinfeatures.attributeAssigner.distribution.AbstractGroupDistributionAssigner