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

A

AbstractHTMLParser<ResultType> - Class in de.bioforscher.singa.core.parser.rest

This class allows handling and parameter definition for simple HTML requests.

AbstractHTMLParser() - Constructor for class de.bioforscher.singa.core.parser.rest.AbstractHTMLParser

AbstractIdentifier - Class in de.bioforscher.singa.core.identifier.model

The most basic, abstract implementation of Identifier.

AbstractIdentifier(String, Pattern) - Constructor for class de.bioforscher.singa.core.identifier.model.AbstractIdentifier

Creates a new identifier by validating it with the given pattern.

AbstractParser<ResultType> - Class in de.bioforscher.singa.core.parser

The class allows definition of resource path and storage for the fetched result.

AbstractParser() - Constructor for class de.bioforscher.singa.core.parser.AbstractParser

AbstractXMLParser<ResultType> - Class in de.bioforscher.singa.core.parser.xml

AbstractXMLParser() - Constructor for class de.bioforscher.singa.core.parser.xml.AbstractXMLParser

add(ParameterValue<?>) - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

add(ParameterValue<Type>) - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

addEventListener(UpdateEventListener<EventType>) - Method in interface de.bioforscher.singa.core.events.UpdateEventEmitter

assertIfValueInRange(Type) - Method in interface de.bioforscher.singa.core.utility.Bounded

Asserts whether the given value is larger than the lower bound and smaller than the upper bound specified for this object.

B

BooleanParameter - Class in de.bioforscher.singa.core.parameters

BooleanParameter(String) - Constructor for class de.bioforscher.singa.core.parameters.BooleanParameter

Bounded<Type extends Comparable<Type>> - Interface in de.bioforscher.singa.core.utility

Defines a Object to be bounded by a lower and upper bound.

C

ChEBIIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is used by the ChEBI Database to identify small molecules.

ChEBIIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.ChEBIIdentifier

Creates a new identifier.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.ChEBIIdentifier

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.ECNumber

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.InChIKey

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.NCBITaxonomyIdentifier

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.PubChemIdentifier

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.SimpleStringIdentifier

Returns true, if the identifier is valid.

check(Identifier) - Static method in class de.bioforscher.singa.core.identifier.UniProtIdentifier

Returns true, if the identifier is valid.

clone() - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

clone() - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

CommutablePair<ValueType> - Class in de.bioforscher.singa.core.utility

This subclass of Pair only implements different equals and hashcode methods.
The values are exchangeable.

CommutablePair(ValueType, ValueType) - Constructor for class de.bioforscher.singa.core.utility.CommutablePair

Creates a new Pair.

D

de.bioforscher.singa.core.biology - package de.bioforscher.singa.core.biology

de.bioforscher.singa.core.events - package de.bioforscher.singa.core.events

de.bioforscher.singa.core.identifier - package de.bioforscher.singa.core.identifier

de.bioforscher.singa.core.identifier.model - package de.bioforscher.singa.core.identifier.model

de.bioforscher.singa.core.parameters - package de.bioforscher.singa.core.parameters

de.bioforscher.singa.core.parser - package de.bioforscher.singa.core.parser

de.bioforscher.singa.core.parser.rest - package de.bioforscher.singa.core.parser.rest

de.bioforscher.singa.core.parser.xml - package de.bioforscher.singa.core.parser.xml

de.bioforscher.singa.core.utility - package de.bioforscher.singa.core.utility

DoubleParameter - Class in de.bioforscher.singa.core.parameters

DoubleParameter(String, double, double) - Constructor for class de.bioforscher.singa.core.parameters.DoubleParameter

E

ECNumber - Class in de.bioforscher.singa.core.identifier

This identifier is used to identify functional classes of enzymes.

ECNumber(String) - Constructor for class de.bioforscher.singa.core.identifier.ECNumber

Creates a new identifier.

emitEvent(EventType) - Method in interface de.bioforscher.singa.core.events.UpdateEventEmitter

equals(Object) - Method in class de.bioforscher.singa.core.identifier.model.AbstractIdentifier

equals(Object) - Method in class de.bioforscher.singa.core.utility.CommutablePair

equals(Object) - Method in class de.bioforscher.singa.core.utility.Pair

error(SAXParseException) - Method in class de.bioforscher.singa.core.parser.xml.XMLErrorHandler

extractFirst(String) - Static method in class de.bioforscher.singa.core.identifier.PDBIdentifier

Extracts the first occurrence of any PDB identifier from a string.

F

fatalError(SAXParseException) - Method in class de.bioforscher.singa.core.parser.xml.XMLErrorHandler

fetchResource() - Method in class de.bioforscher.singa.core.parser.rest.AbstractHTMLParser

fetchResource(String) - Method in class de.bioforscher.singa.core.parser.rest.AbstractHTMLParser

fetchResourceWithQuery() - Method in interface de.bioforscher.singa.core.parser.xml.XMLParser

fetchWithQuery(Map<String, String>) - Method in class de.bioforscher.singa.core.parser.rest.AbstractHTMLParser

Builds a Client and WebTarget with the specified parameters in the query map and sets the input stream as a fetch result.

find(Collection<Identifier>) - Static method in class de.bioforscher.singa.core.identifier.ChEBIIdentifier

Searches a valid PubChem identifier in a collection of identifiers and returns it.

find(Collection<Identifier>) - Static method in class de.bioforscher.singa.core.identifier.PubChemIdentifier

Searches a valid PubChem identifier in a collection of identifiers and returns it.

find(Collection<Identifier>) - Static method in class de.bioforscher.singa.core.identifier.UniProtIdentifier

Searches a valid PubChem identifier in a collection of identifiers and returns it.

G

getCommonName() - Method in class de.bioforscher.singa.core.biology.Organism

Returns a common name (such as "wild boar").

getConsecutiveNumber() - Method in class de.bioforscher.singa.core.identifier.ChEBIIdentifier

Returns the consecutive number without the "CHEBI:" part.

getConsecutiveNumber() - Method in class de.bioforscher.singa.core.identifier.PubChemIdentifier

Returns the consecutive number without the "CID:" part.

getFetchResult() - Method in class de.bioforscher.singa.core.parser.AbstractParser

getFirst() - Method in class de.bioforscher.singa.core.utility.Pair

Returns the first value.

getIdentifier() - Method in class de.bioforscher.singa.core.biology.Organism

getIdentifier() - Method in class de.bioforscher.singa.core.identifier.model.AbstractIdentifier

getIdentifier() - Method in interface de.bioforscher.singa.core.identifier.model.Identifiable

Returns the Identifier.

getIdentifier() - Method in interface de.bioforscher.singa.core.identifier.model.Identifier

Returns the string representation of the identifier.

getLineage() - Method in class de.bioforscher.singa.core.biology.Organism

Returns the linage as a list of Taxons.

getListeners() - Method in interface de.bioforscher.singa.core.events.UpdateEventEmitter

getLowerBound() - Method in class de.bioforscher.singa.core.parameters.BooleanParameter

getLowerBound() - Method in class de.bioforscher.singa.core.parameters.DoubleParameter

getLowerBound() - Method in class de.bioforscher.singa.core.parameters.IntegerParameter

getLowerBound() - Method in interface de.bioforscher.singa.core.utility.Bounded

Returns the lower bound specified for this object.

getLowerBound() - Method in class de.bioforscher.singa.core.utility.Range

getName() - Method in class de.bioforscher.singa.core.biology.Organism

getName() - Method in class de.bioforscher.singa.core.biology.Taxon

getName() - Method in class de.bioforscher.singa.core.parameters.BooleanParameter

getName() - Method in class de.bioforscher.singa.core.parameters.DoubleParameter

getName() - Method in class de.bioforscher.singa.core.parameters.IntegerParameter

getName() - Method in interface de.bioforscher.singa.core.utility.Nameable

Returns the name, by which the object can be referenced.

getParameter() - Method in class de.bioforscher.singa.core.parameters.ParameterValue

getPattern() - Static method in class de.bioforscher.singa.core.identifier.ChEBIIdentifier

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.ECNumber

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.InChIKey

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.NCBITaxonomyIdentifier

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.PubChemIdentifier

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.SimpleStringIdentifier

Returns the pattern used to validate the identifier.

getPattern() - Static method in class de.bioforscher.singa.core.identifier.UniProtIdentifier

Returns the pattern used to validate the identifier.

getPositionFromLabel(LabelType) - Method in interface de.bioforscher.singa.core.utility.Labeled

getRank() - Method in class de.bioforscher.singa.core.biology.Taxon

Returns the rank of this taxon.

getResource() - Method in class de.bioforscher.singa.core.parser.AbstractParser

getResource() - Method in interface de.bioforscher.singa.core.parser.xml.XMLParser

getResourceAsFilepath(String) - Static method in class de.bioforscher.singa.core.utility.Resources

getResourceAsStream(String) - Static method in class de.bioforscher.singa.core.utility.Resources

getScientificName() - Method in class de.bioforscher.singa.core.biology.Organism

Returns the scientific name (such as "Sus scrofa").

getSecond() - Method in class de.bioforscher.singa.core.utility.Pair

Returns the second value.

getUpperBound() - Method in class de.bioforscher.singa.core.parameters.BooleanParameter

getUpperBound() - Method in class de.bioforscher.singa.core.parameters.DoubleParameter

getUpperBound() - Method in class de.bioforscher.singa.core.parameters.IntegerParameter

getUpperBound() - Method in interface de.bioforscher.singa.core.utility.Bounded

Returns the upper bound specified for this object.

getUpperBound() - Method in class de.bioforscher.singa.core.utility.Range

getValue(int, Class<T>) - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

getValue() - Method in class de.bioforscher.singa.core.parameters.ParameterValue

getValue(int) - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

getValueForLabel(LabelType) - Method in interface de.bioforscher.singa.core.utility.Labeled

getValueFromPosition(PositionType) - Method in interface de.bioforscher.singa.core.utility.Labeled

getValues() - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

getValues() - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

getXmlReader() - Method in class de.bioforscher.singa.core.parser.xml.AbstractXMLParser

H

hashCode() - Method in class de.bioforscher.singa.core.identifier.model.AbstractIdentifier

hashCode() - Method in class de.bioforscher.singa.core.utility.CommutablePair

hashCode() - Method in class de.bioforscher.singa.core.utility.Pair

HTMLParser<ResultType> - Interface in de.bioforscher.singa.core.parser.rest

Implements default method to fetch from a defined resource.

I

Identifiable<IdentifierType extends Identifier> - Interface in de.bioforscher.singa.core.identifier.model

The Identifiable interface specifies that, Objects implementing this interface can be identified by a certain Identifier.

Identifier - Interface in de.bioforscher.singa.core.identifier.model

The identifier is used to identify objects that have the same structure.

InChIKey - Class in de.bioforscher.singa.core.identifier

The IUPAC International Chemical Identifier is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web.

InChIKey(String) - Constructor for class de.bioforscher.singa.core.identifier.InChIKey

Creates a new identifier.

IntegerParameter - Class in de.bioforscher.singa.core.parameters

IntegerParameter(String, int, int) - Constructor for class de.bioforscher.singa.core.parameters.IntegerParameter

isInRange(Boolean) - Method in class de.bioforscher.singa.core.parameters.BooleanParameter

isInRange(Type) - Method in interface de.bioforscher.singa.core.utility.Bounded

Checks whether the given value is larger than the lower bound and smaller than the upper bound specified for this object.

L

Labeled<LabelType,PositionType,ValueType> - Interface in de.bioforscher.singa.core.utility

A label is an object (LabelType) das identifies the location or position (PositionType) of something (ValueType) in the object that implements this interface.

labelPosition(LabelType, PositionType) - Method in interface de.bioforscher.singa.core.utility.Labeled

LogManager - Class in de.bioforscher.singa.core.utility

LogManager() - Constructor for class de.bioforscher.singa.core.utility.LogManager

M

MixedParameterList - Class in de.bioforscher.singa.core.parameters

MixedParameterList() - Constructor for class de.bioforscher.singa.core.parameters.MixedParameterList

MixedParameterList(List<ParameterValue<?>>) - Constructor for class de.bioforscher.singa.core.parameters.MixedParameterList

N

Nameable - Interface in de.bioforscher.singa.core.utility

The Nameable interface defines an Object that has a useful name attached to it.

NCBITaxonomyIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is used by the NCBI to uniquely identify any organism on the NCBI Taxonomy Database.

NCBITaxonomyIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.NCBITaxonomyIdentifier

Creates a new identifier.

O

of(Type, Type) - Static method in class de.bioforscher.singa.core.utility.Range

of(Type) - Static method in class de.bioforscher.singa.core.utility.Range

onEventReceived(Type) - Method in interface de.bioforscher.singa.core.events.UpdateEventListener

Organism - Class in de.bioforscher.singa.core.biology

The organism class is used to store information about organisms, such as NCBITaxonomyIdentifier, names, and linage.

Organism(String) - Constructor for class de.bioforscher.singa.core.biology.Organism

Creates a new organism with the given scientific name.

P

Pair<ValueType> - Class in de.bioforscher.singa.core.utility

A Pair is a composition of two objects.

Pair(ValueType, ValueType) - Constructor for class de.bioforscher.singa.core.utility.Pair

Creates a new Pair.

Parameter<Type extends Comparable<Type>> - Interface in de.bioforscher.singa.core.parameters

ParameterSampler - Class in de.bioforscher.singa.core.parameters

ParameterSampler() - Constructor for class de.bioforscher.singa.core.parameters.ParameterSampler

ParameterValue<Type extends Comparable<Type>> - Class in de.bioforscher.singa.core.parameters

ParameterValue(Parameter<Type>, Type) - Constructor for class de.bioforscher.singa.core.parameters.ParameterValue

parse() - Method in interface de.bioforscher.singa.core.parser.Parser

Returns the result of the parsing.

Parser<ResultType> - Interface in de.bioforscher.singa.core.parser

Implements methods to fetch resource and parse articles into the right format.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.ChEBIIdentifier

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.ECNumber

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.InChIKey

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.NCBITaxonomyIdentifier

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.PDBIdentifier

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.PubChemIdentifier

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.SimpleStringIdentifier

The pattern to verify the identifier.

PATTERN - Static variable in class de.bioforscher.singa.core.identifier.UniProtIdentifier

The pattern to verify the identifier.

PDBIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is used by the Protein Database to identify structures.

PDBIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.PDBIdentifier

Creates a new identifier.

PubChemIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is used by the PubChem Database to identify small molecules.

PubChemIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.PubChemIdentifier

Creates a new identifier.

R

Range<Type extends Comparable<Type>> - Class in de.bioforscher.singa.core.utility

Range(Type, Type) - Constructor for class de.bioforscher.singa.core.utility.Range

removeEventListener(UpdateEventListener<EventType>) - Method in interface de.bioforscher.singa.core.events.UpdateEventEmitter

Resources - Class in de.bioforscher.singa.core.utility

Access to commonly used test functions and constants.

Resources() - Constructor for class de.bioforscher.singa.core.utility.Resources

S

sample(BooleanParameter) - Static method in class de.bioforscher.singa.core.parameters.ParameterSampler

sample(DoubleParameter, int) - Static method in class de.bioforscher.singa.core.parameters.ParameterSampler

sample(IntegerParameter, int) - Static method in class de.bioforscher.singa.core.parameters.ParameterSampler

setCommonName(String) - Method in class de.bioforscher.singa.core.biology.Organism

Sets a common name (such as "wild boar").

setDebugLevel(Level) - Static method in class de.bioforscher.singa.core.utility.LogManager

setFetchResult(InputStream) - Method in class de.bioforscher.singa.core.parser.AbstractParser

setFetchResult(String) - Method in interface de.bioforscher.singa.core.parser.xml.XMLParser

setIdentifier(NCBITaxonomyIdentifier) - Method in class de.bioforscher.singa.core.biology.Organism

Sets the NCBITaxonomyIdentifier.

setLineage(List<Taxon>) - Method in class de.bioforscher.singa.core.biology.Organism

Sets the linage for this organism.

setName(String) - Method in class de.bioforscher.singa.core.biology.Taxon

Sets the name of this taxon.

setRank(String) - Method in class de.bioforscher.singa.core.biology.Taxon

Sets the rank of this taxon.

setResource(String) - Method in class de.bioforscher.singa.core.parser.AbstractParser

setScientificName(String) - Method in class de.bioforscher.singa.core.biology.Organism

Sets the scientific name (such as "Sus scrofa").

setValues(List<ParameterValue<?>>) - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

setValues(List<ParameterValue<Type>>) - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

setXmlReader(XMLReader) - Method in class de.bioforscher.singa.core.parser.xml.AbstractXMLParser

SimpleStringIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is just an encapsulated string.

SimpleStringIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.SimpleStringIdentifier

Creates a new identifier.

T

Taxon - Class in de.bioforscher.singa.core.biology

A taxon is usually known by a particular name and given a particular ranking.

Taxon(String, String) - Constructor for class de.bioforscher.singa.core.biology.Taxon

Creates a new Taxon with rank and name.

Taxon(String) - Constructor for class de.bioforscher.singa.core.biology.Taxon

Creates a taxon with unknown or unspecified rank.

toString() - Method in class de.bioforscher.singa.core.identifier.model.AbstractIdentifier

toString() - Method in class de.bioforscher.singa.core.parameters.BooleanParameter

toString() - Method in class de.bioforscher.singa.core.parameters.DoubleParameter

toString() - Method in class de.bioforscher.singa.core.parameters.IntegerParameter

toString() - Method in class de.bioforscher.singa.core.parameters.MixedParameterList

toString() - Method in class de.bioforscher.singa.core.parameters.ParameterValue

toString() - Method in class de.bioforscher.singa.core.parameters.UniqueParameterList

toString() - Method in class de.bioforscher.singa.core.utility.Pair

U

UniProtIdentifier - Class in de.bioforscher.singa.core.identifier

This identifier is used by the Uniprot Database to identify proteins.

UniProtIdentifier(String) - Constructor for class de.bioforscher.singa.core.identifier.UniProtIdentifier

Creates a new identifier.

UniqueParameterList<Type extends Comparable<Type>> - Class in de.bioforscher.singa.core.parameters

UniqueParameterList() - Constructor for class de.bioforscher.singa.core.parameters.UniqueParameterList

UniqueParameterList(List<ParameterValue<Type>>) - Constructor for class de.bioforscher.singa.core.parameters.UniqueParameterList

UpdateEventEmitter<EventType> - Interface in de.bioforscher.singa.core.events

UpdateEventListener<Type> - Interface in de.bioforscher.singa.core.events

W

warning(SAXParseException) - Method in class de.bioforscher.singa.core.parser.xml.XMLErrorHandler

X

XMLErrorHandler - Class in de.bioforscher.singa.core.parser.xml

Your average all purpose SAX Error-Handler.

XMLErrorHandler() - Constructor for class de.bioforscher.singa.core.parser.xml.XMLErrorHandler

XMLParser - Interface in de.bioforscher.singa.core.parser.xml

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