A C D E F G H M P Q S T V X

A

addModel(CrawledModel) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

addModel(CrawledModel) - Method in interface de.unirostock.sems.morre.client.MorreCrawlerInterface

Adds a model to the database.

AGGREGATED_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

aggregatedModelQuery(String, String, String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

aggregatedModelQuery(String, String, String) - Method in interface de.unirostock.sems.morre.client.Morre

Returns the available features for a given query type.

ANNOTATION_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

ANNOTATION_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

AnnotationResult - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for one Result produced by an AnnotationQuery with the MORRE-Interface

AnnotationResult(float, String, List<String>) - Constructor for class de.unirostock.sems.morre.client.dataholder.AnnotationResult

C

CELLML_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

compareTo(AnnotationResult) - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

compareTo(ModelResult) - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

compareTo(PersonResult) - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

compareTo(PublicationResult) - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

CrawledModel - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Object for a model, which is going to be inserted into the database with the MorreCrawlerInterface

CrawledModel(String, String, String, Map<String, List<String>>, Map<String, String>, String) - Constructor for class de.unirostock.sems.morre.client.dataholder.CrawledModel

D

de.unirostock.sems.morre.client - package de.unirostock.sems.morre.client

de.unirostock.sems.morre.client.dataholder - package de.unirostock.sems.morre.client.dataholder

de.unirostock.sems.morre.client.exception - package de.unirostock.sems.morre.client.exception

de.unirostock.sems.morre.client.impl - package de.unirostock.sems.morre.client.impl

doAnnotationQuery(String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doAnnotationQuery(String) - Method in interface de.unirostock.sems.morre.client.Morre

Searches for Annotations on the basis of the given query String.

documentURI - Variable in class de.unirostock.sems.morre.client.dataholder.Model

doModelQuery(String, FeatureSet) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doModelQuery(String, FeatureSet) - Method in interface de.unirostock.sems.morre.client.Morre

Performs a more complex query of the given type The available features can be retrieved by getQueryFeatures.

doPersonQuery(FeatureSet) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doPersonQuery(FeatureSet) - Method in interface de.unirostock.sems.morre.client.Morre

Searches for a Person on the basis of the given features The available features can be retrieved by getQueryFeatures.

doPublicationQuery(FeatureSet) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doPublicationQuery(FeatureSet) - Method in interface de.unirostock.sems.morre.client.Morre

Searches for a Publication on the basis of the given features The available features can be retrieved by getQueryFeatures.

doSimpleAggregatedModelQuery(String, String, String, String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doSimpleAggregatedModelQuery(String, String, String, String) - Method in interface de.unirostock.sems.morre.client.Morre

Searches for a Person on the basis of the given features The available features can be retrieved by getQueryFeatures.

doSimpleModelQuery(String, String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

doSimpleModelQuery(String, String) - Method in interface de.unirostock.sems.morre.client.Morre

Performs a simple query with only one keyword field for the given queryType Note: Only some queryTypes are supporting this method!

E

Entry(K) - Constructor for class de.unirostock.sems.morre.client.FeatureSet.Entry

Entry(K, V) - Constructor for class de.unirostock.sems.morre.client.FeatureSet.Entry

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.Model

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.Person

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

equals(Object) - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

F

FeatureSet - Class in de.unirostock.sems.morre.client

FeatureSet() - Constructor for class de.unirostock.sems.morre.client.FeatureSet

FeatureSet.Entry<K,V> - Class in de.unirostock.sems.morre.client

fileId - Variable in class de.unirostock.sems.morre.client.dataholder.Model

G

getAuthors() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

getDocumentURI() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getEmail() - Method in class de.unirostock.sems.morre.client.dataholder.Person

getFeatures() - Method in class de.unirostock.sems.morre.client.FeatureSet

getFileId() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getFileId() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getFirstName() - Method in class de.unirostock.sems.morre.client.dataholder.Person

getJournal() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

getKey() - Method in class de.unirostock.sems.morre.client.FeatureSet.Entry

getLastName() - Method in class de.unirostock.sems.morre.client.dataholder.Person

getLatestModelVersion(String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

getLatestModelVersion(String) - Method in interface de.unirostock.sems.morre.client.MorreCrawlerInterface

Returns the latest version of a model as dataholder object.

getMeta() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getMetaMap() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getModel() - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

getModelHistory(String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

getModelHistory(String) - Method in interface de.unirostock.sems.morre.client.MorreCrawlerInterface

Returns all available versions of this model as String List.

getModelID() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getModelName() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getModelType() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getModelVersion(String, String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

getModelVersion(String, String) - Method in interface de.unirostock.sems.morre.client.MorreCrawlerInterface

Returns one specific version of a model as dataholder object.

getOrganization() - Method in class de.unirostock.sems.morre.client.dataholder.Person

getParentMap() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getPerson() - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

getPublication() - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

getQueryFeatures(String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

getQueryFeatures(String) - Method in interface de.unirostock.sems.morre.client.Morre

Returns the available features for a given query type and an aggregation type.

getRelatedModelsUri() - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

getRelatedModelsUri() - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

getRelatedModelsUri() - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

getScore() - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

getScore() - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

getScore() - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

getScore() - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

getSynopsis() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

getTitle() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

getUri() - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

getValue() - Method in class de.unirostock.sems.morre.client.FeatureSet.Entry

getVersionId() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getVersionID() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getXmldoc() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

getXmldoc() - Method in class de.unirostock.sems.morre.client.dataholder.Model

getYear() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

H

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.Model

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.Person

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

hashCode() - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

HttpMorreClient - Class in de.unirostock.sems.morre.client.impl

HttpMorreClient(String) - Constructor for class de.unirostock.sems.morre.client.impl.HttpMorreClient

M

META_CRAWLED_DATE - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

META_SOURCE - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

META_VERSION_DATE - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

Model - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for a Model

Model(String, String, String, String, String, String) - Constructor for class de.unirostock.sems.morre.client.dataholder.Model

MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

modelID - Variable in class de.unirostock.sems.morre.client.dataholder.Model

modelName - Variable in class de.unirostock.sems.morre.client.dataholder.Model

modelQuery(String) - Method in class de.unirostock.sems.morre.client.impl.HttpMorreClient

modelQuery(String) - Method in interface de.unirostock.sems.morre.client.Morre

Searches for a model on the basis of a simple query.

ModelResult - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for one Result produced by an ModelQuery with the MORRE-Interface extends the Model Dataholder Class with a score attribute

ModelResult(String, String, String, String, String, String, float) - Constructor for class de.unirostock.sems.morre.client.dataholder.ModelResult

Morre - Interface in de.unirostock.sems.morre.client

Interface for performing search queries to the MORRE database API

MorreClientException - Exception in de.unirostock.sems.morre.client.exception

MorreClientException() - Constructor for exception de.unirostock.sems.morre.client.exception.MorreClientException

MorreClientException(String) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreClientException

MorreClientException(String, Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreClientException

MorreClientException(Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreClientException

MorreCommunicationException - Exception in de.unirostock.sems.morre.client.exception

MorreCommunicationException() - Constructor for exception de.unirostock.sems.morre.client.exception.MorreCommunicationException

MorreCommunicationException(String) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreCommunicationException

MorreCommunicationException(String, Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreCommunicationException

MorreCommunicationException(Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreCommunicationException

MorreCrawlerInterface - Interface in de.unirostock.sems.morre.client

Interface for model crawler to push models to the MORRE Database API

MorreException - Exception in de.unirostock.sems.morre.client.exception

The MORRE database interface has thrown an exception, which the client interface can not handle by it self.

MorreException() - Constructor for exception de.unirostock.sems.morre.client.exception.MorreException

MorreException(String) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreException

MorreException(String, Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreException

MorreException(Throwable) - Constructor for exception de.unirostock.sems.morre.client.exception.MorreException

P

Person - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for a Person returned in a @{link de.unirostock.sems.morre.client.dataholder.PersonResult PersonResult}

Person(String, String, String, String) - Constructor for class de.unirostock.sems.morre.client.dataholder.Person

PERSON_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

PERSON_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

PersonResult - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for one Result produced by an PersonQuery with the MORRE-Interface contains a Person Dataholder Object

PersonResult(float, Person, List<String>) - Constructor for class de.unirostock.sems.morre.client.dataholder.PersonResult

processMeta() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

Publication - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for a Publication returned in a @{link de.unirostock.sems.morre.client.dataholder.PublicationResult PublicationResult}

Publication(String, String, String, String, List<Person>) - Constructor for class de.unirostock.sems.morre.client.dataholder.Publication

PUBLICATION_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

PUBLICATION_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

PublicationResult - Class in de.unirostock.sems.morre.client.dataholder

Dataholder Class for one Result produced by an PublicationQuery with the MORRE-Interface contains a Publication Dataholder Object

PublicationResult(float, Publication, List<String>) - Constructor for class de.unirostock.sems.morre.client.dataholder.PublicationResult

Q

QueryType - Class in de.unirostock.sems.morre.client

All available Query-Types in the MORRE-Interface Note: Not all queries are feature driver, some only expects a keyword.

QueryType() - Constructor for class de.unirostock.sems.morre.client.QueryType

S

set(String, String) - Method in class de.unirostock.sems.morre.client.FeatureSet

setAuthors(List<Person>) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

setDocumentURI(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setEmail(String) - Method in class de.unirostock.sems.morre.client.dataholder.Person

setFileId(String) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setFileId(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setFirstName(String) - Method in class de.unirostock.sems.morre.client.dataholder.Person

setJournal(String) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

setLastName(String) - Method in class de.unirostock.sems.morre.client.dataholder.Person

setMeta(String) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setMetaMap(Map<String, String>) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setModelID(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setModelName(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setModelType(String) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setOrganization(String) - Method in class de.unirostock.sems.morre.client.dataholder.Person

setParentMap(Map<String, List<String>>) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setPerson(Person) - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

setPublication(Publication) - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

setRelatedModelsUri(List<String>) - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

setRelatedModelsUri(List<String>) - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

setRelatedModelsUri(List<String>) - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

setScore(float) - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

setScore(float) - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

setScore(float) - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

setScore(float) - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

setSynopsis(String) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

setTitle(String) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

setUri(String) - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

setValue(V) - Method in class de.unirostock.sems.morre.client.FeatureSet.Entry

setVersionId(String) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setVersionID(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setXmldoc(String) - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

setXmldoc(String) - Method in class de.unirostock.sems.morre.client.dataholder.Model

setYear(String) - Method in class de.unirostock.sems.morre.client.dataholder.Publication

SIMPLE_CELLML_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

SIMPLE_SBML_MODEL_QUERY - Static variable in class de.unirostock.sems.morre.client.QueryType

SOURCE_BIOMODELS_DB - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

SOURCE_PMR2 - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

T

toString() - Method in class de.unirostock.sems.morre.client.dataholder.AnnotationResult

toString() - Method in class de.unirostock.sems.morre.client.dataholder.CrawledModel

toString() - Method in class de.unirostock.sems.morre.client.dataholder.Model

toString() - Method in class de.unirostock.sems.morre.client.dataholder.ModelResult

toString() - Method in class de.unirostock.sems.morre.client.dataholder.Person

toString() - Method in class de.unirostock.sems.morre.client.dataholder.PersonResult

toString() - Method in class de.unirostock.sems.morre.client.dataholder.Publication

toString() - Method in class de.unirostock.sems.morre.client.dataholder.PublicationResult

TYPE_CELLML - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

TYPE_SBML - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

TYPE_SEDML - Static variable in class de.unirostock.sems.morre.client.dataholder.CrawledModel

V

versionID - Variable in class de.unirostock.sems.morre.client.dataholder.Model

X

xmldoc - Variable in class de.unirostock.sems.morre.client.dataholder.Model

A C D E F G H M P Q S T V X