org.bbop.golr.java

Class RetrieveGolrAnnotations

java.lang.Object

org.bbop.golr.java.AbstractRetrieveGolr

org.bbop.golr.java.RetrieveGolrAnnotations

public class RetrieveGolrAnnotations
extends AbstractRetrieveGolr

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RetrieveGolrAnnotations.GolrAnnotationDocument
static class	RetrieveGolrAnnotations.GolrAnnotationExtension

Constructor Summary

Constructors

Constructor and Description
RetrieveGolrAnnotations(String server)
RetrieveGolrAnnotations(String server, int retryCount, boolean ignoreC16ParseErrors)

Method Summary

Methods

Modifier and Type	Method and Description
GafDocument	convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments)
void	convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments, Map<String,Bioentity> entities, GafDocument document)
List<RetrieveGolrAnnotations.GolrAnnotationDocument>	getGolrAnnotations(List<String[]> tagvalues)
List<RetrieveGolrAnnotations.GolrAnnotationDocument>	getGolrAnnotationsForGene(String id)
List<RetrieveGolrAnnotations.GolrAnnotationDocument>	getGolrAnnotationsForGenes(List<String> ids)
List<RetrieveGolrAnnotations.GolrAnnotationDocument>	getGolrAnnotationsForSynonym(String source, List<String> synonyms)
List<RetrieveGolrAnnotations.GolrAnnotationDocument>	getGolrAnnotationsForSynonym(String source, String synonym)
protected List<String>	getRelevantFields()
protected void	handleAnnotationExtension(GeneAnnotation annotation, RetrieveGolrAnnotations.GolrAnnotationDocument document)
protected boolean	isIndentJson()

Methods inherited from class org.bbop.golr.java.AbstractRetrieveGolr

defaultRandomWait, getJsonStringFromUri, getJsonStringFromUri, logRequest, logRequestError, logRetry, parseGolrResponse, randomWait, retryRequest

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RetrieveGolrAnnotations

public RetrieveGolrAnnotations(String server)

RetrieveGolrAnnotations

public RetrieveGolrAnnotations(String server,
                       int retryCount,
                       boolean ignoreC16ParseErrors)

Method Detail

isIndentJson

protected boolean isIndentJson()

Specified by:

isIndentJson in class AbstractRetrieveGolr

getRelevantFields

protected List<String> getRelevantFields()

Specified by:

getRelevantFields in class AbstractRetrieveGolr

convert

public GafDocument convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments)
                    throws IOException

Throws:

IOException

convert

public void convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments,
           Map<String,Bioentity> entities,
           GafDocument document)
             throws IOException,
                    com.google.gson.JsonSyntaxException

Throws:

IOException

com.google.gson.JsonSyntaxException

handleAnnotationExtension

protected void handleAnnotationExtension(GeneAnnotation annotation,
                             RetrieveGolrAnnotations.GolrAnnotationDocument document)
                                  throws com.google.gson.JsonSyntaxException

Throws:

com.google.gson.JsonSyntaxException

getGolrAnnotationsForGenes

public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForGenes(List<String> ids)
                                                                                throws IOException

Throws:

IOException

getGolrAnnotationsForGene

public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForGene(String id)
                                                                               throws IOException

Throws:

IOException

getGolrAnnotationsForSynonym

public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForSynonym(String source,
                                                                                String synonym)
                                                                                  throws IOException

Throws:

IOException

getGolrAnnotationsForSynonym

public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForSynonym(String source,
                                                                                List<String> synonyms)
                                                                                  throws IOException

Throws:

IOException

getGolrAnnotations

public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotations(List<String[]> tagvalues)
                                                                        throws IOException

Throws:

IOException