public class RetrieveGolrAnnotations extends Object
Modifier and Type | Class and Description |
---|---|
static class |
RetrieveGolrAnnotations.GolrAnnotationDocument |
static class |
RetrieveGolrAnnotations.GolrAnnotationExtension |
Constructor and Description |
---|
RetrieveGolrAnnotations(String server) |
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> |
getGolrAnnotationsForSynonym(String source,
String synonym) |
protected String |
getJsonStringFromUri(URI uri) |
protected void |
handleAnnotationExtension(GeneAnnotation annotation,
RetrieveGolrAnnotations.GolrAnnotationDocument document) |
protected void |
logRequest(URI uri) |
protected org.bbop.golr.java.RetrieveGolrAnnotations.GolrResponse |
parseGolrResponse(String response) |
public RetrieveGolrAnnotations(String server)
public GafDocument convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments) throws IOException
IOException
public void convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument> golrAnnotationDocuments, Map<String,Bioentity> entities, GafDocument document) throws IOException
IOException
protected void handleAnnotationExtension(GeneAnnotation annotation, RetrieveGolrAnnotations.GolrAnnotationDocument document) throws IOException
IOException
public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForGene(String id) throws IOException
IOException
public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotationsForSynonym(String source, String synonym) throws IOException
IOException
public List<RetrieveGolrAnnotations.GolrAnnotationDocument> getGolrAnnotations(List<String[]> tagvalues) throws IOException
IOException
protected String getJsonStringFromUri(URI uri) throws IOException
IOException
protected void logRequest(URI uri)
protected org.bbop.golr.java.RetrieveGolrAnnotations.GolrResponse parseGolrResponse(String response) throws IOException
IOException
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