org.molgenis.das

Class RangeHandlingDataSource

java.lang.Object

org.molgenis.das.RangeHandlingDataSource

All Implemented Interfaces:

uk.ac.ebi.mydas.datasource.AnnotationDataSource, uk.ac.ebi.mydas.datasource.RangeHandlingAnnotationDataSource

Direct Known Subclasses:

RepositoryRangeHandlingDataSource

public abstract class RangeHandlingDataSource
extends Object
implements uk.ac.ebi.mydas.datasource.RangeHandlingAnnotationDataSource

Field Summary

Fields inherited from interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

LINK_FIELD_CATEGORY, LINK_FIELD_FEATURE, LINK_FIELD_METHOD, LINK_FIELD_TARGET, LINK_FIELD_TYPE

Constructor Summary

Constructors

Constructor and Description
RangeHandlingDataSource()

Method Summary

Modifier and Type	Method and Description
protected uk.ac.ebi.mydas.model.DasFeature	createDasFeature(Integer start, Integer stop, String identifier, String name, String description, String link, uk.ac.ebi.mydas.model.DasType type, uk.ac.ebi.mydas.model.DasMethod method, String dataSet, String patient, List<String> notes)
void	destroy()
Collection<uk.ac.ebi.mydas.model.DasEntryPoint>	getEntryPoints(Integer segmentId, Integer notUsed)
String	getEntryPointVersion()
Collection<uk.ac.ebi.mydas.model.DasAnnotatedSegment>	getFeatures(Collection<String> arg0, Integer arg1)
Collection<uk.ac.ebi.mydas.model.DasAnnotatedSegment>	getFeatures(Collection<String> arg0, Integer arg1, uk.ac.ebi.mydas.model.Range arg2)
uk.ac.ebi.mydas.model.DasAnnotatedSegment	getFeatures(String arg0, Integer arg1)
uk.ac.ebi.mydas.model.DasAnnotatedSegment	getFeatures(String arg0, Integer arg1, uk.ac.ebi.mydas.model.Range arg2)
uk.ac.ebi.mydas.model.DasAnnotatedSegment	getFeatures(String arg0, int arg1, int arg2, Integer arg3, uk.ac.ebi.mydas.model.Range arg4)
URL	getLinkURL(String arg0, String arg1)
int	getTotalEntryPoints()

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.mydas.datasource.RangeHandlingAnnotationDataSource

getFeatures

Methods inherited from interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

getTotalCountForType, getTypes, init

Constructor Detail

RangeHandlingDataSource

public RangeHandlingDataSource()

Method Detail

createDasFeature

protected uk.ac.ebi.mydas.model.DasFeature createDasFeature(Integer start,
                                                            Integer stop,
                                                            String identifier,
                                                            String name,
                                                            String description,
                                                            String link,
                                                            uk.ac.ebi.mydas.model.DasType type,
                                                            uk.ac.ebi.mydas.model.DasMethod method,
                                                            String dataSet,
                                                            String patient,
                                                            List<String> notes)
                                                     throws uk.ac.ebi.mydas.exceptions.DataSourceException

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

destroy

public void destroy()

Specified by:

destroy in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

getFeatures

public uk.ac.ebi.mydas.model.DasAnnotatedSegment getFeatures(String arg0,
                                                             Integer arg1)
                                                      throws uk.ac.ebi.mydas.exceptions.BadReferenceObjectException,
                                                             uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getFeatures in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.BadReferenceObjectException

uk.ac.ebi.mydas.exceptions.DataSourceException

getFeatures

public Collection<uk.ac.ebi.mydas.model.DasAnnotatedSegment> getFeatures(Collection<String> arg0,
                                                                         Integer arg1,
                                                                         uk.ac.ebi.mydas.model.Range arg2)
                                                                  throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                                                                         uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getFeatures in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException

getLinkURL

public URL getLinkURL(String arg0,
                      String arg1)
               throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                      uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getLinkURL in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException

getTotalEntryPoints

public int getTotalEntryPoints()
                        throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                               uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getTotalEntryPoints in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException

getFeatures

public uk.ac.ebi.mydas.model.DasAnnotatedSegment getFeatures(String arg0,
                                                             int arg1,
                                                             int arg2,
                                                             Integer arg3,
                                                             uk.ac.ebi.mydas.model.Range arg4)
                                                      throws uk.ac.ebi.mydas.exceptions.BadReferenceObjectException,
                                                             uk.ac.ebi.mydas.exceptions.CoordinateErrorException,
                                                             uk.ac.ebi.mydas.exceptions.DataSourceException,
                                                             uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

Specified by:

getFeatures in interface uk.ac.ebi.mydas.datasource.RangeHandlingAnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.BadReferenceObjectException

uk.ac.ebi.mydas.exceptions.CoordinateErrorException

uk.ac.ebi.mydas.exceptions.DataSourceException

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

getFeatures

public uk.ac.ebi.mydas.model.DasAnnotatedSegment getFeatures(String arg0,
                                                             Integer arg1,
                                                             uk.ac.ebi.mydas.model.Range arg2)
                                                      throws uk.ac.ebi.mydas.exceptions.BadReferenceObjectException,
                                                             uk.ac.ebi.mydas.exceptions.DataSourceException,
                                                             uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

Specified by:

getFeatures in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.BadReferenceObjectException

uk.ac.ebi.mydas.exceptions.DataSourceException

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

getFeatures

public Collection<uk.ac.ebi.mydas.model.DasAnnotatedSegment> getFeatures(Collection<String> arg0,
                                                                         Integer arg1)
                                                                  throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                                                                         uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getFeatures in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException

getEntryPointVersion

public String getEntryPointVersion()
                            throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                                   uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getEntryPointVersion in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException

getEntryPoints

public Collection<uk.ac.ebi.mydas.model.DasEntryPoint> getEntryPoints(Integer segmentId,
                                                                      Integer notUsed)
                                                               throws uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException,
                                                                      uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

getEntryPoints in interface uk.ac.ebi.mydas.datasource.AnnotationDataSource

Throws:

uk.ac.ebi.mydas.exceptions.UnimplementedFeatureException

uk.ac.ebi.mydas.exceptions.DataSourceException