org.molgenis.omx.das.impl

Class RepositoryRangeHandlingDataSource

java.lang.Object

org.molgenis.omx.das.RangeHandlingDataSource

org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource

All Implemented Interfaces:

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

public class RepositoryRangeHandlingDataSource
extends RangeHandlingDataSource
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
RepositoryRangeHandlingDataSource()

Method Summary

Methods

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, String dataSet, Double score)
uk.ac.ebi.mydas.model.DasAnnotatedSegment	getFeatures(String segmentParamString, int start, int stop, Integer maxbins)
Integer	getTotalCountForType(uk.ac.ebi.mydas.model.DasType type)
Collection<uk.ac.ebi.mydas.model.DasType>	getTypes()
void	init(javax.servlet.ServletContext servletContext, Map<String,uk.ac.ebi.mydas.configuration.PropertyType> globalParameters, uk.ac.ebi.mydas.configuration.DataSourceConfiguration dataSourceConfig)
protected Iterable<Entity>	queryDataSet(String segmentId, String dataSet, int maxbins)

Methods inherited from class org.molgenis.omx.das.RangeHandlingDataSource

createDasFeature, destroy, getEntryPoints, getEntryPointVersion, getFeatures, getFeatures, getFeatures, getFeatures, getFeatures, getLinkURL, 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

destroy, getEntryPoints, getEntryPointVersion, getFeatures, getFeatures, getFeatures, getFeatures, getLinkURL, getTotalEntryPoints

Constructor Detail

RepositoryRangeHandlingDataSource

public RepositoryRangeHandlingDataSource()
                                  throws uk.ac.ebi.mydas.exceptions.DataSourceException

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

Method Detail

init

public void init(javax.servlet.ServletContext servletContext,
        Map<String,uk.ac.ebi.mydas.configuration.PropertyType> globalParameters,
        uk.ac.ebi.mydas.configuration.DataSourceConfiguration dataSourceConfig)
          throws uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

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

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

getFeatures

public uk.ac.ebi.mydas.model.DasAnnotatedSegment getFeatures(String segmentParamString,
                                                    int start,
                                                    int stop,
                                                    Integer maxbins)
                                                      throws uk.ac.ebi.mydas.exceptions.BadReferenceObjectException,
                                                             uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

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

Throws:

uk.ac.ebi.mydas.exceptions.BadReferenceObjectException

uk.ac.ebi.mydas.exceptions.DataSourceException

queryDataSet

protected Iterable<Entity> queryDataSet(String segmentId,
                            String dataSet,
                            int maxbins)

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,
                                                String dataSet,
                                                Double score)
                                                     throws uk.ac.ebi.mydas.exceptions.DataSourceException

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

getTotalCountForType

public Integer getTotalCountForType(uk.ac.ebi.mydas.model.DasType type)
                             throws uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

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

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

getTypes

public Collection<uk.ac.ebi.mydas.model.DasType> getTypes()
                                                   throws uk.ac.ebi.mydas.exceptions.DataSourceException

Specified by:

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

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException