org.molgenis.omx.das

Class DasOmxDataSource

java.lang.Object

org.molgenis.omx.das.DasOmxDataSource

All Implemented Interfaces:

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

public class DasOmxDataSource
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
DasOmxDataSource()
DasOmxDataSource(Database database)

Method Summary

Methods

Modifier and Type	Method and Description
protected uk.ac.ebi.mydas.model.DasFeature	createDasFeature(Variant variant)
void	destroy()
protected Patient	findPatient(String patient)
protected Chromosome	getChromosome(String segmentId)
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 segmentId, int start, int stop, Integer maxbins)
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)
Integer	getTotalCountForType(uk.ac.ebi.mydas.model.DasType type)
int	getTotalEntryPoints()
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 List<Variant>	queryVariants(String segmentId, int start, int stop, Patient patientObject)

Methods inherited from class java.lang.Object

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

Constructor Detail

DasOmxDataSource

public DasOmxDataSource(Database database)
                 throws uk.ac.ebi.mydas.exceptions.DataSourceException

Throws:

uk.ac.ebi.mydas.exceptions.DataSourceException

DasOmxDataSource

public DasOmxDataSource()
                 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

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

getFeatures

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

uk.ac.ebi.mydas.exceptions.DataSourceException

findPatient

protected Patient findPatient(String patient)
                       throws DatabaseException

Throws:

DatabaseException

queryVariants

protected List<Variant> queryVariants(String segmentId,
                          int start,
                          int stop,
                          Patient patientObject)
                               throws DatabaseException

Throws:

DatabaseException

createDasFeature

protected uk.ac.ebi.mydas.model.DasFeature createDasFeature(Variant variant)
                                                     throws MalformedURLException,
                                                            uk.ac.ebi.mydas.exceptions.DataSourceException

Throws:

MalformedURLException

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

getChromosome

protected Chromosome getChromosome(String segmentId)
                            throws DatabaseException

Throws:

DatabaseException

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