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## Uses of Class
org.ensembl.datamodel.CoordinateSystem

Packages that use CoordinateSystem
org.ensembl | Java library for accessing Ensembl core, compara and variation (SNP) databases.
org.ensembl.datamodel | Data types that appear in the core ensembl databases such as Genes, Exons and Karyotypes and various support classes such as Location.
org.ensembl.driver | Driver and adaptors for accessing ensembl core databases.

Uses of CoordinateSystem in org.ensembl

Methods in org.ensembl with parameters of type CoordinateSystem
`void` | `Example.convertLocationToCoordinateSystemAndGetTheSeqRegionNames(Location sourceLoc, CoordinateSystem targetCS)` Converts location into the target coordinate system and prints the results.
`void` | `Example.fetchKaryotypes(CoordinateSystem coordinateSystem, java.lang.String chromosomeName)` Fetches information about karyotypes (chromosome bands) for the specified chromosome.
`void` | `Example.fetchSequenceRegionsSuchAsChromosomeOrContig(CoordinateSystem coordinateSystem)` Fetches information about the sequence regions.

Uses of CoordinateSystem in org.ensembl.datamodel

Fields in org.ensembl.datamodel declared as CoordinateSystem
`static CoordinateSystem` | `CloneFragmentLocation.DEFAULT_CS`
`static CoordinateSystem` | `AssemblyLocation.DEFAULT_CS` Deprecated.

Methods in org.ensembl.datamodel that return CoordinateSystem
`CoordinateSystem` | `ChainedAssemblyMapper.getCsFirst()`
`CoordinateSystem` | `ChainedAssemblyMapper.getCsLast()`
`CoordinateSystem` | `ChainedAssemblyMapper.getCsMiddle()`
`CoordinateSystem` | `SequenceRegion.getCoordinateSystem()`
`CoordinateSystem[]` | `CoordinateSystemMapping.getPath()`
`CoordinateSystem` | `CoordinateSystemMapping.getFirst()`
`CoordinateSystem` | `CoordinateSystemMapping.getLast()`
`CoordinateSystem` | `Location.getCoordinateSystem()`
`CoordinateSystem` | `SimpleAssemblyMapper.getComponentCoordinateSystem()`
`CoordinateSystem` | `SimpleAssemblyMapper.getAssembledCoordinateSystem()`

Methods in org.ensembl.datamodel with parameters of type CoordinateSystem
`void` | `SequenceRegion.setCoordinateSystem(CoordinateSystem cs)`
`void` | `Location.setCoordinateSystem(CoordinateSystem cs)`
`void` | `Locatable.setCoordinateSystem(CoordinateSystem coordinateSystem, LocationConverter locationConverter)` Converts location to the specified coordinateSystem using the specified locationConverter.
`boolean` | `CoordinateSystem.equals(CoordinateSystem cs)` Test for equality with another Coordinate System.

Constructors in org.ensembl.datamodel with parameters of type CoordinateSystem
`ChainedAssemblyMapper(CoreDriver driver, CoordinateSystem cs1, CoordinateSystem cs2, CoordinateSystem cs3)`
`CloneFragmentLocation(CoordinateSystem cs, boolean gap, int length)` Constructs a location with specified coordinate system, start=1, end=length+1, strand=unset and whether it is a gap.
`CoordinateSystemMapping(CoordinateSystem[] path)` Create a new mapping.
`Location(CoordinateSystem cs, java.lang.String seqRegionName, int start, int end)` Default values: strand = 0, gap = false.
`Location(CoordinateSystem cs, java.lang.String seqRegionName, int start, int end, int strand, boolean gap)`
`Location(CoordinateSystem cs, java.lang.String seqRegionName, int start, int end, int strand)`
`Location(CoordinateSystem cs)` Location representing the whole coordinate system.
`Location(CoordinateSystem cs, java.lang.String seqRegionName)` The whole of the sequence region in the default version of the specified coordinate system.
`Location(CoordinateSystem cs, SequenceRegion seqRegion)`
`Location(CoordinateSystem cs, boolean gap, int length)` Constructs a location with map=CloneFragmentLocation.DEFAULT_CS, start=1, end=length+1, strand=unset and whether it is a gap.
`AssemblyLocation(CoordinateSystem cs, java.lang.String chromosome, int start, int end, int strand)` Deprecated.
`AssemblyLocation(CoordinateSystem cs, boolean gap, int length)` Deprecated. Constructs a location with specified map, start=1, end=length+1, strand=unset and whether it is a gap.
`SimpleAssemblyMapper(CoreDriver driver, CoordinateSystem assembledCoordinateSystem, CoordinateSystem componentCoordinateSystem)`

Uses of CoordinateSystem in org.ensembl.driver

Methods in org.ensembl.driver that return CoordinateSystem
`CoordinateSystem` | `CoordinateSystemAdaptor.fetch(long internalID)` Fetch a CoordinateSystem by its internalID.
`CoordinateSystem` | `CoordinateSystemAdaptor.fetch(java.lang.String name, java.lang.String version)` Fetch a CoordinateSystem by name and version.
`CoordinateSystem` | `CoordinateSystemAdaptor.fetchComplete(CoordinateSystem cs)` Returns a complete CoordinateSystem maching _cs_.name and _cs_.version.
`CoordinateSystem[]` | `CoordinateSystemAdaptor.fetchAll()` Fetch all the coordinate systems defined for this species.
`CoordinateSystem` | `CoordinateSystemAdaptor.fetchSequenceLevel()` Fetch the co-ordinate system that represents the sequence level for this species.
`CoordinateSystem[]` | `CoordinateSystemAdaptor.getMappingPath(CoordinateSystem cs1, CoordinateSystem cs2)` Get the mapping path between two co-ordinate systems, as defined in the meta table.
`CoordinateSystem` | `CoordinateSystemAdaptor.fetchByMap(java.lang.String map)` This function supports old style Locations with Maps.
`CoordinateSystem[]` | `CoordinateSystemAdaptor.fetchAllByFeatureTable(java.lang.String featureTableName)` Retrieve a list of the coordinate systems in which features in a particular table are stored.

Methods in org.ensembl.driver with parameters of type CoordinateSystem
`java.util.List` | `FeatureAdaptor.convertLocations(java.util.List features, CoordinateSystem coordinateSystem)` Converts all feature.location to coordinateSystem.
`java.util.List` | `KaryotypeBandAdaptor.fetch(CoordinateSystem coordSys, java.lang.String chromosome)`
`java.util.List` | `KaryotypeBandAdaptor.fetch(CoordinateSystem coordSys, java.lang.String chromosome, java.lang.String band)`
`SequenceRegion` | `SequenceRegionAdaptor.fetch(java.lang.String name, CoordinateSystem cs)` Fetch a SequenceRegion by name and co-ordinate system.
`SequenceRegion[]` | `SequenceRegionAdaptor.fetchAllByCoordinateSystem(CoordinateSystem cs)` Fetch all the sequence regions for a particular co-ordinate system.
`AssemblyMapper` | `AssemblyMapperAdaptor.fetchByCoordSystems(CoordinateSystem cs1, CoordinateSystem cs2)`
`Location` | `LocationConverter.convert(Location sourceLocation, CoordinateSystem targetCS, boolean includeGaps, boolean allList, boolean includeSequenceRegion)` Create a new location in the target coordinate system that is equivalent to the sourceLocation.
`Location` | `LocationConverter.convert(Location location, CoordinateSystem coordinateSystem)` Converts location into target coordinate system with all gaps and all nodes
`void` | `LocationConverter.cacheSeqRegion(java.lang.String seqRegionName, CoordinateSystem cs, long internalId, int regionLength)` Put given combination of things into a cache.
`long` | `LocationConverter.nameToId(java.lang.String seqRegionName, CoordinateSystem cs)` Convert to an internal id, request from database if not in cache
`long[]` | `LocationConverter.namesToIds(java.lang.String[] names, CoordinateSystem cs)` Convert a number of names in the same coordinate system into an array of internal ids.
`long` | `CoordinateSystemAdaptor.store(CoordinateSystem cs)` Store the CoordinateSystem in the approriate data source and set the internalID.
`CoordinateSystem` | `CoordinateSystemAdaptor.fetchComplete(CoordinateSystem cs)` Returns a complete CoordinateSystem maching _cs_.name and _cs_.version.
`CoordinateSystem[]` | `CoordinateSystemAdaptor.getMappingPath(CoordinateSystem cs1, CoordinateSystem cs2)` Get the mapping path between two co-ordinate systems, as defined in the meta table.

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