Package org.bridgedb.impl

Class InternalUtils

java.lang.Object

org.bridgedb.impl.InternalUtils

public final class InternalUtils
extends Object

To prevent duplication and redundancy, functions that are common to multiple IDMapper implementations can be placed here.

Warning! This class is not part of the public API of BridgeDb. Methods in this class may disappear or change in backwards-incompatible ways. This class should not be used by applications!

Method Summary

Modifier and Type	Method	Description
static InputStream	getInputStream(String source)
static InputStream	getInputStream(URL source)	Start downloading a file from the web and open an InputStream to it.
static Map<DataSource,Set<Xref>>	groupByDataSource(Collection<Xref> srcXrefs)	Split a heterogeneous Xref set into multiple homogeneous Xref sets.
static String	joinIds(Collection<Xref> refs, String sep)	Join the ID part of a collection of Xrefs with a custom separator.
static Map<Xref,Set<Xref>>	mapMultiFromSingle(IDMapper mapper, Collection<Xref> srcXrefs, DataSource... tgt)	call the "single" mapID (Xref, ...) multiple times to perform mapping of a Set.
static Set<Xref>	mapSingleFromMulti(IDMapper mapper, Xref src, DataSource... tgt)	call the "multi" mapID (Set, ...) using a Set with one item to perform mapping of a single ID.
static <T,U> void	multiMapAdd(Map<T,List<U>> map, T key, U val)	Generic method for multimaps, a map that can contain multiple values per key.
static <T,U> void	multiMapPut(Map<T,Set<U>> map, T key, U val)	Generic method for multimaps, a map that can contain multiple values per key.
static <T,U> void	multiMapPutAll(Map<T,Set<U>> map, T key, Collection<U> vals)	Generic method for multimaps, a map that can contain multiple values per key.
static Map<String,String>	parseLocation(String location, String... allowedParams)	parse configuration params of the connection string.
static void	readXmlConfig(InputSource is)	read a configuration file in the bridgedb xml format

Methods inherited from class java.lang.Object

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

Method Detail

mapMultiFromSingle

public static Map<Xref,Set<Xref>> mapMultiFromSingle(IDMapper mapper,
                                                           Collection<Xref> srcXrefs,
                                                           DataSource... tgt)
                                                    throws IDMapperException

call the "single" mapID (Xref, ...) multiple times to perform mapping of a Set.

This is intended for IDMappers that don't gain any advantage of mapping multiple ID's at a time. They can implement mapID(Xref, ...), and use mapMultiFromSingle to simulate mapID(Set, ...)

Parameters:

mapper - used for performing a single mapping

srcXrefs - xrefs to translate

tgt - DataSource(s) to map to, optional.

Returns:

mappings with the translated result for each input Xref. Never returns null, but not each input is a key in the output map.

Throws:

IDMapperException - when mapper.mapID throws IDMapperException

mapSingleFromMulti

public static Set<Xref> mapSingleFromMulti(IDMapper mapper,
                                           Xref src,
                                           DataSource... tgt)
                                    throws IDMapperException

call the "multi" mapID (Set, ...) using a Set with one item to perform mapping of a single ID.

This is intended for IDMappers that have a performance advantage of mapping multiple ID's at a time. They can implement mapID(Set, ...), and use mapSingleFromMulti to simulate mapID(Xref, ...)

Parameters:

mapper - used for performing a multi-mapping

src - xref to translate

tgt - DataSource(s) to map to, optional.

Returns:

Set of translated Xrefs, or an empty set if none were found.

Throws:

IDMapperException - when mapper.mapID throws IDMapperException

parseLocation

public static Map<String,String> parseLocation(String location,
                                                     String... allowedParams)

parse configuration params of the connection string. Connection strings are expected to have a formatting like {base?arg1=val&arg2=val}.

Parameters:

location - - configuration string to parse.

allowedParams - - allowed argument names to appear before =

Returns:

key / value Map of configuration arguments. The base (the part before the ?) is returned in the special key "BASE". If the part before ? is empty, the "BASE" key is not created.

Throws:

IllegalArgumentException - if arguments do not follow the key=val structure, or if the key is not in allowedParams

getInputStream

public static InputStream getInputStream(String source)
                                  throws IOException

Throws:

IOException

getInputStream

public static InputStream getInputStream(URL source)
                                  throws IOException

Start downloading a file from the web and open an InputStream to it.

Parameters:

source - location of file to download.

Returns:

InputStream

Throws:

IOException - after a number of attempts to connect to the remote server have failed.

multiMapPut

public static <T,U> void multiMapPut(Map<T,Set<U>> map,
                                           T key,
                                           U val)

Generic method for multimaps, a map that can contain multiple values per key. Unlike a regular map, if you insert a value for a key that already exists, the previous value will not be discared.

Type Parameters:

T - key type of multimap

U - value type of multimap

Parameters:

map - multimap to work on

key - key of the value to insert

val - value to insert.

multiMapAdd

public static <T,U> void multiMapAdd(Map<T,List<U>> map,
                                           T key,
                                           U val)

Generic method for multimaps, a map that can contain multiple values per key. Unlike a regular map, if you insert a value for a key that already exists, the previous value will not be discarded.

This is like multiMapPut, but uses a list instead of a set for each value of the map.

Type Parameters:

T - key type of multimap

U - value type of multimap

Parameters:

map - multimap to work on

key - key of the value to insert

val - value to insert.

multiMapPutAll

public static <T,U> void multiMapPutAll(Map<T,Set<U>> map,
                                              T key,
                                              Collection<U> vals)

Generic method for multimaps, a map that can contain multiple values per key. Unlike a regular map, if you insert a value for a key that already exists, the previous value will not be discarded.

multiMapPutAll let's you insert a collection of items at once.

Type Parameters:

T - key type of multimap

U - value type of multimap

Parameters:

map - multimap to work on

key - key of the value to insert

vals - values to insert.

groupByDataSource

public static Map<DataSource,Set<Xref>> groupByDataSource(Collection<Xref> srcXrefs)

Split a heterogeneous Xref set into multiple homogeneous Xref sets.

If the input contains {L:3643, L:1234, X:1004_at, X:1234_at}, then the output will contain { L=> {L:3643, L:1234}, X=> {X:1004_at, X:1234_at} }.

Parameters:

srcXrefs - the set to split

Returns:

map with datasources as keys and homogeneous sets as values.

joinIds

public static String joinIds(Collection<Xref> refs,
                             String sep)

Join the ID part of a collection of Xrefs with a custom separator.

Parameters:

refs - Xrefs from which the ids will be concatenated

sep - separator string.

Returns:

concatenation of the ids.

readXmlConfig

public static void readXmlConfig(InputSource is)
                          throws ParserConfigurationException,
                                 SAXException,
                                 IOException

read a configuration file in the bridgedb xml format

Parameters:

is - - the input source

Throws:

ParserConfigurationException - - exception class

SAXException - - exception class

IOException - - exception class