Package org.bridgedb.file

Class IDMapperText

java.lang.Object

org.bridgedb.file.IDMapperFile

org.bridgedb.file.IDMapperText

All Implemented Interfaces:

IDMapper

public class IDMapperText
extends IDMapperFile

Class for mapping ID from delimited text file.

Author:

gjj

Field Summary

Fields inherited from class org.bridgedb.file.IDMapperFile

cap, reader

Constructor Summary

Constructors

Constructor	Description
IDMapperText(URL url)	Constructor from the URL of a tab-delimited text file.
IDMapperText(URL url, char[] dataSourceDelimiters)	Transitivity is unsupported.
IDMapperText(URL url, char[] dataSourceDelimiters, char[] idDelimiters)	Transitivity is unsupported.
IDMapperText(URL url, char[] dataSourceDelimiters, char[] idDelimiters, boolean transitivity)	Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.

Method Summary

Modifier and Type	Method	Description
Set<Xref>	freeSearch(String text, int limit)	Free search is not supported for delimiter-text file.
char[]	getDataSourceDelimiters()
char[]	getIDDelimiters()
boolean	getTransitivity()	Get transitivity support.
URL	getURL()	Get URL of the file.
void	setDataSourceDelimiters(char[] dataSourceDelimiters)	Set delimiters between data sources.
void	setIDDelimiters(char[] idDelimiters)	Set delimiters between data IDs.
void	setTransitivity(boolean transitivity)	Set transitivity support.
String	toString()

Methods inherited from class org.bridgedb.file.IDMapperFile

close, getCapabilities, getIDMappingReader, isConnected, mapID, mapID, xrefExists

Methods inherited from class java.lang.Object

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

Constructor Detail

IDMapperText

public IDMapperText(URL url)
             throws IDMapperException

Constructor from the URL of a tab-delimited text file.

Parameters:

url - URL of the file

Throws:

IDMapperException - if failed to read file

IDMapperText

public IDMapperText(URL url,
                    char[] dataSourceDelimiters)
             throws IDMapperException

Transitivity is unsupported. No delimiter between data sources.

Parameters:

url - url URL of the file

dataSourceDelimiters - delimiters between data sources

Throws:

IDMapperException - if failed to read file

IDMapperText

public IDMapperText(URL url,
                    char[] dataSourceDelimiters,
                    char[] idDelimiters)
             throws IDMapperException

Transitivity is unsupported.

Parameters:

url - url URL of the file

dataSourceDelimiters - delimiters between data sources

idDelimiters - delimiters between IDs

Throws:

IDMapperException - if failed to read file

IDMapperText

public IDMapperText(URL url,
                    char[] dataSourceDelimiters,
                    char[] idDelimiters,
                    boolean transitivity)
             throws IDMapperException

Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.

Parameters:

url - url URL of the file

dataSourceDelimiters - delimiters between data sources

idDelimiters - delimiters between IDs

transitivity - support transitivity if true

Throws:

IDMapperException - if failed to read file

Method Detail

freeSearch

public Set<Xref> freeSearch(String text,
                            int limit)
                     throws IDMapperException

Free search is not supported for delimiter-text file. This will throw UnsupportedOperationException

Parameters:

text - ignored

limit - ignored

Returns:

does not return

Throws:

IDMapperException - will not be thrown

setTransitivity

public void setTransitivity(boolean transitivity)

Set transitivity support.

Parameters:

transitivity - support transitivity if true.

getTransitivity

public boolean getTransitivity()

Get transitivity support.

Returns:

true if support transitivity; false otherwise.

getURL

public URL getURL()

Get URL of the file.

Returns:

URL of the file

getDataSourceDelimiters

public char[] getDataSourceDelimiters()

Returns:

delimiters between data sources

getIDDelimiters

public char[] getIDDelimiters()

Returns:

delimiters between data IDs

setDataSourceDelimiters

public void setDataSourceDelimiters(char[] dataSourceDelimiters)

Set delimiters between data sources.

Parameters:

dataSourceDelimiters - delimiters between data sources

setIDDelimiters

public void setIDDelimiters(char[] idDelimiters)

Set delimiters between data IDs.

Parameters:

idDelimiters - delimiters between data IDs

toString

public String toString()

Overrides:

toString in class Object