org.bridgedb.file
Class IDMappingReaderFromText

java.lang.Object
  org.bridgedb.file.IDMappingReaderFromDelimitedReader
      org.bridgedb.file.IDMappingReaderFromText

All Implemented Interfaces:

IDMappingReader

public class IDMappingReaderFromText
extends IDMappingReaderFromDelimitedReader

Class for reading ID mapping data from delimited text file.

Author:

gjj

Field Summary

protected java.net.URL

url

Fields inherited from class org.bridgedb.file.IDMappingReaderFromDelimitedReader

dsValid, idMappingValid, regExDataSourceDelimiter, regExIDDelimiter

Constructor Summary

IDMappingReaderFromText(java.net.URL url, char[] dataSourceDelimiters)
Transitivity is unsupported.

IDMappingReaderFromText(java.net.URL url, char[] dataSourceDelimiters, char[] regExIDDelimiter)
Transitivity is unsupported.

IDMappingReaderFromText(java.net.URL url, char[] dataSourceDelimiters, char[] regExIDDelimiter, boolean transitivity)
Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.

IDMappingReaderFromText(java.net.URL url, java.lang.String regExDataSourceDelimiter)
Transitivity is unsupported.

IDMappingReaderFromText(java.net.URL url, java.lang.String regExDataSourceDelimiter, java.lang.String regExIDDelimiter)
Transitivity is unsupported.

IDMappingReaderFromText(java.net.URL url, java.lang.String regExDataSourceDelimiter, java.lang.String regExIDDelimiter, boolean transitivity)

Method Summary

void	setDataSourceDelimiters(char[] dataSourceDelimiters) Set delimiters between data sources.
void	setIDDelimiters(char[] idDelimiters) Set delimiters between data IDs.
protected static java.lang.String	strs2regex(char[] chs)

Methods inherited from class org.bridgedb.file.IDMappingReaderFromDelimitedReader

addIDMapping, getDataSources, getIDMappings, getTransitivity, readData, readDataSources, readIDMappings, setDataSources, setTransitivity

Methods inherited from class java.lang.Object

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

Field Detail

url

protected final java.net.URL url

Constructor Detail

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               char[] dataSourceDelimiters)
                        throws IDMapperException

Transitivity is unsupported. No delimiter between IDs.

Parameters:

url - url URL of the file

dataSourceDelimiters - delimiters between data sources

Throws:

IDMapperException - if failed to read file

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               char[] dataSourceDelimiters,
                               char[] regExIDDelimiter)
                        throws IDMapperException

Transitivity is unsupported.

Parameters:

url - url URL of the file

dataSourceDelimiters - delimiters between data sources

regExIDDelimiter - delimiters between IDs

Throws:

IDMapperException - if failed to read file

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               char[] dataSourceDelimiters,
                               char[] regExIDDelimiter,
                               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

regExIDDelimiter - delimiters between IDs

transitivity - support transitivity if true

Throws:

IDMapperException - if failed to read file

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               java.lang.String regExDataSourceDelimiter)
                        throws IDMapperException

Transitivity is unsupported. No delimiters between IDs.

Parameters:

url - the URL of the delimited text file

regExDataSourceDelimiter - regular expression of delimiter between data sources

Throws:

IDMapperException - if failed to read

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               java.lang.String regExDataSourceDelimiter,
                               java.lang.String regExIDDelimiter)
                        throws IDMapperException

Transitivity is unsupported.

Parameters:

url - the URL of the delimited text file

regExDataSourceDelimiter - regular expression of delimiter between data sources

regExIDDelimiter - regular expression of delimiter between IDs

Throws:

IDMapperException - if failed to read

IDMappingReaderFromText

public IDMappingReaderFromText(java.net.URL url,
                               java.lang.String regExDataSourceDelimiter,
                               java.lang.String regExIDDelimiter,
                               boolean transitivity)
                        throws IDMapperException

Parameters:

url - the URL of the delimited text file

regExDataSourceDelimiter - regular expression of delimiter between data sources

regExIDDelimiter - regular expression of delimiter between IDs

transitivity - transitivity support

Throws:

IDMapperException - if failed to read

Method Detail

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

strs2regex

protected static java.lang.String strs2regex(char[] chs)