org.bridgedb.file
Class IDMappingReaderFromDelimitedReader

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

All Implemented Interfaces:

IDMappingReader

Direct Known Subclasses:

IDMappingReaderFromText

public class IDMappingReaderFromDelimitedReader
extends java.lang.Object
implements IDMappingReader

Class for reading ID mapping data from delimited reader.

Author:

gjj

Field Summary

protected boolean	dsValid
protected boolean	idMappingValid
protected java.lang.String	regExDataSourceDelimiter
protected java.lang.String	regExIDDelimiter

Constructor Summary

IDMappingReaderFromDelimitedReader(java.io.Reader reader, java.lang.String regExDataSourceDelimiter, java.lang.String regExIDDelimiter, boolean transitivity)

Method Summary

protected void	addIDMapping(java.util.Set<Xref> xrefs) Add matched references.
java.util.Set<DataSource>	getDataSources() Get DataSources from the file.
java.util.Map<Xref,java.util.Set<Xref>>	getIDMappings() Get Xrefs from the file.
boolean	getTransitivity() Get transitivity support.
protected void	readData(java.io.Reader reader) Read data.
protected void	readDataSources() Read DataSources from the reader.
protected void	readIDMappings() Read ID mappings from the reader.
void	setDataSources(java.util.List<DataSource> dataSources) Set DataSources.
void	setTransitivity(boolean transitivity) Set transitivity support.

Methods inherited from class java.lang.Object

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

Field Detail

regExDataSourceDelimiter

protected java.lang.String regExDataSourceDelimiter

regExIDDelimiter

protected java.lang.String regExIDDelimiter

dsValid

protected boolean dsValid

idMappingValid

protected boolean idMappingValid

Constructor Detail

IDMappingReaderFromDelimitedReader

public IDMappingReaderFromDelimitedReader(java.io.Reader reader,
                                          java.lang.String regExDataSourceDelimiter,
                                          java.lang.String regExIDDelimiter,
                                          boolean transitivity)
                                   throws IDMapperException

Parameters:

reader - a Reader

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

readData

protected void readData(java.io.Reader reader)
                 throws IDMapperException

Read data.

Parameters:

reader - to read data from

Throws:

IDMapperException - when file can't be read

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.

setDataSources

public void setDataSources(java.util.List<DataSource> dataSources)

Set DataSources. This will override the data sources read from the delimited reader.

Parameters:

dataSources - DataSources

getDataSources

public java.util.Set<DataSource> getDataSources()
                                         throws IDMapperException

Get DataSources from the file.

Specified by:

getDataSources in interface IDMappingReader

Returns:

DataSources from the file

Throws:

IDMapperException - if failed to read the file

getIDMappings

public java.util.Map<Xref,java.util.Set<Xref>> getIDMappings()
                                                      throws IDMapperException

Get Xrefs from the file.

Specified by:

getIDMappings in interface IDMappingReader

Returns:

Map from a Xref to the Set of all its matched Xref.

Throws:

IDMapperException - if failed to read the file

readDataSources

protected void readDataSources()
                        throws java.io.IOException

Read DataSources from the reader.

Throws:

java.io.IOException - on failing to read file

readIDMappings

protected void readIDMappings()
                       throws java.io.IOException

Read ID mappings from the reader.

Throws:

java.io.IOException - on file read error

addIDMapping

protected void addIDMapping(java.util.Set<Xref> xrefs)

Add matched references.

Parameters:

xrefs - matched references