edu.mssm.crover.tables.readers
Class LocusLinkTableReader

java.lang.Object
  edu.mssm.crover.tables.readers.LocusLinkTableReader

All Implemented Interfaces:

TableReader

public class LocusLinkTableReader
extends Object
implements TableReader

Reads LocusLink LL.out ascii table format. The format is as follows:

 LL.out -- a tab-delimited file containing summary information for each
 LocusID, one line per combination of LocusID and an identifer from
 the genome-specific database.
 Values:   LocusID, official symbol, interim symbol, MIM number
 (if applicable), chromosome, cytogenetic or genetic localization,
 default gene name (whether the defaults are defined by Human
 Nomenclature Committee is defined in LL_tmpl), NCBI's tax_id,
 the identifier of the genome-specific database (GDB, MGD, RATMAP).
 The tax_id can be used to identify the species of orgin as follows:
 human:  9606
 mouse: 10090
 rat: 10116.
 

MIM number is optional, if not given in the input, zero is stored.

Constructor Summary

LocusLinkTableReader()

Method Summary

static void	addColumns(Table table) Parse the Mineset schema file to extract the column names and types.
static void	addData(Table table, Reader data, Filter filter)
String	getDescription()
String	getShortName()
static void	main(String[] args)
Table	read(InputStream data)
Table	read(Reader data) Parses tabular data and returns the appropriate Table.
static Table	read(Reader data, Filter filter)
boolean	rejectRow(Table.RowIterator ri)

Methods inherited from class java.lang.Object

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

Constructor Detail

LocusLinkTableReader

public LocusLinkTableReader()

Method Detail

getShortName

public String getShortName()

getDescription

public String getDescription()

read

public Table read(InputStream data)
           throws SyntaxErrorException,
                  IOException

Throws:

SyntaxErrorException

IOException

read

public Table read(Reader data)
           throws SyntaxErrorException,
                  IOException

Description copied from interface: TableReader

Parses tabular data and returns the appropriate Table.

Specified by:

read in interface TableReader

Parameters:

data - A reader containing the data to parse

Returns:

A populated table

Throws:

SyntaxErrorException - if there is a problem filling in the Table

IOException - if there is a problem reading the data stream

read

public static Table read(Reader data,
                         Filter filter)
                  throws SyntaxErrorException,
                         IOException

Throws:

SyntaxErrorException

IOException

addColumns

public static void addColumns(Table table)

Parse the Mineset schema file to extract the column names and types. Add these columns to the table. Parses only the content of the input {} block.

addData

public static void addData(Table table,
                           Reader data,
                           Filter filter)
                    throws SyntaxErrorException,
                           IOException

Throws:

SyntaxErrorException

IOException

main

public static void main(String[] args)
                 throws IOException,
                        SyntaxErrorException

Throws:

IOException

SyntaxErrorException

rejectRow

public boolean rejectRow(Table.RowIterator ri)