Package ubic.gemma.core.loader.genome

Class ProbeSequenceParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<String,BioSequence>

ubic.gemma.core.loader.genome.ProbeSequenceParser

All Implemented Interfaces:

LineParser<BioSequence>, Parser<BioSequence>

public class ProbeSequenceParser
extends BasicLineMapParser<String,BioSequence>

Parse probes from a tabular file. First columnn = probe id; Second column = sequence name; Third column = sequence. This is designed primarily to deal with oligonucleotide arrays that have sequence names different from the probe names.

Author:

paul

Field Summary

Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

COMMENT_MARK, log

Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser

MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS

Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
ProbeSequenceParser()

Method Summary

Modifier and Type	Method	Description
boolean	containsKey(String key)
BioSequence	get(String key)
protected String	getKey(BioSequence newItem)
Collection<String>	getKeySet()
Collection<BioSequence>	getResults()
void	parse(InputStream is)	Parse a InputStream.
BioSequence	parseOneLine(String line)	Handle the parsing of a single line from the input.
protected void	put(String key, BioSequence value)

Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

parse, parse

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.util.parser.Parser

getUniqueResult

Constructor Detail

ProbeSequenceParser

public ProbeSequenceParser()

Method Detail

containsKey

public boolean containsKey(String key)

Specified by:

containsKey in class BasicLineMapParser<String,BioSequence>

get

public BioSequence get(String key)

Specified by:

get in class BasicLineMapParser<String,BioSequence>

getKeySet

public Collection<String> getKeySet()

Specified by:

getKeySet in class BasicLineMapParser<String,BioSequence>

getResults

public Collection<BioSequence> getResults()

Specified by:

getResults in interface Parser<BioSequence>

Specified by:

getResults in class BasicLineMapParser<String,BioSequence>

Returns:

the results of the parse.

parse

public void parse(InputStream is)
           throws IOException

Description copied from interface: Parser

Parse a InputStream.

Specified by:

parse in interface Parser<BioSequence>

Overrides:

parse in class BasicLineMapParser<String,BioSequence>

Parameters:

is - input stream

Throws:

IOException - if there is a problem while manipulating the file

parseOneLine

public BioSequence parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<BioSequence>

Specified by:

parseOneLine in class BasicLineMapParser<String,BioSequence>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected String getKey(BioSequence newItem)

Specified by:

getKey in class BasicLineMapParser<String,BioSequence>

put

protected void put(String key,
                   BioSequence value)

Specified by:

put in class BasicLineMapParser<String,BioSequence>