Package ubic.gemma.core.loader.util.parser

Class BasicLineMapParser<K,T>

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T>

All Implemented Interfaces:

LineParser<T>, Parser<T>

Direct Known Subclasses:

AffyProbeReader, IlluminaProbeReader, LineMapParser, NcbiGeneEnsemblFileParser, NcbiGeneHistoryParser, NcbiGeneInfoParser, ProbeSequenceParser, TaxonParser

public abstract class BasicLineMapParser<K,T>
extends Object
implements LineParser<T>

A line parser that produces a Map instead of a Collection. Subclasses must provide a method to generate keys, which is generated from the values. A typical use case of this is when the keys are also known to another class that needs the data provided by the parser; to locate the data it uses the key.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	COMMENT_MARK	Lines starting with this will be ignored.
protected final org.apache.commons.logging.Log	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
BasicLineMapParser()

Method Summary

Modifier and Type	Method	Description
abstract boolean	containsKey(K key)
abstract T	get(K key)
protected abstract K	getKey(T newItem)
abstract Collection<K>	getKeySet()
abstract Collection<T>	getResults()
void	parse(File file)	Parse a File
void	parse(InputStream is)	Parse a InputStream.
void	parse(String filename)	Parse a file identified by its path.
abstract T	parseOneLine(String line)	Handle the parsing of a single line from the input.
protected abstract void	put(K key, T value)

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

Field Details

COMMENT_MARK

protected static final String COMMENT_MARK

Lines starting with this will be ignored.

See Also:

• Constant Field Values

log

protected final org.apache.commons.logging.Log log

Constructor Details

BasicLineMapParser

public BasicLineMapParser()

Method Details

containsKey

public abstract boolean containsKey(K key)

get

public abstract T get(K key)

getKeySet

public abstract Collection<K> getKeySet()

getResults

public abstract Collection<T> getResults()

Specified by:

getResults in interface Parser<K>

Returns:

the results of the parse.

parse

public void parse(File file)
           throws IOException

Description copied from interface: Parser

Parse a File

Specified by:

parse in interface Parser<K>

Parameters:

file - file

Throws:

IOException - if there is a problem while manipulating the file

parse

public void parse(InputStream is)
           throws IOException

Description copied from interface: Parser

Parse a InputStream.

Specified by:

parse in interface Parser<K>

Parameters:

is - input stream

Throws:

IOException - if there is a problem while manipulating the file

parse

public void parse(String filename)
           throws IOException

Description copied from interface: Parser

Parse a file identified by its path.

Specified by:

parse in interface Parser<K>

Parameters:

filename - Absolute path to the file

Throws:

IOException - if there is a problem while manipulating the file

parseOneLine

public abstract T parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<K>

Parameters:

line - line to parse

Returns:

parsed object

getKey

protected abstract K getKey(T newItem)

put

protected abstract void put(K key,
 T value)