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

Class RecordParser<T>

java.lang.Object

ubic.gemma.core.loader.util.parser.RecordParser<T>

All Implemented Interfaces:

Parser<T>

Direct Known Subclasses:

FastaParser, SwissProtParser

public abstract class RecordParser<T>
extends Object
implements Parser<T>

Abstract record-based parser. Records are defined by lines starting with a given record separator. The default record separator is ">".

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected static org.apache.commons.logging.Log	log

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

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
RecordParser()

Method Summary

Modifier and Type	Method	Description
protected abstract void	addResult(Object obj)	Add an object to the results collection.
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.
protected abstract Object	parseOneRecord(String record)	Handle the parsing of a single record from the input.
void	setRecordSeparator(String recordSeparator)

Methods inherited from class java.lang.Object

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

Field Detail

log

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

Constructor Detail

RecordParser

public RecordParser()

Method Detail

getResults

public abstract Collection<T> getResults()

Specified by:

getResults in interface Parser<T>

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<T>

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<T>

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<T>

Parameters:

filename - Absolute path to the file

Throws:

IOException - if there is a problem while manipulating the file

setRecordSeparator

public void setRecordSeparator(String recordSeparator)

parseOneRecord

protected abstract Object parseOneRecord(String record)

Handle the parsing of a single record from the input.

Parameters:

record - record

Returns:

parsed object

addResult

protected abstract void addResult(Object obj)

Add an object to the results collection.

Parameters:

obj - object