net.sf.basedb.util.importer.spotdata
Class SynchronizedSpotDataParser

java.lang.Object
  net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser

All Implemented Interfaces:

BfsParser

public class SynchronizedSpotDataParser
extends Object
implements BfsParser

A parser that synchronizes the parsing of multiple underlying data parsers and a master reporter annotations parser. Before it can be used a master parser must be set by setMasterParser(AnnotationParser). Then, one or more data parsers is needed addDataParser(DataParser). All parsers must have been parsed to beginning-of-file (eg. AnnotationParser.parseToBof() and DataParser.parseToBof()) before they are added to this class. The parse(EventHandler) method will then call AnnotationParser.nextData() and DataParser.nextData() for each parser as long as data is returned. All parsers must resturn at least as many data lines as the master parser or an exception is thrown.

Version:

2.15

Author:

Nicklas

Last modified

$Date: 2010-04-20 10:02:16 +0200 (Tue, 20 Apr 2010) $

Nested Class Summary

static class

SynchronizedSpotDataParser.SynchronizedData This class holds information that is sent to the event handler when DATA_EVENT:s are sent.

Field Summary

static EventType<SynchronizedSpotDataParser.SynchronizedData[]>	DATA_EVENT Event type that is issued for each data line.
private List<DataParser>	dataParsers
private AnnotationParser	masterParser

Constructor Summary

SynchronizedSpotDataParser()
Create a new synchronized data parser.

Method Summary

void	addDataParser(DataParser parser) Adds a data parser.
void	close() Close the parser and relase underlying system resources that are associated with it.
int	getCurrentLine() Get the current line number.
String	getFilename() Get the filename of the file that is being parsed.
long	getFileSize() Get the size of the file that is being parsed.
long	getParsedBytes() Get the number of parsed bytes so far.
void	parse(EventHandler handler) Begin parsing and issue events to the given event handler.
void	setMasterParser(AnnotationParser parser) Sets the master parser.

Methods inherited from class java.lang.Object

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

Field Detail

DATA_EVENT

public static final EventType<SynchronizedSpotDataParser.SynchronizedData[]> DATA_EVENT

Event type that is issued for each data line. The event data is an array with SynchronizedSpotDataParser.SynchronizedData objects. The first entry in the array contains information from the master parser, the following entries contain information for the data parsers in the order they were added.

masterParser

private AnnotationParser masterParser

dataParsers

private List<DataParser> dataParsers

Constructor Detail

SynchronizedSpotDataParser

public SynchronizedSpotDataParser()

Create a new synchronized data parser.

Method Detail

setMasterParser

public void setMasterParser(AnnotationParser parser)

Sets the master parser. This parser should normally parse a reporter annotations file.

addDataParser

public void addDataParser(DataParser parser)

Adds a data parser. The parser should parse a data file that has the same number of data lines as the master parser. Each line contains data identified by the corresponding reporter in the master parser file.

getFilename

public String getFilename()

Description copied from interface: BfsParser

Get the filename of the file that is being parsed.

Specified by:

getFilename in interface BfsParser

Returns:

Always null, since we are parsing multiple files

getFileSize

public long getFileSize()

Description copied from interface: BfsParser

Get the size of the file that is being parsed.

Specified by:

getFileSize in interface BfsParser

Returns:

The file size of the master parser

getCurrentLine

public int getCurrentLine()

Description copied from interface: BfsParser

Get the current line number.

Specified by:

getCurrentLine in interface BfsParser

Returns:

The current line number in the file parsed by the master parser

getParsedBytes

public long getParsedBytes()

Description copied from interface: BfsParser

Get the number of parsed bytes so far.

Specified by:

getParsedBytes in interface BfsParser

Returns:

The number of bytes parsed by the master parser

close

public void close()

Description copied from interface: BfsParser

Close the parser and relase underlying system resources that are associated with it.

Specified by:

close in interface BfsParser

parse

public void parse(EventHandler handler)
           throws IOException

Begin parsing and issue events to the given event handler. For each data line a DATA_EVENT is sent to the event handler. When the end-of-file has been a DataParser.END_OF_FILE_EVENT is sent.

Parameters:

handler - An event handler

Throws:

IOException - If there is an error reading the stream data

NullPointerException - If the event handler or master parser is null