net.sf.basedb.util.bfs
Class AnnotationParser

java.lang.Object
  net.sf.basedb.util.bfs.AnnotationParser

All Implemented Interfaces:

BfsParser

public class AnnotationParser
extends Object
implements BfsParser

Parser implementation that parses a BFS annotation files. Before parsing is started the stream to parse must be specified by calling setInputStream(InputStream). The actual parsing can be done in two different ways:

• "Manual" parsing, using the parseToBof() and nextData() methods.
• Event-based parsing using the parse(EventHandler) method. This parser issues the following events:
  • HEADER_EVENT: When the header-line (should be the first line) has been found.
  • DATA_EVENT: For each data line that is parsed.
  • END_OF_FILE_EVENT: When the end of the file has been reached.
  The AnnotationModel class implements a simple event handler that collects the information from the annotations file and provides methods for accessing it.

This class may be subclassed to provide customized behaviour.

Version:

2.15

Author:

Nicklas

Last modified

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

Field Summary

static EventType<String[]>	DATA_EVENT Event thep that is issued for each data line.
private EncoderDecoder	decoder
static EventType<Object>	END_OF_FILE_EVENT Event type that is issued when the end-of-file had been reached.
private FlatFileParser	ffp
private String	filename
private long	fileSize
static EventType<String[]>	HEADER_EVENT Event type that is issued when the header line is found.
private InputStream	in
private int	numColumns
private Set<Integer>	usedIds

Constructor Summary

AnnotationParser()
Create a new annotation parser.

Method Summary

void	close() Close the parser and relase underlying system resources that are associated with it.
static AnnotationParser	create(File file) Utility method for creating an annotation parser for a file in the BASE file system.
static AnnotationParser	create(File file) Utility method for creating an annotation parser for a file in the local file system.
static AnnotationParser	create(InputStream in, String filename, long size) Utility method for creating an annotation parser when you have an input stream.
protected FlatFileParser	createFlatFileParser(InputStream in) Create a new flat file parser that can parse BFS annotation files.
String	decodeValue(String value) Decode an encoded value.
int	getCurrentLine() Get the current line number.
String	getFilename() Get the file name that this parser is reading from.
long	getFileSize() Get the size in bytes of the file that this parser is reading from.
long	getParsedBytes() Get the number of parsed bytes so far.
protected void	handleData(EventHandler handler, String[] data) Handle the data event.
protected void	handleEndOfFile(EventHandler handler) Handle the end-of-file event.
protected void	handleHeader(EventHandler handler, String[] headers) Handle the header-found event.
String[]	nextData() Get the next data line in the annotations file.
void	parse(EventHandler handler) Parse the input stream and notify the specified event handler with events.
String[]	parseToBof() Parse the header line of the annotations file.
void	setFilename(String filename) Set the file name that this parser is reading from.
void	setFileSize(long fileSize) Set the size of the file or -1 if not known.
void	setInputStream(InputStream in) Set the input stream that should be parsed.

Methods inherited from class java.lang.Object

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

Field Detail

HEADER_EVENT

public static final EventType<String[]> HEADER_EVENT

Event type that is issued when the header line is found. The event data is a string array with the headers, including the ID header.

DATA_EVENT

public static final EventType<String[]> DATA_EVENT

Event thep that is issued for each data line. The event data is a string array with that data, including the ID column.

END_OF_FILE_EVENT

public static final EventType<Object> END_OF_FILE_EVENT

Event type that is issued when the end-of-file had been reached. No event data is submitted.

decoder

private final EncoderDecoder decoder

in

private InputStream in

filename

private String filename

fileSize

private long fileSize

ffp

private FlatFileParser ffp

numColumns

private int numColumns

usedIds

private Set<Integer> usedIds

Constructor Detail

AnnotationParser

public AnnotationParser()

Create a new annotation parser.

Method Detail

create

public static AnnotationParser create(InputStream in,
                                      String filename,
                                      long size)

Utility method for creating an annotation parser when you have an input stream.

Parameters:

in - The input stream the parser should read from

filename - Optional, the name of the file the input stream is reading from

size - The size of the file in bytes, or -1 if not known

create

public static AnnotationParser create(File file)

Utility method for creating an annotation parser for a file in the BASE file system.

Parameters:

file - The file in the BASE file system

create

public static AnnotationParser create(File file)
                               throws IOException

Utility method for creating an annotation parser for a file in the local file system.

Parameters:

file - The file in the local file system

Throws:

IOException

decodeValue

public String decodeValue(String value)

Decode an encoded value. Values are encoded/decoded with a TabCrLfEncoderDecoder.

Parameters:

value - The encoded value

Returns:

The decoded value

getFilename

public String getFilename()

Get the file name that this parser is reading from.

Specified by:

getFilename in interface BfsParser

Returns:

The file name or null if not known

setFilename

public void setFilename(String filename)

Set the file name that this parser is reading from.

getFileSize

public long getFileSize()

Get the size in bytes of the file that this parser is reading from.

Specified by:

getFileSize in interface BfsParser

Returns:

The size or -1 if not known

setFileSize

public void setFileSize(long fileSize)

Set the size of the file or -1 if not known.

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

setInputStream

public void setInputStream(InputStream in)

Set the input stream that should be parsed. This will also reset the parser. All information from a previously parsed file is lost.

Parameters:

in - The stream to parse (in UTF-8 format)

parse

public void parse(EventHandler handler)
           throws IOException

Parse the input stream and notify the specified event handler with events. The event handler is responsible for keeping track of and storing the data of interest.

Parameters:

handler - An event handler

Throws:

IOException - If there is an error reading the stream data

NullPointerException - If the stream or event handler is null

parseToBof

public String[] parseToBof()
                    throws IOException

Parse the header line of the annotations file. This method can only be called once on a given input stream. To parse a second file, call setInputStream(InputStream) again to reset the parser.

Returns:

An array with the column headers

Throws:

IOException - If the header line is not found or if there is any other IO error

IllegalStateException - If the parsing has already started

NullPointerException - If no input stream has been specified

nextData

public String[] nextData()
                  throws IOException

Get the next data line in the annotations file.

Returns:

An array with the data, or null if no more data is found

Throws:

IOException - If there is an IO error or if the data is invalid

IllegalStateException - If not parseToBof() has been called

getCurrentLine

public int getCurrentLine()

Description copied from interface: BfsParser

Get the current line number.

Specified by:

getCurrentLine in interface BfsParser

Returns:

The line number, starting at 1 for the first line in the file, or -1 if not known

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 that has been parsed, or -1 if not known

createFlatFileParser

protected FlatFileParser createFlatFileParser(InputStream in)

Create a new flat file parser that can parse BFS annotation files. This method should set all regular expressions that are needed to parse the stream (assumed to be UTF-8).

handleHeader

protected void handleHeader(EventHandler handler,
                            String[] headers)

Handle the header-found event. The default implemention sends a HEADER_EVENT to the event handler

Parameters:

handler - The event handler from the parse(EventHandler) method

headers - An array with the column headers

handleData

protected void handleData(EventHandler handler,
                          String[] data)

Handle the data event. The default implemention sends a DATA_EVENT to the event handler

Parameters:

handler - The event handler from the parse(EventHandler) method

data - An array with the data

handleEndOfFile

protected void handleEndOfFile(EventHandler handler)

Handle the end-of-file event. The default implementation sends an END_OF_FILE_EVENT notification to the event handler.

Parameters:

handler - The event handler from the parse(EventHandler) method