Package net.sf.basedb.util.bfs
Class AnnotationParser
java.lang.Object
net.sf.basedb.util.bfs.AnnotationParser
- All Implemented Interfaces:
AutoCloseable
,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()
andnextData()
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.
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 (ti, 20 apr 2010) $
-
Field Summary
Modifier and TypeFieldDescriptionEvent thep that is issued for each data line.private final EncoderDecoder
Event type that is issued when the end-of-file had been reached.private FlatFileParser
private String
private long
Event type that is issued when the header line is found.private InputStream
private int
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close the parser and relase underlying system resources that are associated with it.static AnnotationParser
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.static AnnotationParser
Utility method for creating an annotation parser for a file in the BASE file system.protected FlatFileParser
Create a new flat file parser that can parse BFS annotation files.decodeValue
(String value) Decode an encoded value.int
Get the current line number.Get the file name that this parser is reading from.long
Get the size in bytes of the file that this parser is reading from.long
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[]
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
Set the input stream that should be parsed.
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Field Details
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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
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
Event type that is issued when the end-of-file had been reached. No event data is submitted. -
decoder
-
in
-
filename
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fileSize
private long fileSize -
ffp
-
numColumns
private int numColumns -
usedIds
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Constructor Details
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AnnotationParser
public AnnotationParser()Create a new annotation parser.
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Method Details
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create
Utility method for creating an annotation parser when you have an input stream.- Parameters:
in
- The input stream the parser should read fromfilename
- Optional, the name of the file the input stream is reading fromsize
- The size of the file in bytes, or -1 if not known
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create
Utility method for creating an annotation parser for a file in the BASE file system.- Parameters:
file
- The file in the BASE file system
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create
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
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decodeValue
Decode an encoded value. Values are encoded/decoded with aTabCrLfEncoderDecoder
.- Parameters:
value
- The encoded value- Returns:
- The decoded value
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getFilename
Get the file name that this parser is reading from.- Specified by:
getFilename
in interfaceBfsParser
- Returns:
- The file name or null if not known
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setFilename
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 interfaceBfsParser
- Returns:
- The size or -1 if not known
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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 interfaceAutoCloseable
- Specified by:
close
in interfaceBfsParser
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setInputStream
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)
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parse
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 dataNullPointerException
- If the stream or event handler is null
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parseToBof
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, callsetInputStream(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 errorIllegalStateException
- If the parsing has already startedNullPointerException
- If no input stream has been specified
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nextData
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 invalidIllegalStateException
- If notparseToBof()
has been called
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getCurrentLine
public int getCurrentLine()Description copied from interface:BfsParser
Get the current line number.- Specified by:
getCurrentLine
in interfaceBfsParser
- Returns:
- The line number, starting at 1 for the first line in the file, or -1 if not known
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getParsedBytes
public long getParsedBytes()Description copied from interface:BfsParser
Get the number of parsed bytes so far.- Specified by:
getParsedBytes
in interfaceBfsParser
- Returns:
- The number of bytes that has been parsed, or -1 if not known
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createFlatFileParser
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
Handle the header-found event. The default implemention sends aHEADER_EVENT
to the event handler- Parameters:
handler
- The event handler from theparse(EventHandler)
methodheaders
- An array with the column headers
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handleData
Handle the data event. The default implemention sends aDATA_EVENT
to the event handler- Parameters:
handler
- The event handler from theparse(EventHandler)
methoddata
- An array with the data
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handleEndOfFile
Handle the end-of-file event. The default implementation sends anEND_OF_FILE_EVENT
notification to the event handler.- Parameters:
handler
- The event handler from theparse(EventHandler)
method
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