net.sf.jannot.parser
Class Parser

java.lang.Object
  net.sf.jannot.parser.Parser

Direct Known Subclasses:

ALNParser, BedGraphParser, BEDParser, BlastM8Parser, BroadSolexa, EMBLParser, FastaParser, FindPeaksParser, GenbankParser, GeneMarkParser, GFF3Parser, MAFParser, MapViewParser, MaqSNPParser, PTTParser, SIPHTParser, SyntenicParser, TBLParser, TransTermHPParser, TRNAscanParser, WiggleParser

public abstract class Parser
extends java.lang.Object

Field Summary

protected DataKey	dataKey
static Parser[]	parsers

Constructor Summary

Parser(DataKey dataKey)

Method Summary

static Parser	detectParser(java.io.InputStream is, java.lang.Object source)
abstract EntrySet	parse(java.io.InputStream is, EntrySet set) Read all data from an input stream.
void	setDataKey(java.lang.String s)
java.lang.String	toString()
void	write(java.io.OutputStream os, Entry entry) Output everything from the provided entry to the output stream.
void	write(java.io.OutputStream os, Entry entry, DataKey[] dk)

Methods inherited from class java.lang.Object

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

Field Detail

parsers

public static final Parser[] parsers

dataKey

protected DataKey dataKey

Constructor Detail

Parser

public Parser(DataKey dataKey)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

parse

public abstract EntrySet parse(java.io.InputStream is,
                               EntrySet set)

Read all data from an input stream. Set the data source for each item to the supplied source. If and EntrySet is supplied the data will be added to this set, otherwise a new set will be created. Either the supplied or the new EntrySet is returned.

Parameters:

is - inputStream

source - source to set to features

set - TODO

entrySet - the EntrySet to which all stuff will be added

Returns:

either the supplied EntrySet or a new one containing the loaded stuff

write

public void write(java.io.OutputStream os,
                  Entry entry)

Output everything from the provided entry to the output stream.

Parameters:

os - output stream to write data to

e - the entry to save

source - the source to filter on, or null when no filtering is required.

write

public void write(java.io.OutputStream os,
                  Entry entry,
                  DataKey[] dk)

detectParser

public static Parser detectParser(java.io.InputStream is,
                                  java.lang.Object source)
                           throws java.io.IOException

Throws:

java.io.IOException

setDataKey

public void setDataKey(java.lang.String s)