jaligner.util
Class SequenceParser

java.lang.Object
  jaligner.util.SequenceParser

public class SequenceParser

extends java.lang.Object

SequenceParser to sequences from different formats.
Currently the supported formats are:

• Plain sequence
• Sequence

Author:

Ahmed Moustafa (ahmed@users.sf.net)

Constructor Summary

SequenceParser()

Method Summary

static Sequence	parse(java.io.File file) Returns a Sequence parsed and loaded from a file
static Sequence	parse(java.lang.String sequence) Returns a parsed Sequence from a string.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceParser

public SequenceParser()

Method Detail

parse

public static Sequence parse(java.lang.String sequence)
                      throws SequenceParserException

Returns a parsed Sequence from a string.

Parameters:

sequence - string to parse

Returns:

parsed sequence

Throws:

SequenceParserException

See Also:

Sequence

parse

public static Sequence parse(java.io.File file)
                      throws SequenceParserException

Returns a Sequence parsed and loaded from a file

Parameters:

file - to parse

Returns:

parsed sequence

Throws:

SequenceParserException

See Also:

Sequence