alonefichiers
Class FichierBracket

java.lang.Object
  alonefichiers.Fichier
      alonefichiers.FichierBracket

public class FichierBracket
extends Fichier

This class for a Bracket recording file format.
seen also : Lab for Computational Biology - alterRNA
The predicted RNA structure in dot-parenthesis format. The sequence is given from 5' to 3' end, and the structure is given with matching parenthesis denoting a base pair and a dot denoting an unbounded base.

No constructor to read a recorded bracket file like recording here, because of unCompatible palindromes used and can't be easily reverse recognized by a machine...

Author:

Gabriel Chandesris (2008)

See Also:

FichierConvert

Field Summary

private Sequence	cible Current sequence of file.
private PalindromeListe	liste Current list of palindromes of file.

Constructor Summary

FichierBracket(Sequence cible, PalindromeListe liste)
Constructor with given sequence and a list of palindromes.

Method Summary

PalindromeListe	getListe() To get the list of palindromes of current instance.
Sequence	getSequence() To get the sequence of current instance.

Methods inherited from class alonefichiers.Fichier

addToChamps, getChamp, getChamps, getChampsToString, getNom, getType, isValid, length, printFile, readFile, setChamps, setChamps, setValid

Methods inherited from class java.lang.Object

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

Field Detail

cible

private Sequence cible

Current sequence of file.

liste

private PalindromeListe liste

Current list of palindromes of file.

Constructor Detail

FichierBracket

public FichierBracket(Sequence cible,
                      PalindromeListe liste)

Constructor with given sequence and a list of palindromes.

Parameters:

cible - Sequence

liste - PalindromeListe

See Also:

Fichier.Fichier(String, String), Fichier.printFile()

Method Detail

getSequence

public Sequence getSequence()

To get the sequence of current instance.

Returns:

Sequence

getListe

public PalindromeListe getListe()

To get the list of palindromes of current instance.

Returns:

PalindromeListe