alonefichiers
Class FichierRnaViz

java.lang.Object
  alonefichiers.Fichier
      alonefichiers.FichierRnaViz

public class FichierRnaViz
extends Fichier

This class for RNAviz Format Files.

Author:

Stéfan Engelen (2006), Gabriel Chandesris (2008)

Constructor Summary

FichierRnaViz(java.lang.String nom, Sequence adn, PalindromeListe liste)
Constructor.

Method Summary

private void	annotation(Sequence adn, PalindromeListe liste) This procedure to annotate sequence with informations of secondary structure (palindromes tab) in input format of RNAviz.
private static java.lang.String	numerotationHelice(java.lang.String sequenceAnnotee, int[][] tabHelice) This method to number sequence's helix.

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

Constructor Detail

FichierRnaViz

public FichierRnaViz(java.lang.String nom,
                     Sequence adn,
                     PalindromeListe liste)

Constructor.

Parameters:

nom - (String)

adn - (Sequence)

liste - (PalindromeListe)

Method Detail

annotation

private void annotation(Sequence adn,
                        PalindromeListe liste)

This procedure to annotate sequence with informations of secondary structure (palindromes tab) in input format of RNAviz.

Parameters:

adn - (Sequence)

liste - (PalindromeListe)

numerotationHelice

private static java.lang.String numerotationHelice(java.lang.String sequenceAnnotee,
                                                   int[][] tabHelice)

This method to number sequence's helix.
Thus kept that we do not find (because we do not search) pseudoknots. Indeed it is just needed to treat parenthesis information of secondary structure in sequential order. Always in rnaviz file format.

Parameters:

sequenceAnnotee - (String) Annotated sequence.

tabHelice - (int[][]) Halix table.

Returns:

(String)