alonefichiers
Class FichierConvert

java.lang.Object
  alonefichiers.Fichier
      alonefichiers.FichierConvert

public class FichierConvert
extends Fichier

This class for Convert recording file Format.
see also : Lab for Computational Biology - alterRNA
The predicted RNA structure in Connect(.ct) file format. The sequence length is given in the first line. For each nucleotide i, there is a line which consists of: the line number(i), the letter denotion of the nucleotide, the predecessor base index(i-1), the successor base index(i+1), the paired base index(0 if unpaired) and the original base index(i).

Author:

Gabriel Chandesris (2008)

Field Summary

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

Constructor Summary

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

FichierConvert(java.lang.String filename)
Constructor with a given filename.

Method Summary

double[]	comparisonScore(FichierConvert toComputeWith) Comparison between two (2) results of palindrome's search in convert file format.
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 seqquence of file.

liste

private PalindromeListe liste

Current list of palindromes of file.

Constructor Detail

FichierConvert

public FichierConvert(java.lang.String filename)

Constructor with a given filename. Read the file and compute the content : check if valid after...

Parameters:

filename - (String)Path and name of the file.

See Also:

Fichier.readFile(String), Fichier.isValid()

FichierConvert

public FichierConvert(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

comparisonScore

public double[] comparisonScore(FichierConvert toComputeWith)

Comparison between two (2) results of palindrome's search in convert file format. Local instance is reference.

Parameters:

toComputeWith - (FichierConvert)Other structure.

Returns:

(double[])Some pre-compute results.