alonefichiers
Class FichierFasta

java.lang.Object
  alonefichiers.Fichier
      alonefichiers.FichierFasta

public class FichierFasta
extends Fichier

This class for FASTA sequences or ClustalW alignment in FASTA Format.

Author:

Stéfan Engelen (2006), Gabriel Chandesris (2008)

Field Summary

private SequenceListe

liste

Constructor Summary

FichierFasta(SequenceListe liste)
Constructor with a given SequenceListe.

FichierFasta(java.lang.String alignement)
Constructor with a given String of alignment.

FichierFasta(java.lang.String nom, java.lang.String alignement)
Constructor with a given name and a String of alignment.

Method Summary

static java.lang.String	ensureFastaAlignment(java.lang.String alignement) Take care for treatment : aligned sequences are putted on the same line in the way to ensure format is [names on odd lines and alignes sequences in one line (even lines)] Check if it is a fasta alignment before treatment.
SequenceListe[]	getCible(java.lang.String nom) To get a sequence with given name.
SequenceListe	getListe() To get the liste of current instance of FichierFasta.
java.lang.String	getSequencesToString() To get the whole alignment of Sequence's.
static boolean	isFastaAlignment(java.lang.String alignement) To know if the alignment is a FASTA alignment.
private static boolean	isNucleicSequence(java.lang.String sequence) To know if a sequence is a nucleic sequence.
int	length() Length of the current liste of instance of FichierFasta.

Methods inherited from class alonefichiers.Fichier

addToChamps, getChamp, getChamps, getChampsToString, getNom, getType, isValid, 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

liste

private SequenceListe liste

Constructor Detail

FichierFasta

public FichierFasta(java.lang.String alignement)

Constructor with a given String of alignment.

Parameters:

alignement - String

See Also:

Fichier.Fichier(String, String)

FichierFasta

public FichierFasta(java.lang.String nom,
                    java.lang.String alignement)

Constructor with a given name and a String of alignment.
Useful constructor for recording FASTA file.

Parameters:

alignement - String

See Also:

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

FichierFasta

public FichierFasta(SequenceListe liste)

Constructor with a given SequenceListe.

Parameters:

liste - (SequenceListe)

Method Detail

getListe

public SequenceListe getListe()

To get the liste of current instance of FichierFasta.

Returns:

SequenceListe;

length

public int length()

Length of the current liste of instance of FichierFasta.

Overrides:

length in class Fichier

getSequencesToString

public java.lang.String getSequencesToString()

To get the whole alignment of Sequence's.

Returns:

String (as original file).

getCible

public SequenceListe[] getCible(java.lang.String nom)

To get a sequence with given name.
Tab result contain cible Sequence at [0] and other Sequence's in [1].

Parameters:

nom - (String)

Returns:

(SequenceListe[])

isFastaAlignment

public static boolean isFastaAlignment(java.lang.String alignement)

To know if the alignment is a FASTA alignment.

Parameters:

alignement - (String)

Returns:

(boolean)

ensureFastaAlignment

public static java.lang.String ensureFastaAlignment(java.lang.String alignement)

Take care for treatment : aligned sequences are putted on the same line in the way to ensure format is [names on odd lines and alignes sequences in one line (even lines)]
Check if it is a fasta alignment before treatment.

Parameters:

alignement - (String)

Returns:

(String)

See Also:

isFastaAlignment(String)

isNucleicSequence

private static boolean isNucleicSequence(java.lang.String sequence)

To know if a sequence is a nucleic sequence.

Parameters:

sequence - String

Returns:

boolean

See Also:

Base.isBaseOrGap(char)