fasta.c File Reference

Module to handle FASTA sequences. More...

#include "log.h"
#include "format.h"
#include "linestream.h"
#include "stringUtil.h"
#include "common.h"
#include "fasta.h"

Go to the source code of this file.

Functions
void	fasta_deInit (void)
	Deinitialize the FASTA module.
void	fasta_initFromFile (char *fileName)
	Initialize the FASTA module using a file name.
void	fasta_initFromPipe (char *command)
	Initialize the FASTA module using a pipe.
Seq *	fasta_nextSequence (int truncateName)
	Returns a pointer to the next FASTA sequence.
void	fasta_printOneSequence (Seq *currSeq)
	Prints currSeq to stdout.
void	fasta_printSequences (Array seqs)
	Prints seqs to stdout.
Array	fasta_readAllSequences (int truncateName)
	Returns an Array of FASTA sequences.

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Detailed Description

Module to handle FASTA sequences.

Author:

Lukas Habegger (lukas.habegger@yale.edu)

Definition in file fasta.c.

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Function Documentation

void fasta_deInit

(

void

)

Deinitialize the FASTA module.

Frees module internal memory.

Definition at line 39 of file fasta.c.

void fasta_initFromFile

(

char *

fileName

)

Initialize the FASTA module using a file name.

Note:

Use "-" to denote stdin.

Postcondition:

fasta_nextSequence(), fasta_readAllSequences() can be called.

Definition at line 28 of file fasta.c.

void fasta_initFromPipe

(

char *

command

)

Initialize the FASTA module using a pipe.

Postcondition:

fasta_nextSequence(), fasta_readAllSequences() can be called.

Definition at line 50 of file fasta.c.

Seq* fasta_nextSequence

(

int

truncateName

)

Returns a pointer to the next FASTA sequence.

Parameters:

[in]

truncateName

If truncateName > 0, leading spaces of the name are skipped. Furthermore, the name is truncated after the first white space. If truncateName == 0, the name is stored as is.

Note:

The memory belongs to this routine.

Definition at line 124 of file fasta.c.

Array fasta_readAllSequences

(

int

truncateName

)

Returns an Array of FASTA sequences.

Parameters:

[in]

truncateName

If truncateName > 0, leading spaces of the name are skipped. Furthermore, the name is truncated after the first white space. If truncateName == 0, the name is stored as is.

Note:

The memory belongs to this routine.

Definition at line 136 of file fasta.c.