libs/ck-libs/metis/GKlib/seq.c File Reference

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Functions
void	gk_seq_init (gk_seq_t *seq)
gk_i2cc2i_t *	gk_i2cc2i_create_common (char *alphabet)
	This function creates the localizations for the various sequences.
gk_seq_t *	gk_seq_ReadGKMODPSSM (char *filename)
	This function reads a pssm in the format of gkmod pssm.
void	gk_seq_free (gk_seq_t *seq)
	This function frees the memory allocated to the seq structure.

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Function Documentation

void gk_seq_init

(

gk_seq_t *

seq

)

Definition at line 27 of file seq.c.

References gk_seq_t::len, gk_seq_t::name, gk_seq_t::psfm, gk_seq_t::pssm, and gk_seq_t::sequence.

Referenced by gk_seq_ReadGKMODPSSM().

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gk_i2cc2i_t* gk_i2cc2i_create_common

(

char *

alphabet

)

This function creates the localizations for the various sequences.

Parameters:

string

i.e amino acids, nucleotides, sequences

Returns:

gk_i2cc2i_t variable

Definition at line 48 of file seq.c.

References gk_i2cc2i_t::c2i, gk_idx_t, gk_malloc(), gk_i2cc2i_t::i2c, int, gk_i2cc2i_t::n, and PUP::t.

Referenced by gk_seq_ReadGKMODPSSM().

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gk_seq_t* gk_seq_ReadGKMODPSSM

(

char *

filename

)

This function reads a pssm in the format of gkmod pssm.

Parameters:

file_name

is the name of the pssm file

Returns:

gk_seq_t

Definition at line 83 of file seq.c.

References gk_i2cc2i_t::c2i, errexit(), gk_fclose(), gk_fopen(), gk_free(), gk_freetokenslist(), gk_getbasename(), gk_getfilestats(), gk_i2cc2i_create_common(), gk_idx_t, gk_malloc(), gk_seq_init(), gk_strtokenize(), gk_strtoupper(), int, gk_seq_t::len, len, gk_Tokens_t::list, gk_seq_t::name, gk_seq_t::nsymbols, gk_seq_t::psfm, gk_seq_t::pssm, and gk_seq_t::sequence.

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void gk_seq_free

(

gk_seq_t *

seq

)

This function frees the memory allocated to the seq structure.

Parameters:

gk_seq_t

Returns:

nothing

Definition at line 166 of file seq.c.

References gk_free(), gk_seq_t::len, gk_seq_t::name, gk_seq_t::nsymbols, gk_seq_t::psfm, gk_seq_t::pssm, and gk_seq_t::sequence.

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