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/* Functions that create, manipulate or act on cDNA
*
* Wise2_truncate_cDNA
* Wise2_read_fasta_file_cDNA
* Wise2_cDNA_name
* Wise2_cDNA_length
* Wise2_cDNA_seqchar
* Wise2_cDNA_from_Sequence
* Wise2_hard_link_cDNA
* Wise2_cDNA_alloc
* Wise2_replace_baseseq_cDNA
* Wise2_access_baseseq_cDNA
* Wise2_free_cDNA [destructor]
*
*/
/* API for object cDNA */
/* Function: Wise2_truncate_cDNA(cdna,start,stop)
*
* Descrip: Truncates a cDNA sequence. Basically uses
* the /magic_trunc_Sequence function (of course!)
*
* It does not alter cdna, rather it returns a new
* sequence with that truncation
*
*
* Arg: cdna cDNA that is truncated [Wise2_cDNA *]
* Arg: start Undocumented argument [int]
* Arg: stop Undocumented argument [int]
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_truncate_cDNA( Wise2_cDNA * cdna,int start,int stop);
/* Function: Wise2_read_fasta_file_cDNA(filename)
*
* Descrip: Reads a fasta file assuming that it is cDNA.
* Will complain if it is not, and return NULL.
*
*
* Arg: filename filename to be opened and read [char *]
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_read_fasta_file_cDNA( char * filename);
/* Function: Wise2_cDNA_name(cdna)
*
* Descrip: Returns the name of the cDNA
*
*
* Arg: cdna Undocumented argument [Wise2_cDNA *]
*
* Returns Undocumented return value [char *]
*
*/
char * Wise2_cDNA_name( Wise2_cDNA * cdna);
/* Function: Wise2_cDNA_length(cdna)
*
* Descrip: Returns the length of the cDNA
*
*
* Arg: cdna Undocumented argument [Wise2_cDNA *]
*
* Returns Undocumented return value [int]
*
*/
int Wise2_cDNA_length( Wise2_cDNA * cdna);
/* Function: Wise2_cDNA_seqchar(cdna,pos)
*
* Descrip: Returns sequence character at this position.
*
*
* Arg: cdna cDNA [Wise2_cDNA *]
* Arg: pos position in cDNA to get char [int]
*
* Returns Undocumented return value [char]
*
*/
char Wise2_cDNA_seqchar( Wise2_cDNA * cdna,int pos);
/* Function: Wise2_cDNA_from_Sequence(seq)
*
* Descrip: makes a new cDNA from a Sequence. It
* owns the Sequence memory, ie will attempt a /free_Sequence
* on the structure when /free_cDNA is called
*
* If you want to give this cDNA this Sequence and
* forget about it, then just hand it this sequence and set
* seq to NULL (no need to free it). If you intend to use
* the sequence object elsewhere outside of the cDNA datastructure
* then use cDNA_from_Sequence(/hard_link_Sequence(seq))
*
*
*
* Arg: seq Sequence to make cDNA from [Wise2_Sequence *]
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_cDNA_from_Sequence( Wise2_Sequence * seq);
/* Function: Wise2_hard_link_cDNA(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj Object to be hard linked [Wise2_cDNA *]
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_hard_link_cDNA( Wise2_cDNA * obj);
/* Function: Wise2_cDNA_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_cDNA_alloc();
/* Function: Wise2_replace_baseseq_cDNA(obj,baseseq)
*
* Descrip: Replace member variable baseseq
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_cDNA *]
* Arg: baseseq New value of the variable [Wise2_Sequence *]
*
* Returns member variable baseseq [boolean]
*
*/
boolean Wise2_replace_baseseq_cDNA( Wise2_cDNA * obj,Wise2_Sequence * baseseq);
/* Function: Wise2_access_baseseq_cDNA(obj)
*
* Descrip: Access member variable baseseq
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_cDNA *]
*
* Returns member variable baseseq [Wise2_Sequence *]
*
*/
Wise2_Sequence * Wise2_access_baseseq_cDNA( Wise2_cDNA * obj);
/* This is the destructor function, ie, call this to free object*/
/* Function: Wise2_free_cDNA(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj Object that is free'd [Wise2_cDNA *]
*
* Returns Undocumented return value [Wise2_cDNA *]
*
*/
Wise2_cDNA * Wise2_free_cDNA( Wise2_cDNA * obj);
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