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#ifdef _cplusplus
extern "C" {
#endif
#include "cdna.h"
/* Function: 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 [READ ] cDNA that is truncated [cDNA *]
* Arg: start [UNKN ] Undocumented argument [int]
* Arg: stop [UNKN ] Undocumented argument [int]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 45 "cdna.dy"
cDNA * truncate_cDNA(cDNA * cdna,int start,int stop)
{
return cDNA_from_Sequence(magic_trunc_Sequence(cdna->baseseq,start,stop));
}
/* Function: read_fasta_file_cDNA(filename)
*
* Descrip: Reads a fasta file assumming that it is cDNA.
* Will complain if it is not, and return NULL.
*
*
* Arg: filename [UNKN ] filename to be opened and read [char *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 56 "cdna.dy"
cDNA * read_fasta_file_cDNA(char * filename)
{
Sequence * seq;
seq = read_fasta_file_Sequence(filename);
if( seq == NULL ) {
return NULL;
}
return cDNA_from_Sequence(seq);
}
/* Function: read_fasta_cDNA(ifp)
*
* Descrip: Reads a fasta file assumming that it is cDNA.
* Will complain if it is not, and return NULL.
*
*
* Arg: ifp [UNKN ] file point to be read from [FILE *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 75 "cdna.dy"
cDNA * read_fasta_cDNA(FILE * ifp)
{
Sequence * seq;
seq = read_fasta_Sequence(ifp);
if( seq == NULL ) {
return NULL;
}
return cDNA_from_Sequence(seq);
}
/* Function: read_efetch_cDNA(estr)
*
* Descrip: Reads a efetch specified query
* Uses, of course /read_efetch_Sequence
*
*
* Arg: estr [READ ] efetch string which is read [char *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 93 "cdna.dy"
cDNA * read_efetch_cDNA(char * estr)
{
return cDNA_from_Sequence(read_efetch_Sequence(estr));
}
/* Function: read_SRS_cDNA(srsquery)
*
* Descrip: Reads a SRS sequence using srs4 syntax.
* Uses, of course, /read_SRS_Sequence
*
*
*
* Arg: srsquery [READ ] string query representing SRS name [char *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 105 "cdna.dy"
cDNA * read_SRS_cDNA(char * srsquery)
{
return cDNA_from_Sequence(read_SRS_Sequence(srsquery));
}
/* Function: cDNA_name(cdna)
*
* Descrip: Returns the name of the cDNA
*
*
* Arg: cdna [UNKN ] Undocumented argument [cDNA *]
*
* Return [UNKN ] Undocumented return value [char *]
*
*/
# line 115 "cdna.dy"
char * cDNA_name(cDNA * cdna)
{
return cdna->baseseq->name;
}
/* Function: cDNA_length(cdna)
*
* Descrip: Returns the length of the cDNA
*
*
* Arg: cdna [UNKN ] Undocumented argument [cDNA *]
*
* Return [UNKN ] Undocumented return value [int]
*
*/
# line 124 "cdna.dy"
int cDNA_length(cDNA * cdna)
{
return cdna->baseseq->len;
}
/* Function: cDNA_seqchar(cdna,pos)
*
* Descrip: Returns sequence character at this position.
*
*
* Arg: cdna [UNKN ] cDNA [cDNA *]
* Arg: pos [UNKN ] position in cDNA to get char [int]
*
* Return [UNKN ] Undocumented return value [char]
*
*/
# line 135 "cdna.dy"
char cDNA_seqchar(cDNA * cdna,int pos)
{
return cdna->baseseq->seq[pos];
}
/* Function: 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 [OWNER] Sequence to make cDNA from [Sequence *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
# line 155 "cdna.dy"
cDNA * cDNA_from_Sequence(Sequence * seq)
{
cDNA * out;
int conv;
if( seq == NULL ) {
warn("Trying to make a cdna sequence from a NULL baseseq.");
return NULL;
}
if( is_dna_Sequence(seq) == FALSE ) {
warn("Trying to make a cDNA sequence from a non cDNA base sequence [%s].",seq->name);
return NULL;
}
uppercase_Sequence(seq);
force_to_dna_Sequence(seq,1.0,&conv);
if( conv != 0 ) {
log_full_error(INFO,0,"In making %s a cdna sequence, converted %d bases (%2.1f%%) to N's from non ATGCN",seq->name,conv,(double)conv*100/(double)seq->len);
}
out = cDNA_alloc();
out->baseseq = seq;
return out;
}
# line 199 "cdna.c"
/* Function: hard_link_cDNA(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [cDNA *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
cDNA * hard_link_cDNA(cDNA * obj)
{
if( obj == NULL ) {
warn("Trying to hard link to a cDNA object: passed a NULL object");
return NULL;
}
obj->dynamite_hard_link++;
return obj;
}
/* Function: cDNA_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
cDNA * cDNA_alloc(void)
{
cDNA * out; /* out is exported at end of function */
/* call ckalloc and see if NULL */
if((out=(cDNA *) ckalloc (sizeof(cDNA))) == NULL) {
warn("cDNA_alloc failed ");
return NULL; /* calling function should respond! */
}
out->dynamite_hard_link = 1;
#ifdef PTHREAD
pthread_mutex_init(&(out->dynamite_mutex),NULL);
#endif
out->baseseq = NULL;
return out;
}
/* Function: free_cDNA(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [cDNA *]
*
* Return [UNKN ] Undocumented return value [cDNA *]
*
*/
cDNA * free_cDNA(cDNA * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a cDNA obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->baseseq != NULL)
free_Sequence(obj->baseseq);
ckfree(obj);
return NULL;
}
/* Function: replace_baseseq_cDNA(obj,baseseq)
*
* Descrip: Replace member variable baseseq
* For use principly by API functions
*
*
* Arg: obj [UNKN ] Object holding the variable [cDNA *]
* Arg: baseseq [OWNER] New value of the variable [Sequence *]
*
* Return [SOFT ] member variable baseseq [boolean]
*
*/
boolean replace_baseseq_cDNA(cDNA * obj,Sequence * baseseq)
{
if( obj == NULL) {
warn("In replacement function baseseq for object cDNA, got a NULL object");
return FALSE;
}
obj->baseseq = baseseq;
return TRUE;
}
/* Function: access_baseseq_cDNA(obj)
*
* Descrip: Access member variable baseseq
* For use principly by API functions
*
*
* Arg: obj [UNKN ] Object holding the variable [cDNA *]
*
* Return [SOFT ] member variable baseseq [Sequence *]
*
*/
Sequence * access_baseseq_cDNA(cDNA * obj)
{
if( obj == NULL) {
warn("In accessor function baseseq for object cDNA, got a NULL object");
return NULL;
}
return obj->baseseq;
}
#ifdef _cplusplus
}
#endif
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