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#ifdef _cplusplus
extern "C" {
#endif
#include "proteinindexcons.h"
/* Function: new_SeqLookupInterface_from_ProteinIndexConstructor(pic)
*
* Descrip: Makes a new SeqLookupInterface from ProteinIndexConstructor
*
*
* Arg: pic [UNKN ] Undocumented argument [ProteinIndexConstructor *]
*
* Return [UNKN ] Undocumented return value [SeqLookupInterface *]
*
*/
# line 34 "proteinindexcons.dy"
SeqLookupInterface * new_SeqLookupInterface_from_ProteinIndexConstructor(ProteinIndexConstructor * pic)
{
switch(pic->type) {
case ProteinIndexConstructor_Array :
return new_ArraySeq_SeqLookupInterface(SEQLOOKUP_5AA_SIZE,1000);
case ProteinIndexConstructor_Hash :
return new_ghash_SeqLookupInterface();
case ProteinIndexConstructor_Stream :
return new_ProteinStreamedIndex_SeqLookupInterface(pic->waypost);
case ProteinIndexConstructor_Shadow :
return new_ShadowSequenceIndex_SeqLookupInterface(pic->shadowlength,pic->has_maxlen,pic->max_seqlen,pic->shadow_error);
default:
fatal("Cannot process type %d as protein index constructor",pic->type);
}
return NULL;
}
/* Function: show_help_ProteinIndexConstructor(ofp)
*
* Descrip: provides help for protein index constructor
*
*
* Arg: ofp [UNKN ] Undocumented argument [FILE *]
*
*/
# line 59 "proteinindexcons.dy"
void show_help_ProteinIndexConstructor(FILE * ofp)
{
fprintf(ofp,"Protein Index construction options\n");
fprintf(ofp," -pitype [array/hash/stream/shadow] - default array\n");
fprintf(ofp," -piwaypost [number] - waypost for streamed cases, default 3\n");
fprintf(ofp," -pishadow [number] - shadow length for shadow cases, default 15\n");
fprintf(ofp," -pishadow_err [number] - errors per 100 identities tolerated, 3\n");
fprintf(ofp," -piseqmax - indexes can assumme maximum length of seq\n");
fprintf(ofp," -piseqmax_len [number] - assummed max sequnce length, default 1000\n");
return;
}
/* Function: new_ProteinIndexConstructor_from_argv(argc,argv)
*
* Descrip: Provides a ProteinIndexConstructor argument from argv
*
*
* Arg: argc [UNKN ] Undocumented argument [int *]
* Arg: argv [UNKN ] Undocumented argument [char **]
*
* Return [UNKN ] Undocumented return value [ProteinIndexConstructor *]
*
*/
# line 76 "proteinindexcons.dy"
ProteinIndexConstructor * new_ProteinIndexConstructor_from_argv(int * argc,char ** argv)
{
ProteinIndexConstructor * out;
char * temp;
out = ProteinIndexConstructor_alloc();
temp = strip_out_assigned_argument(argc,argv,"pitype");
if( temp != NULL ) {
if( strcmp(temp,"array") == 0 ) {
out->type = ProteinIndexConstructor_Array;
} else if ( strcmp(temp,"hash") == 0 ) {
out->type = ProteinIndexConstructor_Hash;
} else if ( strcmp(temp,"stream") == 0 ) {
out->type = ProteinIndexConstructor_Stream;
} else if ( strcmp(temp,"shadow") == 0 ) {
out->type = ProteinIndexConstructor_Shadow;
} else {
fatal("Could not interpret %s as a protein index type",temp);
}
}
strip_out_integer_argument(argc,argv,"piwaypost",&out->waypost);
strip_out_integer_argument(argc,argv,"pishadow",&out->shadowlength);
strip_out_boolean_def_argument(argc,argv,"piseqmax",&out->waypost);
strip_out_integer_argument(argc,argv,"piseqmax_len",&out->shadowlength);
return out;
}
# line 100 "proteinindexcons.c"
/* Function: hard_link_ProteinIndexConstructor(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 [ProteinIndexConstructor *]
*
* Return [UNKN ] Undocumented return value [ProteinIndexConstructor *]
*
*/
ProteinIndexConstructor * hard_link_ProteinIndexConstructor(ProteinIndexConstructor * obj)
{
if( obj == NULL ) {
warn("Trying to hard link to a ProteinIndexConstructor object: passed a NULL object");
return NULL;
}
obj->dynamite_hard_link++;
return obj;
}
/* Function: ProteinIndexConstructor_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [ProteinIndexConstructor *]
*
*/
ProteinIndexConstructor * ProteinIndexConstructor_alloc(void)
{
ProteinIndexConstructor * out; /* out is exported at end of function */
/* call ckalloc and see if NULL */
if((out=(ProteinIndexConstructor *) ckalloc (sizeof(ProteinIndexConstructor))) == NULL) {
warn("ProteinIndexConstructor_alloc failed ");
return NULL; /* calling function should respond! */
}
out->dynamite_hard_link = 1;
#ifdef PTHREAD
pthread_mutex_init(&(out->dynamite_mutex),NULL);
#endif
out->type = ProteinIndexConstructor_Array;
out->waypost = 3;
out->shadowlength = 15;
out->has_maxlen = 0;
out->max_seqlen = 1000;
out->shadow_error = 3;
return out;
}
/* Function: free_ProteinIndexConstructor(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 [ProteinIndexConstructor *]
*
* Return [UNKN ] Undocumented return value [ProteinIndexConstructor *]
*
*/
ProteinIndexConstructor * free_ProteinIndexConstructor(ProteinIndexConstructor * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a ProteinIndexConstructor 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;
ckfree(obj);
return NULL;
}
#ifdef _cplusplus
}
#endif
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