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%{
#include "arrayseqlookup.h"
#include "subseqhash.h"
#include "proteinstreamedindex.h"
#include "shadowseqindex.h"
typedef enum ProteinIndexConstructorType {
ProteinIndexConstructor_Array = 78,
ProteinIndexConstructor_Hash,
ProteinIndexConstructor_Stream,
ProteinIndexConstructor_Shadow
} ProteinIndexConstructureType;
%}
struct ProteinIndexConstructor
int type !def="ProteinIndexConstructor_Array";
int waypost !def="3"
int shadowlength !def="15"
int has_maxlen !def="0"
int max_seqlen !def="1000"
int shadow_error !def="3"
%{
#include "proteinindexcons.h"
%func
Makes a new SeqLookupInterface from ProteinIndexConstructor
%%
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;
}
%func
provides help for protein index constructor
%%
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 assume maximum length of seq\n");
fprintf(ofp," -piseqmax_len [number] - assumed max sequnce length, default 1000\n");
return;
}
%func
Provides a ProteinIndexConstructor argument from argv
%%
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;
}
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