void ampegdecoder::seekinit3(int discard)
{
int i,j,k;
int extra=(seekmode==seekmodeexact)?1:0;
if ((discard>=seekinitframes)&&extra)
for (i=0; i<2; i++)
for (j=0; j<32; j++)
for (k=0; k<18; k++)
prevblck[i][j][k]=0;
huffoffset=0;
for (i=discard; i<seekinitframes; i++)
if (i<(seekinitframes-extra))
for (j=0; j<(hdrlsf?2:1); j++)
{
if (!decodehdr(0))
return;
readmain(0);
}
else
{
if (!decodehdr(0))
return;
decode3();
}
}
value
grappa_CAML_inv_med
(value medsov, value c_gene1, value c_gene2, value c_gene3, value num_genes,value circular)
{
int debug=0;
CAMLparam5(medsov,c_gene1,c_gene2,c_gene3,num_genes);
CAMLxparam1(circular);
CAMLlocal1(res);
int MEDIAN_SOLVER;
struct genome_struct *g1, *g2, *g3;
struct genome_struct *gen[3];
struct genome_struct *out_genome_list;
struct genome_arr_t *out_genome_arr;
int CIRCULAR;
int NUM_GENES;
int num_cond;
int old_max_num_genes;
//int multichromosome=0;
MEDIAN_SOLVER = Int_val(medsov);
g1 = (struct genome_struct *) Data_custom_val (c_gene1);
g2 = (struct genome_struct *) Data_custom_val (c_gene2);
g3 = (struct genome_struct *) Data_custom_val (c_gene3);
CIRCULAR = Int_val(circular);
NUM_GENES = Int_val(num_genes);
long dims[1]; dims[0] = NUM_GENES;
condense3_mem_t * cond3mem_p; cond3mem_p = &CONDENSE3_MEM;
convert_mem_t * convertmem_p; convertmem_p = &CONVERT_MEM;
old_max_num_genes = cond3mem_p->max_num_genes;
if (debug) {
printf("grappa_interface.grappa_CAML_inv_med,MEDIAN_SOLVER=%d,MAX_NAME=%d\n",MEDIAN_SOLVER,MAX_NAME);
fflush(stdout); }
out_genome_list =
( struct genome_struct * ) malloc ( 1 *
sizeof ( struct genome_struct ) );
if ( out_genome_list == ( struct genome_struct * ) NULL )fprintf ( stderr, "ERROR: genome_list NULL\n" );
out_genome_list[0].gnamePtr =
( char * ) malloc ( MAX_NAME * sizeof ( char ) );
sprintf (out_genome_list[0].gnamePtr, "%i", 0);
if ( out_genome_list[0].gnamePtr == ( char * ) NULL )
{
fprintf ( stderr, "ERROR: gname NULL\n" );
};
out_genome_list[0].genes =( int * ) malloc ( NUM_GENES * sizeof ( int ) );
out_genome_list[0].delimiters = (int *) malloc (NUM_GENES * sizeof (int) );
out_genome_list[0].magic_number = GRAPPA_MAGIC_NUMBER;
out_genome_list[0].encoding = NULL;
if (old_max_num_genes >= NUM_GENES) {}
else
{
//free_mem_4_all ();
ini_mem_4_all (NUM_GENES);
free_mem_4_invdist (&INVDIST_MEM);
ini_mem_4_invdist (NUM_GENES);
free_mem_4_albert ();
ini_mem_4_albert (NUM_GENES);
free_mem_4_siepel ();
ini_mem_4_siepel(NUM_GENES);
free_mem_4_cond3 ();
ini_mem_4_cond3 (NUM_GENES);
free_mem_4_convert();
ini_mem_4_convert(NUM_GENES);
free_mem_4_mgr();
mgr_ini_mem(NUM_GENES);
//3 times of original gene size is the worst case for multi-chromosome.
}
/* debug msg
fprintf(stdout,"in gene list = [");
int x=0;
for(x=0;x<NUM_GENES;x++)
fprintf(stdout,"%d,",g1->genes[x]);
fprintf(stdout,"]; \n");
for(x=0;x<NUM_GENES;x++)
fprintf(stdout,"%d,",g2->genes[x]);
fprintf(stdout,"]; \n");
for(x=0;x<NUM_GENES;x++)
fprintf(stdout,"%d,",g3->genes[x]);
fprintf(stdout,"]; \n");
fflush(stdout);
debug msg */
if(MEDIAN_SOLVER<7)
{
condense3 ( g1->genes,
g2->genes,
g3->genes,
cond3mem_p->con_g1->genes,
cond3mem_p->con_g2->genes,
cond3mem_p->con_g3->genes,
NUM_GENES, &num_cond,
cond3mem_p->pred1, cond3mem_p->pred2,
cond3mem_p->picked, cond3mem_p->decode );
//when 3 input array are the same num_cond = 0
//when 2 out of 3 input array are the same, num_cond could be 0
//either way, median solver in grappa/mgr will crush.
//either way, median3 solver will not be called from genAli.ml.
//I add the if (num_cond>0) else... here just in case.
if (num_cond>0)
{
gen[0] = cond3mem_p->con_g1;
gen[1] = cond3mem_p->con_g2;
gen[2] = cond3mem_p->con_g3;
switch (MEDIAN_SOLVER)
{
case 1: //Alberto Capara median solver
if ( CIRCULAR )
albert_inversion_median_circular
( gen,num_cond,cond3mem_p->con_med->genes );
else
albert_inversion_median_noncircular
(gen,num_cond,cond3mem_p->con_med->genes );
break;
case 2: //A. Siepel median solver
find_reversal_median ( cond3mem_p->con_med, gen, num_cond, &SIEPEL_MEM );
break;
case 3: //Exact median solver
convert2_to_tsp ( gen[0], gen[1], gen[2], convertmem_p->adjl, convertmem_p->adjp,
num_cond, CIRCULAR );
bbtsp ( 2 * num_cond, cond3mem_p->con_med->genes,
FALSE, /* cannot use median that does not exist */
gen[0]->genes, gen[1]->genes, gen[2]->genes,
convertmem_p->adjl,
convertmem_p->neighbors,
convertmem_p->stack,
convertmem_p->outcycle,
convertmem_p->degree,
convertmem_p->otherEnd,
convertmem_p->edges,
CIRCULAR );
break;
case 4: //Greedy median solver
convert2_to_tsp ( gen[0], gen[1], gen[2], convertmem_p->adjl, convertmem_p->adjp,
num_cond, CIRCULAR );
coalestsp ( 2 * num_cond, cond3mem_p->con_med->genes,FALSE,
gen[0]->genes, gen[1]->genes, gen[2]->genes,
convertmem_p->adjl,
convertmem_p->neighbors,
convertmem_p->stack,
convertmem_p->outcycle,
convertmem_p->degree,
convertmem_p->otherEnd,
convertmem_p->edges,
CIRCULAR );
break;
/* case5 and case6 need the CONCORDE package */
// http://www.tsp.gatech.edu//concorde/downloads/downloads.htm
#ifdef USE_CONCORDE
case 5: //SimpleLK TSP median solver
convert_to_tsp ( gen[0], gen[1],
gen[2], num_cond, CIRCULAR,
convertmem_p->weights );
greedylk ( 2 * num_cond, convertmem_p->weights,
cond3mem_p->con_med->genes,
convertmem_p->incycle,
convertmem_p->outcycle );
break;
case 6: //ChainedLK TSP median solver
convert_to_tsp ( gen[0], gen[1],
gen[2], num_cond, CIRCULAR,
convertmem_p->weights );
chlinkern ( 2 * num_cond,
convertmem_p->weights,
cond3mem_p->con_med->genes,
convertmem_p->incycle, convertmem_p->outcycle );
break;
#endif
default:
fprintf(stderr, "unknown choice of median solver !\n");
break;
}
decode3 ( out_genome_list->genes, cond3mem_p->con_med->genes,
cond3mem_p->pred1, cond3mem_p->decode, num_cond );
}
else
{
int x=0;
for(x=0;x<NUM_GENES;x++)
{
out_genome_list->genes[x] = g1->genes[x];
out_genome_list->delimiters[x] = g1->delimiters[x];
}
// memcpy (out_genome_list->genes, g1->genes, NUM_GENES);
// memcpy (out_genome_list->delimiters, g1->delimiters, NUM_GENES);
out_genome_list->deli_num = g1->deli_num;
out_genome_list->genome_num = g1->genome_num;
}
}
else// MEDIAN_SOLVER == 7, MGR median solver
{
mgr_med (g1->genes,g2->genes,g3->genes,g1->delimiters,g2->delimiters,g3->delimiters,g1->deli_num,g2->deli_num,g3->deli_num, NUM_GENES,CIRCULAR,out_genome_list);
}
/* debug msg
fprintf(stdout,"out_genome_list = [");
int xx=0;
for(xx=0;xx<NUM_GENES;xx++)
fprintf(stdout,"%d,",out_genome_list->genes[xx]);
fprintf(stdout,"]; delimiters = [");
for(xx=0;xx<out_genome_list->deli_num;xx++)
fprintf(stdout,"%d",out_genome_list->delimiters[xx]);
fprintf(stdout,"]\n");
fflush(stdout);
debug msg */
CAMLlocal1 (c_genome_arr);
c_genome_arr = alloc_custom(&genomeArrOps, sizeof(struct genome_arr_t), 1, 1000000);
out_genome_arr = (struct genome_arr_t *) Data_custom_val(c_genome_arr);
// fprintf(stdout, "inv_med , genome list addr=%p\n",out_genome_arr);
out_genome_arr->magic_number = GRAPPA_MAGIC_NUMBER;
out_genome_arr->genome_ptr = out_genome_list;
assert( GRAPPA_MAGIC_NUMBER == out_genome_list[0].magic_number);
out_genome_arr->num_genome = 1;
out_genome_arr->num_gene = NUM_GENES;
CAMLreturn(c_genome_arr);
}
