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tools/sctk-2.4.10/src/sclite/net_dp.c
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/*******************************************************************/
/* File: net_dp.c */
/* Desc: Dynamic programming alignment routines for networks. */
/* */
/* Revisions: */
/* 960319 - JGF - Changed Network_dp_align to optionally */
/* output NULLS. */
/* 961009 - JGF - added an option to output a Network of the */
/* aligned networks. */
/*******************************************************************/
#include "sctk.h"
static NET_ALIGN *net_ali = (NET_ALIGN *)0;
PATH *extract_best_NET_ALIGN_result(NET_ALIGN *, NETWORK *, NETWORK *,float wwd(void *, void *, int (*cmp)(void *, void *)));
void find_minimal_paths(NET_ALIGN *, int, int, int *,float wwd(void *, void *, int (*cmp)(void *, void *)),NETWORK *, PATH *, int *);
void create_alinged_NETWORK(NET_ALIGN *, NETWORK *, NETWORK *, void *, int);
void calc_minimum_insert(NET_ALIGN *, int, int, float *, int *);
void calc_minimum_delete(NET_ALIGN *, int, int, float *, int *);
void calc_minimum_substi(NET_ALIGN *, int, int, float *, int *, int *);
static int setup_NET_ALIGN(NET_ALIGN **,NETWORK *,NETWORK *);
static void destroy_NET_ALIGN(NET_ALIGN **net_ali);
PATH *extract_NET_ALIGN_result(NET_ALIGN *,NETWORK *,NETWORK *, int);
static int add_null_network_heads(NETWORK *, char *);
static void calculate_margin_cells(NET_ALIGN *, NETWORK *net_a,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *)));
static void calculate_internal_cells(NET_ALIGN *, NETWORK *,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *)));
int find_arcset_id(ARCSET *arcset, ARC *arc, int from){
int a;
ARC **arclist;
if (from == arcset->num) from --;
for (a=from,arclist = (arcset->arcs) + a; a>=0; a--, arclist--){
if (*arclist == arc)
return(a);
}
for (a=from+1; a<arcset->num; a++){
if (arcset->arcs[a] == arc){
fprintf(scfp,"Error: find_arcset_id found the arc after from
");
return(-1);
}
}
return(-1);
}
void add_to_arcset(ARC *arc, void *ptr){
ARCSET *arcset = (ARCSET *)ptr;
arcset->arcs[arcset->num++] = arc;
}
void calc_minimum_delete(NET_ALIGN *net_ali,int a, int b, float *min_arc_d, int *min_ind_a){
int arc_a_id;
ARC *arc_b, *arc_a;
ARC_LIST_ATOM *arcpa;
*min_arc_d = 999999999.9;
*min_ind_a = -1;
arc_a = net_ali->arcset_a.arcs[a];
arc_b = net_ali->arcset_b.arcs[b];
if (db >= 15) {
printf(" Computing TREE DELETE COST [%d][%d]:
",a,b);
printf(" ");
print_arc(arc_a,0);
printf(" ");
print_arc(arc_b,0);
}
for (arcpa = arc_a->from_node->in_arcs; arcpa != NULL;arcpa = arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,a)) <0){
fprintf(stderr,"Error: find_arcset_id failed in
");
exit(1);
}
if (db >= 15) {printf(" look back to cell: %d,%d
",arc_a_id, b);
printf(" ");
print_arc(arcpa->arc,0);
printf(" ");
print_arc(arc_b,0);}
if (net_ali->cell[arc_a_id][b].min_d < *min_arc_d){
*min_arc_d = net_ali->cell[arc_a_id][b].min_d;
*min_ind_a = arc_a_id;
}
}
if (db >= 15)
printf(" Min_d=%4.2f cell [%d][%d]
",
*min_arc_d, *min_ind_a, b);
}
void calc_minimum_insert(NET_ALIGN *net_ali,int a, int b, float *min_arc_d, int *min_ind_b){
int arc_b_id;
ARC *arc_b, *arc_a;
ARC_LIST_ATOM *arcpb;
*min_arc_d = 999999999.9;
*min_ind_b = -1;
arc_a = net_ali->arcset_a.arcs[a];
arc_b = net_ali->arcset_b.arcs[b];
if (db >= 15) {
printf(" Computing TREE INSERT COST [%d][%d]:
",a,b);
printf(" ");
print_arc(arc_a,0);
printf(" ");
print_arc(arc_b,0);
}
for (arcpb = arc_b->from_node->in_arcs; arcpb != NULL;arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),arcpb->arc,b)) <0){
fprintf(stderr,"Error: find_arcset_id failed
");
exit(1);
}
if (db >= 15) {printf(" look back to cell: %d,%d
",a, arc_b_id);
printf(" ");
print_arc(arc_a,0);
printf(" ");
print_arc(arcpb->arc,0);}
if (net_ali->cell[a][arc_b_id].min_d < *min_arc_d){
*min_arc_d = net_ali->cell[a][arc_b_id].min_d;
*min_ind_b = arc_b_id;
}
}
if (db >= 15)
printf(" Min_d=%4.2f cell [%d][%d]
",
*min_arc_d, a, *min_ind_b);
}
void calc_minimum_substi(NET_ALIGN *net_ali,int a, int b, float *min_arc_d, int *min_ind_a, int *min_ind_b){
int arc_a_id, arc_b_id;
ARC *arc_a, *arc_b;
ARC_LIST_ATOM *arcpa, *arcpb;
*min_arc_d = 999999999.9;
*min_ind_b = *min_ind_a = -1;
arc_a = net_ali->arcset_a.arcs[a];
arc_b = net_ali->arcset_b.arcs[b];
if (db >= 15) {
printf(" Computing TREE SUBSITUTION Cost [%d][%d]:
",a,b);
printf(" ");print_arc(arc_a,0);printf(" ");
print_arc(arc_b,0);
}
for (arcpa = arc_a->from_node->in_arcs; arcpa != NULL;arcpa = arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,a)) <0){
fprintf(stderr,"Error: netA find_arcset_id failed
");
exit(1);
}
for (arcpb = arc_b->from_node->in_arcs; arcpb != NULL;
arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),
arcpb->arc,b)) <0){
fprintf(stderr,"Error: netB find_arcset_id failed
");
exit(1);
}
if (db >= 15) {printf(" look back to cell: %d,%d
",
arc_a_id, arc_b_id);
printf(" ");print_arc(arcpa->arc,0);
printf(" ");print_arc(arcpb->arc,0);}
if (net_ali->cell[arc_a_id][arc_b_id].min_d < *min_arc_d){
*min_arc_d = net_ali->cell[arc_a_id][arc_b_id].min_d;
*min_ind_b = arc_b_id;
*min_ind_a = arc_a_id;
}
}
}
if (db >= 15)
printf(" Min_d=%4.2f cell [%d][%d]
",
*min_arc_d, *min_ind_a, *min_ind_b);
}
static int add_null_network_heads(NETWORK *net, char *proc){
if (Network_add_arc_to_head(net,(void *)0) > 0){
fprintf(stderr,"%s: Unable to add (void *)0 to Net A
",proc);
return(1);
}
return(0);
}
static void calculate_margin_cells(NET_ALIGN *net_ali, NETWORK *net_a,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *))){
int a,b;
float min_arc_d;
int min_ind_a, min_ind_b;
/* Pre-Calculate the margin Cells */
for (a=0,b=1; b<net_ali->arcset_b.num; b++){
calc_minimum_insert(net_ali,0,b,&min_arc_d,&min_ind_b);
net_ali->cell[0][b].min_d = min_arc_d +
wwd(NULL_WORD,net_ali->arcset_b.arcs[b]->data,
net_a->arc_func.equal);
net_ali->cell[0][b].back_a = 0;
net_ali->cell[0][b].back_b = min_ind_b;
if (db >= 15)
printf(" Min_d=%4.2f back_a=%d back_b=%d
",
net_ali->cell[a][b].min_d,
net_ali->cell[a][b].back_a,
net_ali->cell[a][b].back_b);
}
for (b=0,a=1; a<net_ali->arcset_a.num; a++){
calc_minimum_delete(net_ali,a,0,&min_arc_d,&min_ind_a);
net_ali->cell[a][0].min_d = min_arc_d +
wwd(net_ali->arcset_a.arcs[a]->data,NULL_WORD,
net_a->arc_func.equal);
net_ali->cell[a][0].back_a = min_ind_a;
net_ali->cell[a][0].back_b = 0;
if (db >= 15)
printf(" Min_d=%4.2f back_a=%d back_b=%d
",
net_ali->cell[a][b].min_d,
net_ali->cell[a][b].back_a,
net_ali->cell[a][b].back_b);
}
}
static void calculate_internal_cells(NET_ALIGN *net_ali, NETWORK *net_a,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *))){
int a,b;
for (a=1; a<net_ali->arcset_a.num; a++){
for (b=1; b<net_ali->arcset_b.num; b++){
/* for (b=1; b<2; b++){ */
int ins_min_ind_b, del_min_ind_a, sub_min_ind_a, sub_min_ind_b;
float ins_min_d, del_min_d, sub_min_d;
if (db >= 15){
printf("Computing minimized cost of [%d][%d]:
",a,b);
print_arc(net_ali->arcset_a.arcs[a],0);
print_arc(net_ali->arcset_b.arcs[b],0);
}
calc_minimum_insert(net_ali,a,b,&ins_min_d,&ins_min_ind_b);
calc_minimum_delete(net_ali,a,b,&del_min_d,&del_min_ind_a);
calc_minimum_substi(net_ali,a,b,&sub_min_d,&sub_min_ind_a,
&sub_min_ind_b);
if (db >= 15)
printf(" Tree: Ins = %f Del = %f Sub = %f
",
ins_min_d, del_min_d, sub_min_d);
sub_min_d += wwd(net_ali->arcset_a.arcs[a]->data,
net_ali->arcset_b.arcs[b]->data,
net_a->arc_func.equal);
del_min_d += wwd(net_ali->arcset_a.arcs[a]->data,0,
net_a->arc_func.equal);
ins_min_d += wwd(0,net_ali->arcset_b.arcs[b]->data,
net_a->arc_func.equal);
if (db >= 15)
printf(" Tree+wwd: Ins = %f Del = %f Sub = %f
",
ins_min_d, del_min_d, sub_min_d);
if (sub_min_d <= del_min_d && sub_min_d <= ins_min_d){
net_ali->cell[a][b].min_d = sub_min_d;
net_ali->cell[a][b].back_a = sub_min_ind_a;
net_ali->cell[a][b].back_b = sub_min_ind_b;
} else if (del_min_d < ins_min_d) {
net_ali->cell[a][b].min_d = del_min_d;
net_ali->cell[a][b].back_a = del_min_ind_a;
net_ali->cell[a][b].back_b = b;
} else {
net_ali->cell[a][b].min_d = ins_min_d;
net_ali->cell[a][b].back_a = a;
net_ali->cell[a][b].back_b = ins_min_ind_b;
}
if (db >= 15)
printf(" Min_d=%4.2f back_a=%d back_b=%d
",
net_ali->cell[a][b].min_d,
net_ali->cell[a][b].back_a,
net_ali->cell[a][b].back_b);
if (db >= 15) printf("
");
}
}
}
void cleanup_NET_ALIGN(void){
char *proc="cleanup_NET_ALIGN";
if (db >= 1) printf("Entering %s:
",proc);
Network_dpalign((NETWORK *)0,(NETWORK *)0, 0, (PATH **)0, 0);
}
static int setup_NET_ALIGN(NET_ALIGN **net_ali,NETWORK *net_a,NETWORK *net_b){
char *proc="setup_NET_ALIGN";
/* make sure there is enough room in the data structure */
if (((*net_ali) = alloc_NET_ALIGN((*net_ali),net_a->arc_count,
net_b->arc_count)) == NET_ALIGN_NULL){
fprintf(stderr,"%s: alloc_NET_ALIGN failed
",proc);
return(1);
}
/* link the arcs into the structure */
Network_traverse(net_a,0,0,add_to_arcset,(void *)&((*net_ali)->arcset_a),
NT_CA_For + NT_Inorder);
Network_traverse(net_b,0,0,add_to_arcset,(void *)&((*net_ali)->arcset_b),
NT_CA_For + NT_Inorder);
/* initialize the [0][0] Cell */
(*net_ali)->cell[0][0].back_a = -1;
(*net_ali)->cell[0][0].back_b = -1;
(*net_ali)->cell[0][0].min_d = 0.0;
if (db >= 15) dump_NET_ALIGN((*net_ali),stdout);
return(0);
}
PATH *extract_NET_ALIGN_result(NET_ALIGN *net_ali,NETWORK *net_a,NETWORK *net_b, int include_nulls){
PATH *t_path;
ARC_LIST_ATOM *arcpa, *arcpb;
int back_path, min_a, min_b, hops;
int a, b;
int arc_a_id, arc_b_id;
float min_arc_d;
/*********************************/
/* Beginning Back Trace */
/* Find the minimal network termination node, */
/* !!!! It's not just max x,y any more !!!!*/
min_arc_d = 999999.9;
a = b = -1;
for (arcpa = net_a->stop_node->in_arcs; arcpa != NULL;arcpa =arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,
net_ali->arcset_a.num)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
for (arcpb = net_b->stop_node->in_arcs; arcpb != NULL;
arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),arcpb->arc,
net_ali->arcset_b.num)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (min_arc_d > net_ali->cell[arc_a_id][arc_b_id].min_d){
min_arc_d = net_ali->cell[arc_a_id][arc_b_id].min_d;
a = arc_a_id; b = arc_b_id;
}
}
}
min_a = a;
min_b = b;
{if (getenv("DBL") != NULL) { db=(int)atof(getenv("DBL")); }}
if (db >= 25) dump_NET_ALIGN(net_ali,stdout);
/* first do a back trace, counting the hops */
a = min_a ; b = min_b; hops = 0;
while (a > 0 || b > 0){
int la, lb;
if (db >= 15)
printf("Counting hops a=%d b=%d %d,%d
",a,b,
net_ali->cell[a][b].back_b,net_ali->cell[a][b].back_a);
hops ++;
/* check for an insertion of "@", and ignore it */
if (b == net_ali->cell[a][b].back_b) {
if (!include_nulls &&
net_a->arc_func.is_null_alt(net_ali->arcset_a.arcs[a]->data)){
if (db >= 15) printf("Insertion of nulls
");
hops --;
}
} else if (a == net_ali->cell[a][b].back_a) {
/* check for a deletion of "@", and ignore it */
if (!include_nulls &&
net_b->arc_func.is_null_alt(net_ali->arcset_b.arcs[b]->data)){
if (db >= 15) printf("deletion of null
");
hops --;
}
} else {
/* check for a substitution of "@", and ignore it */
if (!include_nulls &&
(net_a->arc_func.is_null_alt(net_ali->arcset_a.arcs[a]->data))&&
(net_b->arc_func.is_null_alt(net_ali->arcset_b.arcs[b]->data))){
printf("substition of to nulls
");
hops --;
}
}
la = a; lb = b;
a = net_ali->cell[la][lb].back_a;
b = net_ali->cell[la][lb].back_b;
}
a = min_a ; b = min_b;
if (db >= 10)
printf("Minimal Start point: D(%d,%d) = %f hops(%d)
",
a,b,min_arc_d,hops);
t_path = PATH_alloc(hops);
back_path = hops - 1;
a = min_a ; b = min_b;
while (a > 0 || b > 0){
int la, lb;
enum edits back;
back = (a == net_ali->cell[a][b].back_a) ? INS :
((b == net_ali->cell[a][b].back_b) ? DEL : SUB);
switch (back){
case DEL:
if (include_nulls ||
!net_a->arc_func.is_null_alt(net_ali->arcset_a.arcs[a]->data)){
if (! net_a->arc_func.is_opt_del(net_ali->arcset_a.arcs[a]->data)){
t_path->pset[back_path].a_ptr = net_ali->arcset_a.arcs[a]->data;
net_a->arc_func.use_count(net_ali->arcset_a.arcs[a]->data,1);
t_path->pset[back_path].b_ptr = (void *)0;
if (db >= 15){
printf("Del %d %d
",a,b);
print_arc(net_ali->arcset_a.arcs[a],0);
printf(" *
");
}
t_path->pset[back_path].eval = P_DEL;
} else {
/**** OPTIONALLY deletable, make it correct */
t_path->pset[back_path].a_ptr = net_ali->arcset_a.arcs[a]->data;
net_a->arc_func.use_count(net_ali->arcset_a.arcs[a]->data,1);
t_path->pset[back_path].b_ptr =
net_a->arc_func.make_empty((void*)0);
if (db >= 15){
printf("Corr Del %d %d
",a,b);
print_arc(net_ali->arcset_a.arcs[a],0);
}
t_path->pset[back_path].eval = P_CORR;
}
--back_path; t_path->num ++;
}
break;
case SUB:
if(include_nulls ||
!(net_b->arc_func.is_null_alt(net_ali->arcset_a.arcs[a]->data)&&
net_b->arc_func.is_null_alt(net_ali->arcset_b.arcs[b]->data))){
t_path->pset[back_path].a_ptr = net_ali->arcset_a.arcs[a]->data;
net_a->arc_func.use_count(net_ali->arcset_a.arcs[a]->data,1);
t_path->pset[back_path].b_ptr = net_ali->arcset_b.arcs[b]->data;
net_a->arc_func.use_count(net_ali->arcset_b.arcs[b]->data,1);
if (db >= 15){
printf("Sub %d %d
",a,b);
print_arc(net_ali->arcset_a.arcs[a],0);
print_arc(net_ali->arcset_b.arcs[b],0);
}
if (net_a->arc_func.equal(t_path->pset[back_path].a_ptr,
t_path->pset[back_path].b_ptr) == 0)
t_path->pset[back_path].eval = P_CORR;
else
t_path->pset[back_path].eval = P_SUB;
--back_path; t_path->num ++;
}
break;
case INS:
if (include_nulls ||
!net_b->arc_func.is_null_alt(net_ali->arcset_b.arcs[b]->data)){
if (! net_b->arc_func.is_opt_del(net_ali->arcset_b.arcs[b]->data)){
t_path->pset[back_path].a_ptr = (void *)0;
t_path->pset[back_path].b_ptr = net_ali->arcset_b.arcs[b]->data;
net_a->arc_func.use_count(net_ali->arcset_b.arcs[b]->data,1);
if (db >= 15){
printf("INS %d %d
",a,b);
printf(" *
");
print_arc(net_ali->arcset_b.arcs[b],0);
}
t_path->pset[back_path].eval = P_INS;
} else {
t_path->pset[back_path].a_ptr =
net_b->arc_func.make_empty((void*)0);
t_path->pset[back_path].b_ptr = net_ali->arcset_b.arcs[b]->data;
net_a->arc_func.use_count(net_ali->arcset_b.arcs[b]->data,1);
if (db >= 15){
printf("CORR INS %d %d
",a,b);
printf(" *
");
print_arc(net_ali->arcset_b.arcs[b],0);
}
t_path->pset[back_path].eval = P_CORR;
}
--back_path; t_path->num ++;
}
}
la = a;
lb = b;
a = net_ali->cell[la][lb].back_a;
b = net_ali->cell[la][lb].back_b;
}
return(t_path);
}
int Network_dpalign(NETWORK *net_a,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *)), PATH **out_path, int include_nulls){
char *proc = "Network_dpalign";
int prev_db;
prev_db = db;
if (getenv("NET_DP_DBL") != NULL) { db=(int)atof(getenv("NET_DP_DBL")); }
if (db >= 1) printf("Entering %s:
%s",proc,proc);
if (net_a == (NETWORK *)0 && net_b == (NETWORK *)0){
if (db >= 1) printf("destroying %s's data
",proc);
destroy_NET_ALIGN(&net_ali);
return (1);
}
/* Add Null words to the beginning of Net A and B */
if (add_null_network_heads(net_a,proc) != 0) return(1);
if (add_null_network_heads(net_b,proc) != 0) return(1);
if (setup_NET_ALIGN(&net_ali,net_a,net_b) != 0)
return(1);
calculate_margin_cells(net_ali,net_a,net_b,wwd);
calculate_internal_cells(net_ali,net_a,net_b,wwd);
if (db >= 15) dump_NET_ALIGN(net_ali,stdout);
*out_path = extract_NET_ALIGN_result(net_ali, net_a, net_b, include_nulls);
db=prev_db;
return(0);
}
int Network_dpalign_n_networks(NETWORK **in_nets, int n_nets, float wwd(void *, void *, int (*cmp)(void *, void *)), NETWORK **out_net, void *null_alt){
char *proc = "Network_dpalign_n_networks";
NETWORK **copy_in_nets;
int new_db = db, n, rtn=0;
if (getenv("NET_DP_DBL") != NULL)
new_db =(int)atof(getenv("NET_DP_DBL"));
alloc_singZ(copy_in_nets,n_nets,NETWORK *,(NETWORK *)0);
if (new_db >= 1) printf("Entering %s:
",proc);
/* make a copy of the networks and align to those. This allows */
/* the return network function to work from the copy to make the */
/* output network */
for (n=0; n<n_nets; n++){
if ((copy_in_nets[n] = Network_copy(in_nets[n])) == (NETWORK *)0){
fprintf(scfp,"Error: %s unable to copy networks
",proc);
goto ERROR;
}
if (add_null_network_heads(copy_in_nets[n],proc) != 0) {
goto ERROR;
}
if (new_db >= 10) {
printf("%s: ----------------------------------------
",proc);
printf("%s: Input network %d
",proc,n);
if (n == 0) printf("%s: STARTING OUTPUT NETOWRK
",proc);
Network_traverse(copy_in_nets[n],0,0,print_arc,0,
NT_CA_For+NT_Verbose);
}
}
if (new_db >= 10)
printf("%s: ----------------------------------------
",proc);
/* now loop through the networks, aligning them, then merging them */
for (n=1; n<n_nets; n++){
if (setup_NET_ALIGN(&net_ali,copy_in_nets[0],copy_in_nets[n]) != 0){
goto ERROR;
}
calculate_margin_cells(net_ali,copy_in_nets[0],copy_in_nets[n],wwd);
calculate_internal_cells(net_ali,copy_in_nets[0],copy_in_nets[n],wwd);
if (new_db >= 15) dump_NET_ALIGN(net_ali,stdout);
create_alinged_NETWORK(net_ali,copy_in_nets[0],copy_in_nets[n],
null_alt,n);
if (new_db >= 10) {
printf("%s: ----------------------------------------
",proc);
printf("%s: Output Network %d
",proc,n);
Network_traverse(copy_in_nets[0],0,0,print_arc,0,
NT_CA_For+NT_Verbose);
}
}
Network_delete_null_arcs(copy_in_nets[0]);
*out_net = copy_in_nets[0];
rtn = 0;
goto CLEANUP;
ERROR:
rtn = 1;
CLEANUP:
for (n=1; n<n_nets; n++)
Network_destroy(copy_in_nets[n]);
free_singarr(copy_in_nets,NETWORK *);
return(rtn);
}
/*** THIS CODE MAKES THE ASSUMPTION THE net_b network is a linear network */
/*** without branching */
void create_alinged_NETWORK(NET_ALIGN *net_ali, NETWORK *net_a, NETWORK *net_b, void *null_alt, int iteration){
char *proc = "create_alinged_NETWORK";
ARC_LIST_ATOM *arcpa, *arcpb;
void *copy_b_arc_data;
int min_a, min_b;
int a, b, i;
int arc_a_id, arc_b_id;
float min_arc_d;
int new_db = 0;
if (getenv("ALIGN_NET_DBL") != NULL)
new_db=(int)atof(getenv("ALIGN_NET_DBL"));
if (new_db >= 10) printf("Entering %s:
",proc);
/* Find the minimal network termination node, */
/* !!!! It's not just max x,y any more !!!!*/
min_arc_d = 999999.9;
a = b = -1;
for (arcpa = net_a->stop_node->in_arcs; arcpa != NULL;arcpa =arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,
net_ali->arcset_a.num)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
for (arcpb = net_b->stop_node->in_arcs; arcpb != NULL;
arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),arcpb->arc,
net_ali->arcset_b.num)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (min_arc_d > net_ali->cell[arc_a_id][arc_b_id].min_d){
min_arc_d = net_ali->cell[arc_a_id][arc_b_id].min_d;
a = arc_a_id; b = arc_b_id;
}
}
}
min_a = a;
min_b = b;
/*******************************************************************/
/* Beginning the Back Trace copying the B-arcs onto A_net */
if (new_db >= 10)
printf("Minimal Start point: D(%d,%d) = %f
",min_a,min_b,min_arc_d);
a = min_a ; b = min_b;
while (a > 0 || b > 0){
int la = a, lb = b;
ARC *a_arc, *b_arc;
enum edits back;
back = (a == net_ali->cell[a][b].back_a) ? INS :
((b == net_ali->cell[a][b].back_b) ? DEL : SUB);
b_arc = net_ali->arcset_b.arcs[b];
a_arc = net_ali->arcset_a.arcs[a];
switch (back){
case SUB:
/* insert a copy the B_arc onto the from_node and to_node of the
A_arc */
if (new_db >= 10){
printf("%s: SUB
",proc);
printf("%s: Insert copy of B_arc",proc);
print_arc(b_arc,stdout);
printf("%s: between A_arcs(from)",proc);
print_node(a_arc->from_node,stdout);
printf("%s: A_arcs(to) ",proc);
print_node(a_arc->to_node,stdout);
}
if (NETWORK_insert_arc_between_node(net_a, a_arc->from_node,
a_arc->to_node,
b_arc->net->arc_func.copy(b_arc->data)) != 0)
goto ERROR;
break;
case DEL:
/* insert a @ arc onto the from_node and to_node of the A_arc */
if (new_db >= 10){
printf("%s: DEL
",proc);
printf("%s: Insert copy of null_alt
",proc);
printf("%s: between A_arcs(from)",proc);
print_node(a_arc->from_node,stdout);
printf("%s: A_arcs(to) ",proc);
print_node(a_arc->to_node,stdout);
}
if (NETWORK_insert_arc_between_node(net_a, a_arc->from_node,
a_arc->to_node,
a_arc->net->arc_func.copy(null_alt)) != 0)
goto ERROR;
break;
case INS:
/* insert a subnetwork of { @ / B_arc } onto the from_node */
/* and to_node of the A_arc, There will be 'iteration' @'s */
/* inside this network */
if (new_db >= 10){
printf("%s: INS
",proc);
printf("%s: Insert a subnet with %d null arcs and a "
"copy of b_arc
",proc,iteration);
printf("%s: Insert copy of B_arc",proc);
print_arc(b_arc,stdout);
printf("%s: At A_arcs(to_node) ",proc);
print_node(a_arc->to_node,stdout);
}
/* first, insert the copy of b_arc's data into the A_net */
copy_b_arc_data = a_arc->net->arc_func.copy(b_arc->data);
if (NETWORK_insert_arc_before_node(a_arc->net,
a_arc->to_node,
copy_b_arc_data) != 0)
goto ERROR;
/* Find, in A_net, the new arc */
for (arcpa = a_arc->to_node->out_arcs; arcpa != NULL;
arcpa = arcpa->next)
if (arcpa->arc->data == copy_b_arc_data){
break;
}
if (arcpa == NULL){
fprintf(scfp,"Internal Error
");
goto ERROR;
}
for (i=0; i<iteration; i++)
if (NETWORK_insert_arc_between_node(arcpa->arc->net,
arcpa->arc->from_node,
arcpa->arc->to_node,
a_arc->net->arc_func.copy(null_alt)) != 0)
goto ERROR;
break;
}
la = a; lb = b;
a = net_ali->cell[la][lb].back_a; b = net_ali->cell[la][lb].back_b;
}
goto CLEANUP;
ERROR:
printf("ERROR OCCURED
");
CLEANUP:
return;
}
void dump_NET_ALIGN(NET_ALIGN *net_ali,FILE *fp){
int aa, bb;
printf("Dump of net_ali:
");
printf("
Arc List from Network A
");
for (aa=0; aa<net_ali->arcset_a.num; aa++){
printf(" %2d: ",aa);
print_arc(net_ali->arcset_a.arcs[aa],0);
}
printf("
Arc List from Network B
");
for (bb=0; bb<net_ali->arcset_b.num; bb++){
printf(" %2d: ",bb);
print_arc(net_ali->arcset_b.arcs[bb],0);
}
printf("
");
for (bb=0; bb<net_ali->arcset_b.num; bb++)
printf(" %3d ",bb);
printf("
");
for (aa=0; aa<net_ali->arcset_a.num; aa++) {
printf(" %3d ",aa);
for (bb=0; bb<net_ali->arcset_b.num; bb++)
printf("D%6.3f ",net_ali->cell[aa][bb].min_d);
printf("
");
printf(" ");
for (bb=0; bb<net_ali->arcset_b.num; bb++){
if (aa == net_ali->cell[aa][bb].back_a)
printf("I=");
else if (bb == net_ali->cell[aa][bb].back_b)
printf("D=");
else
printf("S=");
printf("%2d,%2d ",net_ali->cell[aa][bb].back_a,
net_ali->cell[aa][bb].back_b);
}
printf("
");
}
}
void alloc_ARCSET(ARCSET *arcset, int n){
arcset->max = n;
arcset->num = 0;
alloc_singarr(arcset->arcs,arcset->max,ARC *);
}
void free_ARCSET(ARCSET *arcset){
arcset->max = 0;
arcset->num = 0;
free_singarr(arcset->arcs,ARC *);
}
static void destroy_NET_ALIGN(NET_ALIGN **net_ali){
char *proc = "destroy_NET_ALIGN";
if (db >= 1) printf("Entering %s:
",proc);
/* free the cell array */
free_2dimarr((*net_ali)->cell,(*net_ali)->arcset_a.max,CELL);
/* the arcsets */
free_ARCSET(&((*net_ali)->arcset_a));
free_ARCSET(&((*net_ali)->arcset_b));
/* the structure */
free_singarr((*net_ali),NET_ALIGN);
*net_ali = (NET_ALIGN *)0;
}
NET_ALIGN *alloc_NET_ALIGN(NET_ALIGN *net_ali, int na, int nb){
char *proc = "alloc_NET_ALIGN";
int alloc_data, init_size=100;
if (db >= 1) printf("Entering %s:
",proc);
if (na < init_size) na = init_size;
if (nb < init_size) nb = init_size;
if (db >= 2)
printf("NET_ALIGN: %p na=%d nb=%d
",net_ali,na,nb);
if (net_ali == NET_ALIGN_NULL) {
/* do the first initialization */
alloc_singarr(net_ali,1,NET_ALIGN);
alloc_data = T;
} else if (net_ali->arcset_a.max < na || net_ali->arcset_b.max < nb) {
/* Then ... Re-allocate the structure */
if (db >= 5)
printf("%s: Free-ing previous data structure
",proc);
/* free the old memory */
free_2dimarr(net_ali->cell,net_ali->arcset_a.max,CELL);
free_ARCSET(&(net_ali->arcset_a));
free_ARCSET(&(net_ali->arcset_b));
alloc_data = T;
} else
alloc_data = F;
if (alloc_data){
alloc_ARCSET(&(net_ali->arcset_a),(int)(na * 1.05));
alloc_ARCSET(&(net_ali->arcset_b),(int)(nb * 1.05));
alloc_2dimarr(net_ali->cell,
net_ali->arcset_a.max,net_ali->arcset_b.max,CELL);
}
/* erase the data cells and arcs */
#ifdef full
clear_sing(net_ali->arcset_a.arcs,net_ali->arcset_a.max,(ARC *)0);
clear_sing(net_ali->arcset_b.arcs,net_ali->arcset_b.max,(ARC *)0);
for (a=0; a<net_ali->arcset_a.max; a++)
for (b=0; b<net_ali->arcset_b.max; b++){
c = &(net_ali->cell[a][b]);
c->min_d = 0.0;
c->back_a = c->back_b = 0;
}
#endif
net_ali->arcset_a.num = 0;
net_ali->arcset_b.num = 0;
return(net_ali);
}
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
PATH *extract_best_NET_ALIGN_result(NET_ALIGN *net_ali,NETWORK *net_a,NETWORK *net_b,float wwd(void *, void *, int (*cmp)(void *, void *))){
ARC_LIST_ATOM *arcpa, *arcpb;
int min_a, min_b, hops=0;
int a, b;
int arc_a_id, arc_b_id;
float min_arc_d;
int r=0, count=0;
PATH *path;
path = PATH_alloc(100);
/*********************************/
/* Beginning Back Trace */
/* Find the minimal network termination node, */
/* !!!! It's not just max x,y any more !!!!*/
min_arc_d = 999999.9;
a = b = -1;
for (arcpa = net_a->stop_node->in_arcs; arcpa != NULL;arcpa =arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,
net_ali->arcset_a.num)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
for (arcpb = net_b->stop_node->in_arcs; arcpb != NULL;
arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),arcpb->arc,
net_ali->arcset_b.num)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (min_arc_d > net_ali->cell[arc_a_id][arc_b_id].min_d){
min_arc_d = net_ali->cell[arc_a_id][arc_b_id].min_d;
a = arc_a_id; b = arc_b_id;
}
}
}
min_a = a;
min_b = b;
/*
dump_NET_ALIGN(net_ali,stdout);
*/
for (arcpa = net_a->stop_node->in_arcs; arcpa != NULL;arcpa =arcpa->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),arcpa->arc,
net_ali->arcset_a.num)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
for (arcpb = net_b->stop_node->in_arcs; arcpb != NULL;
arcpb = arcpb->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),arcpb->arc,
net_ali->arcset_b.num)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (min_arc_d == net_ali->cell[arc_a_id][arc_b_id].min_d){
printf("Minimal Start point: D(%d,%d) = %f hops(%d)
",
arc_a_id,arc_b_id,min_arc_d,hops);
find_minimal_paths(net_ali,arc_a_id,arc_b_id,
&r,wwd, net_a, path,&count);
printf("Count = %d
",count);
(count) = 0;
}
}
}
db = 0;
return((PATH *)0);
}
void find_minimal_paths(NET_ALIGN *net_ali, int a, int b, int *rlev,float wwd(void *, void *, int (*cmp)(void *, void *)),NETWORK *net_a, PATH *path,int *count)
{
ARC_LIST_ATOM *oarc_a, *oarc_b;
ARC *arc_a, *arc_b;
int la, lb, cost;
int arc_a_id, arc_b_id,d;
int db = 0;
char buf[100];
sprintf(buf,rsprintf("%%0%ds",*rlev),"");
if (a == 0 && b == 0){
if (db > 5) printf("END recursion
");
if (db > 2) {
printf("Count = %d
",*count);
PATH_print(path,stdout,100);
}
(*count)++;
return;
}
arc_a = net_ali->arcset_a.arcs[a];
arc_b = net_ali->arcset_b.arcs[b];
cost = net_ali->cell[a][b].min_d;
if (db > 5){
printf("%sCurrent position: D(%d,%d) = %d
",buf,a,b,cost);
printf("%s ",buf); print_arc(arc_a,0);
printf("%s ",buf); print_arc(arc_b,0);
}
/* loop through the net A in_arcs, seaching for possible paths */
for (oarc_a = arc_a->from_node->in_arcs; oarc_a != NULL;
oarc_a=oarc_a->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),oarc_a->arc,
a)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
if (db > 5) {
printf("%s Checking deletion arcs:
",buf);
printf("%s A:",buf); print_arc(oarc_a->arc,0);
}
if (net_ali->cell[arc_a_id][b].min_d <= cost &&
(wwd(arc_a->data,NULL_WORD,net_a->arc_func.equal) +
net_ali->cell[arc_a_id][b].min_d) <= cost){
if (db > 5) printf("%s Possible PATH
",buf);
if (db > 5) printf("%s ***** Delete %s
",buf,
((WORD*)(arc_b->data))->value);
*rlev += 2;
PATH_append(path,arc_a->data,0,P_DEL);
find_minimal_paths(net_ali,arc_a_id,b,rlev,wwd,net_a,path,count);
PATH_remove(path);
*rlev -= 2;
}
}
for (oarc_b = arc_b->from_node->in_arcs; oarc_b != NULL;
oarc_b = oarc_b->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),oarc_b->arc,
b)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (db > 5) {
printf("%s Checking insertion arcs:
",buf);
printf("%s B:",buf); print_arc(oarc_b->arc,0);
}
if (net_ali->cell[a][arc_b_id].min_d <= cost &&
(wwd(NULL_WORD,arc_b->data,net_a->arc_func.equal) +
net_ali->cell[a][arc_b_id].min_d) <= cost){
if (db > 5) printf("%s Possible PATH
",buf);
if (db > 5) printf("%s ***** Insert %s
",buf,
((WORD*)(arc_b->data))->value);
*rlev += 2;
PATH_append(path,0,arc_b->data,P_INS);
find_minimal_paths(net_ali,a,arc_b_id,rlev,wwd,net_a,path,count);
PATH_remove(path);
*rlev -= 2;
}
}
for (oarc_a = arc_a->from_node->in_arcs; oarc_a != NULL;
oarc_a=oarc_a->next){
if ((arc_a_id = find_arcset_id(&(net_ali->arcset_a),oarc_a->arc,
a)) <0){
fprintf(stderr,"Error: find_arcset_id for Net A failed
");
exit(1);
}
for (oarc_b = arc_b->from_node->in_arcs; oarc_b != NULL;
oarc_b = oarc_b->next){
if ((arc_b_id = find_arcset_id(&(net_ali->arcset_b),oarc_b->arc,
b)) < 0){
fprintf(stderr,"Error: find_arcset_id for Net B failed
");
exit(1);
}
if (db > 5) {
printf("%s Checking substitution arcs: (%d,%d)
",buf,
arc_a_id,arc_b_id);
printf("%s A:",buf); print_arc(oarc_a->arc,0);
printf("%s B:",buf); print_arc(oarc_b->arc,0);
}
if (net_ali->cell[arc_a_id][arc_b_id].min_d <= cost &&
((d=wwd(arc_a->data,arc_b->data,net_a->arc_func.equal)) +
net_ali->cell[arc_a_id][arc_b_id].min_d) <= cost){
if (db > 5){
printf("%s Possible PATH
",buf);
printf("%s ***** Substitute %s and %s
",buf,
((WORD*)(arc_a->data))->value,
((WORD*)(arc_b->data))->value);
}
*rlev += 2;
PATH_append(path,arc_a->data,arc_b->data,(d==0)?P_CORR:P_SUB);
find_minimal_paths(net_ali,arc_a_id,arc_b_id,rlev,wwd,net_a,path,count);
PATH_remove(path);
*rlev -= 2;
}
}
}
la = a; lb = b;
a = net_ali->cell[la][lb].back_a;
b = net_ali->cell[la][lb].back_b;
}
|