graph_t *mkGraphABCDE()
{
graph_t *g = graph_new(streq);
graph_add_node(g, strdup("A"));
graph_add_node(g, strdup("B"));
graph_add_node(g, strdup("C"));
graph_add_node(g, strdup("D"));
graph_add_node(g, strdup("E"));
return g;
}
graph_s *border_graph(msw_s *ms)
{
graph_s *n = graph_new();
int *r = ms->revealed;
int *graph_perm = malloc(ms->g->nodes * sizeof(int));
int j = 0;
for(int i = 0; i < ms->g->nodes;i++){
if (r[i] == 0){
graph_add_node(n,ms->g->node_list[i]);
graph_perm[i]=j;
j++;
}
}
int neighb;
for(int i = 0; i < ms->g->nodes;i++){
for(int j = 0; j < ms->g->neighb_count[i]; j++){
neighb = ms->g->neighb_list[i][j];
if (r[i] > 0 && r[neighb] == 0){
graph_add_arc(n,graph_perm[neighb],i);
}
}
}
free(graph_perm);
return n;
}
static sexpr sexpr_to_graph (sexpr sx)
{
sexpr g = graph_create ();
sexpr c = car(sx);
while (consp(c))
{
sexpr cx = car (c);
sexpr cxcar = car (cx);
graph_add_node (g, cxcar);
c = cdr (c);
}
c = cdr(sx);
while (consp(c))
{
sexpr cx = car (c);
sexpr cxcar = car (cx);
sexpr cxcdr = cdr (cx);
sexpr cxcadr = car (cxcdr);
sexpr cxcddr = cdr (cxcdr);
struct graph_node *ns = graph_search_node (g, cxcar);
struct graph_node *nt = graph_search_node (g, cxcadr);
if ((ns != (struct graph_node *)0) && (nt != (struct graph_node *)0))
{
graph_node_add_edge (ns, nt, cxcddr);
}
c = cdr (c);
}
c = car(sx);
while (consp(c))
{
sexpr cx = car (c);
sexpr cxcar = car (cx);
sexpr cxcdr = cdr (cx);
struct graph_node *n = graph_search_node (g, cxcar);
if (n != (struct graph_node *)0)
{
n->label = cxcdr;
}
c = cdr (c);
}
return g;
}
/* Abre el archivo `filename` y crea un grafo con la lista de adyacencia
* inscrita en el. Cada linea del archivo debe cumplir la siguiente expresion
* regular (con BL como el BUFFER_LEN): '\d{1,BL}:( \d{1,BL})*\n'
* Retorno: Un grafo G (descrito en structures.h)*/
struct graph *file_to_graph(const char * filename)
{
char ch = '\0',
buffer[BUFFER_LEN] = ""; // Se puede calcular por el nro de lineas.
unsigned int i, id, size, *tmp;
struct list *last_list;
struct node *last_node;
struct graph *G;
FILE *fp = fopen(filename, "r");
if(fp == NULL){
fprintf(stderr,"No se puede leer el archivo \"%s\".\n", filename);
return NULL;
}
size = count_lines(fp);
G = new_graph(size);
IDC = (int*) calloc(size, sizeof(int));
ODC = (int*) malloc(size * sizeof(int));
while (1) {
i = 0;
do {
ch = getc(fp);
if (ch == EOF) {
fclose(fp);
return G;
} else if (ch == ':') {
id = atoi(buffer);
last_list = new_list();
ch = getc(fp);
if (ch == '\n'){
break;
}
i = 0;
memset(buffer, 0, BUFFER_LEN);
} else if (ch == ' ' || ch == '\n') {
tmp = (int *) malloc(sizeof(int));
buffer[i] = '\0';
*tmp = atoi(buffer);
list_add(last_list, tmp);
IDC[*tmp]++;
i = 0;
memset(buffer, 0, BUFFER_LEN);
} else {
buffer[i++] = ch;
}
} while (ch != '\n');
ODC[id] = last_list->size;
last_node = new_node(id, last_list);
graph_add_node(G, last_node);
last_node = NULL;
last_list = NULL;
}
}
int main(int argc, char **argv){
// user didn't specify the input file name containing the graph structure
if(argc != 2){
printf("Usage: ./main <file_name>..\n");
return(1);
}
FILE *fpr = NULL;
char line[LEN];
int i, j, node_value, edges, list_value, weight;
int num_nodes = 8;
graph *gr = NULL;
// graph initialization
gr = graph_init(num_nodes);
if(gr == NULL){
return(1);
}
// open the file again
fpr = open_file(argv[1], "r");
i = 0;
while(fscanf(fpr, "%d %d", &node_value, &edges) != EOF){
gr->nodes[i]->value = node_value;
// read all the node adjacent to the current one
for(j = 0; j<edges; j++){
fscanf(fpr, "%d %d", &list_value, &weight);
gr = graph_add_node(gr, i, list_value, weight);
if(gr == NULL){
return(1);
}
}
i++;
}
fclose(fpr);
//print_graph(gr);
//depth_first_search(gr, 0);
//breadth_first_search(gr);
dijkstra(gr, 0);
for(j=0; j<gr->num_nodes; j++){
printf("Node: %d\tweight: %d\n", gr->nodes[j]->value, gr->nodes[j]->distance);
}
return (0);
}
int main(int argc, char **argv) {
GRAPH *g = graph_new(NODES_MAX);
int i;
names = calloc(NODES_MAX, sizeof(char **));
srand(time(NULL));
for (i = 0; i < NODES_MAX; i++)
graph_add_node(g);
for (i = 0; i < NODES_MAX; i++) {
graph_add_link(g, i, i / 4, 1, 1);
}
fprintf(stderr, "Found %i nodes\n", determine_links(g, 0));
return 0;
}
int
main (void)
{
Graph *test_graph = graph_new ();
GraphNode *a = graph_add_node (test_graph, NULL);
GraphNode *b = graph_add_node (test_graph, NULL);
GraphNode *c = graph_add_node (test_graph, NULL);
GraphNode *c1 = graph_add_node (test_graph, NULL);
GraphNode *c2 = graph_add_node (test_graph, NULL);
GraphNode *c11 = graph_add_node (test_graph, NULL);
GraphNode *d = graph_add_node (test_graph, NULL);
GraphEdge *ab = graph_add_edge (test_graph, a, b, NULL);
GraphEdge *bc = graph_add_edge (test_graph, b, c, NULL);
GraphEdge *cd = graph_add_edge (test_graph, c, d, NULL);
GraphEdge *da = graph_add_edge (test_graph, d, a, NULL);
graph_add_edge (test_graph, c, c1, NULL);
graph_add_edge (test_graph, c1, c11, NULL);
graph_add_edge (test_graph, c, c2, NULL);
graph_dump_by_edges (test_graph, "test_graph.dot", NULL);
GQueue *path;
gboolean result = graph_node_in_cycle (test_graph, a, &path);
g_assert (result);
g_assert (g_queue_peek_head (path) == da);
g_assert (g_queue_peek_nth (path, 1) == cd);
g_assert (g_queue_peek_nth (path, 2) == bc);
g_assert (g_queue_peek_tail (path) == ab);
g_queue_free (path);
exit (EXIT_SUCCESS);
}
int rdis_user_function (struct _rdis * rdis, uint64_t address)
{
// get a tree of all functions reachable at this address
struct _map * functions = loader_function_address(rdis->loader,
rdis->memory,
address);
// add in this address as a new function as well
struct _function * function = function_create(address);
map_insert(functions, function->address, function);
object_delete(function);
// for each newly reachable function
struct _map_it * mit;
for (mit = map_iterator(functions); mit != NULL; mit = map_it_next(mit)) {
struct _function * function = map_it_data(mit);
uint64_t fitaddress = function->address;
// if we already have this function, skip it
if (map_fetch(rdis->functions, function->address) != NULL)
continue;
// add this function to the rdis->function_tree
map_insert(rdis->functions, function->address, function);
// add label
struct _label * label = loader_label_address(rdis->loader,
rdis->memory,
fitaddress);
map_insert(rdis->labels, fitaddress, label);
object_delete(label);
// if this function is already in our graph, all we need to do is make
// sure its a separate node and then remove function predecessors
struct _graph_node * node = graph_fetch_node_max(rdis->graph, fitaddress);
if (node != NULL) {
// already a node, remove function predecessors
if (node->index == address) {
remove_function_predecessors(rdis->graph, rdis->functions);
continue;
}
// search for instruction with given address
struct _list * ins_list = node->data;
struct _list_it * it;
for (it = list_iterator(ins_list); it != NULL; it = it->next) {
struct _ins * ins = it->data;
// found instruction
if (ins->address == fitaddress) {
// create a new instruction list.
// add remaining instructions to new list while removing them from
// the current list
struct _list * new_ins_list = list_create();
while (1) {
list_append(new_ins_list, it->data);
it = list_remove(ins_list, it);
if (it == NULL)
break;
}
// create a new graph node for this new function
graph_add_node(rdis->graph, fitaddress, new_ins_list);
// all graph successors from old node are added to new node
struct _queue * queue = queue_create();
struct _list * successors = graph_node_successors(node);
struct _list_it * sit;
for (sit = list_iterator(successors);
sit != NULL;
sit = sit->next) {
struct _graph_edge * edge = sit->data;
graph_add_edge(rdis->graph,
fitaddress,
edge->tail,
edge->data);
queue_push(queue, edge);
}
object_delete(successors);
// and removed from old node
while (queue->size > 0) {
struct _graph_edge * edge = queue_peek(queue);
graph_remove_edge(rdis->graph, edge->head, edge->tail);
queue_pop(queue);
}
object_delete(queue);
// that was easy
break;
}
}
if (it != NULL)
continue;
}
// we need to create a new graph for this node
struct _graph * graph = loader_graph_address(rdis->loader,
rdis->memory,
fitaddress);
graph_merge(rdis->graph, graph);
object_delete(graph);
}
object_delete(functions);
rdis_callback(rdis, RDIS_CALLBACK_ALL);
return 0;
}
int main(){
struct graph* graph;
struct graph* clone;
char node_desc[NODE_DESCRIPTION_LENGTH];
char edge_desc[EDGE_DESCRIPTION_LENGTH];
struct node* node_asterix;
struct node* node_obelix;
struct node* node_idefix;
struct node* node_abraracourcix;
graph = graph_create(NODE_DESCRIPTION_LENGTH, EDGE_DESCRIPTION_LENGTH);
graph_register_dotPrint_callback(graph, NULL, asterix_dotPrint_node, asterix_dotPrint_edge, NULL)
/* add nodes */
snprintf(node_desc, NODE_DESCRIPTION_LENGTH, "asterix");
node_asterix = graph_add_node(graph, &node_desc);
if (node_asterix == NULL){
log_err("unable to add node to graph");
}
snprintf(node_desc, NODE_DESCRIPTION_LENGTH, "obelix");
node_obelix = graph_add_node(graph, &node_desc);
if (node_obelix == NULL){
log_err("unable to add node to graph");
}
snprintf(node_desc, NODE_DESCRIPTION_LENGTH, "idefix");
node_idefix = graph_add_node(graph, &node_desc);
if (node_idefix == NULL){
log_err("unable to add node to graph");
}
snprintf(node_desc, NODE_DESCRIPTION_LENGTH, "abraracourcix");
node_abraracourcix = graph_add_node(graph, &node_desc);
if (node_abraracourcix == NULL){
log_err("unable to add node to graph");
}
/* add edges */
snprintf(edge_desc, EDGE_DESCRIPTION_LENGTH, "friend");
if (graph_add_edge(graph, node_obelix, node_asterix, &edge_desc) == NULL){
log_err("unable to add edge to graph");
}
snprintf(edge_desc, EDGE_DESCRIPTION_LENGTH, "obey");
if (graph_add_edge(graph, node_idefix, node_obelix, &edge_desc) == NULL){
log_err("unable to add edge to graph");
}
snprintf(edge_desc, EDGE_DESCRIPTION_LENGTH, "rule");
if (graph_add_edge(graph, node_abraracourcix, node_obelix, &edge_desc) == NULL){
log_err("unable to add edge to graph");
}
snprintf(edge_desc, EDGE_DESCRIPTION_LENGTH, "rule");
if (graph_add_edge(graph, node_abraracourcix, node_asterix, &edge_desc) == NULL){
log_err("unable to add edge to graph");
}
clone = graph_clone(graph, asterix_copy_node, asterix_copy_edge, NULL);
graph_delete(graph);
/* print graph */
if (graphPrintDot_print(clone, "asterix.dot", NULL)){
log_err("unable to print graph to dot format");
}
graph_delete(clone);
return 0;
}
static void
handle_graph_message(UiConnection *self, const gchar *command, JsonObject *payload,
SoupWebsocketConnection *ws)
{
g_return_if_fail(payload);
Graph *graph = NULL;
if (g_strcmp0(command, "clear") != 0) {
// All other commands must have graph
// TODO: change FBP protocol to use 'graph' instead of 'id'?
const gchar *graph_id = json_object_get_string_member(payload, "graph");
Network *net = (graph_id) ? g_hash_table_lookup(self->network_map, graph_id) : NULL;
graph = (net) ? net->graph : NULL;
g_return_if_fail(graph);
}
if (g_strcmp0(command, "clear") == 0) {
const gchar *graph_id = json_object_get_string_member(payload, "id");
Graph *graph = graph_new(graph_id, self->component_lib);
Network *network = network_new(graph);
ui_connection_add_network(self, graph_id, network);
} else if (g_strcmp0(command, "addnode") == 0) {
graph_add_node(graph,
json_object_get_string_member(payload, "id"),
json_object_get_string_member(payload, "component")
);
} else if (g_strcmp0(command, "removenode") == 0) {
graph_remove_node(graph,
json_object_get_string_member(payload, "id")
);
} else if (g_strcmp0(command, "changenode") == 0) {
// Just metadata, ignored
} else if (g_strcmp0(command, "addinitial") == 0) {
JsonObject *tgt = json_object_get_object_member(payload, "tgt");
JsonObject *src = json_object_get_object_member(payload, "src");
GValue data = G_VALUE_INIT;
json_node_get_value(json_object_get_member(src, "data"), &data);
graph_add_iip(graph,
json_object_get_string_member(tgt, "node"),
json_object_get_string_member(tgt, "port"),
&data
);
g_value_unset(&data);
} else if (g_strcmp0(command, "removeinitial") == 0) {
JsonObject *tgt = json_object_get_object_member(payload, "tgt");
graph_remove_iip(graph,
json_object_get_string_member(tgt, "node"),
json_object_get_string_member(tgt, "port")
);
} else if (g_strcmp0(command, "addedge") == 0) {
JsonObject *src = json_object_get_object_member(payload, "src");
JsonObject *tgt = json_object_get_object_member(payload, "tgt");
graph_add_edge(graph,
json_object_get_string_member(src, "node"),
json_object_get_string_member(src, "port"),
json_object_get_string_member(tgt, "node"),
json_object_get_string_member(tgt, "port")
);
} else if (g_strcmp0(command, "removeedge") == 0) {
JsonObject *src = json_object_get_object_member(payload, "src");
JsonObject *tgt = json_object_get_object_member(payload, "tgt");
graph_remove_edge(graph,
json_object_get_string_member(src, "node"),
json_object_get_string_member(src, "port"),
json_object_get_string_member(tgt, "node"),
json_object_get_string_member(tgt, "port")
);
} else if (g_strcmp0(command, "changeedge") == 0) {
// Just metadata, ignored
} else {
imgflo_warning("Unhandled message on protocol 'graph', command='%s'", command);
}
}
int main(int argc, char *argv[]) {
int nv, ne, i, ind1, ind2, len;
double mf;
FILE *fp, *fp_meas;
int tt;
char str1[256] = "";
char *sg;
char *ms_f;
char *of;
int legacy = 0;
int ii = 1;
sf *sf;
if (argc < 4) {
printf(
"Usage: exampleProgram nameSizeGraph nameFileValues outputFile \n");
exit(-1);
}
if (argc >= 4){
if (!strcmp("-l",argv[ii])){
legacy = 1;
ii++;
printf("Legacy output mode\n");
}
}
sg = argv[ii++];
ms_f = argv[ii++];
of = argv[ii++];
if ((fp = fopen(sg, "r")) == NULL) {
printf("Error (Reading): unable to open .size!\n");
return (0);
}
if ((fp_meas = fopen(ms_f, "r")) == NULL) {
printf("Error (Reading): unable to open measuring function file!\n");
return (0);
}
tt = fscanf(fp, "%d\n %d\n", &nv, &ne);
Graph *G = new_graph(nv);
for (i = 0; i < nv; i++) {
tt = fscanf(fp_meas, "%lf", &mf);
graph_add_node(G,mf);
}
printf("Done\n");
int x, y;
for (i = 0; i < ne; i++) {
tt = fscanf(fp, "%d %d \n", &ind1, &ind2);
x = ind1;
y = ind2;
add_new_edge_graph(G,x,y);
}
fclose(fp);
fclose(fp_meas);
sf = newDeltaStarReductionAlgorithm(G);
printf("Delta star reduction: done\n");
destroy_graph(G);
write_ang_pt(sf, of, legacy);
printf("Sf printed\n");
sf_destroy(sf);
return 0;
}
/**
* Builds a snp graph from the snps array
*/
graph *graph_from_snps(GapIO *io, snp_t *snp, int nsnps, double c_offset) {
graph *g = NULL;
int i, j;
int ntemplates, *templates = NULL;
node **tmpl_map = NULL;
int lookup[256];
if (verbosity)
puts("Building graph");
/* lookup table for fast base to index conversion */
for (i = 0; i < 256; i++)
lookup[i] = 0;
lookup['A'] = lookup['a'] = 1;
lookup['C'] = lookup['c'] = 2;
lookup['G'] = lookup['g'] = 3;
lookup['T'] = lookup['t'] = 4;
lookup['*'] = 5;
g = graph_create();
g->correlation_offset = c_offset;
/*
* Obtain a list of unique template numbers, by collecting and sorting.
* For each unique template we initialise the graph node.
*
* At the end of this we have ntemplates unique templates and
* tmpl_map[] indexed by Gap4 template number maps us to the
* node in the graph.
*/
for (ntemplates = i = 0; i < nsnps; i++) {
ntemplates += snp[i].nseqs;
}
templates = (int *)malloc(ntemplates * sizeof(int));
for (ntemplates = i = 0; i < nsnps; i++) {
for (j = 0; j < snp[i].nseqs; j++) {
templates[ntemplates++] = snp[i].seqs[j].tmplate;
}
}
tmpl_map = (node **)xcalloc(Ntemplates(io)+1, sizeof(*tmpl_map));
qsort(templates, ntemplates, sizeof(int), int_compare);
for (i = j = 0; i < ntemplates; j++) {
tmpl_map[templates[i]] = graph_add_node(g);
tmpl_map[templates[i]]->number = j;
tmpl_map[templates[i]]->tname =
strdup(get_template_name(io, templates[i]));
do {
i++;
} while (i < ntemplates && templates[i] == templates[i-1]);
}
xfree(templates);
ntemplates = j;
g->nsnps = nsnps;
g->ntemplates = ntemplates;
/*
* The matrix is of size nsnps by ntemplates. It initially will consist
* of entirely empty vectors.
*/
g->matrix = (int (*)[6])malloc(ntemplates * nsnps * sizeof(*g->matrix));
memset(&g->matrix[0][0], 0, ntemplates * nsnps * 6 * sizeof(int));
for (i = j = 0; j < ntemplates; i++) {
if (!tmpl_map[i])
continue;
tmpl_map[i]->matrix = &g->matrix[j * nsnps];
j++;
}
/* Create the snp_score array */
g->snp_scores = (double *)malloc(nsnps * sizeof(*g->snp_scores));
for (i = 0; i < nsnps; i++) {
g->snp_scores[i] = snp[i].score;
}
/* Now add basecalls to the matrix from snp info */
for (i = 0; i < nsnps; i++) {
for (j = 0; j < snp[i].nseqs; j++) {
node *n = tmpl_map[snp[i].seqs[j].tmplate];
n->matrix[i][lookup[snp[i].seqs[j].base]]++;
n->tscore = snp[i].seqs[j].tscore;
/* FIXME: confidence not yet used */
}
for (j = 0; j < ntemplates; j++) {
if (!g->nodes->node[j]->matrix[i][1] &&
!g->nodes->node[j]->matrix[i][2] &&
!g->nodes->node[j]->matrix[i][3] &&
!g->nodes->node[j]->matrix[i][4] &&
!g->nodes->node[j]->matrix[i][5])
g->nodes->node[j]->matrix[i][0]++;
}
}
return g;
}
/*
* This is the initial phase, used to populate the graph with all reachable
* nodes. We will worry about fixing edges from jmp-like mnemonics later.
*/
void x8664_graph_0 (struct _graph * graph,
uint64_t address,
struct _map * memory)
{
ud_t ud_obj;
int continue_disassembling = 1;
uint64_t last_address = -1;
int edge_type = INS_EDGE_NORMAL;
struct _buffer * buffer = map_fetch_max(memory, address);
if (buffer == NULL)
return;
uint64_t base_address = map_fetch_max_key(memory, address);
if (base_address + buffer->size < address)
return;
uint64_t offset = address - base_address;
ud_init (&ud_obj);
ud_set_mode (&ud_obj, 64);
ud_set_syntax(&ud_obj, UD_SYN_INTEL);
ud_set_input_buffer(&ud_obj, &(buffer->bytes[offset]), buffer->size - offset);
while (continue_disassembling == 1) {
size_t bytes_disassembled = ud_disassemble(&ud_obj);
if (bytes_disassembled == 0) {
break;
}
// even if we have already added this node, make sure we add the edge
// from the preceeding node, in case this node was added from a jump
// previously. otherwise we won't have an edge from its preceeding
// instruction
if (graph_fetch_node(graph, address) != NULL) {
if (last_address != -1) {
// not concerned if this call fails
struct _ins_edge * ins_edge = ins_edge_create(edge_type);
graph_add_edge(graph, last_address, address, ins_edge);
object_delete(ins_edge);
}
break;
}
// create graph node for this instruction
struct _ins * ins = x8664_ins(address, &ud_obj);
struct _list * ins_list = list_create();
list_append(ins_list, ins);
graph_add_node(graph, address, ins_list);
object_delete(ins_list);
object_delete(ins);
// add edge from previous instruction to this instruction
if (last_address != -1) {
struct _ins_edge * ins_edge = ins_edge_create(edge_type);
graph_add_edge(graph, last_address, address, ins_edge);
object_delete(ins_edge);
}
// these mnemonics cause us to continue disassembly somewhere else
struct ud_operand * operand;
switch (ud_obj.mnemonic) {
case UD_Ijo :
case UD_Ijno :
case UD_Ijb :
case UD_Ijae :
case UD_Ijz :
case UD_Ijnz :
case UD_Ijbe :
case UD_Ija :
case UD_Ijs :
case UD_Ijns :
case UD_Ijp :
case UD_Ijnp :
case UD_Ijl :
case UD_Ijge :
case UD_Ijle :
case UD_Ijg :
case UD_Ijmp :
case UD_Iloop :
//case UD_Icall :
operand = &(ud_obj.operand[0]);
if (operand->type != UD_OP_JIMM)
break;
if (ud_obj.mnemonic == UD_Icall)
edge_type = INS_EDGE_NORMAL;
else if (ud_obj.mnemonic == UD_Ijmp)
edge_type = INS_EDGE_NORMAL; // not important, will terminate
else
edge_type = INS_EDGE_JCC_FALSE;
if (operand->type == UD_OP_JIMM) {
x8664_graph_0(graph,
address
+ ud_insn_len(&ud_obj)
+ udis86_sign_extend_lval(operand),
memory);
}
break;
default :
edge_type = INS_EDGE_NORMAL;
break;
}
// these mnemonics cause disassembly to stop
switch (ud_obj.mnemonic) {
case UD_Iret :
case UD_Ihlt :
case UD_Ijmp :
continue_disassembling = 0;
break;
default :
break;
}
last_address = address;
address += bytes_disassembled;
}
}
struct _graph * redis_x86_graph (uint64_t address, struct _map * memory)
{
uint64_t next_index = 1;
uint64_t this_index = 0;
uint64_t last_index = 0;
struct _redis_x86 * redis_x86 = redis_x86_create();
redis_x86_mem_from_mem_map(redis_x86, memory);
redis_x86->regs[RED_EIP] = address;
redis_x86_false_stack(redis_x86);
struct _map * ins_map = map_create();
struct _graph * graph = graph_create();
while (redis_x86_step(redis_x86) == REDIS_SUCCESS) {
uint64_t address = redis_x86->ins_addr;
// do we have an instruction at this address already?
struct _index * index = map_fetch(ins_map, address);
// we have an instruction, fetch it, make sure it matches
if (index) {
struct _graph_node * node = graph_fetch_node(graph, index->index);
struct _ins * ins = list_first(node->data);
// instructions diverge, create new instruction
if ( (ins->size != redis_x86->ins_size)
|| (memcmp(ins->bytes, redis_x86->ins_bytes, redis_x86->ins_size))) {
ins = redis_x86_create_ins(redis_x86);
if (ins == NULL) {
fprintf(stderr, "could not create ins, eip=%llx\n",
(unsigned long long) redis_x86->ins_addr);
break;
}
struct _list * list = list_create();
list_append(list, ins);
object_delete(ins);
graph_add_node(graph, next_index, list);
object_delete(list);
map_remove(ins_map, redis_x86->ins_addr);
index = index_create(next_index++);
map_insert(ins_map, redis_x86->ins_addr, index);
this_index = index->index;
object_delete(index);
}
else
this_index = index->index;
}
// no instruction at this address, create it
else {
struct _ins * ins = redis_x86_create_ins(redis_x86);
if (ins == NULL) {
fprintf(stderr, "could not create ins eip=%llx\n",
(unsigned long long) redis_x86->ins_addr);
break;
}
struct _list * list = list_create();
list_append(list, ins);
object_delete(ins);
graph_add_node(graph, next_index, list);
object_delete(list);
index = index_create(next_index++);
map_insert(ins_map, redis_x86->ins_addr, index);
this_index = index->index;
object_delete(index);
}
/*
* create an edge from last index to this index
* because our graph library enforces both the condition that the head
* and tail nodes are valid, and that there exists only one edge per
* head->tail combination, we can blindly add edges here and let the
* graph library work out the details
*/
printf("[edge] %llx -> %llx\n",
(unsigned long long) last_index,
(unsigned long long) this_index);
struct _ins_edge * ins_edge = ins_edge_create(INS_EDGE_NORMAL);
graph_add_edge(graph, last_index, this_index, ins_edge);
object_delete(ins_edge);
last_index = this_index;
printf("%llx -> %llx\n",
(unsigned long long) last_index,
(unsigned long long) this_index);
}
object_delete(ins_map);
object_delete(redis_x86);
return graph;
}
struct _graph * recursive_disassemble (const struct _map * mem_map,
uint64_t entry,
struct _ins * (* ins_callback) (const struct _map *, uint64_t))
{
struct _queue * queue = queue_create();
struct _map * map = map_create();
struct _index * index = index_create(entry);
queue_push(queue, index);
object_delete(index);
while (queue->size > 0) {
struct _index * index = queue_peek(queue);
if (map_fetch(map, index->index)) {
queue_pop(queue);
continue;
}
struct _ins * ins = ins_callback(mem_map, index->index);
if (ins == NULL) {
queue_pop(queue);
continue;
}
map_insert(map, index->index, ins);
struct _list_it * lit;
for (lit = list_iterator(ins->successors); lit != NULL; lit = lit->next) {
struct _ins_value * successor = lit->data;
if (successor->type == INS_SUC_CALL)
continue;
struct _index * index = index_create(successor->address);
queue_push(queue, index);
object_delete(index);
}
queue_pop(queue);
}
object_delete(queue);
// create graph nodes
struct _graph * graph = graph_create();
struct _map_it * mit;
for (mit = map_iterator(map); mit != NULL; mit = map_it_next(mit)) {
graph_add_node(graph, map_it_key(mit), map_it_data(mit));
}
// create graph edges
for (mit = map_iterator(map); mit != NULL; mit = map_it_next(mit)) {
struct _ins * ins = map_it_data(mit);
struct _list_it * lit;
for (lit = list_iterator(ins->successors); lit != NULL; lit = lit->next) {
struct _ins_value * successor = lit->data;
// don't add call edges
if (successor->type == INS_SUC_CALL)
continue;
graph_add_edge(graph, ins->address, successor->address, successor);
}
}
object_delete(map);
return graph;
}
node_t *graph_add_sam(graph_t *g, bam1_t *b, ref_t *ref, int32_t use_threads)
{
bam_aln_t *aln = NULL;
int32_t aln_start, aln_index, ref_index, aln_ref_index;
int32_t i;
node_t *prev_node=NULL, *cur_node=NULL, *ret_node=NULL;
uint8_t type, strand;
aln_start = b->core.pos+1;
aln_ref_index = b->core.tid;
aln = bam_aln_init(b, ref);
strand = bam1_strand(b);
// --- SYNC ON ---
if(1 == use_threads) pthread_mutex_lock(&graph_mutex); // synchronize start
if(aln_start < g->position_start) {
int32_t diff = g->position_start - aln_start;
graph_nodes_realloc(g, g->position_end - aln_start + 1); // alloc more memory if needed
// shift up
for(i=g->position_end-g->position_start;0<=i;i--) {
// swap
node_list_t *list = g->nodes[i+diff];
g->nodes[i+diff] = g->nodes[i];
g->nodes[i] = list;
}
g->position_start = aln_start;
}
if(1 == g->is_empty) {
for(i=0;i<g->position_end - g->position_start + 1;i++) {
node_list_clear(g->nodes[i]);
assert(0 == g->nodes[i]->length); // DEBUG
}
g->position_start = aln_start;
if(ALN_GAP == aln->ref[0]) {
g->position_start--;
}
g->position_end = g->position_start;
g->contig = aln_ref_index + 1;
g->is_empty = 0;
}
if(1 == use_threads) pthread_mutex_unlock(&graph_mutex); // synchronize end
// --- SYNC OFF ---
for(aln_index=0,ref_index=-1;aln_index<aln->length;aln_index++,prev_node=cur_node) {
// Skip over a deletion
while(ALN_GAP == aln->read[aln_index]) {
aln_index++;
ref_index++;
}
if(aln->read[aln_index] == aln->ref[aln_index]) { // match
type = NODE_MATCH;
}
else if(aln->ref[aln_index] == ALN_GAP) { // insertion
type = NODE_INSERTION;
}
else { // mismatch
type = NODE_MISMATCH;
}
if(NULL == prev_node || NODE_INSERTION != __node_type(prev_node)) { // previous was an insertion, already on the position
ref_index++;
}
cur_node = graph_add_node(g,
node_init(aln->read[aln_index], type, g->contig, aln_start + ref_index, prev_node),
prev_node,
use_threads);
if(NULL == prev_node && 0 == strand) { // first node and forward strand
ret_node = cur_node;
}
}
if(1 == strand) {
ret_node = cur_node;
}
bam_aln_free(aln);
return ret_node;
}
