void biosal_assembly_graph_store_set_vertex_flag(struct thorium_actor *self,
struct thorium_message *message)
{
char *buffer;
int count;
int flag;
struct biosal_dna_kmer transport_kmer;
struct biosal_assembly_vertex *vertex;
struct biosal_assembly_graph_store *concrete_self;
struct core_memory_pool *ephemeral_memory;
int position;
concrete_self = thorium_actor_concrete_actor(self);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
biosal_dna_kmer_init_empty(&transport_kmer);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
position = 0;
position += biosal_dna_kmer_unpack(&transport_kmer, buffer, concrete_self->kmer_length,
ephemeral_memory, &concrete_self->transport_codec);
core_memory_copy(&flag, buffer + position, sizeof(flag));
position += sizeof(flag);
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(position, count);
CORE_DEBUGGER_ASSERT(flag >= BIOSAL_VERTEX_FLAG_START_VALUE);
CORE_DEBUGGER_ASSERT(flag <= BIOSAL_VERTEX_FLAG_END_VALUE);
if (flag == BIOSAL_VERTEX_FLAG_UNITIG) {
++concrete_self->unitig_vertex_count;
}
#if 0
printf("DEBUG ACTION_SET_VERTEX_FLAG %d\n", flag);
#endif
vertex = biosal_assembly_graph_store_find_vertex(self, &transport_kmer);
CORE_DEBUGGER_ASSERT_NOT_NULL(vertex);
biosal_dna_kmer_destroy(&transport_kmer, ephemeral_memory);
biosal_assembly_vertex_set_flag(vertex, flag);
thorium_actor_send_reply_empty(self, ACTION_SET_VERTEX_FLAG_REPLY);
}
void biosal_assembly_graph_store_get_vertex(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_vertex vertex;
struct biosal_dna_kmer kmer;
void *buffer;
struct biosal_assembly_graph_store *concrete_self;
struct core_memory_pool *ephemeral_memory;
struct thorium_message new_message;
int new_count;
void *new_buffer;
struct biosal_assembly_vertex *canonical_vertex;
int is_canonical;
int path;
int position;
int count;
path = -1;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
biosal_dna_kmer_init_empty(&kmer);
position = 0;
position += biosal_dna_kmer_unpack(&kmer, buffer, concrete_self->kmer_length,
ephemeral_memory,
&concrete_self->transport_codec);
/*
* Check if a path index was provided too.
*/
if (position < count) {
position += thorium_message_unpack_int(message, position, &path);
}
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(position, count);
CORE_DEBUGGER_ASSERT(position == count);
canonical_vertex = biosal_assembly_graph_store_find_vertex(self, &kmer);
biosal_assembly_vertex_init_copy(&vertex, canonical_vertex);
is_canonical = biosal_dna_kmer_is_canonical(&kmer, concrete_self->kmer_length,
&concrete_self->transport_codec);
if (!is_canonical) {
biosal_assembly_vertex_invert_arcs(&vertex);
}
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
new_count = biosal_assembly_vertex_pack_size(&vertex);
new_buffer = thorium_actor_allocate(self, new_count);
biosal_assembly_vertex_pack(&vertex, new_buffer);
thorium_message_init(&new_message, ACTION_ASSEMBLY_GET_VERTEX_REPLY,
new_count, new_buffer);
thorium_actor_send_reply(self, &new_message);
thorium_message_destroy(&new_message);
}
static void source_receive(struct thorium_actor *self, struct thorium_message *message)
{
int action;
void *buffer;
int leader;
int source;
int count;
struct source *concrete_self;
int name;
concrete_self = (struct source *)thorium_actor_concrete_actor(self);
action = thorium_message_action(message);
buffer = thorium_message_buffer(message);
source = thorium_message_source(message);
name = thorium_actor_name(self);
count = thorium_message_count(message);
if (action == ACTION_ASK_TO_STOP) {
thorium_actor_log(self, "sent %d ACTION_PING messages\n",
concrete_self->message_count);
thorium_actor_send_to_self_empty(self, ACTION_STOP);
} else if (action == ACTION_NOTIFY) {
#ifdef LATENCY_PROBE_USE_MULTIPLEXER
thorium_actor_send_to_self_empty(self, ACTION_ENABLE_MULTIPLEXER);
#endif
CORE_DEBUGGER_ASSERT(core_vector_empty(&concrete_self->targets));
core_vector_unpack(&concrete_self->targets, buffer);
if (source_is_important(self)) {
printf("%d (node %d worker %d) has %d targets\n", thorium_actor_name(self),
thorium_actor_node_name(self),
thorium_actor_worker_name(self),
(int)core_vector_size(&concrete_self->targets));
}
concrete_self->leader = source;
source_send_ping(self);
} else if (action == ACTION_PING_REPLY) {
CORE_DEBUGGER_ASSERT(count == 0);
++concrete_self->message_count;
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(count, 0);
CORE_DEBUGGER_ASSERT_IS_NULL(buffer);
if (concrete_self->message_count % PERIOD == 0 || concrete_self->event_count < 500) {
if (source_is_important(self)) {
printf("progress %d %d/%d\n",
name, concrete_self->message_count, concrete_self->event_count);
}
}
if (concrete_self->message_count == concrete_self->event_count) {
leader = concrete_self->leader;
thorium_actor_send_empty(self, leader, ACTION_NOTIFY_REPLY);
if (source_is_important(self))
printf("%d (ACTION_PING sent: %d)"
" sends ACTION_NOTIFY_REPLY to %d\n", thorium_actor_name(self),
concrete_self->message_count,
leader);
} else {
source_send_ping(self);
}
}
}
