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Remove dead tree apis #1936

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merged 1 commit into from
Nov 24, 2021
Merged

Remove dead tree apis #1936

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3 changes: 0 additions & 3 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -74,16 +74,13 @@ check_trees_identical(tsk_tree_t *self, tsk_tree_t *other)
CU_ASSERT_EQUAL_FATAL(self->num_samples == NULL, other->num_samples == NULL)
CU_ASSERT_EQUAL_FATAL(
self->num_tracked_samples == NULL, other->num_tracked_samples == NULL)
CU_ASSERT_EQUAL_FATAL(self->marked == NULL, other->marked == NULL)
if (self->num_samples != NULL) {
CU_ASSERT_FATAL(tsk_memcmp(self->num_samples, other->num_samples,
N * sizeof(*self->num_samples))
== 0);
CU_ASSERT_FATAL(tsk_memcmp(self->num_tracked_samples, other->num_tracked_samples,
N * sizeof(*self->num_tracked_samples))
== 0);
CU_ASSERT_FATAL(
tsk_memcmp(self->marked, other->marked, N * sizeof(*self->marked)) == 0);
}

CU_ASSERT_EQUAL_FATAL(self->left_sample == NULL, other->left_sample == NULL)
Expand Down
63 changes: 3 additions & 60 deletions c/tskit/trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3263,9 +3263,7 @@ tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t
if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
self->num_samples = tsk_calloc(N, sizeof(*self->num_samples));
self->num_tracked_samples = tsk_calloc(N, sizeof(*self->num_tracked_samples));
self->marked = tsk_calloc(N, sizeof(*self->marked));
if (self->num_samples == NULL || self->num_tracked_samples == NULL
|| self->marked == NULL) {
if (self->num_samples == NULL || self->num_tracked_samples == NULL) {
goto out;
}
}
Expand Down Expand Up @@ -3321,7 +3319,6 @@ tsk_tree_free(tsk_tree_t *self)
tsk_safe_free(self->right_sib);
tsk_safe_free(self->num_samples);
tsk_safe_free(self->num_tracked_samples);
tsk_safe_free(self->marked);
tsk_safe_free(self->left_sample);
tsk_safe_free(self->right_sample);
tsk_safe_free(self->next_sample);
Expand Down Expand Up @@ -3442,52 +3439,6 @@ tsk_tree_track_descendant_samples(tsk_tree_t *self, tsk_id_t node)
return ret;
}

/* TODO REMOVE ME */
int TSK_WARN_UNUSED
tsk_tree_set_tracked_samples_from_sample_list(
tsk_tree_t *self, tsk_tree_t *other, tsk_id_t node)
{
int ret = TSK_ERR_GENERIC;
tsk_id_t u, stop, index;
const tsk_id_t *next = other->next_sample;
const tsk_id_t *samples = other->tree_sequence->samples;
tsk_size_t num_tracked_samples = 0;

if (!tsk_tree_has_sample_lists(other)) {
ret = TSK_ERR_UNSUPPORTED_OPERATION;
goto out;
}
/* TODO This is not needed when the tree is new. We should use the
* state machine to check and only reset the tracked samples when needed.
*/
ret = tsk_tree_reset_tracked_samples(self);
if (ret != 0) {
goto out;
}

index = other->left_sample[node];
if (index != TSK_NULL) {
stop = other->right_sample[node];
while (true) {
u = samples[index];
num_tracked_samples++;
tsk_bug_assert(self->num_tracked_samples[u] == 0);
/* Propagate this upwards */
while (u != TSK_NULL) {
self->num_tracked_samples[u] += 1;
u = self->parent[u];
}
if (index == stop) {
break;
}
index = next[index];
}
}
self->num_tracked_samples[self->virtual_root] = num_tracked_samples;
out:
return ret;
}

int TSK_WARN_UNUSED
tsk_tree_copy(const tsk_tree_t *self, tsk_tree_t *dest, tsk_flags_t options)
{
Expand Down Expand Up @@ -3527,7 +3478,6 @@ tsk_tree_copy(const tsk_tree_t *self, tsk_tree_t *dest, tsk_flags_t options)
tsk_memcpy(dest->num_samples, self->num_samples, N * sizeof(*self->num_samples));
tsk_memcpy(dest->num_tracked_samples, self->num_tracked_samples,
N * sizeof(*self->num_tracked_samples));
tsk_memcpy(dest->marked, self->marked, N * sizeof(*self->marked));
}
if (dest->options & TSK_SAMPLE_LISTS) {
if (!(self->options & TSK_SAMPLE_LISTS)) {
Expand Down Expand Up @@ -3984,8 +3934,8 @@ tsk_tree_print_state(const tsk_tree_t *self, FILE *out)
(long long) self->right_sample[j]);
}
if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
fprintf(out, "\t%lld\t%lld\t%lld", (long long) self->num_samples[j],
(long long) self->num_tracked_samples[j], (long long) self->marked[j]);
fprintf(out, "\t%lld\t%lld", (long long) self->num_samples[j],
(long long) self->num_tracked_samples[j]);
}
fprintf(out, "\n");
}
Expand Down Expand Up @@ -4107,8 +4057,6 @@ tsk_tree_remove_edge(tsk_tree_t *self, tsk_id_t p, tsk_id_t c)
tsk_id_t *restrict parent = self->parent;
tsk_size_t *restrict num_samples = self->num_samples;
tsk_size_t *restrict num_tracked_samples = self->num_tracked_samples;
uint8_t *restrict marked = self->marked;
const uint8_t mark = self->mark;
const tsk_size_t root_threshold = self->root_threshold;
tsk_id_t u;
tsk_id_t path_end = TSK_NULL;
Expand All @@ -4126,7 +4074,6 @@ tsk_tree_remove_edge(tsk_tree_t *self, tsk_id_t p, tsk_id_t c)
path_end_was_root = POTENTIAL_ROOT(u);
num_samples[u] -= num_samples[c];
num_tracked_samples[u] -= num_tracked_samples[c];
marked[u] = mark;
u = parent[u];
}

Expand All @@ -4149,8 +4096,6 @@ tsk_tree_insert_edge(tsk_tree_t *self, tsk_id_t p, tsk_id_t c)
tsk_id_t *restrict parent = self->parent;
tsk_size_t *restrict num_samples = self->num_samples;
tsk_size_t *restrict num_tracked_samples = self->num_tracked_samples;
uint8_t *restrict marked = self->marked;
const uint8_t mark = self->mark;
const tsk_size_t root_threshold = self->root_threshold;
tsk_id_t u;
tsk_id_t path_end = TSK_NULL;
Expand All @@ -4165,7 +4110,6 @@ tsk_tree_insert_edge(tsk_tree_t *self, tsk_id_t p, tsk_id_t c)
path_end_was_root = POTENTIAL_ROOT(u);
num_samples[u] += num_samples[c];
num_tracked_samples[u] += num_tracked_samples[c];
marked[u] = mark;
u = parent[u];
}

Expand Down Expand Up @@ -4445,7 +4389,6 @@ tsk_tree_clear(tsk_tree_t *self)

if (sample_counts) {
tsk_memset(self->num_samples, 0, N * sizeof(*self->num_samples));
tsk_memset(self->marked, 0, N * sizeof(*self->marked));
/* We can't reset the tracked samples via memset because we don't
* know where the tracked samples are.
*/
Expand Down
9 changes: 0 additions & 9 deletions c/tskit/trees.h
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Original file line number Diff line number Diff line change
Expand Up @@ -182,13 +182,6 @@ typedef struct {
* counts or roots are available. */
tsk_size_t *num_samples;
tsk_size_t *num_tracked_samples;
/* TODO the only place this feature seems to be used is in the ld_calculator.
* when this is being replaced we should come up with a better way of doing
* whatever this is being used for. */
/* All nodes that are marked during a particular transition are marked
* with a given value. */
uint8_t *marked;
uint8_t mark;
/* These are for the optional sample list tracking. */
tsk_id_t *left_sample;
tsk_id_t *right_sample;
Expand Down Expand Up @@ -488,8 +481,6 @@ int tsk_tree_copy(const tsk_tree_t *self, tsk_tree_t *dest, tsk_flags_t options)
int tsk_tree_track_descendant_samples(tsk_tree_t *self, tsk_id_t node);
int tsk_tree_set_tracked_samples(
tsk_tree_t *self, tsk_size_t num_tracked_samples, const tsk_id_t *tracked_samples);
int tsk_tree_set_tracked_samples_from_sample_list(
tsk_tree_t *self, tsk_tree_t *other, tsk_id_t node);

int tsk_tree_get_branch_length(
const tsk_tree_t *self, tsk_id_t u, double *branch_length);
Expand Down