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benjefferybenjeffery
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Takeset indexes
1 parent fd2a4ff commit 37a8f44

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3 files changed

+14
-47
lines changed

3 files changed

+14
-47
lines changed

‎c/tests/test_tables.c

Lines changed: 0 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -451,23 +451,14 @@ test_reference_sequence_take(void)
451451
tsk_reference_sequence_t r1;
452452
tsk_reference_sequence_t r2;
453453
const char *const_data = "data";
454-
const char *const_url = "url";
455-
const char *const_metadata_schema = "metadata_schema";
456454
const char *const_metadata = "metadata";
457455
char *takeset_data = strdup(const_data);
458-
char *takeset_url = strdup(const_url);
459-
char *takeset_metadata_schema = strdup(const_metadata_schema);
460456
char *takeset_metadata = strdup(const_metadata);
461457

462458
ret = tsk_reference_sequence_init(&r1, 0);
463459

464460
ret = tsk_reference_sequence_set_data(&r1, const_data, strlen(const_data));
465461
CU_ASSERT_EQUAL_FATAL(ret, 0);
466-
ret = tsk_reference_sequence_set_url(&r1, const_url, strlen(const_url));
467-
CU_ASSERT_EQUAL_FATAL(ret, 0);
468-
ret = tsk_reference_sequence_set_metadata_schema(
469-
&r1, const_metadata_schema, strlen(const_metadata_schema));
470-
CU_ASSERT_EQUAL_FATAL(ret, 0);
471462
ret = tsk_reference_sequence_set_metadata(
472463
&r1, const_metadata, strlen(const_metadata));
473464
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -478,13 +469,6 @@ test_reference_sequence_take(void)
478469
ret = tsk_reference_sequence_takeset_data(&r2, takeset_data, strlen(takeset_data));
479470
CU_ASSERT_EQUAL_FATAL(ret, 0);
480471
CU_ASSERT_FALSE(tsk_reference_sequence_equals(&r1, &r2, 0));
481-
ret = tsk_reference_sequence_takeset_url(&r2, takeset_url, strlen(takeset_url));
482-
CU_ASSERT_EQUAL_FATAL(ret, 0);
483-
CU_ASSERT_FALSE(tsk_reference_sequence_equals(&r1, &r2, 0));
484-
ret = tsk_reference_sequence_takeset_metadata_schema(
485-
&r2, takeset_metadata_schema, strlen(takeset_metadata_schema));
486-
CU_ASSERT_EQUAL_FATAL(ret, 0);
487-
CU_ASSERT_FALSE(tsk_reference_sequence_equals(&r1, &r2, 0));
488472
ret = tsk_reference_sequence_takeset_metadata(
489473
&r2, takeset_metadata, strlen(takeset_metadata));
490474
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -493,11 +477,6 @@ test_reference_sequence_take(void)
493477
/* Writing over these with copies doesn't lose memory */
494478
ret = tsk_reference_sequence_set_data(&r2, const_data, strlen(const_data));
495479
CU_ASSERT_EQUAL_FATAL(ret, 0);
496-
ret = tsk_reference_sequence_set_url(&r2, const_url, strlen(const_url));
497-
CU_ASSERT_EQUAL_FATAL(ret, 0);
498-
ret = tsk_reference_sequence_set_metadata_schema(
499-
&r2, const_metadata_schema, strlen(const_metadata_schema));
500-
CU_ASSERT_EQUAL_FATAL(ret, 0);
501480
ret = tsk_reference_sequence_set_metadata(
502481
&r2, const_metadata, strlen(const_metadata));
503482
CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -506,18 +485,11 @@ test_reference_sequence_take(void)
506485

507486
/* The original copies are gone, make some new ones */
508487
takeset_data = strdup(const_data);
509-
takeset_url = strdup(const_url);
510-
takeset_metadata_schema = strdup(const_metadata_schema);
511488
takeset_metadata = strdup(const_metadata);
512489

513490
CU_ASSERT_EQUAL_FATAL(ret, 0);
514491
ret = tsk_reference_sequence_takeset_data(&r1, takeset_data, strlen(takeset_data));
515492
CU_ASSERT_EQUAL_FATAL(ret, 0);
516-
ret = tsk_reference_sequence_takeset_url(&r1, takeset_url, strlen(takeset_url));
517-
CU_ASSERT_EQUAL_FATAL(ret, 0);
518-
ret = tsk_reference_sequence_takeset_metadata_schema(
519-
&r1, takeset_metadata_schema, strlen(takeset_metadata_schema));
520-
CU_ASSERT_EQUAL_FATAL(ret, 0);
521493
ret = tsk_reference_sequence_takeset_metadata(
522494
&r1, takeset_metadata, strlen(takeset_metadata));
523495
CU_ASSERT_EQUAL_FATAL(ret, 0);

‎c/tskit/tables.c

Lines changed: 8 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -842,13 +842,6 @@ tsk_reference_sequence_takeset_data(
842842
return takeset_string(&self->data, &self->data_length, data, data_length);
843843
}
844844

845-
int
846-
tsk_reference_sequence_takeset_url(
847-
tsk_reference_sequence_t *self, char *url, tsk_size_t url_length)
848-
{
849-
return takeset_string(&self->url, &self->url_length, url, url_length);
850-
}
851-
852845
int
853846
tsk_reference_sequence_takeset_metadata(
854847
tsk_reference_sequence_t *self, char *metadata, tsk_size_t metadata_length)
@@ -857,14 +850,6 @@ tsk_reference_sequence_takeset_metadata(
857850
&self->metadata, &self->metadata_length, metadata, metadata_length);
858851
}
859852

860-
int
861-
tsk_reference_sequence_takeset_metadata_schema(tsk_reference_sequence_t *self,
862-
char *metadata_schema, tsk_size_t metadata_schema_length)
863-
{
864-
return takeset_string(&self->metadata_schema, &self->metadata_schema_length,
865-
metadata_schema, metadata_schema_length);
866-
}
867-
868853
/*************************
869854
* individual table
870855
*************************/
@@ -10547,6 +10532,14 @@ tsk_table_collection_set_metadata(
1054710532
&self->metadata, &self->metadata_length, metadata, metadata_length);
1054810533
}
1054910534

10535+
int
10536+
tsk_table_collection_takeset_metadata(
10537+
tsk_table_collection_t *self, char *metadata, tsk_size_t metadata_length)
10538+
{
10539+
return takeset_string(
10540+
&self->metadata, &self->metadata_length, metadata, metadata_length);
10541+
}
10542+
1055010543
int
1055110544
tsk_table_collection_set_metadata_schema(tsk_table_collection_t *self,
1055210545
const char *metadata_schema, tsk_size_t metadata_schema_length)

‎c/tskit/tables.h

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -4015,6 +4015,9 @@ Copies the metadata string to this table collection, replacing any existing.
40154015
int tsk_table_collection_set_metadata(
40164016
tsk_table_collection_t *self, const char *metadata, tsk_size_t metadata_length);
40174017

4018+
int tsk_table_collection_takeset_metadata(
4019+
tsk_table_collection_t *self, char *metadata, tsk_size_t metadata_length);
4020+
40184021
/**
40194022
@brief Set the metadata schema
40204023
@rst
@@ -4089,6 +4092,9 @@ int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t o
40894092
int tsk_table_collection_set_indexes(tsk_table_collection_t *self,
40904093
tsk_id_t *edge_insertion_order, tsk_id_t *edge_removal_order);
40914094

4095+
int tsk_table_collection_takeset_indexes(tsk_table_collection_t *self,
4096+
tsk_id_t *edge_insertion_order, tsk_id_t *edge_removal_order);
4097+
40924098
/**
40934099
@brief Runs integrity checks on this table collection.
40944100
@@ -4205,12 +4211,8 @@ int tsk_reference_sequence_set_metadata_schema(tsk_reference_sequence_t *self,
42054211
const char *metadata_schema, tsk_size_t metadata_schema_length);
42064212
int tsk_reference_sequence_takeset_data(
42074213
tsk_reference_sequence_t *self, char *data, tsk_size_t data_length);
4208-
int tsk_reference_sequence_takeset_url(
4209-
tsk_reference_sequence_t *self, char *url, tsk_size_t url_length);
42104214
int tsk_reference_sequence_takeset_metadata(
42114215
tsk_reference_sequence_t *self, char *metadata, tsk_size_t metadata_length);
4212-
int tsk_reference_sequence_takeset_metadata_schema(tsk_reference_sequence_t *self,
4213-
char *metadata_schema, tsk_size_t metadata_schema_length);
42144216

42154217
/**
42164218
@defgroup TABLE_SORTER_API_GROUP Low-level table sorter API.

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