doc: start book sections on tree sequences

Author: molpopgen

book/src/SUMMARY.md

@@ -8,3 +8,7 @@
   - [Accessing table columns](./table_collection_column_access.md)
   - [Accessing table rows](./table_collection_row_access.md)
   - [Validating table collection contents](./table_collection_validation.md)
+
+- [Working with tree sequences](./working_with_tree_sequences.md)
+  - [Initialization from a table collection](./tree_sequence_from_table_collection.md)
+  - [Iterating over trees](./tree_sequence_iterate_trees.md)

book/src/tree_sequence_from_table_collection.md

@@ -0,0 +1,45 @@
+## Initialization from a table collection
+
+The steps are:
+
+* Add rows to a table
+* Sort the table
+* Index the table
+* Create the tree sequence
+
+For brevity, we skip careful pattern matching of return values
+and instead just unwrap them.
+
+### Adding rows
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:build_tables}}
+```
+
+### Sorting
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:sort_tables}}
+```
+
+See the [API docs](https://docs.rs) for the details of sorting.
+The behavior of this function can be confusing at first.
+Only tables with strict sorting requirements are affected.
+
+### Indexing
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:index_tables}}
+```
+
+### Create the tree sequence
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:create_tree_sequence}}
+```
+
+Notes:
+
+* We could have skipped `tables.build_index()` and passed `TreeSquenceFlags::BUILD_INDEXES` instead of the default flags.
+* Creating a tree sequence from a table collection takes ownership of the table data and consumes the table collection variable.
+  Any further attempts to manipulate the table collection variable will result in a compiler error.

book/src/tree_sequence_iterate_trees.md

@@ -0,0 +1,17 @@
+## Iterating over trees
+
+To iterate over trees left-to-right:
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:iterate_trees}}
+```
+
+This API depends on traits most easily brought into scope via the crate prelude:
+
+```rust, noplayground, ignore
+use tskit::prelude::*;
+```
+
+A `next_back()` function allows iteration to the next tree left of the current tree.
+We currently do not have an API expressing "build me an iterator starting from the rightmost tree".
+Such an thing is certainly doable.

book/src/working_with_tree_sequences.md

@@ -0,0 +1,21 @@
+# Working with tree sequences <img align="right" width="73" height="45" src="https://raw.githubusercontent.com/tskit-dev/administrative/main/logos/svg/tskit-rust/Tskit_rust_logo.eps.svg">
+
+The next several sections provide examples based on a tree sequence with two trees.
+
+The first tree is:
+
+     0
+    +++
+    | |  1
+    | | +++
+    2 3 4 5
+
+The second tree is:
+
+         0
+       +-+-+
+       1   |
+     +-+-+ |
+     2 4 5 3
+
+

tests/book_trees.rs

@@ -0,0 +1,76 @@
+#[test]
+fn initialize_from_table_collection() {
+    // ANCHOR: build_tables
+    use tskit::prelude::*;
+    use tskit::TableCollection;
+    use tskit::TableSortOptions;
+    use tskit::TreeFlags;
+    use tskit::TreeSequenceFlags;
+
+    let mut tables = TableCollection::new(1000.).unwrap();
+    tables
+        .add_node(0, 2.0, PopulationId::NULL, IndividualId::NULL)
+        .unwrap();
+    tables
+        .add_node(0, 1.0, PopulationId::NULL, IndividualId::NULL)
+        .unwrap();
+    tables
+        .add_node(
+            TSK_NODE_IS_SAMPLE,
+            0.0,
+            PopulationId::NULL,
+            IndividualId::NULL,
+        )
+        .unwrap();
+    tables
+        .add_node(
+            TSK_NODE_IS_SAMPLE,
+            0.0,
+            PopulationId::NULL,
+            IndividualId::NULL,
+        )
+        .unwrap();
+    tables
+        .add_node(
+            TSK_NODE_IS_SAMPLE,
+            0.0,
+            PopulationId::NULL,
+            IndividualId::NULL,
+        )
+        .unwrap();
+    tables
+        .add_node(
+            TSK_NODE_IS_SAMPLE,
+            0.0,
+            PopulationId::NULL,
+            IndividualId::NULL,
+        )
+        .unwrap();
+    tables.add_edge(500., 1000., 0, 1).unwrap();
+    tables.add_edge(0., 500., 0, 2).unwrap();
+    tables.add_edge(0., 1000., 0, 3).unwrap();
+    tables.add_edge(500., 1000., 1, 2).unwrap();
+    tables.add_edge(0., 1000., 1, 4).unwrap();
+    tables.add_edge(0., 1000., 1, 5).unwrap();
+    // ANCHOR_END: build_tables
+
+    // ANCHOR: sort_tables
+    tables.full_sort(TableSortOptions::default()).unwrap();
+    // ANCHOR_END: sort_tables
+
+    // ANCHOR: index_tables
+    tables.build_index().unwrap();
+    // ANCHOR_END: index_tables
+
+    // ANCHOR: create_tree_sequence
+    let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
+    // ANCHOR_END: create_tree_sequence
+
+    // ANCHOR: iterate_trees
+    let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
+
+    while let Some(_tree) = tree_iterator.next() {
+        // _tree is a tskit::Tree
+    }
+    // ANCHOR_END: iterate_trees
+}