cool

Author: molpopgen

src/sys/flags.rs

@@ -39,7 +39,18 @@ macro_rules! bits {
         pub fn bits(&self) -> RawFlags {
             self.0
         }
-    }
+    };
+}
+
+macro_rules! contains {
+    () => {
+        pub fn contains<I>(&self, bit: I) -> bool
+        where
+            I: Into<Self> + Copy,
+        {
+            bit.into().0 == 0 || (self.0 & bit.into().0) != 0
+        }
+    };
 }
 
 /// Control the behavior of table simplification.
@@ -79,29 +90,29 @@ pub struct SimplificationOptions(RawFlags);
 
 impl SimplificationOptions {
     /// Default behavior
-    const NONE: RawFlags = 0;
-    const FILTER_SITES: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_SITES;
+    pub const NONE: RawFlags = 0;
+    pub const FILTER_SITES: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_SITES;
     /// If True, remove any populations that are not referenced by
     /// nodes after simplification; new population IDs are allocated
     /// sequentially from zero.
     /// If False, the population table will not be altered in any way.
-    const FILTER_POPULATIONS: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_POPULATIONS;
+    pub const FILTER_POPULATIONS: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_POPULATIONS;
     /// If True, remove any individuals that are not referenced by nodes
     /// after simplification; new individual IDs are allocated sequentially
     /// from zero. If False, the individual table will not be altered in any way.
-    const FILTER_INDIVIDUALS: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_INDIVIDUALS;
+    pub const FILTER_INDIVIDUALS: RawFlags = ll_bindings::TSK_SIMPLIFY_FILTER_INDIVIDUALS;
     /// Whether to reduce the topology down to the trees that are present at sites.
-    const REDUCE_TO_SITE_TOPOLOGY: RawFlags = ll_bindings::TSK_SIMPLIFY_REDUCE_TO_SITE_TOPOLOGY;
+    pub const REDUCE_TO_SITE_TOPOLOGY: RawFlags = ll_bindings::TSK_SIMPLIFY_REDUCE_TO_SITE_TOPOLOGY;
     /// If True, preserve unary nodes (i.e. nodes with exactly one child)
     /// that exist on the path from samples to root.
-    const KEEP_UNARY: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY;
+    pub const KEEP_UNARY: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY;
     /// Whether to retain history ancestral to the MRCA of the samples.
-    const KEEP_INPUT_ROOTS: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_INPUT_ROOTS;
+    pub const KEEP_INPUT_ROOTS: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_INPUT_ROOTS;
     ///  If True, preserve unary nodes that exist on the path from samples
     ///  to root, but only if they are associated with an individual
     ///  in the individuals table.
     ///  Cannot be specified at the same time as `KEEP_UNARY`.
-    const KEEP_UNARY_IN_INDIVIDUALS: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVIDUALS;
+    pub const KEEP_UNARY_IN_INDIVIDUALS: RawFlags = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVIDUALS;
 
     flag_builder_api!(
     /// Update to set [`KEEP_INPUT_ROOTS`](crate::SimplificationOptions::KEEP_INPUT_ROOTS).
@@ -188,6 +199,7 @@ impl SimplificationOptions {
     => filter_individuals, FILTER_INDIVIDUALS);
 
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::clear`].
@@ -251,6 +263,7 @@ impl TableClearOptions {
         /// Set [`CLEAR_PROVENANCE`](crate::TableClearOptions::CLEAR_PROVENANCE)
         => clear_provenance, CLEAR_PROVENANCE);
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::equals`].
@@ -326,6 +339,7 @@ impl TableEqualityOptions {
         /// Set [`IGNORE_TIMESTAMPS`](crate::TableEqualityOptions::IGNORE_TIMESTAMPS)
         => ignore_timestamps, IGNORE_TIMESTAMPS);
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::sort`].
@@ -362,6 +376,7 @@ impl TableSortOptions {
         /// Set [`NO_CHECK_INTEGRITY`](crate::TableSortOptions::NO_CHECK_INTEGRITY)
         => no_check_integrity, NO_CHECK_INTEGRITY);
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::sort_individuals`].
@@ -383,6 +398,7 @@ impl IndividualTableSortOptions {
     /// Default behavior.
     pub const NONE: RawFlags = 0;
     bits!();
+    contains!();
 }
 
 /// Specify the behavior of iterating over [`Tree`] objects.
@@ -433,6 +449,7 @@ impl TreeFlags {
         /// Set [`NO_SAMPLE_COUNTS`](crate::TreeFlags::NO_SAMPLE_COUNTS)
         => no_sample_counts, NO_SAMPLE_COUNTS);
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::dump`].
@@ -461,6 +478,7 @@ pub struct TableOutputOptions(RawFlags);
 
 impl TableOutputOptions {
     bits!();
+    contains!();
 }
 
 /// Modify behavior of [`crate::TableCollection::tree_sequence`]
@@ -499,6 +517,7 @@ impl TreeSequenceFlags {
         /// Set [`BUILD_INDEXES`](crate::TreeSequenceFlags::BUILD_INDEXES)
         => build_indexes, BUILD_INDEXES);
     bits!();
+    contains!();
 }
 
 /// Flags to affect the behavior of
@@ -613,6 +632,7 @@ impl TableIntegrityCheckFlags {
         /// Set [`CHECK_TREES`](crate::TableIntegrityCheckFlags::CHECK_TREES)
         => check_trees, CHECK_TREES);
     bits!();
+    contains!();
 }
 
 #[derive(Default, Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
@@ -653,13 +673,7 @@ impl NodeFlags {
     }
 
     bits!();
-
-    pub fn contains<I>(&self, bit: I) -> bool
-    where
-        I: Into<Self> + Copy,
-    {
-        bit.into().0 == 0 || (self.0 & bit.into().0) != 0
-    }
+    contains!();
 
     pub fn toggle(&mut self, bit: tsk_flags_t) {
         self.0 ^= bit
@@ -693,6 +707,8 @@ impl IndividualFlags {
     pub fn is_valid(&self) -> bool {
         true
     }
+    bits!();
+    contains!();
 }
 
 impl_flags!(SimplificationOptions);