From 842022d3f060888fa3bfd25c87c7725c1bca3d1e Mon Sep 17 00:00:00 2001
From: Koki Kato <koki.kato1994@gmail.com>
Date: Fri, 31 Jan 2025 09:14:30 +0900
Subject: [PATCH 1/4] Rename existing `suffix_array` module to `sample`

---
 benches/locate.rs                  | 2 +-
 src/builder.rs                     | 2 +-
 src/fm_index.rs                    | 4 ++--
 src/lib.rs                         | 2 +-
 src/rlfmi.rs                       | 4 ++--
 src/{suffix_array.rs => sample.rs} | 0
 src/search.rs                      | 2 +-
 7 files changed, 8 insertions(+), 8 deletions(-)
 rename src/{suffix_array.rs => sample.rs} (100%)

diff --git a/benches/locate.rs b/benches/locate.rs
index 16b8c48..ae59841 100644
--- a/benches/locate.rs
+++ b/benches/locate.rs
@@ -1,4 +1,4 @@
-use fm_index::suffix_array::HasPosition;
+use fm_index::sample::HasPosition;
 use fm_index::{FMIndexBackend, SearchIndexBuilder};
 
 use criterion::{criterion_group, criterion_main};
diff --git a/src/builder.rs b/src/builder.rs
index b5e9341..229a16a 100644
--- a/src/builder.rs
+++ b/src/builder.rs
@@ -3,7 +3,7 @@ use crate::converter;
 
 use crate::{
     converter::{Converter, IdConverter},
-    suffix_array::SuffixOrderSampledArray,
+    sample::SuffixOrderSampledArray,
     Character, FMIndex, RLFMIndex,
 };
 
diff --git a/src/fm_index.rs b/src/fm_index.rs
index 1e65965..6edab17 100644
--- a/src/fm_index.rs
+++ b/src/fm_index.rs
@@ -3,7 +3,7 @@ use crate::character::{prepare_text, Character};
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
 use crate::iter::FMIndexBackend;
-use crate::suffix_array::{self, HasPosition, SuffixOrderSampledArray};
+use crate::sample::{self, HasPosition, SuffixOrderSampledArray};
 use crate::{sais, seal, HeapSize};
 use crate::{util, Search};
 
@@ -39,7 +39,7 @@ where
     C: Converter<T>,
 {
     pub(crate) fn new(text: Vec<T>, converter: C, level: usize) -> Self {
-        Self::create(text, converter, |sa| suffix_array::sample(sa, level))
+        Self::create(text, converter, |sa| sample::sample(sa, level))
     }
 }
 
diff --git a/src/lib.rs b/src/lib.rs
index dc36428..c0b73f9 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -135,7 +135,7 @@
 #![warn(missing_docs)]
 
 pub mod converter;
-pub mod suffix_array;
+pub mod sample;
 
 mod builder;
 mod character;
diff --git a/src/rlfmi.rs b/src/rlfmi.rs
index 9ec199b..3f645f4 100644
--- a/src/rlfmi.rs
+++ b/src/rlfmi.rs
@@ -3,7 +3,7 @@ use crate::character::{prepare_text, Character};
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
 use crate::iter::FMIndexBackend;
-use crate::suffix_array::{self, HasPosition, SuffixOrderSampledArray};
+use crate::sample::{self, HasPosition, SuffixOrderSampledArray};
 use crate::{sais, HeapSize, Search};
 use crate::{seal, util};
 
@@ -41,7 +41,7 @@ where
     C: Converter<T>,
 {
     pub(crate) fn new(text: Vec<T>, converter: C, level: usize) -> Self {
-        Self::create(text, converter, |sa| suffix_array::sample(sa, level))
+        Self::create(text, converter, |sa| sample::sample(sa, level))
     }
 }
 
diff --git a/src/suffix_array.rs b/src/sample.rs
similarity index 100%
rename from src/suffix_array.rs
rename to src/sample.rs
diff --git a/src/search.rs b/src/search.rs
index 6725586..9924b09 100644
--- a/src/search.rs
+++ b/src/search.rs
@@ -5,8 +5,8 @@ use crate::converter;
 
 use crate::converter::IndexWithConverter;
 use crate::iter::FMIndexBackend;
+use crate::sample::HasPosition;
 use crate::seal;
-use crate::suffix_array::HasPosition;
 
 /// An object containing the result of a search.
 ///

From 7cd094400f3170cd042676698a87cefea7ba9f0c Mon Sep 17 00:00:00 2001
From: Koki Kato <koki.kato1994@gmail.com>
Date: Fri, 31 Jan 2025 09:25:15 +0900
Subject: [PATCH 2/4] Move HasPosition to iter module

HasPosition is a property (trait) of a search index, so it might be more
intuitive to move this to iter module, where other traits for indexes
are located.
---
 benches/locate.rs |  3 +--
 src/fm_index.rs   |  4 ++--
 src/iter.rs       | 10 ++++++++++
 src/lib.rs        |  2 +-
 src/rlfmi.rs      |  4 ++--
 src/sample.rs     | 10 +---------
 src/search.rs     |  3 +--
 7 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/benches/locate.rs b/benches/locate.rs
index ae59841..2352f66 100644
--- a/benches/locate.rs
+++ b/benches/locate.rs
@@ -1,5 +1,4 @@
-use fm_index::sample::HasPosition;
-use fm_index::{FMIndexBackend, SearchIndexBuilder};
+use fm_index::{FMIndexBackend, HasPosition, SearchIndexBuilder};
 
 use criterion::{criterion_group, criterion_main};
 use criterion::{BatchSize, BenchmarkId, Criterion, Throughput};
diff --git a/src/fm_index.rs b/src/fm_index.rs
index 6edab17..6090044 100644
--- a/src/fm_index.rs
+++ b/src/fm_index.rs
@@ -2,8 +2,8 @@ use crate::character::{prepare_text, Character};
 #[cfg(doc)]
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
-use crate::iter::FMIndexBackend;
-use crate::sample::{self, HasPosition, SuffixOrderSampledArray};
+use crate::iter::{FMIndexBackend, HasPosition};
+use crate::sample::{self, SuffixOrderSampledArray};
 use crate::{sais, seal, HeapSize};
 use crate::{util, Search};
 
diff --git a/src/iter.rs b/src/iter.rs
index 1cb9df0..b241332 100644
--- a/src/iter.rs
+++ b/src/iter.rs
@@ -1,5 +1,7 @@
 use crate::character::Character;
 use crate::converter::{Converter, IndexWithConverter};
+#[cfg(doc)]
+use crate::sample::SuffixOrderSampledArray;
 use crate::seal;
 use crate::search::Search;
 
@@ -68,6 +70,14 @@ pub trait HeapSize {
     fn size(&self) -> usize;
 }
 
+/// A trait for an index that supports locate queries.
+///
+/// This is only supported when [`SuffixOrderSampledArray`] is passed in.
+pub trait HasPosition {
+    #[doc(hidden)]
+    fn get_sa<L: seal::IsLocal>(&self, i: u64) -> u64;
+}
+
 /// An iterator that goes backwards through the text, producing [`Character`].
 pub struct BackwardIterator<'a, I>
 where
diff --git a/src/lib.rs b/src/lib.rs
index c0b73f9..e55f1f9 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -152,5 +152,5 @@ pub use crate::rlfmi::RLFMIndex;
 
 pub use builder::SearchIndexBuilder;
 pub use character::Character;
-pub use iter::{BackwardIterator, FMIndexBackend, ForwardIterator, HeapSize};
+pub use iter::{BackwardIterator, FMIndexBackend, ForwardIterator, HasPosition, HeapSize};
 pub use search::Search;
diff --git a/src/rlfmi.rs b/src/rlfmi.rs
index 3f645f4..a80574e 100644
--- a/src/rlfmi.rs
+++ b/src/rlfmi.rs
@@ -2,8 +2,8 @@ use crate::character::{prepare_text, Character};
 #[cfg(doc)]
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
-use crate::iter::FMIndexBackend;
-use crate::sample::{self, HasPosition, SuffixOrderSampledArray};
+use crate::iter::{FMIndexBackend, HasPosition};
+use crate::sample::{self, SuffixOrderSampledArray};
 use crate::{sais, HeapSize, Search};
 use crate::{seal, util};
 
diff --git a/src/sample.rs b/src/sample.rs
index 21a3056..40892f7 100644
--- a/src/sample.rs
+++ b/src/sample.rs
@@ -1,20 +1,12 @@
 //! Suffix arrays, used to construct the index.
 //!
 //! Can also be used in sampled fashion to perform locate queries.
-use crate::{seal, util};
+use crate::util;
 use std::fmt;
 
 use serde::{Deserialize, Serialize};
 use vers_vecs::BitVec;
 
-/// A trait for an index that supports locate queries.
-///
-/// This is only supported when [`SuffixOrderSampledArray`] is passed in.
-pub trait HasPosition {
-    #[doc(hidden)]
-    fn get_sa<L: seal::IsLocal>(&self, i: u64) -> u64;
-}
-
 /// A sampled suffix array, stored within the index.
 #[derive(Serialize, Deserialize)]
 pub struct SuffixOrderSampledArray {
diff --git a/src/search.rs b/src/search.rs
index 9924b09..a713f68 100644
--- a/src/search.rs
+++ b/src/search.rs
@@ -4,8 +4,7 @@ use crate::character::Character;
 use crate::converter;
 
 use crate::converter::IndexWithConverter;
-use crate::iter::FMIndexBackend;
-use crate::sample::HasPosition;
+use crate::iter::{FMIndexBackend, HasPosition};
 use crate::seal;
 
 /// An object containing the result of a search.

From f2e72d38031b80d3c7da995f0d3aeadef523110f Mon Sep 17 00:00:00 2001
From: Koki Kato <koki.kato1994@gmail.com>
Date: Fri, 31 Jan 2025 09:34:40 +0900
Subject: [PATCH 3/4] Move sample module under suffix_array

---
 src/builder.rs                   | 2 +-
 src/fm_index.rs                  | 2 +-
 src/lib.rs                       | 2 +-
 src/rlfmi.rs                     | 2 +-
 src/suffix_array.rs              | 5 +++++
 src/{ => suffix_array}/sample.rs | 4 +---
 6 files changed, 10 insertions(+), 7 deletions(-)
 create mode 100644 src/suffix_array.rs
 rename src/{ => suffix_array}/sample.rs (95%)

diff --git a/src/builder.rs b/src/builder.rs
index 229a16a..faf4f0a 100644
--- a/src/builder.rs
+++ b/src/builder.rs
@@ -3,7 +3,7 @@ use crate::converter;
 
 use crate::{
     converter::{Converter, IdConverter},
-    sample::SuffixOrderSampledArray,
+    suffix_array::sample::SuffixOrderSampledArray,
     Character, FMIndex, RLFMIndex,
 };
 
diff --git a/src/fm_index.rs b/src/fm_index.rs
index 6090044..3a4f1fb 100644
--- a/src/fm_index.rs
+++ b/src/fm_index.rs
@@ -3,7 +3,7 @@ use crate::character::{prepare_text, Character};
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
 use crate::iter::{FMIndexBackend, HasPosition};
-use crate::sample::{self, SuffixOrderSampledArray};
+use crate::suffix_array::sample::{self, SuffixOrderSampledArray};
 use crate::{sais, seal, HeapSize};
 use crate::{util, Search};
 
diff --git a/src/lib.rs b/src/lib.rs
index e55f1f9..4067369 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -135,7 +135,6 @@
 #![warn(missing_docs)]
 
 pub mod converter;
-pub mod sample;
 
 mod builder;
 mod character;
@@ -145,6 +144,7 @@ mod rlfmi;
 mod sais;
 mod seal;
 mod search;
+mod suffix_array;
 mod util;
 
 pub use crate::fm_index::FMIndex;
diff --git a/src/rlfmi.rs b/src/rlfmi.rs
index a80574e..0f0d2ff 100644
--- a/src/rlfmi.rs
+++ b/src/rlfmi.rs
@@ -3,7 +3,7 @@ use crate::character::{prepare_text, Character};
 use crate::converter;
 use crate::converter::{Converter, IndexWithConverter};
 use crate::iter::{FMIndexBackend, HasPosition};
-use crate::sample::{self, SuffixOrderSampledArray};
+use crate::suffix_array::sample::{self, SuffixOrderSampledArray};
 use crate::{sais, HeapSize, Search};
 use crate::{seal, util};
 
diff --git a/src/suffix_array.rs b/src/suffix_array.rs
new file mode 100644
index 0000000..3068146
--- /dev/null
+++ b/src/suffix_array.rs
@@ -0,0 +1,5 @@
+//! Suffix arrays, used to construct the index.
+//!
+//! Can also be used in sampled fashion to perform locate queries.
+
+pub mod sample;
diff --git a/src/sample.rs b/src/suffix_array/sample.rs
similarity index 95%
rename from src/sample.rs
rename to src/suffix_array/sample.rs
index 40892f7..e3df26b 100644
--- a/src/sample.rs
+++ b/src/suffix_array/sample.rs
@@ -1,6 +1,4 @@
-//! Suffix arrays, used to construct the index.
-//!
-//! Can also be used in sampled fashion to perform locate queries.
+//! Sampled suffix arrays to perform locate queries.
 use crate::util;
 use std::fmt;
 

From b9a31004b637a973510ff1fef1b6a3263ac2e37b Mon Sep 17 00:00:00 2001
From: Koki Kato <koki.kato1994@gmail.com>
Date: Fri, 31 Jan 2025 09:43:42 +0900
Subject: [PATCH 4/4] Fix doc

---
 src/iter.rs | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/iter.rs b/src/iter.rs
index b241332..e6f6aa3 100644
--- a/src/iter.rs
+++ b/src/iter.rs
@@ -1,7 +1,5 @@
 use crate::character::Character;
 use crate::converter::{Converter, IndexWithConverter};
-#[cfg(doc)]
-use crate::sample::SuffixOrderSampledArray;
 use crate::seal;
 use crate::search::Search;
 
@@ -71,8 +69,6 @@ pub trait HeapSize {
 }
 
 /// A trait for an index that supports locate queries.
-///
-/// This is only supported when [`SuffixOrderSampledArray`] is passed in.
 pub trait HasPosition {
     #[doc(hidden)]
     fn get_sa<L: seal::IsLocal>(&self, i: u64) -> u64;