Add diagram

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "block-aligner"
-version = "0.5.0"
+version = "0.5.1"
 authors = ["c0deb0t <[email protected]>"]
 edition = "2018"
 license = "MIT"

README.md

@@ -45,6 +45,10 @@ assert_eq!(cigar.to_string(), "2=6I16=3D");
 ```
 See the [docs](https://docs.rs/block-aligner) for detailed API information.
 
+<p align = "center">
+<img src = "block_aligner_modes.png" width = "400px">
+</p>
+
 ## Algorithm
 Block aligner provides a new efficient way to compute pairwise alignments on proteins, DNA sequences,
 and byte strings with dynamic programming.

src/scan_block.rs

@@ -1,4 +1,4 @@
-//! Main block aligner algorithm and supporting data structures.
+//! Main Block Aligner algorithm and supporting data structures.
 
 #[cfg(feature = "simd_sse2")]
 use crate::sse2::*;
@@ -82,7 +82,10 @@ struct StateProfile<'a, P: Profile> {
     x_drop: i32
 }
 
-/// Data structure storing the settings for block aligner.
+/// Data structure storing the settings for Block Aligner.
+///
+/// A diagram showing different ways Block Aligner can be used:
+/// ![Block Aligner modes](https://raw.githubusercontent.com/Daniel-Liu-c0deb0t/block-aligner/main/block_aligner_modes.png)
 pub struct Block<const TRACE: bool, const X_DROP: bool = false, const LOCAL_START: bool = false, const FREE_QUERY_START_GAPS: bool = false, const FREE_QUERY_END_GAPS: bool = false> {
     res: AlignResult,
     allocated: Allocated

src/scores.rs

@@ -137,6 +137,8 @@ impl Matrix for AAMatrix {
 /// Nucleotide scoring matrix.
 ///
 /// Supports characters `A`, `C`, `G`, `N`, and `T`. Lowercase characters are uppercased.
+///
+/// If a larger alphabet is needed (for example, with IUPAC characters), use `AAMatrix` instead.
 #[repr(C, align(32))]
 #[derive(Clone, PartialEq, Debug)]
 pub struct NucMatrix {