renaming fields for clarity and removing warnings on test

Author: LCrossman

ROADMAP.md

@@ -27,7 +27,7 @@ Protein parameters such as:
 - [x]  Counted amino acids & as percentage
 - [x] Aromaticity
 - [ ]  Parsing phylogenetic trees 
-- [ ]  Parsing multiple sequence alignments
+- [x]  Parsing multiple sequence alignments
 - [ ]  Methylation data parsing
 - [x]  pyo3 integration
 

microBioRust/src/align.rs

@@ -231,11 +231,11 @@ impl<Kind> Alignment<Kind> {
         let stdout = io::stdout();
         let mut handle = BufWriter::new(stdout.lock());
         let max_id_width = rows.clone().map(|i| self.ids[i].len()).max().unwrap_or(10).min(20); //capped at 20
-        // 1. Iterate through columns in "blocks"
+        //iterate through columns in "blocks"
         for block_start in (cols.start..cols.end).step_by(block_width) {
             let block_end = (block_start + block_width).min(cols.end);
 
-            // 2. For each block, print every requested row
+            //for each block, print every requested row
             for r_idx in rows.clone() {
                 if let Some(id) = self.ids.get(r_idx) {
                     //truncate or pad ID for alignment

microBioRust/src/lib.rs

@@ -10,6 +10,7 @@
 //!
 #![allow(non_snake_case)]
 pub mod embl;
+pub mod align;
 pub mod gbk;
 pub mod blast;
 pub mod record;