Update usage of the next_diff functions. (#551)

Update usage of the next_diff functions.

enclone_paper/src/bin/insertion_analysis.rs

@@ -443,7 +443,7 @@ fn main() {
     let mut bounds2 = Vec::<(usize, usize, Vec<usize>, Vec<usize>)>::new();
     let mut i = 0;
     while i < data.len() {
-        // let j = next_diff12_9(&data, i as i32) as usize;
+        // let j = next_diff12_9(&data, i);
         let mut j = i + 1;
         while j < data.len() {
             if data[j].0 != data[i].0 || data[j].1 != data[i].1 {

enclone_paper/src/bin/public_light_chain_analysis.rs

@@ -469,7 +469,7 @@ fn main() {
     let mut bounds2 = Vec::<(usize, usize, Vec<usize>, Vec<usize>)>::new();
     let mut i = 0;
     while i < data.len() {
-        // let j = next_diff12_9(&data, i as i32) as usize;
+        // let j = next_diff12_9(&data, i);
         let mut j = i + 1;
         while j < data.len() {
             if data[j].0 != data[i].0 || data[j].1 != data[i].1 {

enclone_paper/src/bin/weighted_light_chain_analysis.rs

@@ -95,7 +95,7 @@ fn main() {
     let mut bounds = Vec::<(usize, usize, Vec<Vec<(usize, usize, usize, usize)>>)>::new();
     let mut i = 0;
     while i < data.len() {
-        // let j = next_diff12_9(&data, i as i32) as usize;
+        // let j = next_diff12_9(&data, i);
         let mut j = i + 1;
         while j < data.len() {
             if data[j].0 != data[i].0 || data[j].1 != data[i].1 {

enclone_tail/src/group.rs

@@ -549,7 +549,7 @@ pub fn group_and_print_clonotypes(
                         } else {
                             let mut k = 0;
                             while k < pg[id].len() {
-                                let l = next_diff1_3(&pg[id], k as i32) as usize;
+                                let l = next_diff1_3(&pg[id], k);
                                 let mut s = Vec::<String>::new();
                                 for m in k..l {
                                     s.push(format!("{}={}", pg[id][m].1 as char, pg[id][m].2));
@@ -584,7 +584,7 @@ pub fn group_and_print_clonotypes(
                     } else {
                         let mut k = 0;
                         while k < pg[id].len() {
-                            let l = next_diff1_3(&pg[id], k as i32) as usize;
+                            let l = next_diff1_3(&pg[id], k);
                             let mut s = Vec::<String>::new();
                             for m in k..l {
                                 s.push(format!("{}={}", pg[id][m].1 as char, pg[id][m].2));

enclone_tail/src/grouper.rs

@@ -80,7 +80,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);
@@ -121,7 +121,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);
@@ -152,7 +152,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     if all[i].0.is_empty() {
                         for k in i..j {
                             let g = vec![all[k].1];
@@ -192,7 +192,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     if all[i].0.is_empty() {
                         for k in i..j {
                             let g = vec![all[k].1];
@@ -240,7 +240,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     if all[i].0.is_empty() {
                         for k in i..j {
                             let g = vec![all[k].1];
@@ -277,7 +277,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);
@@ -307,7 +307,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);
@@ -339,7 +339,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);
@@ -371,7 +371,7 @@ pub fn grouper(
                 all.sort();
                 let mut i = 0;
                 while i < all.len() {
-                    let j = next_diff1_2(&all, i as i32) as usize;
+                    let j = next_diff1_2(&all, i);
                     let mut g = Vec::<usize>::new();
                     for k in i..j {
                         g.push(all[k].1);