Restructure modules.

src/cli/concat.rs → src/cli/align/concat.rs

@@ -1,7 +1,7 @@
 use std::path::PathBuf;
 
-use super::{collect_paths, AlignSeqInput, ConcatCli, InputCli, OutputCli};
 use crate::cli::args::AlignConcatArgs;
+use crate::cli::{collect_paths, AlignSeqInput, ConcatCli, InputCli, OutputCli};
 use crate::core::align::concat::AlignmentConcatenation;
 use crate::helper::logger::AlignSeqLogger;
 

src/cli/convert.rs → src/cli/align/convert.rs

@@ -4,7 +4,7 @@ use crate::{core::align::convert::AlignmentConversion, helper::logger::AlignSeqL
 
 use crate::cli::args::AlignConvertArgs;
 
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for ConvertParser<'_> {}
 impl OutputCli for ConvertParser<'_> {}

src/cli/filter.rs → src/cli/align/filter.rs

@@ -2,6 +2,8 @@ use std::path::PathBuf;
 
 use colored::Colorize;
 
+use crate::cli::args::AlignFilterArgs;
+use crate::cli::collect_paths;
 use crate::cli::{AlignSeqInput, ConcatCli, InputCli, OutputCli};
 use crate::core::align::filter::{AlignmentFiltering, FilteringParameters};
 use crate::helper::finder::IDs;
@@ -10,9 +12,6 @@ use crate::helper::types::{DataType, InputFmt, PartitionFmt};
 use crate::helper::utils;
 use crate::parser::txt;
 
-use super::args::AlignFilterArgs;
-use super::collect_paths;
-
 impl InputCli for FilterParser<'_> {}
 impl OutputCli for FilterParser<'_> {}
 impl ConcatCli for FilterParser<'_> {}

src/cli/align/mod.rs

@@ -0,0 +1,6 @@
+pub(crate) mod concat;
+pub(crate) mod convert;
+pub(crate) mod filter;
+pub(crate) mod partition;
+pub(crate) mod split;
+pub(crate) mod summarize;

src/cli/partition.rs → src/cli/align/partition.rs

@@ -3,8 +3,8 @@ use crate::helper::partition::construct_partition_path;
 use crate::helper::types::PartitionFmt;
 use crate::helper::{logger, utils};
 
-use super::args::PartitionArgs;
-use super::{AlignSeqInput, ConcatCli, InputCli, OutputCli};
+use crate::cli::args::PartitionArgs;
+use crate::cli::{AlignSeqInput, ConcatCli, InputCli, OutputCli};
 
 impl InputCli for PartParser<'_> {}
 impl ConcatCli for PartParser<'_> {}

src/cli/split.rs → src/cli/align/split.rs

@@ -4,8 +4,8 @@ use crate::core::align::split::AlignmentSplitting;
 use crate::helper::logger::AlignSeqLogger;
 use crate::helper::types::PartitionFmt;
 
-use super::args::AlignSplitArgs;
-use super::{AlignSeqInput, ConcatCli, InputCli, OutputCli};
+use crate::cli::args::AlignSplitArgs;
+use crate::cli::{AlignSeqInput, ConcatCli, InputCli, OutputCli};
 
 impl OutputCli for SplitParser<'_> {}
 impl InputCli for SplitParser<'_> {}

src/cli/summarize.rs → src/cli/align/summarize.rs

@@ -3,8 +3,8 @@ use std::path::PathBuf;
 use crate::core::align::summarize::AlignmentSummary;
 use crate::helper::logger::AlignSeqLogger;
 
-use super::args::AlignSummaryArgs;
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::args::AlignSummaryArgs;
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for SummaryParser<'_> {}
 impl OutputCli for SummaryParser<'_> {}

src/cli/commands.rs

@@ -1,23 +1,23 @@
+use crate::cli::align::concat::ConcatParser;
+use crate::cli::align::convert::ConvertParser;
+use crate::cli::align::filter::FilterParser;
+use crate::cli::align::partition::PartParser;
+use crate::cli::align::split::SplitParser;
+use crate::cli::align::summarize::SummaryParser;
 use crate::cli::args::MainSubcommand;
-use crate::cli::concat::ConcatParser;
-use crate::cli::convert::ConvertParser;
-use crate::cli::extract::ExtractParser;
-use crate::cli::filter::FilterParser;
-use crate::cli::id::IdParser;
-use crate::cli::partition::PartParser;
-use crate::cli::read::ReadSummaryCliParser;
-use crate::cli::remove::RemoveParser;
-use crate::cli::rename::RenameParser;
-use crate::cli::split::SplitParser;
-use crate::cli::summarize::SummaryParser;
-use crate::cli::translate::TranslateParser;
+use crate::cli::read::summarize::ReadSummaryCliParser;
+use crate::cli::sequence::extract::ExtractParser;
+use crate::cli::sequence::id::IdParser;
+use crate::cli::sequence::remove::RemoveParser;
+use crate::cli::sequence::rename::RenameParser;
+use crate::cli::sequence::translate::TranslateParser;
 
 use super::{
     args::{
         AlignmentSubcommand, ContigSubcommand, PartitionSubcommand, SeqReadSubcommand,
         SequenceSubcommand,
     },
-    contigs::ContigCliParser,
+    contig::summarize::ContigCliParser,
 };
 
 pub(crate) fn match_cli_subcommand(subcommand: &MainSubcommand) {

src/cli/contig/mod.rs

@@ -0,0 +1 @@
+pub(crate) mod summarize;

src/cli/contigs.rs → src/cli/contig/summarize.rs

@@ -1,6 +1,6 @@
 use std::path::PathBuf;
 
-use super::{args::ContigSummaryArgs, collect_paths, ContigInputCli, InputCli, OutputCli};
+use crate::cli::{args::ContigSummaryArgs, collect_paths, ContigInputCli, InputCli, OutputCli};
 use crate::core::contig::summarize::ContigSummaryHandler;
 use crate::helper::logger::ContigLogger;
 

src/cli/mod.rs

@@ -1,19 +1,10 @@
 //! Command line interface for parsing and executing commands.
+mod align;
 mod args;
 mod commands;
-mod concat;
-mod contigs;
-mod convert;
-mod extract;
-mod filter;
-mod id;
-mod partition;
+mod contig;
 mod read;
-mod remove;
-mod rename;
-mod split;
-mod summarize;
-mod translate;
+mod sequence;
 
 #[cfg(target_os = "windows")]
 use glob::glob;

src/cli/read/mod.rs

@@ -0,0 +1 @@
+pub(crate) mod summarize;

src/cli/read.rs → src/cli/read/summarize.rs

@@ -2,7 +2,7 @@ use std::path::PathBuf;
 
 use crate::{core::read::summarize::GenomicReadSummary, helper::logger::ReadLogger};
 
-use super::{args::SeqReadSummaryArgs, collect_paths, InputCli, OutputCli, RawInputCli};
+use crate::cli::{args::SeqReadSummaryArgs, collect_paths, InputCli, OutputCli, RawInputCli};
 
 impl InputCli for ReadSummaryCliParser<'_> {}
 impl OutputCli for ReadSummaryCliParser<'_> {}

src/cli/extract.rs → src/cli/sequence/extract.rs

@@ -6,8 +6,8 @@ use crate::core::sequence::extract::{SeqExtractionParameters, SequenceExtraction
 use crate::helper::logger::AlignSeqLogger;
 use crate::parser::txt;
 
-use super::args::SequenceExtractArgs;
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::args::SequenceExtractArgs;
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for ExtractParser<'_> {}
 impl OutputCli for ExtractParser<'_> {}

src/cli/id.rs → src/cli/sequence/id.rs

@@ -3,8 +3,8 @@ use std::path::PathBuf;
 use crate::core::sequence::id::SequenceID;
 use crate::helper::logger::AlignSeqLogger;
 
-use super::args::SequenceIdArgs;
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::args::SequenceIdArgs;
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for IdParser<'_> {}
 impl OutputCli for IdParser<'_> {}

src/cli/sequence/mod.rs

@@ -0,0 +1,5 @@
+pub(crate) mod extract;
+pub(crate) mod id;
+pub(crate) mod remove;
+pub(crate) mod rename;
+pub(crate) mod translate;

src/cli/remove.rs → src/cli/sequence/remove.rs

@@ -7,7 +7,7 @@ use crate::{
     helper::logger::AlignSeqLogger,
 };
 
-use super::{args::SequenceRemoveArgs, collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::{args::SequenceRemoveArgs, collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for RemoveParser<'_> {}
 impl OutputCli for RemoveParser<'_> {}

src/cli/rename.rs → src/cli/sequence/rename.rs

@@ -7,8 +7,8 @@ use crate::helper::logger::AlignSeqLogger;
 use crate::helper::utils;
 use crate::parser::delimited;
 
-use super::args::SequenceRenameArgs;
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::args::SequenceRenameArgs;
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for RenameParser<'_> {}
 impl OutputCli for RenameParser<'_> {}

src/cli/translate.rs → src/cli/sequence/translate.rs

@@ -5,8 +5,8 @@ use crate::helper::logger::AlignSeqLogger;
 use crate::helper::types::GeneticCodes;
 use colored::Colorize;
 
-use super::args::SequenceTranslateArgs;
-use super::{collect_paths, AlignSeqInput, InputCli, OutputCli};
+use crate::cli::args::SequenceTranslateArgs;
+use crate::cli::{collect_paths, AlignSeqInput, InputCli, OutputCli};
 
 impl InputCli for TranslateParser<'_> {}
 impl OutputCli for TranslateParser<'_> {}