segul 0.18.1

An ultrafast and memory efficient alignment tool for phylogenomics
Documentation 
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use std::path::PathBuf;

use clap::ArgMatches;

use crate::cli::{ConcatCli, InputCli, InputPrint, OutputCli};
use crate::handler::concat::ConcatHandler;
use crate::helper::filenames;

impl ConcatCli for ConcatParser<'_> {}
impl InputPrint for ConcatParser<'_> {}
impl OutputCli for ConcatParser<'_> {}
impl InputCli for ConcatParser<'_> {}

pub(in crate::cli) struct ConcatParser<'a> {
    matches: &'a ArgMatches,
    input_dir: Option<PathBuf>,
}

impl<'a> ConcatParser<'a> {
    pub(in crate::cli) fn new(matches: &'a ArgMatches) -> Self {
        Self {
            matches,
            input_dir: None,
        }
    }

    pub(in crate::cli) fn concat(&mut self) {
        let input_fmt = self.parse_input_fmt(self.matches);
        let datatype = self.parse_datatype(self.matches);
        let output_fmt = self.parse_output_fmt(self.matches);
        let dir = self.parse_output(self.matches);
        let prefix = self.parse_prefix(self.matches, &dir);
        let output = filenames::create_output_fname(&dir, &prefix, &output_fmt);
        let part_fmt = self.parse_partition_fmt(self.matches);
        self.check_partition_format(&output_fmt, &part_fmt);
        let task_desc = "Alignment concatenation";
        let mut files = if self.matches.is_present("dir") {
            let dir = self.parse_dir_input(self.matches);
            self.input_dir = Some(PathBuf::from(dir));
            self.get_files(dir, &input_fmt)
        } else {
            self.parse_input(self.matches)
        };
        self.print_input(
            &self.input_dir,
            task_desc,
            files.len(),
            &input_fmt,
            &datatype,
        );

        let is_overwrite = self.parse_overwrite_opts(self.matches);
        self.check_output_dir_exist(&dir, is_overwrite);

        let mut concat = ConcatHandler::new(&input_fmt, &output, &output_fmt, &part_fmt);
        concat.concat_alignment(&mut files, &datatype);
    }
}