use dna_parsing::base::Base;
use dna_parsing::parser::Parser;
use std::env;
use std::fs;
use std::io;
use std::io::Write;

fn main() {
    let args: Vec<String> = env::args().collect();
    if args.len() < 3 {
        println!("Usage: {} <dna file> <offset>", args[0]);
        return;
    }

    let Ok(dna) = fs::read_to_string(&args[1]) else {
        println!("Failed to read dna file at {}", &args[1]);
        return;
    };
    let Ok(offset): Result<usize, _> = args[2].parse() else {
        println!("Failed to parse offset {}", &args[2]);
        return;
    };

    let mut index = 0;
    loop {
        print!("> ");
        let _ = io::stdout().flush();
        let mut line = String::new();
        if !io::stdin().read_line(&mut line).is_ok() {
            println!("Failed to read response line");
            return;
        }
        line = line.trim().to_string();
        if !line.is_empty() {
            let Ok(new_index): Result<usize, _> = line.parse() else {
                println!("Failed to parse {}", line);
                continue;
            };
            index = new_index;
        }

        let mut parser = Parser::new(
            dna[index + offset..]
                .chars()
                .filter_map(|c| Base::from_char(c)),
        );
        let mut rna = Vec::new();
        let Some(pattern) = parser.pattern(&mut rna) else {
            println!("Failed to parse pattern");
            continue;
        };
        let Some(template) = parser.template(&mut rna) else {
            println!("Failed to parse template");
            continue;
        };

        if !rna.is_empty() {
            println!("RNA output:");
            for r in rna.iter() {
                let rna_str: String = r.iter().map(|b| b.to_char()).collect();
                println!("    {}", rna_str);
            }
            println!();
        }
        println!("{} ; {} ;", pattern, template);
        index += parser.index();
        println!("Now at: {}", index);
    }
}