sbml-sim 0.1.2

Simulator for SBML models.
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mod integrators;
use integrators::main::*;
pub mod structs;
pub use structs::assignment_rule::*;
pub use structs::compartment::*;
pub use structs::derivative::*;
pub use structs::initial_assignment::*;
pub use structs::local_parameter::*;
pub use structs::methods::*;
pub use structs::parameter::*;
pub use structs::rate_rule::*;
pub use structs::reaction::*;
pub use structs::species::*;
extern crate clap;
use clap::{App, Arg};

fn main() {
    let matches = App::new("SBML Simulator in Rust")
        .version("1.0")
        .author("Pranav Ballaney <ballaneypranav@gmail.com>")
        .about("A simulator for SBML models.")
        .arg(
            Arg::with_name("INPUT")
                .help("Sets the input file to use")
                .required(true)
                .index(1),
        )
        .arg(
            Arg::with_name("TIME")
                .help("Simulation duration in seconds")
                .required(true),
        )
        .arg(
            Arg::with_name("STEPS")
                .help("Number of steps for numerical integration")
                .required(true),
        )
        .arg(
            Arg::with_name("METHOD")
                .help("Numerical integration algorithm")
                .required(false)
                .possible_values(&Methods::variants())
                .default_value("RKF45"),
        )
        .arg(
            Arg::with_name("RELATIVE_TOLERANCE")
                .help("Relative error tolerance")
                .required(false)
                .default_value("1e-10"),
        )
        .arg(
            Arg::with_name("ABSOLUTE_TOLERANCE")
                .help("Absolute error tolerance")
                .required(false)
                .default_value("1e-16"),
        )
        .arg(
            Arg::with_name("amounts")
                .short("a")
                .help("Print amounts instead of concentrations"),
        )
        .arg(
            Arg::with_name("v")
                .short("v")
                .multiple(true)
                .help("Sets the level of verbosity"),
        )
        .arg(
            Arg::with_name("debug")
                .short("d")
                .help("Print debug information"),
        )
        .get_matches();
    //
    // Vary the output based on how many times the user used the "verbose" flag
    // (i.e. 'myprog -v -v -v' or 'myprog -vvv' vs 'myprog -v'
    match matches.occurrences_of("v") {
        0 => {}
        1 => println!("Some verbose info"),
        2 => println!("Tons of verbose info"),
        _ => println!("Don't be crazy"),
    }

    // Calling .unwrap() is safe here because "INPUT" is required (if "INPUT" wasn't
    // required we could have used an 'if let' to conditionally get the value)
    let filename = matches.value_of("INPUT").unwrap();
    let time = matches.value_of("TIME").unwrap().parse::<f64>().unwrap();
    let steps = matches.value_of("STEPS").unwrap().parse::<i32>().unwrap();
    let method = matches
        .value_of("METHOD")
        .unwrap()
        .parse::<Methods>()
        .unwrap();
    let rtol = matches
        .value_of("RELATIVE_TOLERANCE")
        .unwrap()
        .parse::<f64>()
        .unwrap();
    let atol = matches
        .value_of("ABSOLUTE_TOLERANCE")
        .unwrap()
        .parse::<f64>()
        .unwrap();
    println!("Using {} on input file: {}", method, filename);
    println!("{} seconds with {} steps.", time, steps);

    let DEBUG = matches.is_present("debug");
    let print_amounts = matches.is_present("amounts");

    let step_size = time / (steps as f64);
    let model = sbml_rs::parse_with_converted_species(&filename).expect("Couldn't parse model.");
    let result = integrate(
        &model,
        time,
        steps,
        step_size,
        method,
        rtol,
        atol,
        print_amounts,
        DEBUG,
    )
    .unwrap();

    print!("t           \t");
    // print!("t      ");
    let mut headings = Vec::<String>::new();
    for heading in result.iter().nth(1).unwrap().keys() {
        if heading != "t" {
            headings.push(heading.clone());
        }
    }
    headings.sort();
    for heading in &headings {
        print!("{:24}", heading);
        //print!("{:16}", heading);
    }
    println!();
    for iteration in result.iter().step_by(1) {
        let t = iteration.get("t").unwrap();
        print!("{:.10}\t", t);
        //print!("{:.2}  ", t);
        for heading in &headings {
            print!("{:.20}\t", iteration.get(heading).unwrap());
            //print!("{:.12}\t", iteration.get(heading).unwrap());
        }
        println!();
    }
}