VARNA.cs

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using UnityEngine;
using System.Collections;
using System.Diagnostics;
using System.Collections.Generic;
using System.Text;

public class VARNA : MonoBehaviour {
    public static string generateStructureString(int sequenceLength, List<int[]> pairs)
    {
        StringBuilder structure = new StringBuilder(new string('.', sequenceLength), sequenceLength);
        int pair_count = pairs.Count;
        for (int i = 0; i < pair_count; i++) 
        {
            int n1 = pairs[i][0];
            int n2 = pairs[i][1];
            if(n1 > n2) {
                int temp = n1;
                n1 = n2;
                n2 = temp;
            }
            if (n1 <= pair_count && n2 <= pair_count && n1 != n2) {
                structure[n1 - 1] = '(';
                structure[n2 - 1] = ')';
            }
        }
        return structure.ToString();
    }
    
    public static Process generateImage(string sequence, string structure, string outputDirectory, string filename)
    {       
        string cmd = "java";
        ProcessStartInfo startInfo = new ProcessStartInfo(cmd);
        startInfo.WorkingDirectory = outputDirectory;
        startInfo.UseShellExecute = false;
        startInfo.RedirectStandardInput = false;
        startInfo.RedirectStandardOutput = false;
        startInfo.Arguments = "-cp /Users/sebastien/Downloads/VARNAv3-9-src.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN " + sequence + " -structureDBN " + structure + " -o " + filename;
        
        Process process = new Process();
        process.StartInfo = startInfo;
                
        process.EnableRaisingEvents = true;
        
        return process;
    }
}