/**
 *
 * @author rli
 */
package oligo3;
import java.io.File;
import java.io.IOException;
import java.util.Properties;

public class Params {

    static int input_file_mode = 2;
    static int sequence_validation = 0;
    static int ORF_components = 1;
    static int minimum_ORF_length = 66;
    static int oligo_probe_length = 60;
    static float remove_similarity = 0.01f;
    static float eliminate_homology = 0.0f;
    static String parameters_file = "parameters.lst";
    static String input_genes_file = "input-genes.ffn";
    static String output_genes_file = "output-genes.ffn";
    static String out_overlaps_file = "overlap-genes.tdt";
    static String ORF_stats_file = "orf-stats.txt";
    static String ORF_tags_file = "orf-tags.txt";
    static String ORF_start_codons = "atg,gtg,ttg,ctg,att";
    static String ORF_id_prefix = "";
    static Properties params = new Properties();
    public static final String workdir = System.getProperty("user.dir");
    static String input_files_dir = workdir;
    static String output_files_dir = workdir;
    static String usage ="\nUsage: java -jar OliGo3.jar [switches]\n\nSwitches:\n"
    + "\n-p <parameters-file>\n-f <input-genes-file>\n-h <program-usage-info>\n";

    // Load parameters from parameters_file if it is used.
    public static void loadParams() throws IOException {
      if (InputFile.OpenOkay(workdir, parameters_file)) {
      // Read parameters set in parameters_file and override defaults.
        try {
          params.load(InputFile.br);
        } catch (IOException e) {
          System.err.println("I/O File Load Error: " + e.getMessage());
        } catch (IllegalArgumentException e) {
          System.err.println("Illegal Argument Error: " + e.getMessage());
        }
        // Parse and validate loaded parameters
        // Filenames except output have format requirements
        String s = "";
        if ((s = getParam("input_file_mode", "^[123]$"))!= null) {
           input_file_mode = Integer.parseInt(s);
        }
        if ((s = getParam("sequence_validation", "^[01]$"))!= null) {
           sequence_validation = Integer.parseInt(s);
        }
        if ((s = getParam("ORF_components", "^[123]$"))!= null) {
           ORF_components = Integer.parseInt(s);
        }
        if ((s = getParam("minimum_ORF_length", "^\\d{2,}$"))!= null) {
           minimum_ORF_length = Integer.parseInt(s);
        }
        if ((s = getParam("oligo_probe_length", "^\\d{2}$"))!= null) {
           oligo_probe_length = Integer.parseInt(s);
        }
        if ((s = getParam("remove_similarity", "^0?\\.\\d+$"))!= null) {
           remove_similarity = Float.parseFloat(s);
        }
        if ((s = getParam("eliminate_homology", "^0?\\.\\d+$"))!= null) {
           eliminate_homology = Float.parseFloat(s);
        }
        if ((s = getParam("input_files_dir", ""))!= null) {
           input_files_dir = s;
        }
        if (!ParseOptions.flag) {
        if ((s=getParam("input_genes_file","^\\w[\\w\\s\\(\\)\\.,-]*[\\w\\)]*$"))!=null) {
           input_genes_file = s;
        }}
        if ((s = getParam("output_files_dir", ""))!= null) {
           output_files_dir = s;
        }
        if ((s = getParam("output_genes_file", ".+"))!= null) {
           output_genes_file = s;
        }
        if ((s = getParam("out_overlaps_file", ".+"))!= null) {
           out_overlaps_file = s;
        }
        if ((s = getParam("ORF_stats_file", ".+"))!= null) {
           ORF_stats_file = s;
        }
        if ((s = getParam("ORF_tags_file", ".+"))!= null) {
           ORF_tags_file = s;
        }
        // Read in a comma-separated list of strings into ORF_start_codons
        if ((s = getParam("ORF_start_codons", ".+"))!= null) {
           ORF_start_codons = s;
        }
        // Parse and validate ORF start codons fetched from either file or default
        if (!ORF_start_codons.matches("(?i)^(?:[acgt]{3},)*[acgt]{3}$")) {
           System.out.println(ORF_start_codons + ": Invalid start codons!");
           System.exit(1);
        }
        if ((s = params.getProperty("ORF_id_prefix"))== null) {
           System.out.println("The property key ORF_id_prefix is not found.");
           System.exit(1);
        } else if (!s.equals("")) {
           if (s.trim().length() < 5) { //Up to 4 characters
              ORF_id_prefix = s.trim();
           } else {
              System.out.println(s + ": has invalid prefix length!");
              System.exit(1);
           }
        }
        // End of loading and validating parameters
      }
    }

    public static String getParam(String p, String v) throws IOException {
      String s = "";
      if ((s = params.getProperty(p))== null) {
         System.out.println("The property key " + p + " is not found.");
         System.exit(1);
      } else if (s.equals("")) {
         System.out.println("The property key " + p + " has no value."
         + "\nThe default value is used instead.\n");
      } else if (p.endsWith("dir")) {
         // Check and validate the directory of input/output files
         File d = new File(s);
         if (!d.exists()) {
            System.out.println("The directory: " + s + " does not exist.");
            System.exit(1);
         } else if (!d.isDirectory()) {
            System.out.println("The path: " + s + " is not a directory.");
            System.exit(1);
         } else {
           return s.trim();
         }
      } else {
        if (s.trim().matches(v)) {
           return s.trim();
        } else {
           System.out.println(s + ": Invalid parameter!");
           System.exit(1);
        }
      }
      return null;
    }

    public static void printParams() {
      System.out.println("\nThis program will run based on the following settings:\n"
      + "\nparameters_file     = " + parameters_file
      + "\ninput_file_mode     = " + input_file_mode
      + "\ninput_files_dir     = " + input_files_dir
      + "\ninput_genes_file    = " + input_genes_file
      + "\noutput_files_dir    = " + output_files_dir
      + "\noutput_genes_file   = " + output_genes_file
      + "\nout_overlaps_file   = " + out_overlaps_file
      + "\norf_stats_file      = " + ORF_stats_file
      + "\norf_tags_file       = " + ORF_tags_file
      + "\norf_id_prefix       = " + ORF_id_prefix
      + "\nsequence_validation = " + sequence_validation
      + "\norf_start_codons    = " + ORF_start_codons
      + "\norf_components      = " + ORF_components
      + "\nminimum_orf_length  = " + minimum_ORF_length
      + "\noligo_probe_length  = " + oligo_probe_length
      + "\nremove_similarity   = " + remove_similarity
      + "\neliminate_homology  = " + eliminate_homology
      + "\n\nType in -h for help and make your own settings in parameters.lst.\n");
    }
}