/**
 * This class provides commonly used utilities for biological sequence processing
 * @author rli
 */
package oligo3;

public class BioSeq {

    static String se = "";
    static String si = "";
    static int i = 0;
    static int j = 0;

    public static void getSeq(String line) {
      // Build biological sequence from each fasta line
      if (Fasta.key) {
         // Initialize a new sequence
         Fasta.sb = new StringBuilder(line);
         // Turn StringBuilder constructor off
         Fasta.key = false;
      } else {
         // Concatenate sequence lines
         Fasta.sb.append(line);
      }
    }

    public static void getHeader(String line) {
      // Extract fasta header data while its line hits
      if (Fasta.gbk_p0.matcher(line).matches()) {
         Fasta.readNCBI(); // data from GenBank databases
      } else {
         Fasta.readJGI(); // data from JGI and other databases
      }
    }

    public static boolean validSeq(String seq) {
      // Validate biological sequence fetched from each sequence block
      if ((Fasta.m=Fasta.valid_p.matcher(seq)).find()) {
         OutputFile.stats.println("Error in File " + Fasta.file
         + "! Sequence block contains characters (" + Fasta.m.group(1)
         + ") other than ACGT letters, which precedes Header: " + Fasta.line);
         if (Params.sequence_validation > 0) {
            Fasta.ss = seq.substring(0, Fasta.m.start(1));
            if (inFrame(Fasta.ss)) {
               OutputFile.stats.println("Sequence error"
               + " has been fixed and sequence retained.");
            } else {
               OutputFile.stats.println("Sequence error"
               + " cannot be fixed and sequence dropped.");
               return false;
            }
         }
      }
      return true;
    }

    public static int findDupSeq(String seq) {
      // Find duplicate sequence by global alignment
      if (Fasta.e > 0) {
         for (i = Fasta.e - 1; i >= 0; i--) {
          if (seq.equals(ORF.seq.get(i))) break;
         }
         return i;
      }
      return 0;
    }
    
    public static boolean inFrame(String dna) {
      // Check if DNA sequence is in-frame
      for (i=0, j=3; j <= dna.length(); i+=3, j+=3) {
       if ((ORF.m=ORF.stop_cd.matcher(dna).region(i, j)).find()) {
          return true; // stop codon found
       }
      }
      return false; // stop codon not found
    }

    public static void deleteSeq(int i) {
      // Build biological sequence from each fasta line
      ORF.gid.remove(i);
      ORF.acn.remove(i);
      ORF.gsb.remove(i);
      ORF.loc.remove(i);
      ORF.prd.remove(i);
      ORF.seq.remove(i);
    }

    public static void setSeqInfo(int e) {
      // Set gene information for each distinct sequence
      if (ORF.gsb.get(e).equals("gene_symbol")
           && ORF.loc.get(e).equals("gene_locus")
           && ORF.prd.get(e).equals("product_name")) {
         ORF.gsb.set(e, ORF.gid.get(e));
         // Customize a sequence/orf/gene ID
         ORF.gid.set(e, Fasta.text+"_"+String.format("%04d", e+1));
      }
    }

    public static void integrateSeqInfo(int i, int e) {
      // Integrate gene information at element index i with duplicate seq info at element index e
      if (ORF.loc.get(i).equals("gene_locus") && !ORF.loc.get(e).equals("gene_locus")) {
         ORF.loc.set(i, ORF.loc.get(e));
      }
      if (ORF.acn.get(i).equals("gene_accession") && !ORF.acn.get(e).equals("gene_accession")) {
         ORF.acn.set(i, ORF.acn.get(e));
      }
      if ((ORF.gsb.get(i).equals("gene_symbol") && !ORF.gsb.get(e).equals("gene_symbol")) || (
        !ORF.gsb.get(i).matches("^\\w{3,}_\\w*\\d{4}$")&&ORF.gsb.get(e).matches("^\\w{3,}_\\w*\\d{4}$"))) {
         ORF.gsb.set(i, ORF.gsb.get(e));
      }
      if ((ORF.prd.get(i).equals("product_name") && !ORF.prd.get(e).equals("product_name")) || (
         ORF.prd.get(i).matches("(?i)hypothetical") && !ORF.prd.get(e).matches("(?i)hypothetical"))) {
         ORF.prd.set(i, ORF.prd.get(e));
      } else if (!ORF.prd.get(e).matches("(?i)hypothetical") && !ORF.prd.get(e).equals("product_name")) {
        // strip differential characters off product names and lowercase them to make them comparable
        se = ORF.prd.get(e).toLowerCase().replaceAll("[-,\\s]", "");
        si = ORF.prd.get(i).toLowerCase().replaceAll("[-,\\s]", "");
        if (!se.equals(si)) {
           if (se.contains(si)) { // if se contains si
              ORF.prd.set(i, ORF.prd.get(e));
           }
           else if (si.contains(se)) {} // do nothing if si contains se
           else {
            ORF.prd.set(i, ORF.prd.get(i)+"|"+ORF.prd.get(e)); // merge info delimited by |
           }
        }
      }
    }
}