Method startElement

src/openms/source/FORMAT/XTandemXMLFile.cpp:86–327

  }

  void XTandemXMLFile::startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const Attributes& attributes)
  {
    tag_ = String(sm_.convert(qname));

    if (tag_ == "domain")
    {
      String id_string = attributeAsString_(attributes, "id");
      UInt id = id_string.prefix('.').toInt();
      current_id_ = id;

      PeptideEvidence pe;
      // get amino acid before
      String pre = attributeAsString_(attributes, "pre");
      if (!pre.empty())
      {
        pe.setAABefore(pre[pre.size()-1]);
      }
      // get amino acid after
      String post = attributeAsString_(attributes, "post");
      if (!post.empty())
      {
        pe.setAAAfter(post[0]);
      }

      current_start_ = attributeAsInt_(attributes, "start");
      pe.setStart(current_start_ - 1);
      current_stop_ = attributeAsInt_(attributes, "end");
      pe.setEnd(current_stop_ - 1);
        
      pe.setProteinAccession(current_protein_);
 
      String seq = attributeAsString_(attributes, "seq");
      // is this the same peptide as before, just in a different protein (scores will be the same)?
      if ((peptide_hits_.find(id) == peptide_hits_.end()) || (seq != previous_seq_))
      {
        PeptideHit hit;
        // can't parse sequences permissively because that would skip characters
        // that X! Tandem includes when calculating e.g. modification positions,
        // potentially leading to errors when assigning mods to residues:
        hit.setSequence(AASequence::fromString(seq, false));
        hit.setCharge(current_charge_);
        
        // get scores etc.:
        hit.setMetaValue("nextscore", attributeAsDouble_(attributes, "nextscore"));
        hit.setMetaValue("delta", attributeAsDouble_(attributes, "delta"));
        hit.setMetaValue("mass", attributeAsDouble_(attributes, "mh")); // note the different names
        hit.setMetaValue("E-Value", attributeAsDouble_(attributes, "expect")); // note the different names
        double hyperscore = attributeAsDouble_(attributes, "hyperscore");
        hit.setMetaValue("hyperscore", hyperscore);
        hit.setScore(hyperscore);

        // try to get a, b, c, x, y, z score (optional)
        String ions = "abcxyz";
        String ion_score = " _score";
        String ion_count = " _ions";
        for (String::iterator it = ions.begin(); it != ions.end(); ++it)
        {
          ion_score[0] = *it;