Method removeLuciphorTargetMods_

src/topp/LuciphorAdapter.cpp:343–384

remove all modifications which are LuciPHOr2 target modifications, because for these LuciPHOr2 could predict a different position.

  // remove all modifications which are LuciPHOr2 target modifications,
  // because for these LuciPHOr2 could predict a different position.
  AASequence removeLuciphorTargetMods_(const AASequence& original_seq, const map<String, String>& target_mods_conv)
  {
    if (!original_seq.isModified()) {
      return original_seq;
    }
    
    AASequence seq_converted = AASequence::fromString(original_seq.toUnmodifiedString());
    
    // set C-term/N-term modification
    if (original_seq.hasNTerminalModification())
    {
      seq_converted.setNTerminalModification(original_seq.getNTerminalModificationName());
    }
    if (original_seq.hasCTerminalModification())
    {
      seq_converted.setCTerminalModification(original_seq.getCTerminalModificationName());
    }
    
    // set all modifications, which were not changed by LuciPHOr2
    for (Size i = 0; i < original_seq.size(); ++i)
    {
      if (original_seq.getResidue(i).isModified())
      {
        String mod = original_seq.getResidue(i).getModificationName();
        
        // no target modification, modification can be set
        bool found = false;
        for (map<String, String>::const_iterator iter = target_mods_conv.begin(); iter != target_mods_conv.end() && !found; ++iter)
        {
          if (mod == iter->second)
          {
            found = true;
          }
        }
        if (!found)
        {
          seq_converted.setModification(i, mod);
        }
      }
    }
    return seq_converted;    
  }
  
  // set modifications changed by LuciPHOr2
  ExitCodes setLuciphorTargetMods_(AASequence& seq, String seq_luciphor, const map<String, String>& target_mods_conv)