content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package act.installer.sequence;
  
  import java.util.List;
  import java.util.ArrayList;
  import java.util.Set;
  import java.util.HashSet;
  import java.util.HashMap;
  import com.mongodb.DBObject;
  import org.json.JSONObject;
  import org.json.JSONArray;
  import org.json.JSONException;
  import org.json.XML;
  import act.shared.helpers.MongoDBToJSON;
  import act.shared.helpers.P;
  import act.shared.sar.SAR;
  
  public class GenBankEntry extends SequenceEntry {
    JSONObject data;
    JSONObject desc;
  
    public static Set<P<JSONObject, JSONObject>> get_seq_entry_objs(JSONObject root) {
      // differentiates between multiple entries (CASE 1) and single entry (CASE 2)
      //
      // CASE 1:
      // {"Bioseq-set": {"Bioseq-set_seq-set": {"Seq-entry": {"Seq-entry_set": {"Bioseq-set": {
      //     "Bioseq-set_annot": {...}
      //     "Bioseq-set_seq-set": {"Seq-entry": [
      //         {"Seq-entry_seq": {"Bioseq": {
      // CASE 2:
      // {"Bioseq-set": {"Bioseq-set_seq-set": {"Seq-entry": {"Seq-entry_seq": {"Bioseq": {
      // The way we do that is to:
      // a. traverse Bioseq-set -> Bioseq-set_seq-set -> Seq-entry
      // b. check if we encounter a Seq-entry_set (multiple) or Seq-entry_seq (single)
      // c. If multip:
      //      c.A traverse Seq-entry_set -> Bioseq-set
      //      c.B get Seq-entry array within Bioseq-set_seq-set
      //      c.C iterate array and traverse Seq-entry_seq -> Bioseq within each
      // d. If single: traverse Seq-entry_seq -> Bioseq within it
  
      Set<P<JSONObject, JSONObject>> all = new HashSet<P<JSONObject, JSONObject>>();
      // a. traverse Bioseq-set -> Bioseq-set_seq-set -> Seq-entry
      String[] init_path = new String[] { "Bioseq-set", "Bioseq-set_seq-set", "Seq-entry" };
      JSONObject inside = traverse(root, init_path);
  
  
      // b. check if we encounter a Seq-entry_set (multiple) or Seq-entry_seq (single)
      if (inside.has("Seq-entry_set")) { // multiple entries
        System.out.println("###### Received multiple entries");
  
        //      c.A traverse Seq-entry_set -> Bioseq-set
        String[] m_path = new String[] { "Seq-entry_set", "Bioseq-set"};
        JSONObject main = traverse(inside, m_path);
        String[] desc_path = new String[] { "Bioseq-set_descr", "Seq-descr" };
        JSONObject desc = traverse(main, desc_path);
  
        //      c.B get Seq-entry array within Bioseq-set_seq-set
        JSONArray entries = main.getJSONObject("Bioseq-set_seq-set").getJSONArray("Seq-entry");
  
        //      c.C iterate array and traverse Seq-entry_seq -> Bioseq within each
        String[] inside_path = new String[] { "Seq-entry_seq", "Bioseq" };
        for (int i=0; i<entries.length(); i++) {
          JSONObject entry = traverse(entries.getJSONObject(i), inside_path);
          all.add(new P<JSONObject, JSONObject>(entry, desc));
        }
  
      } else { // single entry
  
        // d. If single: traverse Seq-entry_seq -> Bioseq within it
        String[] inside_path = new String[] { "Seq-entry_seq", "Bioseq" };
        JSONObject entry = traverse(inside, inside_path);
        String[] desc_path = new String[] { "Bioseq_descr", "Seq-descr" };
        JSONObject desc = traverse(entry, desc_path);
        all.add(new P<JSONObject, JSONObject>(entry, desc));
  
      }
      return all;
    }
  
    public static Set<SequenceEntry> parsePossiblyMany(String xml) {
  
      // This file is written to handle rettype=native calls. (Output has Bioseq_ etc.)
      // The alternative call of using rettype=fasta returns compact seq data
      //      but is formatted differently (with TSeq_ etc.)
      // See examples at the end of this file.
  
      Set<SequenceEntry> all_entries = new HashSet<SequenceEntry>();
      JSONObject jo = null;
      try {
        jo = XML.toJSONObject(xml);
        Set<P<JSONObject, JSONObject>> seq_entries = get_seq_entry_objs(jo);
        for (P<JSONObject, JSONObject> gene_entry : seq_entries) {
          try {
            GenBankEntry entry = new GenBankEntry(gene_entry.fst(), gene_entry.snd());
            all_entries.add(entry);
          } catch (JSONException e) {
  
            System.out.println("Data: " + gene_entry.fst().toString(4));
            System.out.println("Desc: " + gene_entry.snd().toString(4));
            System.out.println("Failed to extract some field in Genbank. Err: " + e);
          }
        }
      } catch (JSONException e) {
  
        System.out.println("Failed to parse GenBank XML. Err: " + e);
  
      }
      return all_entries;
    }
  
    private GenBankEntry(JSONObject gene_entry, JSONObject desc_entry) {
      this.data = gene_entry;
      this.desc = desc_entry;
  
      this.accessions = extract_accessions();
      this.refs = extract_pmids();
      this.org_id = extract_org_id();
      this.sequence = extract_seq();
      this.ec = extract_ec();
  
      // inits this.catalyzed_{rxns, substrates, products}
      // optionally; if there are some that we NLP out of the
      // "catalysis activity" field read from this entry
      extract_catalyzed_reactions();
  
      // new Seq(..) looks at the metadata in this.data for SwissProt fields:
      // this.data { "name" : gene_name_eg_Adh1 }
      // this.data { "proteinExistence": { "type" : "evidence at transcript level" });
      // this.data { "comment": [ { "type": "catalytic activity", "text": uniprot_activity_annotation } ] }
      // this.data { "accession" : ["Q23412", "P87D78"] }
      // we manually add these fields so that we have consistent data
      JSONArray accs = new JSONArray();
      for (String a : this.accessions)
        accs.put(a);
      JSONObject evidence = new JSONObject(), activity = new JSONObject();
      String name = "";
  
      this.data.put("name", name);
      this.data.put("proteinExistence", evidence);
      this.data.put("comment", new JSONArray(new JSONObject[] { activity }));
      this.data.put("accession", accs);
  
      // extract_metadata processes this.data, so do that only after updating
      // this.data with the proxy fields from above.
      this.metadata = extract_metadata();
    }
  
    DBObject metadata;
    Set<String> accessions;
    List<JSONObject> refs;
    String sequence;
    Long org_id;
    String ec;
    Set<Long> catalyzed_rxns;
    Set<Long> catalyzed_substrates_diverse, catalyzed_substrates_uniform;
    Set<Long> catalyzed_products_diverse, catalyzed_products_uniform;
    HashMap<Long, Set<Long>> catalyzed_rxns_to_substrates, catalyzed_rxns_to_products;
    SAR sar;
  
    DBObject getMetadata() { return this.metadata; }
    Set<String> getAccessions() { return this.accessions; }
    List<JSONObject> getRefs() { return this.refs; }
    Long getOrgId() { return this.org_id; }
    String getSeq() { return this.sequence; }
    String getEc() { return this.ec; }
    Set<Long> getCatalyzedRxns() { return this.catalyzed_rxns; }
    Set<Long> getCatalyzedSubstratesUniform() { return this.catalyzed_substrates_uniform; }
    Set<Long> getCatalyzedSubstratesDiverse() { return this.catalyzed_substrates_diverse; }
    Set<Long> getCatalyzedProductsUniform() { return this.catalyzed_products_uniform; }
    Set<Long> getCatalyzedProductsDiverse() { return this.catalyzed_products_diverse; }
    HashMap<Long, Set<Long>> getCatalyzedRxnsToSubstrates() { return this.catalyzed_rxns_to_substrates; }
    HashMap<Long, Set<Long>> getCatalyzedRxnsToProducts() { return this.catalyzed_rxns_to_products; }
    SAR getSar() { return this.sar; }
  
    private DBObject extract_metadata() {
      // cannot directly return this.data coz in Seq.java
      // we expect certain specific JSON format fields
      return MongoDBToJSON.conv(this.data);
    }
  
    private Set<String> extract_accessions() {
      Set<String> accessions = new HashSet<String>();
      // "Bioseq_id": {"Seq-id": [
      //     {"Seq-id_ddbj": {"Textseq-id": {
      //         "Textseq-id_version": 1,
      //         "Textseq-id_accession": "E07950"
  
  
      accessions.addAll(extract_accessions_under("Seq-id_ddbj"));
      accessions.addAll(extract_accessions_under("Seq-id_embl"));
      accessions.addAll(extract_accessions_under("Seq-id_genbank"));
      accessions.addAll(extract_accessions_under("Seq-id_swissprot"));
      accessions.addAll(extract_accessions_under("Seq-id_other"));
  
      if (accessions.size() == 0) {
        System.out.println("Got 0 accessions from: " + this.data.toString(2));
        System.console().readLine();
      }
      return accessions;
    }
  
    Set<String> extract_accessions_under(String key) {
      Set<String> accessions = new HashSet<String>();
      String[] initpath = new String[] {"Bioseq_id"};
      Set<JSONObject> os = get_inarray(this.data, key, initpath, "Seq-id");
      for (JSONObject o : os)
        accessions.add(o.getJSONObject(key).getJSONObject("Textseq-id").getString("Textseq-id_accession"));
      return accessions;
    }
  
    private Set<JSONObject> get_desc_obj(String haskey) {
      // the description object is a wierd beast: need it for get_org_id + get_pmids
      // 1. We have to traverse down to this.data -> "Bioseq_descr" -> "Seq-descr" -> "Seqdesc" : JSONArray
      // 2. Then within this array there are objects like below:
      //        {"Seqdesc_title": "gDNA encoding NAD synthetase."},
      //        {"Seqdesc_comment": "OS   Bacillus ste ...
      //        {"Seqdesc_genbank": {"GB-block": { ...
      //        {"Seqdesc_pub": {"Pubdesc": {"Pubdesc_pub": {"Pub-equiv": {"Pub": {"Pub_patent ...
      //        {"Seqdesc_source": {"BioSource": {"BioSource_org": {"Org-ref": {  ...
      //        {"Seqdesc_update-date": {"Date": ...
      //        {"Seqdesc_create-date": {"Date":
      //
      // For get_org_id and get_pmids we have to retrieve the objects that have fields
      // Seqdesc_source and Seqdesc_pub, respectively. We first get the array and then search
      // each object within it for one that has the @param field
  
      return get_inarray(this.desc, haskey, new String[] {}, "Seqdesc");
    }
  
    private Set<JSONObject> get_inarray(JSONObject in_obj, String has_key, String[] initpath, String pathend) {
      Set<JSONObject> objs_having_key = new HashSet<JSONObject>();
  
      JSONObject container = traverse(in_obj, initpath);
      Object x = container.get(pathend);
      if (x instanceof JSONArray) {
        JSONArray desc_array = (JSONArray)x;
  
        for (int i=0; i<desc_array.length(); i++) {
          JSONObject o = desc_array.getJSONObject(i);
          if (o.has(has_key))
            objs_having_key.add(o);
        }
      } else if (x instanceof JSONObject) {
        JSONObject o = (JSONObject)x;
        if (o.has(has_key))
          objs_having_key.add(o);
      }
  
      return objs_having_key;
    }
  
    void extract_catalyzed_reactions() {
      // optionally add reactions to actfamilies by processing
      // "catalytic activity" annotations and then return those
      // catalyzed reaction ids (Long _id of actfamilies). This
      // function SHOULD NOT infer which actfamilies refer to
      // this object, as that is done in map_seq install.
      this.catalyzed_rxns = new HashSet<Long>();
      this.catalyzed_substrates_uniform = new HashSet<Long>();
      this.catalyzed_substrates_diverse = new HashSet<Long>();
      this.catalyzed_products_diverse = new HashSet<Long>();
      this.catalyzed_products_uniform = new HashSet<Long>();
      this.catalyzed_rxns_to_substrates = new HashMap<Long, Set<Long>>();
      this.catalyzed_rxns_to_products = new HashMap<Long, Set<Long>>();
      this.sar = new SAR();
    }
  
    private List<JSONObject> extract_pmids() {
      // See comments in get_desc_obj for how we traverse to an array
      // and then find an object within with a particular field
  
      List<String> pmids = new ArrayList<String>();
      // the pub's contain patents (and probably paper references)
      // For patents it looks like:
      // {"Seqdesc_pub": {"Pubdesc": {"Pubdesc_pub": {"Pub-equiv": {"Pub": {"Pub_patent": {"Cit-pat": { ...
      // For publications it looks like:
      // {"Seqdesc_pub": {"Pubdesc": {"Pubdesc_pub": {"Pub-equiv": {"Pub": [
      //     {"Pub_article": {"Cit-art": {...
      //     {"Pub_pmid": {"PubMedId": 15057458}}
      Set<JSONObject> sourceflds = get_desc_obj("Seqdesc_pub") ;
      for (JSONObject sourcefld : sourceflds) {
        String[] toPub_path = new String[] { "Seqdesc_pub", "Pubdesc", "Pubdesc_pub", "Pub-equiv" };
        Set<JSONObject> o = get_inarray(sourcefld, "Pub_pmid", toPub_path, "Pub");
        for (JSONObject pmid_obj : o)
          pmids.add(pmid_obj.getJSONObject("Pub_pmid").getInt("PubMedId") + "");
      }
  
      List<JSONObject> pmidReferences = new ArrayList<>();
      for (String pmid : pmids) {
        JSONObject obj = new JSONObject();
        obj.put("val", pmid);
        obj.put("src", "PMID");
        pmidReferences.add(obj);
      }
  
      return pmidReferences;
    }
  
    private Long extract_org_id() {
      // See comments in get_desc_obj for how we traverse to an array
      // and then find an object within with a particular field
  
      Long org_id = null;
      Set<JSONObject> sourceflds = get_desc_obj("Seqdesc_source") ;
      if (sourceflds.size() > 1)
        System.out.println("WARN: Genbank entry has more than one source organism id.");
      for (JSONObject sourcefld : sourceflds) {
        String[] path = new String[] { "Seqdesc_source", "BioSource", "BioSource_org", "Org-ref",
                                        "Org-ref_db", "Dbtag", "Dbtag_tag", "Object-id" };
        JSONObject o = traverse(sourcefld, path);
        org_id = new Long(o.getInt("Object-id_id"));
      }
  
      if (org_id == null) {
        System.out.println("org_id == null. Multiple entries? We dont traverse down to the right desc for that case");
        System.console().readLine();
      }
      return org_id;
  
      // We have to navigate this structure to get to the Object-id_id value...
      //
      //  {"Seqdesc_source": {"BioSource": {"BioSource_org": {"Org-ref": {
      //      "Org-ref_orgname": {"OrgName": {
      //          "OrgName_lineage": "Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus",
      //          "OrgName_div": "BCT",
      //          "OrgName_mod": {"OrgMod": {
      //              "OrgMod_subtype": {
      //                  "value": "old-name",
      //                  "content": 254
      //              },
      //              "OrgMod_subname": "Bacillus stearothermophilus"
      //          }},
      //          "OrgName_name": {"OrgName_name_binomial": {"BinomialOrgName": {
      //              "BinomialOrgName_genus": "Geobacillus",
      //              "BinomialOrgName_species": "stearothermophilus"
      //          }}},
      //          "OrgName_gcode": 11
      //      }},
      //      "Org-ref_taxname": "Geobacillus stearothermophilus",
      //      "Org-ref_db": {"Dbtag": {
      //          "Dbtag_tag": {"Object-id": {"Object-id_id": 1422}},
      //          "Dbtag_db": "taxon"
      //      }}
      //  }}}}},
    }
  
    private String extract_seq() {
      // "Bioseq_inst": {"Seq-inst": {
      //    "Seq-inst_mol": {"value": "dna"},
      //    "Seq-inst_length": 1238,
      //    "Seq-inst_seq-data": {"Seq-data": {"Seq-data_iupacna": {"IUPACna": "GCATGCGCTCT
      // OR
      // "Bioseq_inst": {"Seq-inst": {
      //   "Seq-inst_mol": {"value": "aa"},
      //   "Seq-inst_length": 770,
      //   "Seq-inst_seq-data": {"Seq-data": {"Seq-data_iupacaa": {"IUPACaa": "MTT
  
      String pathend_e, seq_e;
      String[] type_path = new String[] {"Bioseq_inst", "Seq-inst", "Seq-inst_mol" };
      String seq_type = traverse(this.data, type_path).getString("value");
      // seq_type == dna | rna | aa
      boolean dna = "dna".equals(seq_type);
      boolean rna = "rna".equals(seq_type);
  
      if (dna || rna) { // NT seq
        pathend_e = "Seq-data_iupacna";
        seq_e = "IUPACna";
      } else { // AA seq
        pathend_e = "Seq-data_iupacaa";
        seq_e = "IUPACaa";
      }
      String[] seq_path = new String[] {"Bioseq_inst", "Seq-inst", "Seq-inst_seq-data", "Seq-data", pathend_e };
      JSONObject o = traverse(this.data, seq_path);
      String seq = o.getString(seq_e);
      return seq;
    }
  
    private String extract_ec() {
      // genbank entries dont seem to have the ec#
      return null;
    }
  
    static JSONObject traverse(JSONObject container, String[] xpath) {
      return traverse(container, xpath, 0);
    }
  
    static JSONObject traverse(JSONObject container, String[] xpath, int idx) {
      if (idx == xpath.length)
        return container;
      else
        return traverse(container.getJSONObject(xpath[idx]), xpath, idx + 1);
    }
  
    public String toString() {
      return this.desc.toString() + " -> " + this.data.toString();
    }
  
  }
  
  /*
  Difference between rettype=native and rettype=fasta for NCBI genbank calls.
  
  E.g.,
  Case A]  16     lines in curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=GI:6320033&rettype=fasta&retmode=xml"
  Case B]  3209 lines in curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=GI:6320033&rettype=native&retmode=xml" | wc -l
  
  Case A] 16 lines from "fasta" have format:
  {
    "TSeqSet": {
      "TSeq": {
        "TSeq_seqtype": { "-value": "protein" },
        "TSeq_gi": "6320033",
        "TSeq_accver": "NP_010113.1",
        "TSeq_taxid": "559292",
        "TSeq_orgname": "Saccharomyces cerevisiae S288c",
        "TSeq_defline": "bifunctional alcohol dehydrogenase/S-(hydroxymethyl)glutathione dehydrogenase [Saccharomyces cerevisiae S288c]",
        "TSeq_length": "386",
        "TSeq_sequence": "MSAATVGKPIKCIAAVAYDAKKPLSVEEITVDAPKAHEVRIKIEYTAVCHTDAYTLSGSDPEGLFPCVLGHEGAGIVESVGDDVITVKPGDHVIALYTAECGKCKFCTSGKTNLCGAVRATQGKGVMPDGTTRFHNAKGEDIYHFMGCSTFSEYTVVADVSVVAIDPKAPLDAACLLGCGVTTGFGAALKTANVQKGDTVAVFGCGTVGLSVIQGAKLRGASKIIAIDINNKKKQYCSQFGATDFVNPKEDLAKDQTIVEKLIEMTDGGLDFTFDCTGNTKIMRDALEACHKGWGQSIIIGVAAAGEEISTRPFQLVTGRVWKGSAFGGIKGRSEMGGLIKDYQKGALKVEEFITHRRPFKEINQAFEDLHNGDCLRTVLKSDEIK"
      }
    }
  }
  
  Case B] 3k lines (can go upto 1M+) from "native" have format:
  {
    "Bioseq-set": {
      "Bioseq-set_seq-set": {
        "Seq-entry": {
          "Seq-entry_set": {
            "Bioseq-set": {
              "Bioseq-set_class": { "-value": "nuc-prot" },
              "Bioseq-set_descr": {
                "Seq-descr": {
                  "Seqdesc": [
                    {
                      "Seqdesc_source": {
                        "BioSource": {
                          "BioSource_genome": {
                            "-value": "chromosome",
                            "#text": "21"
                          },
                          "BioSource_org": {
                            "Org-ref": {
                              "Org-ref_taxname": "Saccharomyces cerevisiae S288c",
                              "Org-ref_db": {
                                "Dbtag": {
                                  "Dbtag_db": "taxon",
                                  "Dbtag_tag": {
                                    "Object-id": { "Object-id_id": "559292" }
                                  }
                                }
                              },
                              "Org-ref_orgname": {
                                "OrgName": {
                                  "OrgName_name": {
                                    "OrgName_name_binomial": {
                                      "BinomialOrgName": {
                                        "BinomialOrgName_genus": "Saccharomyces",
                                        "BinomialOrgName_species": "cerevisiae"
                                      }
                                    }
                                  },
                                  "OrgName_mod": {
                                    "OrgMod": {
                                      "OrgMod_subtype": {
                                        "-value": "strain",
                                        "#text": "2"
                                      },
                                      "OrgMod_subname": "S288c"
                                    }
                                  },
                                  "OrgName_lineage": "Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces",
                                  "OrgName_gcode": "1",
                                  "OrgName_mgcode": "3",
                                  "OrgName_div": "PLN"
                                }
                              }
                            }
                          },
                          "BioSource_subtype": {
                            "SubSource": {
                              "SubSource_subtype": {
                                "-value": "chromosome",
                                "#text": "1"
                              },
                              "SubSource_name": "IV"
                            }
                          }
                        }
                      }
                    },
                    {
                      "Seqdesc_pub": {
                        "Pubdesc": {
                          "Pubdesc_pub": {
                            "Pub-equiv": {
                              "Pub": {
                                "Pub_sub": {
                                  "Cit-sub": {
                                    "Cit-sub_authors": {
                                      "Auth-list": {
                                        "Auth-list_names": {
                                          "Auth-list_names_std": {
                                            "Author": {
                                              "Author_name": {
                                                "Person-id": { "Person-id_consortium": "Saccharomyces Genome Database" }
                                              }
                                            }
                                          }
                                        },
                                        "Auth-list_affil": {
                                          "Affil": {
                                            "Affil_std": {
                                              "Affil_std_affil": "Stanford University",
                                              "Affil_std_div": "Department of Genetics",
                                              "Affil_std_city": "Stanford",
                                              "Affil_std_sub": "CA",
                                              "Affil_std_country": "USA",
                                              "Affil_std_postal-code": "94305-5120"
                                            }
                                          }
                                        }
                                      }
                                    },
                                    "Cit-sub_date": {
                                      "Date": {
                                        "Date_std": {
                                          "Date-std": {
                                            "Date-std_year": "2009",
                                            "Date-std_month": "12",
                                            "Date-std_day": "11"
                                          }
                                        }
                                      }
                                    }
                                  }
                                }
                              }
                            }
                          }
                        }
                      }
                    },
                    {
                      "Seqdesc_pub": {
                        "Pubdesc": {
                          "Pubdesc_pub": {
                            "Pub-equiv": {
                              "Pub": [
                                {
                                  "Pub_article": {
                                    "Cit-art": {
                                      "Cit-art_title": {
                                        "Title": {
                                          "Title_E": { "Title_E_name": "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." }
                                        }
                                      },
                                      "Cit-art_authors": {
                                        "Auth-list": {
                                          "Auth-list_names": {
                                            "Auth-list_names_std": {
                                              "Author": [
                                                {
                                                  "Author_name": {
                                                    "Person-id": {
                                                      "Person-id_name": {
                                                        "Name-std": {
                                                          "Name-std_last": "Jacq",
                                                          "Name-std_first": "C",
                                                          "Name-std_initials": "C."
                                                        }
                                                      }
                                                    }
                                                  }
                                                },
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                                      "Seq-feat_ext": {
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                                          "User-object_data": {
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                                                "User-field_label": {
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                                                "User-field_data": { "User-field_data_real": "1" }
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                                              {
                                                "User-field_label": {
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                                                "User-field_data": { "User-field_data_int": "3" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "specific" }
                                                },
                                                "User-field_data": {
                                                  "User-field_data_bool": { "-value": "true" }
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                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "nonredundant" }
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                                                "User-field_data": {
                                                  "User-field_data_bool": { "-value": "true" }
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                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "definition" }
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                                                "User-field_data": { "User-field_data_str": "cd08300" }
                                              },
                                              {
                                                "User-field_label": {
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                                                "User-field_data": { "User-field_data_str": "alcohol_DH_class_III" }
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                                              {
                                                "User-field_label": {
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                                                },
                                                "User-field_data": { "User-field_data_int": "9" }
                                              },
                                              {
                                                "User-field_label": {
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                                                "User-field_data": { "User-field_data_int": "380" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "score" }
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                                                "User-field_data": { "User-field_data_int": "1838" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "evalue" }
                                                },
                                                "User-field_data": { "User-field_data_real": "0" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "bit_score" }
                                                },
                                                "User-field_data": { "User-field_data_real": "711.692" }
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                                            ]
                                          }
                                        }
                                      },
                                      "Seq-feat_dbxref": {
                                        "Dbtag": {
                                          "Dbtag_db": "CDD",
                                          "Dbtag_tag": {
                                            "Object-id": { "Object-id_id": "176260" }
                                          }
                                        }
                                      }
                                    },
                                    {
                                      "Seq-feat_data": {
                                        "SeqFeatData": {
                                          "SeqFeatData_site": { "-value": "other" }
                                        }
                                      },
                                      "Seq-feat_comment": "structural Zn binding site [ion binding]",
                                      "Seq-feat_location": {
                                        "Seq-loc": {
                                          "Seq-loc_mix": {
                                            "Seq-loc-mix": {
                                              "Seq-loc": [
                                                {
                                                  "Seq-loc_pnt": {
                                                    "Seq-point": {
                                                      "Seq-point_point": "100",
                                                      "Seq-point_id": {
                                                        "Seq-id": { "Seq-id_gi": "6320033" }
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                                                },
                                                {
  
                                                },
                                                {
                                                  "Seq-loc_pnt": {
                                                    "Seq-point": {
                                                      "Seq-point_point": "103",
                                                      "Seq-point_id": {
                                                        "Seq-id": { "Seq-id_gi": "6320033" }
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                                                  }
                                                },
                                                {
  
                                                },
                                                {
                                                  "Seq-loc_pnt": {
                                                    "Seq-point": {
                                                      "Seq-point_point": "106",
                                                      "Seq-point_id": {
                                                        "Seq-id": { "Seq-id_gi": "6320033" }
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                                                },
                                                {
  
                                                },
                                                {
                                                  "Seq-loc_pnt": {
                                                    "Seq-point": {
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                                                      "Seq-point_id": {
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                                              ]
                                            }
                                          }
                                        }
                                      },
                                      "Seq-feat_ext": {
                                        "User-object": {
                                          "User-object_type": {
                                            "Object-id": { "Object-id_str": "cddSiteScoreData" }
                                          },
                                          "User-object_data": {
                                            "User-field": [
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                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "completeness" }
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                                                "User-field_data": { "User-field_data_real": "1" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "feature-ID" }
                                                },
                                                "User-field_data": { "User-field_data_int": "4" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "specific" }
                                                },
                                                "User-field_data": {
                                                  "User-field_data_bool": { "-value": "true" }
                                                }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "nonredundant" }
                                                },
                                                "User-field_data": {
                                                  "User-field_data_bool": { "-value": "true" }
                                                }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "definition" }
                                                },
                                                "User-field_data": { "User-field_data_str": "cd08300" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "short_name" }
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                                                "User-field_data": { "User-field_data_str": "alcohol_DH_class_III" }
                                              },
                                              {
                                                "User-field_label": {
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                                                "User-field_data": { "User-field_data_int": "9" }
                                              },
                                              {
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                                                "User-field_data": { "User-field_data_int": "380" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "score" }
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                                                "User-field_data": { "User-field_data_int": "1838" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "evalue" }
                                                },
                                                "User-field_data": { "User-field_data_real": "0" }
                                              },
                                              {
                                                "User-field_label": {
                                                  "Object-id": { "Object-id_str": "bit_score" }
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                                                "User-field_data": { "User-field_data_real": "711.692" }
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                                          }
                                        }
                                      },
                                      "Seq-feat_dbxref": {
                                        "Dbtag": {
                                          "Dbtag_db": "CDD",
                                          "Dbtag_tag": {
                                            "Object-id": { "Object-id_id": "176260" }
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                                      }
                                    }
                                  ]
                                }
                              }
                            }
                          ]
                        }
                      }
                    }
                  }
                ]
              },
              "Bioseq-set_annot": {
                "Seq-annot": {
                  "Seq-annot_data": {
                    "Seq-annot_data_ftable": {
                      "Seq-feat": {
                        "Seq-feat_data": {
                          "SeqFeatData": {
                            "SeqFeatData_cdregion": {
                              "Cdregion": {
                                "Cdregion_frame": { "-value": "one" },
                                "Cdregion_code": {
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                                    "Genetic-code_E": { "Genetic-code_E_id": "1" }
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                              }
                            }
                          }
                        },
                        "Seq-feat_comment": "Bifunctional alcohol dehydrogenase and formaldehyde dehydrogenase; formaldehyde dehydrogenase activity is glutathione-dependent; functions in formaldehyde detoxification and formation of long chain and complex alcohols, regulated by Hog1p-Sko1p; protein abundance increases in response to DNA replication stress",
                        "Seq-feat_product": {
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                            "Seq-loc_whole": {
                              "Seq-id": { "Seq-id_gi": "6320033" }
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                        },
                        "Seq-feat_location": {
                          "Seq-loc": {
                            "Seq-loc_int": {
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                                "Seq-interval_to": "1160",
                                "Seq-interval_strand": {
                                  "Na-strand": { "-value": "plus" }
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                                "Seq-interval_id": {
                                  "Seq-id": { "Seq-id_gi": "296143201" }
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                        "Seq-feat_dbxref": {
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                            "Dbtag_db": "SGD",
                            "Dbtag_tag": {
                              "Object-id": { "Object-id_str": "S000002327" }
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                        }
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  }
  
  */
  