/*************************************************************************
* *
* 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.metacyc.entities;
import act.installer.metacyc.BPElement;
import act.installer.metacyc.JsonHelper;
import act.installer.metacyc.NXT;
import act.installer.metacyc.OrganismComposition;
import act.installer.metacyc.Resource;
import org.json.JSONObject;
import java.util.HashSet;
import java.util.Set;
public class ProteinRNARef extends BPElement {
Resource organism; // referring to the BioSource this protein is in
String sequence; // protein AA sequence
String standardName;
Set<String> comments;
Set<Resource> memberEntityRef; // references to other proteins?
// we call these when looking up date in OrganismCompositionMongoWriter:getSequence(Catalysis)
public String getSeq() { return this.sequence; }
public Resource getOrg() { return this.organism; }
// Allow access to standard name that was in BPElement
public String getStandardName() {
if (this.standardName == null) {
return super.getStandardName();
} else {
return this.standardName;
}
}
public Set<String> getComments() { return this.comments; }
public Set<Resource> getRefs() { return this.memberEntityRef; }
public ProteinRNARef(BPElement basics, Resource org, String seq, String standardName, Set<String> comments, Set<Resource> memRef) {
super(basics);
this.organism = org;
this.sequence = seq;
this.memberEntityRef = memRef;
}
@Override
public Set<Resource> field(NXT typ) {
Set<Resource> s = new HashSet<Resource>();
if (typ == NXT.organism) {
s.add(this.organism);
}
return s;
}
public JSONObject expandedJSON(OrganismComposition src) {
JsonHelper o = new JsonHelper(src);
o.add("seq", sequence);
if (organism != null)
o.add("org", src.resolve(organism).expandedJSON(src));
if (memberEntityRef != null)
for (BPElement m : src.resolve(memberEntityRef))
o.add("members", m.expandedJSON(src));
return o.getJSON();
}
}
/*
<bp:ProteinReference rdf:ID="ProteinReference1733619">
<bp:organism rdf:resource="#BioSource1698655"/>
<bp:sequence rdf:datatype="http://www.w3.org/2001/ XMLSchema#string">MVTLSPRKRHGGSLKAGRSLQWPRSSR*GVLAIKGSCCRLKQGRGRS* SSPAGWWDVLRGGNLLLCPRGTTYADATLTAIA*RPKCLRAGWCPQLVLSASALWL* PRANMKTNSYLSVDGRSPFDNLF*VACCVVLSSSI*PCRQD*PRACREPRDCSRGLP* KPCTLTQGFDNHFNQAFYLYQAPKRLVYKHELNSFNPRRTSCVGATGKVKQNLLCYVDIIECRERLGYLL*KD* PALALQGITSYSNREQQKPK*GAIKMHRVR*NGTNTVISVKVKV*SRKAKWN* ATGLTLFSFENTVSLLPRLGVRSKGLIGLQSWFIFAVTVVA*AALELVLSQPPE*LGCTTCPHNLSLLSPASHAC* GPWTSGYRLRSWGHPAEGCQGRPLGTLSFDLCWALLLQLPRCRHLQSGCHAVEALTWVQHFDCVPPCLCFTNAVHLAVRGDEG*AHWWAECLLITWLFSEFIC*GRGLRS*VRPFVSLCSILH*VWALAHSLAVRLNIS*AHVAFDHHFLRRAS*LLSG*EHLFSQEGGLFPPELDFA*SSKVFPLEPPILVQVTPALLMALLLGNI*SGDALND*FV* VLGRRLRKAGFRQVQFREFSLFVD*NMTDCKQTTLQMYLNCAEVSCPKV*D*VINCLPTVGVVNEKESVL*KNKIFK* NII</bp:sequence>
<bp:xref rdf:resource="#UnificationXref1733621"/>
<bp:xref rdf:resource="#UnificationXref1733620"/>
<bp:standardName rdf:datatype="http://www.w3.org/2001/ XMLSchema#string">succinate dehydrogenase complex, subunit D, integral membrane protein</bp:standardName>
<bp:comment rdf:datatype="http://www.w3.org/2001/ XMLSchema#string">GO:0005506</bp:comment>
</bp:ProteinReference>
*/