<commit_before>package com.bio4j.model.uniprot.vertices;

import com.bio4j.model.enzymedb.vertices.Enzyme;
import com.bio4j.model.go.vertices.GoTerm;
import com.bio4j.model.ncbiTaxonomy.vertices.NCBITaxon;
import com.bio4j.model.uniprot.UniprotGraph;
import com.bio4j.model.uniprot.edges.*;
import com.bio4j.model.uniprot_enzymedb.edges.EnzymaticActivity;
import com.bio4j.model.uniprot_go.edges.GoAnnotation;
import com.bio4j.model.uniprot_ncbiTaxonomy.edges.ProteinNCBITaxon;
import com.bio4j.model.uniprot_uniref.edges.*;
import com.bio4j.model.uniref.vertices.UniRef100Cluster;
import com.bio4j.model.uniref.vertices.UniRef50Cluster;
import com.bio4j.model.uniref.vertices.UniRef90Cluster;
import com.bio4j.angulillos.UntypedGraph;

import java.util.Date;
import java.util.List;
import java.util.Optional;
import java.util.stream.Stream;

/**
 * Created by ppareja on 7/23/2014.
 */
public final class Protein <I extends UntypedGraph<RV, RVT, RE, RET>, RV, RVT, RE, RET>
		extends UniprotGraph.UniprotVertex<
		Protein<I, RV, RVT, RE, RET>,
		UniprotGraph<I, RV, RVT, RE, RET>.ProteinType,
		I, RV, RVT, RE, RET
		> {

	public Protein(RV vertex, UniprotGraph<I, RV, RVT, RE, RET>.ProteinType type) {
		super(vertex, type);
	}

	@Override
	public Protein<I, RV, RVT, RE, RET> self() {
		return this;
	}

	// properties
	public String accession() {
		return get(type().accession);
	}
	public String shortName() {
		return get(type().shortName);
	}
    public String name() { return get(type().name); }
	public String sequence() {
		return get(type().sequence);
	}
	public String fullName() {
	return get(type().fullName);
	}
	public Date modifiedDate() {
		return get(type().modifiedDate);
	}
	public Date createdDate() {
		return get(type().createdDate);
	}
	public String mass() {
		return get(type().mass);
	}
	public Integer version() {
		return get(type().version);
	}
	public Integer length() {
		return get(type().length);
	}

	//////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////////////////
	// relationships
	////////////////////////////////////////////////////////////////////////////////////////////////////////

	// proteinOrganism
	// outgoing
	public ProteinOrganism<I, RV, RVT, RE, RET> proteinOrganism_out(){
		return outOne(graph().ProteinOrganism());
	}
	public Organism<I, RV, RVT, RE, RET>  proteinOrganism_outV(){
		return outOneV(graph().ProteinOrganism());
	}

	// proteinComment
	// outgoing
	public Optional<Stream<ProteinComment<I, RV, RVT, RE, RET>>> proteinComment_out(){
		return outManyOptional(graph().ProteinComment());
	}
	public Optional<Stream<CommentType<I, RV, RVT, RE, RET>>>  proteinComment_outV(){
		return outManyOptionalV(graph().ProteinComment());
	}

	// proteinRefSeq
	// outgoing
	public Optional<Stream<ProteinRefSeq<I, RV, RVT, RE, RET>>> proteinRefSeq_out(){
		return outManyOptional(graph().ProteinRefSeq());
	}
	public Optional<Stream<RefSeq<I, RV, RVT, RE, RET>>>  proteinRefSeq_outV(){
		return outManyOptionalV(graph().ProteinRefSeq());
	}

	// proteinSequenceCaution
	// outgoing
	public Optional<Stream<ProteinSequenceCaution<I, RV, RVT, RE, RET>>> proteinSequenceCaution_out(){
		return outManyOptional(graph().ProteinSequenceCaution());
	}
	public Optional<Stream<SequenceCaution<I, RV, RVT, RE, RET>>>  proteinSequenceCaution_outV(){
		return outManyOptionalV(graph().ProteinSequenceCaution());
	}

	// proteinSubcellularLocation
	// outgoing
	public Optional<Stream<ProteinSubcellularLocation<I, RV, RVT, RE, RET>>> proteinSubcellularLocation_out(){
		return outManyOptional(graph().ProteinSubcellularLocation());
	}
	public Optional<Stream<SubcellularLocation<I, RV, RVT, RE, RET>>>  proteinSubcellularLocation_outV(){
		return outManyOptionalV(graph().ProteinSubcellularLocation());
	}

	// proteinPIR
	// outgoing
	public Optional<Stream<ProteinPIR<I, RV, RVT, RE, RET>>> proteinPIR_out(){
		return outManyOptional(graph().ProteinPIR());
	}
	public Optional<Stream<PIR<I, RV, RVT, RE, RET>>>  proteinPIR_outV(){
		return outManyOptionalV(graph().ProteinPIR());
	}

	// proteinFeature
	// outgoing
	public Optional<Stream<ProteinFeature<I, RV, RVT, RE, RET>>> proteinFeature_out(){
		return outManyOptional(graph().ProteinFeature());
	}
	public Optional<Stream<FeatureType<I, RV, RVT, RE, RET>>>  proteinFeature_outV(){
		return outManyOptionalV(graph().ProteinFeature());
	}

	// proteinEMBL
	// outgoing
	public Optional<Stream<ProteinEMBL<I, RV, RVT, RE, RET>>> proteinEMBL_out(){
		return outManyOptional(graph().ProteinEMBL());
	}
	public Optional<Stream<EMBL<I, RV, RVT, RE, RET>>>  proteinEMBL_outV(){
		return outManyOptionalV(graph().ProteinEMBL());
	}

	// proteinDisease
	// outgoing
	public Optional<Stream<ProteinDisease<I, RV, RVT, RE, RET>>> proteinDisease_out(){
		return outManyOptional(graph().ProteinDisease());
	}
	public Optional<Stream<Disease<I, RV, RVT, RE, RET>>>  proteinDisease_outV(){
		return outManyOptionalV(graph().ProteinDisease());
	}

	// proteinDataset
	// outgoing
	public ProteinDataset<I, RV, RVT, RE, RET> proteinDataset_out(){
		return outOne(graph().ProteinDataset());
	}
	public Dataset<I, RV, RVT, RE, RET>  proteinDataset_outV(){
		return outOneV(graph().ProteinDataset());
	}

	// proteinInterpro
	// outgoing
	public Optional<Stream<ProteinInterpro<I, RV, RVT, RE, RET>>> proteinIntepro_out(){
		return outManyOptional(graph().ProteinInterpro());
	}
	public Optional<Stream<Interpro<I, RV, RVT, RE, RET>>>  proteinInterpro_outV(){
		return outManyOptionalV(graph().ProteinInterpro());
	}

	// proteinReactomeTerm
	// outgoing
	public Optional<Stream<ProteinReactomeTerm<I, RV, RVT, RE, RET>>> proteinReactomeTerm_out(){
		return outManyOptional(graph().ProteinReactomeTerm());
	}
	public Optional<Stream<ReactomeTerm<I, RV, RVT, RE, RET>>>  proteinReactomeTerm_outV(){
		return outManyOptionalV(graph().ProteinReactomeTerm());<commit_msg>Fixed a typo in the method name<commit_after>package com.bio4j.model.uniprot.vertices;

import com.bio4j.model.enzymedb.vertices.Enzyme;
import com.bio4j.model.go.vertices.GoTerm;
import com.bio4j.model.ncbiTaxonomy.vertices.NCBITaxon;
import com.bio4j.model.uniprot.UniprotGraph;
import com.bio4j.model.uniprot.edges.*;
import com.bio4j.model.uniprot_enzymedb.edges.EnzymaticActivity;
import com.bio4j.model.uniprot_go.edges.GoAnnotation;
import com.bio4j.model.uniprot_ncbiTaxonomy.edges.ProteinNCBITaxon;
import com.bio4j.model.uniprot_uniref.edges.*;
import com.bio4j.model.uniref.vertices.UniRef100Cluster;
import com.bio4j.model.uniref.vertices.UniRef50Cluster;
import com.bio4j.model.uniref.vertices.UniRef90Cluster;
import com.bio4j.angulillos.UntypedGraph;

import java.util.Date;
import java.util.List;
import java.util.Optional;
import java.util.stream.Stream;

/**
 * Created by ppareja on 7/23/2014.
 */
public final class Protein <I extends UntypedGraph<RV, RVT, RE, RET>, RV, RVT, RE, RET>
		extends UniprotGraph.UniprotVertex<
		Protein<I, RV, RVT, RE, RET>,
		UniprotGraph<I, RV, RVT, RE, RET>.ProteinType,
		I, RV, RVT, RE, RET
		> {

	public Protein(RV vertex, UniprotGraph<I, RV, RVT, RE, RET>.ProteinType type) {
		super(vertex, type);
	}

	@Override
	public Protein<I, RV, RVT, RE, RET> self() {
		return this;
	}

	// properties
	public String accession() {
		return get(type().accession);
	}
	public String shortName() {
		return get(type().shortName);
	}
    public String name() { return get(type().name); }
	public String sequence() {
		return get(type().sequence);
	}
	public String fullName() {
	return get(type().fullName);
	}
	public Date modifiedDate() {
		return get(type().modifiedDate);
	}
	public Date createdDate() {
		return get(type().createdDate);
	}
	public String mass() {
		return get(type().mass);
	}
	public Integer version() {
		return get(type().version);
	}
	public Integer length() {
		return get(type().length);
	}

	//////////////////////////////////////////////////////////////////////////////////////////////

	////////////////////////////////////////////////////////////////////////////////////////////////////////
	// relationships
	////////////////////////////////////////////////////////////////////////////////////////////////////////

	// proteinOrganism
	// outgoing
	public ProteinOrganism<I, RV, RVT, RE, RET> proteinOrganism_out(){
		return outOne(graph().ProteinOrganism());
	}
	public Organism<I, RV, RVT, RE, RET>  proteinOrganism_outV(){
		return outOneV(graph().ProteinOrganism());
	}

	// proteinComment
	// outgoing
	public Optional<Stream<ProteinComment<I, RV, RVT, RE, RET>>> proteinComment_out(){
		return outManyOptional(graph().ProteinComment());
	}
	public Optional<Stream<CommentType<I, RV, RVT, RE, RET>>>  proteinComment_outV(){
		return outManyOptionalV(graph().ProteinComment());
	}

	// proteinRefSeq
	// outgoing
	public Optional<Stream<ProteinRefSeq<I, RV, RVT, RE, RET>>> proteinRefSeq_out(){
		return outManyOptional(graph().ProteinRefSeq());
	}
	public Optional<Stream<RefSeq<I, RV, RVT, RE, RET>>>  proteinRefSeq_outV(){
		return outManyOptionalV(graph().ProteinRefSeq());
	}

	// proteinSequenceCaution
	// outgoing
	public Optional<Stream<ProteinSequenceCaution<I, RV, RVT, RE, RET>>> proteinSequenceCaution_out(){
		return outManyOptional(graph().ProteinSequenceCaution());
	}
	public Optional<Stream<SequenceCaution<I, RV, RVT, RE, RET>>>  proteinSequenceCaution_outV(){
		return outManyOptionalV(graph().ProteinSequenceCaution());
	}

	// proteinSubcellularLocation
	// outgoing
	public Optional<Stream<ProteinSubcellularLocation<I, RV, RVT, RE, RET>>> proteinSubcellularLocation_out(){
		return outManyOptional(graph().ProteinSubcellularLocation());
	}
	public Optional<Stream<SubcellularLocation<I, RV, RVT, RE, RET>>>  proteinSubcellularLocation_outV(){
		return outManyOptionalV(graph().ProteinSubcellularLocation());
	}

	// proteinPIR
	// outgoing
	public Optional<Stream<ProteinPIR<I, RV, RVT, RE, RET>>> proteinPIR_out(){
		return outManyOptional(graph().ProteinPIR());
	}
	public Optional<Stream<PIR<I, RV, RVT, RE, RET>>>  proteinPIR_outV(){
		return outManyOptionalV(graph().ProteinPIR());
	}

	// proteinFeature
	// outgoing
	public Optional<Stream<ProteinFeature<I, RV, RVT, RE, RET>>> proteinFeature_out(){
		return outManyOptional(graph().ProteinFeature());
	}
	public Optional<Stream<FeatureType<I, RV, RVT, RE, RET>>>  proteinFeature_outV(){
		return outManyOptionalV(graph().ProteinFeature());
	}

	// proteinEMBL
	// outgoing
	public Optional<Stream<ProteinEMBL<I, RV, RVT, RE, RET>>> proteinEMBL_out(){
		return outManyOptional(graph().ProteinEMBL());
	}
	public Optional<Stream<EMBL<I, RV, RVT, RE, RET>>>  proteinEMBL_outV(){
		return outManyOptionalV(graph().ProteinEMBL());
	}

	// proteinDisease
	// outgoing
	public Optional<Stream<ProteinDisease<I, RV, RVT, RE, RET>>> proteinDisease_out(){
		return outManyOptional(graph().ProteinDisease());
	}
	public Optional<Stream<Disease<I, RV, RVT, RE, RET>>>  proteinDisease_outV(){
		return outManyOptionalV(graph().ProteinDisease());
	}

	// proteinDataset
	// outgoing
	public ProteinDataset<I, RV, RVT, RE, RET> proteinDataset_out(){
		return outOne(graph().ProteinDataset());
	}
	public Dataset<I, RV, RVT, RE, RET>  proteinDataset_outV(){
		return outOneV(graph().ProteinDataset());
	}

	// proteinInterpro
	// outgoing
	public Optional<Stream<ProteinInterpro<I, RV, RVT, RE, RET>>> proteinInterpro_out(){
		return outManyOptional(graph().ProteinInterpro());
	}
	public Optional<Stream<Interpro<I, RV, RVT, RE, RET>>>  proteinInterpro_outV(){
		return outManyOptionalV(graph().ProteinInterpro());
	}

	// proteinReactomeTerm
	// outgoing
	public Optional<Stream<ProteinReactomeTerm<I, RV, RVT, RE, RET>>> proteinReactomeTerm_out(){
		return outManyOptional(graph().ProteinReactomeTerm());
	}
	public Optional<Stream<ReactomeTerm<I, RV, RVT, RE, RET>>>  proteinReactomeTerm_outV(){
		return outManyOptionalV(graph().ProteinReactomeTerm());
{'fraction_non_alphanumeric': 0.18911031435003753, 'fraction_numerical': 0.0046693904777787044, 'mean_word_length': 4.189961055819992, 'pattern_counts': {'":': 0, '<': 145, '<?xml version=': 0, '>': 145, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '135597', 'n_tokens_mistral': 4211, 'n_tokens_neox': 3859, 'n_words': 775}