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org.intermine.model.bio.SOTermShadow Maven / Gradle / Ivy
package org.intermine.model.bio;
import org.intermine.objectstore.ObjectStore;
import org.intermine.objectstore.intermine.NotXmlParser;
import org.intermine.objectstore.intermine.NotXmlRenderer;
import org.intermine.objectstore.proxy.ProxyCollection;
import org.intermine.objectstore.proxy.ProxyReference;
import org.intermine.model.StringConstructor;
import org.intermine.metadata.TypeUtil;
import org.intermine.util.DynamicUtil;
import org.intermine.model.ShadowClass;
public class SOTermShadow implements SOTerm, ShadowClass
{
public static final Class shadowOf = SOTerm.class;
// Attr: org.intermine.model.bio.OntologyTerm.identifier
protected java.lang.String identifier;
public java.lang.String getIdentifier() { return identifier; }
public void setIdentifier(final java.lang.String identifier) { this.identifier = identifier; }
// Attr: org.intermine.model.bio.OntologyTerm.description
protected java.lang.String description;
public java.lang.String getDescription() { return description; }
public void setDescription(final java.lang.String description) { this.description = description; }
// Attr: org.intermine.model.bio.OntologyTerm.obsolete
protected java.lang.Boolean obsolete;
public java.lang.Boolean getObsolete() { return obsolete; }
public void setObsolete(final java.lang.Boolean obsolete) { this.obsolete = obsolete; }
// Attr: org.intermine.model.bio.OntologyTerm.name
protected java.lang.String name;
public java.lang.String getName() { return name; }
public void setName(final java.lang.String name) { this.name = name; }
// Attr: org.intermine.model.bio.OntologyTerm.namespace
protected java.lang.String namespace;
public java.lang.String getNamespace() { return namespace; }
public void setNamespace(final java.lang.String namespace) { this.namespace = namespace; }
// Ref: org.intermine.model.bio.OntologyTerm.ontology
protected org.intermine.model.InterMineObject ontology;
public org.intermine.model.bio.Ontology getOntology() { if (ontology instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Ontology) ((org.intermine.objectstore.proxy.ProxyReference) ontology).getObject()); }; return (org.intermine.model.bio.Ontology) ontology; }
public void setOntology(final org.intermine.model.bio.Ontology ontology) { this.ontology = ontology; }
public void proxyOntology(final org.intermine.objectstore.proxy.ProxyReference ontology) { this.ontology = ontology; }
public org.intermine.model.InterMineObject proxGetOntology() { return ontology; }
// Col: org.intermine.model.bio.OntologyTerm.relations
protected java.util.Set relations = new java.util.HashSet();
public java.util.Set getRelations() { return relations; }
public void setRelations(final java.util.Set relations) { this.relations = relations; }
public void addRelations(final org.intermine.model.bio.OntologyRelation arg) { relations.add(arg); }
// Col: org.intermine.model.bio.OntologyTerm.synonyms
protected java.util.Set synonyms = new java.util.HashSet();
public java.util.Set getSynonyms() { return synonyms; }
public void setSynonyms(final java.util.Set synonyms) { this.synonyms = synonyms; }
public void addSynonyms(final org.intermine.model.bio.OntologyTermSynonym arg) { synonyms.add(arg); }
// Col: org.intermine.model.bio.OntologyTerm.ontologyAnnotations
protected java.util.Set ontologyAnnotations = new java.util.HashSet();
public java.util.Set getOntologyAnnotations() { return ontologyAnnotations; }
public void setOntologyAnnotations(final java.util.Set ontologyAnnotations) { this.ontologyAnnotations = ontologyAnnotations; }
public void addOntologyAnnotations(final org.intermine.model.bio.OntologyAnnotation arg) { ontologyAnnotations.add(arg); }
// Col: org.intermine.model.bio.OntologyTerm.parents
protected java.util.Set parents = new java.util.HashSet();
public java.util.Set getParents() { return parents; }
public void setParents(final java.util.Set parents) { this.parents = parents; }
public void addParents(final org.intermine.model.bio.OntologyTerm arg) { parents.add(arg); }
// Col: org.intermine.model.bio.OntologyTerm.dataSets
protected java.util.Set dataSets = new java.util.HashSet();
public java.util.Set getDataSets() { return dataSets; }
public void setDataSets(final java.util.Set dataSets) { this.dataSets = dataSets; }
public void addDataSets(final org.intermine.model.bio.DataSet arg) { dataSets.add(arg); }
// Col: org.intermine.model.bio.OntologyTerm.crossReferences
protected java.util.Set crossReferences = new java.util.HashSet();
public java.util.Set getCrossReferences() { return crossReferences; }
public void setCrossReferences(final java.util.Set crossReferences) { this.crossReferences = crossReferences; }
public void addCrossReferences(final org.intermine.model.bio.OntologyTerm arg) { crossReferences.add(arg); }
// Attr: org.intermine.model.InterMineObject.id
protected java.lang.Integer id;
public java.lang.Integer getId() { return id; }
public void setId(final java.lang.Integer id) { this.id = id; }
@Override public boolean equals(Object o) { return (o instanceof SOTerm && id != null) ? id.equals(((SOTerm)o).getId()) : this == o; }
@Override public int hashCode() { return (id != null) ? id.hashCode() : super.hashCode(); }
@Override public String toString() { return "SOTerm [description=" + (description == null ? "null" : "\"" + description + "\"") + ", id=" + id + ", identifier=" + (identifier == null ? "null" : "\"" + identifier + "\"") + ", name=" + (name == null ? "null" : "\"" + name + "\"") + ", namespace=" + (namespace == null ? "null" : "\"" + namespace + "\"") + ", obsolete=" + (obsolete == null ? "null" : "\"" + obsolete + "\"") + ", ontology=" + (ontology == null ? "null" : (ontology.getId() == null ? "no id" : ontology.getId().toString())) + "]"; }
public Object getFieldValue(final String fieldName) throws IllegalAccessException {
if ("identifier".equals(fieldName)) {
return identifier;
}
if ("description".equals(fieldName)) {
return description;
}
if ("obsolete".equals(fieldName)) {
return obsolete;
}
if ("name".equals(fieldName)) {
return name;
}
if ("namespace".equals(fieldName)) {
return namespace;
}
if ("ontology".equals(fieldName)) {
if (ontology instanceof ProxyReference) {
return ((ProxyReference) ontology).getObject();
} else {
return ontology;
}
}
if ("relations".equals(fieldName)) {
return relations;
}
if ("synonyms".equals(fieldName)) {
return synonyms;
}
if ("ontologyAnnotations".equals(fieldName)) {
return ontologyAnnotations;
}
if ("parents".equals(fieldName)) {
return parents;
}
if ("dataSets".equals(fieldName)) {
return dataSets;
}
if ("crossReferences".equals(fieldName)) {
return crossReferences;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
return TypeUtil.getFieldValue(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public Object getFieldProxy(final String fieldName) throws IllegalAccessException {
if ("identifier".equals(fieldName)) {
return identifier;
}
if ("description".equals(fieldName)) {
return description;
}
if ("obsolete".equals(fieldName)) {
return obsolete;
}
if ("name".equals(fieldName)) {
return name;
}
if ("namespace".equals(fieldName)) {
return namespace;
}
if ("ontology".equals(fieldName)) {
return ontology;
}
if ("relations".equals(fieldName)) {
return relations;
}
if ("synonyms".equals(fieldName)) {
return synonyms;
}
if ("ontologyAnnotations".equals(fieldName)) {
return ontologyAnnotations;
}
if ("parents".equals(fieldName)) {
return parents;
}
if ("dataSets".equals(fieldName)) {
return dataSets;
}
if ("crossReferences".equals(fieldName)) {
return crossReferences;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
return TypeUtil.getFieldProxy(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public void setFieldValue(final String fieldName, final Object value) {
if ("identifier".equals(fieldName)) {
identifier = (java.lang.String) value;
} else if ("description".equals(fieldName)) {
description = (java.lang.String) value;
} else if ("obsolete".equals(fieldName)) {
obsolete = (java.lang.Boolean) value;
} else if ("name".equals(fieldName)) {
name = (java.lang.String) value;
} else if ("namespace".equals(fieldName)) {
namespace = (java.lang.String) value;
} else if ("ontology".equals(fieldName)) {
ontology = (org.intermine.model.InterMineObject) value;
} else if ("relations".equals(fieldName)) {
relations = (java.util.Set) value;
} else if ("synonyms".equals(fieldName)) {
synonyms = (java.util.Set) value;
} else if ("ontologyAnnotations".equals(fieldName)) {
ontologyAnnotations = (java.util.Set) value;
} else if ("parents".equals(fieldName)) {
parents = (java.util.Set) value;
} else if ("dataSets".equals(fieldName)) {
dataSets = (java.util.Set) value;
} else if ("crossReferences".equals(fieldName)) {
crossReferences = (java.util.Set) value;
} else if ("id".equals(fieldName)) {
id = (java.lang.Integer) value;
} else {
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
DynamicUtil.setFieldValue(this, fieldName, value);
return;
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
public Class getFieldType(final String fieldName) {
if ("identifier".equals(fieldName)) {
return java.lang.String.class;
}
if ("description".equals(fieldName)) {
return java.lang.String.class;
}
if ("obsolete".equals(fieldName)) {
return java.lang.Boolean.class;
}
if ("name".equals(fieldName)) {
return java.lang.String.class;
}
if ("namespace".equals(fieldName)) {
return java.lang.String.class;
}
if ("ontology".equals(fieldName)) {
return org.intermine.model.bio.Ontology.class;
}
if ("relations".equals(fieldName)) {
return java.util.Set.class;
}
if ("synonyms".equals(fieldName)) {
return java.util.Set.class;
}
if ("ontologyAnnotations".equals(fieldName)) {
return java.util.Set.class;
}
if ("parents".equals(fieldName)) {
return java.util.Set.class;
}
if ("dataSets".equals(fieldName)) {
return java.util.Set.class;
}
if ("crossReferences".equals(fieldName)) {
return java.util.Set.class;
}
if ("id".equals(fieldName)) {
return java.lang.Integer.class;
}
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
return TypeUtil.getFieldType(org.intermine.model.bio.SOTerm.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public StringConstructor getoBJECT() {
if (!org.intermine.model.bio.SOTermShadow.class.equals(getClass())) {
return NotXmlRenderer.render(this);
}
StringConstructor sb = new StringConstructor();
sb.append("$_^org.intermine.model.bio.SOTerm");
if (identifier != null) {
sb.append("$_^aidentifier$_^");
String string = identifier;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (description != null) {
sb.append("$_^adescription$_^");
String string = description;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (obsolete != null) {
sb.append("$_^aobsolete$_^").append(obsolete);
}
if (name != null) {
sb.append("$_^aname$_^");
String string = name;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (namespace != null) {
sb.append("$_^anamespace$_^");
String string = namespace;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (ontology != null) {
sb.append("$_^rontology$_^").append(ontology.getId());
}
if (id != null) {
sb.append("$_^aid$_^").append(id);
}
return sb;
}
public void setoBJECT(String notXml, ObjectStore os) {
setoBJECT(NotXmlParser.SPLITTER.split(notXml), os);
}
public void setoBJECT(final String[] notXml, final ObjectStore os) {
if (!org.intermine.model.bio.SOTermShadow.class.equals(getClass())) {
throw new IllegalStateException("Class " + getClass().getName() + " does not match code (org.intermine.model.bio.SOTerm)");
}
for (int i = 2; i < notXml.length;) {
int startI = i;
if ((i < notXml.length) && "aidentifier".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
identifier = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "adescription".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
description = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "aobsolete".equals(notXml[i])) {
i++;
obsolete = Boolean.valueOf(notXml[i]);
i++;
}
if ((i < notXml.length) && "aname".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
name = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "anamespace".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
namespace = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) &&"rontology".equals(notXml[i])) {
i++;
ontology = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Ontology.class);
i++;
};
if ((i < notXml.length) && "aid".equals(notXml[i])) {
i++;
id = Integer.valueOf(notXml[i]);
i++;
}
if (startI == i) {
throw new IllegalArgumentException("Unknown field " + notXml[i]);
}
}
relations = new ProxyCollection(os, this, "relations", org.intermine.model.bio.OntologyRelation.class);
synonyms = new ProxyCollection(os, this, "synonyms", org.intermine.model.bio.OntologyTermSynonym.class);
ontologyAnnotations = new ProxyCollection(os, this, "ontologyAnnotations", org.intermine.model.bio.OntologyAnnotation.class);
parents = new ProxyCollection(os, this, "parents", org.intermine.model.bio.OntologyTerm.class);
dataSets = new ProxyCollection(os, this, "dataSets", org.intermine.model.bio.DataSet.class);
crossReferences = new ProxyCollection(os, this, "crossReferences", org.intermine.model.bio.OntologyTerm.class);
}
public void addCollectionElement(final String fieldName, final org.intermine.model.InterMineObject element) {
if ("relations".equals(fieldName)) {
relations.add((org.intermine.model.bio.OntologyRelation) element);
} else if ("synonyms".equals(fieldName)) {
synonyms.add((org.intermine.model.bio.OntologyTermSynonym) element);
} else if ("ontologyAnnotations".equals(fieldName)) {
ontologyAnnotations.add((org.intermine.model.bio.OntologyAnnotation) element);
} else if ("parents".equals(fieldName)) {
parents.add((org.intermine.model.bio.OntologyTerm) element);
} else if ("dataSets".equals(fieldName)) {
dataSets.add((org.intermine.model.bio.DataSet) element);
} else if ("crossReferences".equals(fieldName)) {
crossReferences.add((org.intermine.model.bio.OntologyTerm) element);
} else {
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
TypeUtil.addCollectionElement(this, fieldName, element);
return;
}
throw new IllegalArgumentException("Unknown collection " + fieldName);
}
}
public Class getElementType(final String fieldName) {
if ("relations".equals(fieldName)) {
return org.intermine.model.bio.OntologyRelation.class;
}
if ("synonyms".equals(fieldName)) {
return org.intermine.model.bio.OntologyTermSynonym.class;
}
if ("ontologyAnnotations".equals(fieldName)) {
return org.intermine.model.bio.OntologyAnnotation.class;
}
if ("parents".equals(fieldName)) {
return org.intermine.model.bio.OntologyTerm.class;
}
if ("dataSets".equals(fieldName)) {
return org.intermine.model.bio.DataSet.class;
}
if ("crossReferences".equals(fieldName)) {
return org.intermine.model.bio.OntologyTerm.class;
}
if (!org.intermine.model.bio.SOTerm.class.equals(getClass())) {
return TypeUtil.getElementType(org.intermine.model.bio.SOTerm.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
