org.intermine.model.bio.OrganismShadow 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.model.StringConstructor;
import org.intermine.metadata.TypeUtil;
import org.intermine.util.DynamicUtil;
import org.intermine.model.ShadowClass;
public class OrganismShadow implements Organism, ShadowClass
{
public static final Class shadowOf = Organism.class;
// Attr: org.intermine.model.bio.Organism.species
protected java.lang.String species;
public java.lang.String getSpecies() { return species; }
public void setSpecies(final java.lang.String species) { this.species = species; }
// Attr: org.intermine.model.bio.Organism.genus
protected java.lang.String genus;
public java.lang.String getGenus() { return genus; }
public void setGenus(final java.lang.String genus) { this.genus = genus; }
// Attr: org.intermine.model.bio.Organism.taxonId
protected java.lang.String taxonId;
public java.lang.String getTaxonId() { return taxonId; }
public void setTaxonId(final java.lang.String taxonId) { this.taxonId = taxonId; }
// Attr: org.intermine.model.bio.Organism.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.Organism.commonName
protected java.lang.String commonName;
public java.lang.String getCommonName() { return commonName; }
public void setCommonName(final java.lang.String commonName) { this.commonName = commonName; }
// Attr: org.intermine.model.bio.Organism.shortName
protected java.lang.String shortName;
public java.lang.String getShortName() { return shortName; }
public void setShortName(final java.lang.String shortName) { this.shortName = shortName; }
// Col: org.intermine.model.bio.Organism.strains
protected java.util.Set strains = new java.util.HashSet();
public java.util.Set getStrains() { return strains; }
public void setStrains(final java.util.Set strains) { this.strains = strains; }
public void addStrains(final org.intermine.model.bio.Strain arg) { strains.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 Organism && id != null) ? id.equals(((Organism)o).getId()) : this == o; }
@Override public int hashCode() { return (id != null) ? id.hashCode() : super.hashCode(); }
@Override public String toString() { return "Organism [commonName=" + (commonName == null ? "null" : "\"" + commonName + "\"") + ", genus=" + (genus == null ? "null" : "\"" + genus + "\"") + ", id=" + id + ", name=" + (name == null ? "null" : "\"" + name + "\"") + ", shortName=" + (shortName == null ? "null" : "\"" + shortName + "\"") + ", species=" + (species == null ? "null" : "\"" + species + "\"") + ", taxonId=" + (taxonId == null ? "null" : "\"" + taxonId + "\"") + "]"; }
public Object getFieldValue(final String fieldName) throws IllegalAccessException {
if ("species".equals(fieldName)) {
return species;
}
if ("genus".equals(fieldName)) {
return genus;
}
if ("taxonId".equals(fieldName)) {
return taxonId;
}
if ("name".equals(fieldName)) {
return name;
}
if ("commonName".equals(fieldName)) {
return commonName;
}
if ("shortName".equals(fieldName)) {
return shortName;
}
if ("strains".equals(fieldName)) {
return strains;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
return TypeUtil.getFieldValue(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public Object getFieldProxy(final String fieldName) throws IllegalAccessException {
if ("species".equals(fieldName)) {
return species;
}
if ("genus".equals(fieldName)) {
return genus;
}
if ("taxonId".equals(fieldName)) {
return taxonId;
}
if ("name".equals(fieldName)) {
return name;
}
if ("commonName".equals(fieldName)) {
return commonName;
}
if ("shortName".equals(fieldName)) {
return shortName;
}
if ("strains".equals(fieldName)) {
return strains;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
return TypeUtil.getFieldProxy(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public void setFieldValue(final String fieldName, final Object value) {
if ("species".equals(fieldName)) {
species = (java.lang.String) value;
} else if ("genus".equals(fieldName)) {
genus = (java.lang.String) value;
} else if ("taxonId".equals(fieldName)) {
taxonId = (java.lang.String) value;
} else if ("name".equals(fieldName)) {
name = (java.lang.String) value;
} else if ("commonName".equals(fieldName)) {
commonName = (java.lang.String) value;
} else if ("shortName".equals(fieldName)) {
shortName = (java.lang.String) value;
} else if ("strains".equals(fieldName)) {
strains = (java.util.Set) value;
} else if ("id".equals(fieldName)) {
id = (java.lang.Integer) value;
} else {
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
DynamicUtil.setFieldValue(this, fieldName, value);
return;
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
public Class getFieldType(final String fieldName) {
if ("species".equals(fieldName)) {
return java.lang.String.class;
}
if ("genus".equals(fieldName)) {
return java.lang.String.class;
}
if ("taxonId".equals(fieldName)) {
return java.lang.String.class;
}
if ("name".equals(fieldName)) {
return java.lang.String.class;
}
if ("commonName".equals(fieldName)) {
return java.lang.String.class;
}
if ("shortName".equals(fieldName)) {
return java.lang.String.class;
}
if ("strains".equals(fieldName)) {
return java.util.Set.class;
}
if ("id".equals(fieldName)) {
return java.lang.Integer.class;
}
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
return TypeUtil.getFieldType(org.intermine.model.bio.Organism.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public StringConstructor getoBJECT() {
if (!org.intermine.model.bio.OrganismShadow.class.equals(getClass())) {
return NotXmlRenderer.render(this);
}
StringConstructor sb = new StringConstructor();
sb.append("$_^org.intermine.model.bio.Organism");
if (species != null) {
sb.append("$_^aspecies$_^");
String string = species;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (genus != null) {
sb.append("$_^agenus$_^");
String string = genus;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (taxonId != null) {
sb.append("$_^ataxonId$_^");
String string = taxonId;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (name != null) {
sb.append("$_^aname$_^");
String string = name;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (commonName != null) {
sb.append("$_^acommonName$_^");
String string = commonName;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (shortName != null) {
sb.append("$_^ashortName$_^");
String string = shortName;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (id != null) {
sb.append("$_^aid$_^").append(id);
}
return sb;
}
public void setoBJECT(String notXml, ObjectStore os) {
setoBJECT(NotXmlParser.SPLITTER.split(notXml), os);
}
public void setoBJECT(final String[] notXml, final ObjectStore os) {
if (!org.intermine.model.bio.OrganismShadow.class.equals(getClass())) {
throw new IllegalStateException("Class " + getClass().getName() + " does not match code (org.intermine.model.bio.Organism)");
}
for (int i = 2; i < notXml.length;) {
int startI = i;
if ((i < notXml.length) && "aspecies".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
species = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "agenus".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("$_^").append(notXml[i].substring(1));
}
genus = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "ataxonId".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
taxonId = string == null ? notXml[i] : string.toString();
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("$_^").append(notXml[i].substring(1));
}
name = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "acommonName".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
commonName = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "ashortName".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));
}
shortName = string == null ? notXml[i] : string.toString();
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]);
}
}
strains = new ProxyCollection(os, this, "strains", org.intermine.model.bio.Strain.class);
}
public void addCollectionElement(final String fieldName, final org.intermine.model.InterMineObject element) {
if ("strains".equals(fieldName)) {
strains.add((org.intermine.model.bio.Strain) element);
} else {
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
TypeUtil.addCollectionElement(this, fieldName, element);
return;
}
throw new IllegalArgumentException("Unknown collection " + fieldName);
}
}
public Class getElementType(final String fieldName) {
if ("strains".equals(fieldName)) {
return org.intermine.model.bio.Strain.class;
}
if (!org.intermine.model.bio.Organism.class.equals(getClass())) {
return TypeUtil.getElementType(org.intermine.model.bio.Organism.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}