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org.intermine.model.bio.PublicationShadow 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 PublicationShadow implements Publication, ShadowClass
{
public static final Class shadowOf = Publication.class;
// Attr: org.intermine.model.bio.Publication.year
protected java.lang.Integer year;
public java.lang.Integer getYear() { return year; }
public void setYear(final java.lang.Integer year) { this.year = year; }
// Attr: org.intermine.model.bio.Publication.issue
protected java.lang.String issue;
public java.lang.String getIssue() { return issue; }
public void setIssue(final java.lang.String issue) { this.issue = issue; }
// Attr: org.intermine.model.bio.Publication.title
protected java.lang.String title;
public java.lang.String getTitle() { return title; }
public void setTitle(final java.lang.String title) { this.title = title; }
// Attr: org.intermine.model.bio.Publication.pages
protected java.lang.String pages;
public java.lang.String getPages() { return pages; }
public void setPages(final java.lang.String pages) { this.pages = pages; }
// Attr: org.intermine.model.bio.Publication.doi
protected java.lang.String doi;
public java.lang.String getDoi() { return doi; }
public void setDoi(final java.lang.String doi) { this.doi = doi; }
// Attr: org.intermine.model.bio.Publication.volume
protected java.lang.String volume;
public java.lang.String getVolume() { return volume; }
public void setVolume(final java.lang.String volume) { this.volume = volume; }
// Attr: org.intermine.model.bio.Publication.journal
protected java.lang.String journal;
public java.lang.String getJournal() { return journal; }
public void setJournal(final java.lang.String journal) { this.journal = journal; }
// Attr: org.intermine.model.bio.Publication.firstAuthor
protected java.lang.String firstAuthor;
public java.lang.String getFirstAuthor() { return firstAuthor; }
public void setFirstAuthor(final java.lang.String firstAuthor) { this.firstAuthor = firstAuthor; }
// Attr: org.intermine.model.bio.Publication.month
protected java.lang.String month;
public java.lang.String getMonth() { return month; }
public void setMonth(final java.lang.String month) { this.month = month; }
// Attr: org.intermine.model.bio.Publication.abstractText
protected java.lang.String abstractText;
public java.lang.String getAbstractText() { return abstractText; }
public void setAbstractText(final java.lang.String abstractText) { this.abstractText = abstractText; }
// Attr: org.intermine.model.bio.Publication.pubMedId
protected java.lang.String pubMedId;
public java.lang.String getPubMedId() { return pubMedId; }
public void setPubMedId(final java.lang.String pubMedId) { this.pubMedId = pubMedId; }
// Col: org.intermine.model.bio.Publication.authors
protected java.util.Set authors = new java.util.HashSet();
public java.util.Set getAuthors() { return authors; }
public void setAuthors(final java.util.Set authors) { this.authors = authors; }
public void addAuthors(final org.intermine.model.bio.Author arg) { authors.add(arg); }
// Col: org.intermine.model.bio.Publication.entities
protected java.util.Set entities = new java.util.HashSet();
public java.util.Set getEntities() { return entities; }
public void setEntities(final java.util.Set entities) { this.entities = entities; }
public void addEntities(final org.intermine.model.bio.Annotatable arg) { entities.add(arg); }
// Col: org.intermine.model.bio.Publication.meshTerms
protected java.util.Set meshTerms = new java.util.HashSet();
public java.util.Set getMeshTerms() { return meshTerms; }
public void setMeshTerms(final java.util.Set meshTerms) { this.meshTerms = meshTerms; }
public void addMeshTerms(final org.intermine.model.bio.MeshTerm arg) { meshTerms.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 Publication && id != null) ? id.equals(((Publication)o).getId()) : this == o; }
@Override public int hashCode() { return (id != null) ? id.hashCode() : super.hashCode(); }
@Override public String toString() { return "Publication [abstractText=" + (abstractText == null ? "null" : "\"" + abstractText + "\"") + ", doi=" + (doi == null ? "null" : "\"" + doi + "\"") + ", firstAuthor=" + (firstAuthor == null ? "null" : "\"" + firstAuthor + "\"") + ", id=" + id + ", issue=" + (issue == null ? "null" : "\"" + issue + "\"") + ", journal=" + (journal == null ? "null" : "\"" + journal + "\"") + ", month=" + (month == null ? "null" : "\"" + month + "\"") + ", pages=" + (pages == null ? "null" : "\"" + pages + "\"") + ", pubMedId=" + (pubMedId == null ? "null" : "\"" + pubMedId + "\"") + ", title=" + (title == null ? "null" : "\"" + title + "\"") + ", volume=" + (volume == null ? "null" : "\"" + volume + "\"") + ", year=" + year + "]"; }
public Object getFieldValue(final String fieldName) throws IllegalAccessException {
if ("year".equals(fieldName)) {
return year;
}
if ("issue".equals(fieldName)) {
return issue;
}
if ("title".equals(fieldName)) {
return title;
}
if ("pages".equals(fieldName)) {
return pages;
}
if ("doi".equals(fieldName)) {
return doi;
}
if ("volume".equals(fieldName)) {
return volume;
}
if ("journal".equals(fieldName)) {
return journal;
}
if ("firstAuthor".equals(fieldName)) {
return firstAuthor;
}
if ("month".equals(fieldName)) {
return month;
}
if ("abstractText".equals(fieldName)) {
return abstractText;
}
if ("pubMedId".equals(fieldName)) {
return pubMedId;
}
if ("authors".equals(fieldName)) {
return authors;
}
if ("entities".equals(fieldName)) {
return entities;
}
if ("meshTerms".equals(fieldName)) {
return meshTerms;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
return TypeUtil.getFieldValue(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public Object getFieldProxy(final String fieldName) throws IllegalAccessException {
if ("year".equals(fieldName)) {
return year;
}
if ("issue".equals(fieldName)) {
return issue;
}
if ("title".equals(fieldName)) {
return title;
}
if ("pages".equals(fieldName)) {
return pages;
}
if ("doi".equals(fieldName)) {
return doi;
}
if ("volume".equals(fieldName)) {
return volume;
}
if ("journal".equals(fieldName)) {
return journal;
}
if ("firstAuthor".equals(fieldName)) {
return firstAuthor;
}
if ("month".equals(fieldName)) {
return month;
}
if ("abstractText".equals(fieldName)) {
return abstractText;
}
if ("pubMedId".equals(fieldName)) {
return pubMedId;
}
if ("authors".equals(fieldName)) {
return authors;
}
if ("entities".equals(fieldName)) {
return entities;
}
if ("meshTerms".equals(fieldName)) {
return meshTerms;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
return TypeUtil.getFieldProxy(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public void setFieldValue(final String fieldName, final Object value) {
if ("year".equals(fieldName)) {
year = (java.lang.Integer) value;
} else if ("issue".equals(fieldName)) {
issue = (java.lang.String) value;
} else if ("title".equals(fieldName)) {
title = (java.lang.String) value;
} else if ("pages".equals(fieldName)) {
pages = (java.lang.String) value;
} else if ("doi".equals(fieldName)) {
doi = (java.lang.String) value;
} else if ("volume".equals(fieldName)) {
volume = (java.lang.String) value;
} else if ("journal".equals(fieldName)) {
journal = (java.lang.String) value;
} else if ("firstAuthor".equals(fieldName)) {
firstAuthor = (java.lang.String) value;
} else if ("month".equals(fieldName)) {
month = (java.lang.String) value;
} else if ("abstractText".equals(fieldName)) {
abstractText = (java.lang.String) value;
} else if ("pubMedId".equals(fieldName)) {
pubMedId = (java.lang.String) value;
} else if ("authors".equals(fieldName)) {
authors = (java.util.Set) value;
} else if ("entities".equals(fieldName)) {
entities = (java.util.Set) value;
} else if ("meshTerms".equals(fieldName)) {
meshTerms = (java.util.Set) value;
} else if ("id".equals(fieldName)) {
id = (java.lang.Integer) value;
} else {
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
DynamicUtil.setFieldValue(this, fieldName, value);
return;
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
public Class getFieldType(final String fieldName) {
if ("year".equals(fieldName)) {
return java.lang.Integer.class;
}
if ("issue".equals(fieldName)) {
return java.lang.String.class;
}
if ("title".equals(fieldName)) {
return java.lang.String.class;
}
if ("pages".equals(fieldName)) {
return java.lang.String.class;
}
if ("doi".equals(fieldName)) {
return java.lang.String.class;
}
if ("volume".equals(fieldName)) {
return java.lang.String.class;
}
if ("journal".equals(fieldName)) {
return java.lang.String.class;
}
if ("firstAuthor".equals(fieldName)) {
return java.lang.String.class;
}
if ("month".equals(fieldName)) {
return java.lang.String.class;
}
if ("abstractText".equals(fieldName)) {
return java.lang.String.class;
}
if ("pubMedId".equals(fieldName)) {
return java.lang.String.class;
}
if ("authors".equals(fieldName)) {
return java.util.Set.class;
}
if ("entities".equals(fieldName)) {
return java.util.Set.class;
}
if ("meshTerms".equals(fieldName)) {
return java.util.Set.class;
}
if ("id".equals(fieldName)) {
return java.lang.Integer.class;
}
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
return TypeUtil.getFieldType(org.intermine.model.bio.Publication.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public StringConstructor getoBJECT() {
if (!org.intermine.model.bio.PublicationShadow.class.equals(getClass())) {
return NotXmlRenderer.render(this);
}
StringConstructor sb = new StringConstructor();
sb.append("$_^org.intermine.model.bio.Publication");
if (year != null) {
sb.append("$_^ayear$_^").append(year);
}
if (issue != null) {
sb.append("$_^aissue$_^");
String string = issue;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (title != null) {
sb.append("$_^atitle$_^");
String string = title;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (pages != null) {
sb.append("$_^apages$_^");
String string = pages;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (doi != null) {
sb.append("$_^adoi$_^");
String string = doi;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (volume != null) {
sb.append("$_^avolume$_^");
String string = volume;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (journal != null) {
sb.append("$_^ajournal$_^");
String string = journal;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (firstAuthor != null) {
sb.append("$_^afirstAuthor$_^");
String string = firstAuthor;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (month != null) {
sb.append("$_^amonth$_^");
String string = month;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (abstractText != null) {
sb.append("$_^aabstractText$_^");
String string = abstractText;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (pubMedId != null) {
sb.append("$_^apubMedId$_^");
String string = pubMedId;
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$_^").append(id);
}
return sb;
}
public void setoBJECT(String notXml, ObjectStore os) {
setoBJECT(NotXmlParser.SPLITTER.split(notXml), os);
}
public void setoBJECT(final String[] notXml, final ObjectStore os) {
if (!org.intermine.model.bio.PublicationShadow.class.equals(getClass())) {
throw new IllegalStateException("Class " + getClass().getName() + " does not match code (org.intermine.model.bio.Publication)");
}
for (int i = 2; i < notXml.length;) {
int startI = i;
if ((i < notXml.length) && "ayear".equals(notXml[i])) {
i++;
year = Integer.valueOf(notXml[i]);
i++;
}
if ((i < notXml.length) && "aissue".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
issue = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "atitle".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("$_^").append(notXml[i].substring(1));
}
title = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "apages".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
pages = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "adoi".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("$_^").append(notXml[i].substring(1));
}
doi = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "avolume".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
volume = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "ajournal".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("$_^").append(notXml[i].substring(1));
}
journal = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "afirstAuthor".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
firstAuthor = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "amonth".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("$_^").append(notXml[i].substring(1));
}
month = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "aabstractText".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
abstractText = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "apubMedId".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));
}
pubMedId = 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]);
}
}
authors = new ProxyCollection(os, this, "authors", org.intermine.model.bio.Author.class);
entities = new ProxyCollection(os, this, "entities", org.intermine.model.bio.Annotatable.class);
meshTerms = new ProxyCollection(os, this, "meshTerms", org.intermine.model.bio.MeshTerm.class);
}
public void addCollectionElement(final String fieldName, final org.intermine.model.InterMineObject element) {
if ("authors".equals(fieldName)) {
authors.add((org.intermine.model.bio.Author) element);
} else if ("entities".equals(fieldName)) {
entities.add((org.intermine.model.bio.Annotatable) element);
} else if ("meshTerms".equals(fieldName)) {
meshTerms.add((org.intermine.model.bio.MeshTerm) element);
} else {
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
TypeUtil.addCollectionElement(this, fieldName, element);
return;
}
throw new IllegalArgumentException("Unknown collection " + fieldName);
}
}
public Class getElementType(final String fieldName) {
if ("authors".equals(fieldName)) {
return org.intermine.model.bio.Author.class;
}
if ("entities".equals(fieldName)) {
return org.intermine.model.bio.Annotatable.class;
}
if ("meshTerms".equals(fieldName)) {
return org.intermine.model.bio.MeshTerm.class;
}
if (!org.intermine.model.bio.Publication.class.equals(getClass())) {
return TypeUtil.getElementType(org.intermine.model.bio.Publication.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
