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org.intermine.model.bio.IntronShadow 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 IntronShadow implements Intron, ShadowClass
{
public static final Class shadowOf = Intron.class;
// Col: org.intermine.model.bio.Intron.genes
protected java.util.Set genes = new java.util.HashSet();
public java.util.Set getGenes() { return genes; }
public void setGenes(final java.util.Set genes) { this.genes = genes; }
public void addGenes(final org.intermine.model.bio.Gene arg) { genes.add(arg); }
// Attr: org.intermine.model.bio.SequenceFeature.score
protected java.lang.Double score;
public java.lang.Double getScore() { return score; }
public void setScore(final java.lang.Double score) { this.score = score; }
// Attr: org.intermine.model.bio.SequenceFeature.scoreType
protected java.lang.String scoreType;
public java.lang.String getScoreType() { return scoreType; }
public void setScoreType(final java.lang.String scoreType) { this.scoreType = scoreType; }
// Attr: org.intermine.model.bio.SequenceFeature.length
protected java.lang.Integer length;
public java.lang.Integer getLength() { return length; }
public void setLength(final java.lang.Integer length) { this.length = length; }
// Ref: org.intermine.model.bio.SequenceFeature.strain
protected org.intermine.model.InterMineObject strain;
public org.intermine.model.bio.Strain getStrain() { if (strain instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Strain) ((org.intermine.objectstore.proxy.ProxyReference) strain).getObject()); }; return (org.intermine.model.bio.Strain) strain; }
public void setStrain(final org.intermine.model.bio.Strain strain) { this.strain = strain; }
public void proxyStrain(final org.intermine.objectstore.proxy.ProxyReference strain) { this.strain = strain; }
public org.intermine.model.InterMineObject proxGetStrain() { return strain; }
// Ref: org.intermine.model.bio.SequenceFeature.sequenceOntologyTerm
protected org.intermine.model.InterMineObject sequenceOntologyTerm;
public org.intermine.model.bio.SOTerm getSequenceOntologyTerm() { if (sequenceOntologyTerm instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.SOTerm) ((org.intermine.objectstore.proxy.ProxyReference) sequenceOntologyTerm).getObject()); }; return (org.intermine.model.bio.SOTerm) sequenceOntologyTerm; }
public void setSequenceOntologyTerm(final org.intermine.model.bio.SOTerm sequenceOntologyTerm) { this.sequenceOntologyTerm = sequenceOntologyTerm; }
public void proxySequenceOntologyTerm(final org.intermine.objectstore.proxy.ProxyReference sequenceOntologyTerm) { this.sequenceOntologyTerm = sequenceOntologyTerm; }
public org.intermine.model.InterMineObject proxGetSequenceOntologyTerm() { return sequenceOntologyTerm; }
// Ref: org.intermine.model.bio.SequenceFeature.chromosomeLocation
protected org.intermine.model.InterMineObject chromosomeLocation;
public org.intermine.model.bio.Location getChromosomeLocation() { if (chromosomeLocation instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Location) ((org.intermine.objectstore.proxy.ProxyReference) chromosomeLocation).getObject()); }; return (org.intermine.model.bio.Location) chromosomeLocation; }
public void setChromosomeLocation(final org.intermine.model.bio.Location chromosomeLocation) { this.chromosomeLocation = chromosomeLocation; }
public void proxyChromosomeLocation(final org.intermine.objectstore.proxy.ProxyReference chromosomeLocation) { this.chromosomeLocation = chromosomeLocation; }
public org.intermine.model.InterMineObject proxGetChromosomeLocation() { return chromosomeLocation; }
// Ref: org.intermine.model.bio.SequenceFeature.sequence
protected org.intermine.model.InterMineObject sequence;
public org.intermine.model.bio.Sequence getSequence() { if (sequence instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Sequence) ((org.intermine.objectstore.proxy.ProxyReference) sequence).getObject()); }; return (org.intermine.model.bio.Sequence) sequence; }
public void setSequence(final org.intermine.model.bio.Sequence sequence) { this.sequence = sequence; }
public void proxySequence(final org.intermine.objectstore.proxy.ProxyReference sequence) { this.sequence = sequence; }
public org.intermine.model.InterMineObject proxGetSequence() { return sequence; }
// Ref: org.intermine.model.bio.SequenceFeature.chromosome
protected org.intermine.model.InterMineObject chromosome;
public org.intermine.model.bio.Chromosome getChromosome() { if (chromosome instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Chromosome) ((org.intermine.objectstore.proxy.ProxyReference) chromosome).getObject()); }; return (org.intermine.model.bio.Chromosome) chromosome; }
public void setChromosome(final org.intermine.model.bio.Chromosome chromosome) { this.chromosome = chromosome; }
public void proxyChromosome(final org.intermine.objectstore.proxy.ProxyReference chromosome) { this.chromosome = chromosome; }
public org.intermine.model.InterMineObject proxGetChromosome() { return chromosome; }
// Col: org.intermine.model.bio.SequenceFeature.overlappingFeatures
protected java.util.Set overlappingFeatures = new java.util.HashSet();
public java.util.Set getOverlappingFeatures() { return overlappingFeatures; }
public void setOverlappingFeatures(final java.util.Set overlappingFeatures) { this.overlappingFeatures = overlappingFeatures; }
public void addOverlappingFeatures(final org.intermine.model.bio.SequenceFeature arg) { overlappingFeatures.add(arg); }
// Col: org.intermine.model.bio.SequenceFeature.childFeatures
protected java.util.Set childFeatures = new java.util.HashSet();
public java.util.Set getChildFeatures() { return childFeatures; }
public void setChildFeatures(final java.util.Set childFeatures) { this.childFeatures = childFeatures; }
public void addChildFeatures(final org.intermine.model.bio.SequenceFeature arg) { childFeatures.add(arg); }
// Attr: org.intermine.model.bio.BioEntity.symbol
protected java.lang.String symbol;
public java.lang.String getSymbol() { return symbol; }
public void setSymbol(final java.lang.String symbol) { this.symbol = symbol; }
// Attr: org.intermine.model.bio.BioEntity.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.BioEntity.secondaryIdentifier
protected java.lang.String secondaryIdentifier;
public java.lang.String getSecondaryIdentifier() { return secondaryIdentifier; }
public void setSecondaryIdentifier(final java.lang.String secondaryIdentifier) { this.secondaryIdentifier = secondaryIdentifier; }
// Ref: org.intermine.model.bio.BioEntity.organism
protected org.intermine.model.InterMineObject organism;
public org.intermine.model.bio.Organism getOrganism() { if (organism instanceof org.intermine.objectstore.proxy.ProxyReference) { return ((org.intermine.model.bio.Organism) ((org.intermine.objectstore.proxy.ProxyReference) organism).getObject()); }; return (org.intermine.model.bio.Organism) organism; }
public void setOrganism(final org.intermine.model.bio.Organism organism) { this.organism = organism; }
public void proxyOrganism(final org.intermine.objectstore.proxy.ProxyReference organism) { this.organism = organism; }
public org.intermine.model.InterMineObject proxGetOrganism() { return organism; }
// Col: org.intermine.model.bio.BioEntity.locatedFeatures
protected java.util.Set locatedFeatures = new java.util.HashSet();
public java.util.Set getLocatedFeatures() { return locatedFeatures; }
public void setLocatedFeatures(final java.util.Set locatedFeatures) { this.locatedFeatures = locatedFeatures; }
public void addLocatedFeatures(final org.intermine.model.bio.Location arg) { locatedFeatures.add(arg); }
// Col: org.intermine.model.bio.BioEntity.locations
protected java.util.Set locations = new java.util.HashSet();
public java.util.Set getLocations() { return locations; }
public void setLocations(final java.util.Set locations) { this.locations = locations; }
public void addLocations(final org.intermine.model.bio.Location arg) { locations.add(arg); }
// Col: org.intermine.model.bio.BioEntity.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.Synonym arg) { synonyms.add(arg); }
// Col: org.intermine.model.bio.BioEntity.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.BioEntity.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.CrossReference arg) { crossReferences.add(arg); }
// Attr: org.intermine.model.bio.Annotatable.primaryIdentifier
protected java.lang.String primaryIdentifier;
public java.lang.String getPrimaryIdentifier() { return primaryIdentifier; }
public void setPrimaryIdentifier(final java.lang.String primaryIdentifier) { this.primaryIdentifier = primaryIdentifier; }
// Col: org.intermine.model.bio.Annotatable.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.Annotatable.publications
protected java.util.Set publications = new java.util.HashSet();
public java.util.Set getPublications() { return publications; }
public void setPublications(final java.util.Set publications) { this.publications = publications; }
public void addPublications(final org.intermine.model.bio.Publication arg) { publications.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 Intron && id != null) ? id.equals(((Intron)o).getId()) : this == o; }
@Override public int hashCode() { return (id != null) ? id.hashCode() : super.hashCode(); }
@Override public String toString() { return "Intron [chromosome=" + (chromosome == null ? "null" : (chromosome.getId() == null ? "no id" : chromosome.getId().toString())) + ", chromosomeLocation=" + (chromosomeLocation == null ? "null" : (chromosomeLocation.getId() == null ? "no id" : chromosomeLocation.getId().toString())) + ", id=" + id + ", length=" + length + ", name=" + (name == null ? "null" : "\"" + name + "\"") + ", organism=" + (organism == null ? "null" : (organism.getId() == null ? "no id" : organism.getId().toString())) + ", primaryIdentifier=" + (primaryIdentifier == null ? "null" : "\"" + primaryIdentifier + "\"") + ", score=" + score + ", scoreType=" + (scoreType == null ? "null" : "\"" + scoreType + "\"") + ", secondaryIdentifier=" + (secondaryIdentifier == null ? "null" : "\"" + secondaryIdentifier + "\"") + ", sequence=" + (sequence == null ? "null" : (sequence.getId() == null ? "no id" : sequence.getId().toString())) + ", sequenceOntologyTerm=" + (sequenceOntologyTerm == null ? "null" : (sequenceOntologyTerm.getId() == null ? "no id" : sequenceOntologyTerm.getId().toString())) + ", strain=" + (strain == null ? "null" : (strain.getId() == null ? "no id" : strain.getId().toString())) + ", symbol=" + (symbol == null ? "null" : "\"" + symbol + "\"") + "]"; }
public Object getFieldValue(final String fieldName) throws IllegalAccessException {
if ("genes".equals(fieldName)) {
return genes;
}
if ("score".equals(fieldName)) {
return score;
}
if ("scoreType".equals(fieldName)) {
return scoreType;
}
if ("length".equals(fieldName)) {
return length;
}
if ("strain".equals(fieldName)) {
if (strain instanceof ProxyReference) {
return ((ProxyReference) strain).getObject();
} else {
return strain;
}
}
if ("sequenceOntologyTerm".equals(fieldName)) {
if (sequenceOntologyTerm instanceof ProxyReference) {
return ((ProxyReference) sequenceOntologyTerm).getObject();
} else {
return sequenceOntologyTerm;
}
}
if ("chromosomeLocation".equals(fieldName)) {
if (chromosomeLocation instanceof ProxyReference) {
return ((ProxyReference) chromosomeLocation).getObject();
} else {
return chromosomeLocation;
}
}
if ("sequence".equals(fieldName)) {
if (sequence instanceof ProxyReference) {
return ((ProxyReference) sequence).getObject();
} else {
return sequence;
}
}
if ("chromosome".equals(fieldName)) {
if (chromosome instanceof ProxyReference) {
return ((ProxyReference) chromosome).getObject();
} else {
return chromosome;
}
}
if ("overlappingFeatures".equals(fieldName)) {
return overlappingFeatures;
}
if ("childFeatures".equals(fieldName)) {
return childFeatures;
}
if ("symbol".equals(fieldName)) {
return symbol;
}
if ("name".equals(fieldName)) {
return name;
}
if ("secondaryIdentifier".equals(fieldName)) {
return secondaryIdentifier;
}
if ("organism".equals(fieldName)) {
if (organism instanceof ProxyReference) {
return ((ProxyReference) organism).getObject();
} else {
return organism;
}
}
if ("locatedFeatures".equals(fieldName)) {
return locatedFeatures;
}
if ("locations".equals(fieldName)) {
return locations;
}
if ("synonyms".equals(fieldName)) {
return synonyms;
}
if ("dataSets".equals(fieldName)) {
return dataSets;
}
if ("crossReferences".equals(fieldName)) {
return crossReferences;
}
if ("primaryIdentifier".equals(fieldName)) {
return primaryIdentifier;
}
if ("ontologyAnnotations".equals(fieldName)) {
return ontologyAnnotations;
}
if ("publications".equals(fieldName)) {
return publications;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
return TypeUtil.getFieldValue(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public Object getFieldProxy(final String fieldName) throws IllegalAccessException {
if ("genes".equals(fieldName)) {
return genes;
}
if ("score".equals(fieldName)) {
return score;
}
if ("scoreType".equals(fieldName)) {
return scoreType;
}
if ("length".equals(fieldName)) {
return length;
}
if ("strain".equals(fieldName)) {
return strain;
}
if ("sequenceOntologyTerm".equals(fieldName)) {
return sequenceOntologyTerm;
}
if ("chromosomeLocation".equals(fieldName)) {
return chromosomeLocation;
}
if ("sequence".equals(fieldName)) {
return sequence;
}
if ("chromosome".equals(fieldName)) {
return chromosome;
}
if ("overlappingFeatures".equals(fieldName)) {
return overlappingFeatures;
}
if ("childFeatures".equals(fieldName)) {
return childFeatures;
}
if ("symbol".equals(fieldName)) {
return symbol;
}
if ("name".equals(fieldName)) {
return name;
}
if ("secondaryIdentifier".equals(fieldName)) {
return secondaryIdentifier;
}
if ("organism".equals(fieldName)) {
return organism;
}
if ("locatedFeatures".equals(fieldName)) {
return locatedFeatures;
}
if ("locations".equals(fieldName)) {
return locations;
}
if ("synonyms".equals(fieldName)) {
return synonyms;
}
if ("dataSets".equals(fieldName)) {
return dataSets;
}
if ("crossReferences".equals(fieldName)) {
return crossReferences;
}
if ("primaryIdentifier".equals(fieldName)) {
return primaryIdentifier;
}
if ("ontologyAnnotations".equals(fieldName)) {
return ontologyAnnotations;
}
if ("publications".equals(fieldName)) {
return publications;
}
if ("id".equals(fieldName)) {
return id;
}
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
return TypeUtil.getFieldProxy(this, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public void setFieldValue(final String fieldName, final Object value) {
if ("genes".equals(fieldName)) {
genes = (java.util.Set) value;
} else if ("score".equals(fieldName)) {
score = (java.lang.Double) value;
} else if ("scoreType".equals(fieldName)) {
scoreType = (java.lang.String) value;
} else if ("length".equals(fieldName)) {
length = (java.lang.Integer) value;
} else if ("strain".equals(fieldName)) {
strain = (org.intermine.model.InterMineObject) value;
} else if ("sequenceOntologyTerm".equals(fieldName)) {
sequenceOntologyTerm = (org.intermine.model.InterMineObject) value;
} else if ("chromosomeLocation".equals(fieldName)) {
chromosomeLocation = (org.intermine.model.InterMineObject) value;
} else if ("sequence".equals(fieldName)) {
sequence = (org.intermine.model.InterMineObject) value;
} else if ("chromosome".equals(fieldName)) {
chromosome = (org.intermine.model.InterMineObject) value;
} else if ("overlappingFeatures".equals(fieldName)) {
overlappingFeatures = (java.util.Set) value;
} else if ("childFeatures".equals(fieldName)) {
childFeatures = (java.util.Set) value;
} else if ("symbol".equals(fieldName)) {
symbol = (java.lang.String) value;
} else if ("name".equals(fieldName)) {
name = (java.lang.String) value;
} else if ("secondaryIdentifier".equals(fieldName)) {
secondaryIdentifier = (java.lang.String) value;
} else if ("organism".equals(fieldName)) {
organism = (org.intermine.model.InterMineObject) value;
} else if ("locatedFeatures".equals(fieldName)) {
locatedFeatures = (java.util.Set) value;
} else if ("locations".equals(fieldName)) {
locations = (java.util.Set) value;
} else if ("synonyms".equals(fieldName)) {
synonyms = (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 ("primaryIdentifier".equals(fieldName)) {
primaryIdentifier = (java.lang.String) value;
} else if ("ontologyAnnotations".equals(fieldName)) {
ontologyAnnotations = (java.util.Set) value;
} else if ("publications".equals(fieldName)) {
publications = (java.util.Set) value;
} else if ("id".equals(fieldName)) {
id = (java.lang.Integer) value;
} else {
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
DynamicUtil.setFieldValue(this, fieldName, value);
return;
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
public Class getFieldType(final String fieldName) {
if ("genes".equals(fieldName)) {
return java.util.Set.class;
}
if ("score".equals(fieldName)) {
return java.lang.Double.class;
}
if ("scoreType".equals(fieldName)) {
return java.lang.String.class;
}
if ("length".equals(fieldName)) {
return java.lang.Integer.class;
}
if ("strain".equals(fieldName)) {
return org.intermine.model.bio.Strain.class;
}
if ("sequenceOntologyTerm".equals(fieldName)) {
return org.intermine.model.bio.SOTerm.class;
}
if ("chromosomeLocation".equals(fieldName)) {
return org.intermine.model.bio.Location.class;
}
if ("sequence".equals(fieldName)) {
return org.intermine.model.bio.Sequence.class;
}
if ("chromosome".equals(fieldName)) {
return org.intermine.model.bio.Chromosome.class;
}
if ("overlappingFeatures".equals(fieldName)) {
return java.util.Set.class;
}
if ("childFeatures".equals(fieldName)) {
return java.util.Set.class;
}
if ("symbol".equals(fieldName)) {
return java.lang.String.class;
}
if ("name".equals(fieldName)) {
return java.lang.String.class;
}
if ("secondaryIdentifier".equals(fieldName)) {
return java.lang.String.class;
}
if ("organism".equals(fieldName)) {
return org.intermine.model.bio.Organism.class;
}
if ("locatedFeatures".equals(fieldName)) {
return java.util.Set.class;
}
if ("locations".equals(fieldName)) {
return java.util.Set.class;
}
if ("synonyms".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 ("primaryIdentifier".equals(fieldName)) {
return java.lang.String.class;
}
if ("ontologyAnnotations".equals(fieldName)) {
return java.util.Set.class;
}
if ("publications".equals(fieldName)) {
return java.util.Set.class;
}
if ("id".equals(fieldName)) {
return java.lang.Integer.class;
}
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
return TypeUtil.getFieldType(org.intermine.model.bio.Intron.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
public StringConstructor getoBJECT() {
if (!org.intermine.model.bio.IntronShadow.class.equals(getClass())) {
return NotXmlRenderer.render(this);
}
StringConstructor sb = new StringConstructor();
sb.append("$_^org.intermine.model.bio.Intron");
if (score != null) {
sb.append("$_^ascore$_^").append(score);
}
if (scoreType != null) {
sb.append("$_^ascoreType$_^");
String string = scoreType;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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 (length != null) {
sb.append("$_^alength$_^").append(length);
}
if (strain != null) {
sb.append("$_^rstrain$_^").append(strain.getId());
}
if (sequenceOntologyTerm != null) {
sb.append("$_^rsequenceOntologyTerm$_^").append(sequenceOntologyTerm.getId());
}
if (chromosomeLocation != null) {
sb.append("$_^rchromosomeLocation$_^").append(chromosomeLocation.getId());
}
if (sequence != null) {
sb.append("$_^rsequence$_^").append(sequence.getId());
}
if (chromosome != null) {
sb.append("$_^rchromosome$_^").append(chromosome.getId());
}
if (symbol != null) {
sb.append("$_^asymbol$_^");
String string = symbol;
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 (secondaryIdentifier != null) {
sb.append("$_^asecondaryIdentifier$_^");
String string = secondaryIdentifier;
while (string != null) {
int delimPosition = string.indexOf("$_^");
if (delimPosition == -1) {
sb.append(string);
string = null;
} else {
sb.append(string.substring(0, delimPosition + 3));
sb.append("d");
string = string.substring(delimPosition + 3);
}
}
}
if (organism != null) {
sb.append("$_^rorganism$_^").append(organism.getId());
}
if (primaryIdentifier != null) {
sb.append("$_^aprimaryIdentifier$_^");
String string = primaryIdentifier;
while (string != null) {
int delimPosition = string.indexOf("$_^");
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.IntronShadow.class.equals(getClass())) {
throw new IllegalStateException("Class " + getClass().getName() + " does not match code (org.intermine.model.bio.Intron)");
}
for (int i = 2; i < notXml.length;) {
int startI = i;
if ((i < notXml.length) && "ascore".equals(notXml[i])) {
i++;
score = Double.valueOf(notXml[i]);
i++;
}
if ((i < notXml.length) && "ascoreType".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("$_^").append(notXml[i].substring(1));
}
scoreType = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "alength".equals(notXml[i])) {
i++;
length = Integer.valueOf(notXml[i]);
i++;
}
if ((i < notXml.length) &&"rstrain".equals(notXml[i])) {
i++;
strain = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Strain.class);
i++;
};
if ((i < notXml.length) &&"rsequenceOntologyTerm".equals(notXml[i])) {
i++;
sequenceOntologyTerm = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.SOTerm.class);
i++;
};
if ((i < notXml.length) &&"rchromosomeLocation".equals(notXml[i])) {
i++;
chromosomeLocation = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Location.class);
i++;
};
if ((i < notXml.length) &&"rsequence".equals(notXml[i])) {
i++;
sequence = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Sequence.class);
i++;
};
if ((i < notXml.length) &&"rchromosome".equals(notXml[i])) {
i++;
chromosome = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Chromosome.class);
i++;
};
if ((i < notXml.length) && "asymbol".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
symbol = 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("$_^").append(notXml[i].substring(1));
}
name = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) && "asecondaryIdentifier".equals(notXml[i])) {
i++;
StringBuilder string = null;
while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == 'd')) {
if (string == null) string = new StringBuilder(notXml[i]);
i++;
string.append("$_^").append(notXml[i].substring(1));
}
secondaryIdentifier = string == null ? notXml[i] : string.toString();
i++;
}
if ((i < notXml.length) &&"rorganism".equals(notXml[i])) {
i++;
organism = new ProxyReference(os, Integer.valueOf(notXml[i]), org.intermine.model.bio.Organism.class);
i++;
};
if ((i < notXml.length) && "aprimaryIdentifier".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));
}
primaryIdentifier = 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]);
}
}
genes = new ProxyCollection(os, this, "genes", org.intermine.model.bio.Gene.class);
overlappingFeatures = new ProxyCollection(os, this, "overlappingFeatures", org.intermine.model.bio.SequenceFeature.class);
childFeatures = new ProxyCollection(os, this, "childFeatures", org.intermine.model.bio.SequenceFeature.class);
locatedFeatures = new ProxyCollection(os, this, "locatedFeatures", org.intermine.model.bio.Location.class);
locations = new ProxyCollection(os, this, "locations", org.intermine.model.bio.Location.class);
synonyms = new ProxyCollection(os, this, "synonyms", org.intermine.model.bio.Synonym.class);
dataSets = new ProxyCollection(os, this, "dataSets", org.intermine.model.bio.DataSet.class);
crossReferences = new ProxyCollection(os, this, "crossReferences", org.intermine.model.bio.CrossReference.class);
ontologyAnnotations = new ProxyCollection(os, this, "ontologyAnnotations", org.intermine.model.bio.OntologyAnnotation.class);
publications = new ProxyCollection(os, this, "publications", org.intermine.model.bio.Publication.class);
}
public void addCollectionElement(final String fieldName, final org.intermine.model.InterMineObject element) {
if ("genes".equals(fieldName)) {
genes.add((org.intermine.model.bio.Gene) element);
} else if ("overlappingFeatures".equals(fieldName)) {
overlappingFeatures.add((org.intermine.model.bio.SequenceFeature) element);
} else if ("childFeatures".equals(fieldName)) {
childFeatures.add((org.intermine.model.bio.SequenceFeature) element);
} else if ("locatedFeatures".equals(fieldName)) {
locatedFeatures.add((org.intermine.model.bio.Location) element);
} else if ("locations".equals(fieldName)) {
locations.add((org.intermine.model.bio.Location) element);
} else if ("synonyms".equals(fieldName)) {
synonyms.add((org.intermine.model.bio.Synonym) 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.CrossReference) element);
} else if ("ontologyAnnotations".equals(fieldName)) {
ontologyAnnotations.add((org.intermine.model.bio.OntologyAnnotation) element);
} else if ("publications".equals(fieldName)) {
publications.add((org.intermine.model.bio.Publication) element);
} else {
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
TypeUtil.addCollectionElement(this, fieldName, element);
return;
}
throw new IllegalArgumentException("Unknown collection " + fieldName);
}
}
public Class getElementType(final String fieldName) {
if ("genes".equals(fieldName)) {
return org.intermine.model.bio.Gene.class;
}
if ("overlappingFeatures".equals(fieldName)) {
return org.intermine.model.bio.SequenceFeature.class;
}
if ("childFeatures".equals(fieldName)) {
return org.intermine.model.bio.SequenceFeature.class;
}
if ("locatedFeatures".equals(fieldName)) {
return org.intermine.model.bio.Location.class;
}
if ("locations".equals(fieldName)) {
return org.intermine.model.bio.Location.class;
}
if ("synonyms".equals(fieldName)) {
return org.intermine.model.bio.Synonym.class;
}
if ("dataSets".equals(fieldName)) {
return org.intermine.model.bio.DataSet.class;
}
if ("crossReferences".equals(fieldName)) {
return org.intermine.model.bio.CrossReference.class;
}
if ("ontologyAnnotations".equals(fieldName)) {
return org.intermine.model.bio.OntologyAnnotation.class;
}
if ("publications".equals(fieldName)) {
return org.intermine.model.bio.Publication.class;
}
if (!org.intermine.model.bio.Intron.class.equals(getClass())) {
return TypeUtil.getElementType(org.intermine.model.bio.Intron.class, fieldName);
}
throw new IllegalArgumentException("Unknown field " + fieldName);
}
}
