diff --git a/org/gmod/schema/analysis/Analysis.java b/org/gmod/schema/analysis/Analysis.java
new file mode 100644
index 0000000000000000000000000000000000000000..280da6955b89a20dd7fe372198d00bdfa98bda3c
--- /dev/null
+++ b/org/gmod/schema/analysis/Analysis.java
@@ -0,0 +1,242 @@
+package org.gmod.schema.analysis;
+
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+public class Analysis implements Serializable {
+
+ // Fields
+
+
+ private int analysisId;
+
+
+ private String name;
+
+
+ private String description;
+
+
+ private String program;
+
+
+ private String programVersion;
+
+
+ private String algorithm;
+
+
+ private String sourceName;
+
+
+ private String sourceVersion;
+
+
+ private String sourceUri;
+
+
+ private Date timeExecuted;
+
+
+ private Set<AnalysisFeature> analysisFeatures = new HashSet<AnalysisFeature>(0);
+
+
+ private Set<AnalysisProp> analysisProps = new HashSet<AnalysisProp>(0);
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getAnalysisId()
+ */
+ public int getAnalysisId() {
+ return this.analysisId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setAnalysisId(int)
+ */
+ public void setAnalysisId(int analysisId) {
+ this.analysisId = analysisId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getName()
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setName(java.lang.String)
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getDescription()
+ */
+ public String getDescription() {
+ return this.description;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setDescription(java.lang.String)
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getProgram()
+ */
+ public String getProgram() {
+ return this.program;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setProgram(java.lang.String)
+ */
+ public void setProgram(String program) {
+ this.program = program;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getProgramversion()
+ */
+ public String getProgramVersion() {
+ return this.programVersion;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setProgramversion(java.lang.String)
+ */
+ public void setProgramVersion(String programVersion) {
+ this.programVersion = programVersion;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getAlgorithm()
+ */
+ public String getAlgorithm() {
+ return this.algorithm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setAlgorithm(java.lang.String)
+ */
+ public void setAlgorithm(String algorithm) {
+ this.algorithm = algorithm;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getSourcename()
+ */
+ public String getSourceName() {
+ return this.sourceName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setSourcename(java.lang.String)
+ */
+ public void setSourceName(String sourceName) {
+ this.sourceName = sourceName;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getSourceversion()
+ */
+ public String getSourceVersion() {
+ return this.sourceVersion;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setSourceversion(java.lang.String)
+ */
+ public void setSourceVersion(String sourceVersion) {
+ this.sourceVersion = sourceVersion;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getSourceuri()
+ */
+ public String getSourceUri() {
+ return this.sourceUri;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setSourceuri(java.lang.String)
+ */
+ public void setSourceUri(String sourceUri) {
+ this.sourceUri = sourceUri;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getTimeexecuted()
+ */
+ public Date getTimeExecuted() {
+ return this.timeExecuted;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setTimeexecuted(java.util.Date)
+ */
+ public void setTimeExecuted(Date timeExecuted) {
+ this.timeExecuted = timeExecuted;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getAnalysisfeatures()
+ */
+ public Collection<AnalysisFeature> getAnalysisFeatures() {
+ return this.analysisFeatures;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setAnalysisfeatures(java.util.Set)
+ */
+ public void setAnalysisFeatures(Set<AnalysisFeature> analysisFeatures) {
+ this.analysisFeatures = analysisFeatures;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#getAnalysisprops()
+ */
+ public Collection<AnalysisProp> getAnalysisProps() {
+ return this.analysisProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisI#setAnalysisprops(java.util.Set)
+ */
+ private void setAnalysisProps(Set<AnalysisProp> analysisProps) {
+ this.analysisProps = analysisProps;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/analysis/AnalysisFeature.java b/org/gmod/schema/analysis/AnalysisFeature.java
new file mode 100644
index 0000000000000000000000000000000000000000..5bff33006ca81d8a9233619b58df5e08de0cd9b6
--- /dev/null
+++ b/org/gmod/schema/analysis/AnalysisFeature.java
@@ -0,0 +1,176 @@
+package org.gmod.schema.analysis;
+
+import org.gmod.schema.sequence.Feature;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class AnalysisFeature implements Serializable {
+
+ // Fields
+
+
+
+ private int analysisFeatureId;
+
+
+
+ private Analysis analysis;
+
+
+
+ private Feature feature;
+
+
+ private Double rawScore;
+
+
+ private Double normScore;
+
+
+ private Double significance;
+
+
+ private Double identity;
+
+ // Constructors
+
+ /** default constructor */
+ public AnalysisFeature() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public AnalysisFeature(Analysis analysis, Feature feature) {
+ this.analysis = analysis;
+ this.feature = feature;
+ }
+ /** full constructor */
+ public AnalysisFeature(Analysis analysis, Feature feature, Double rawScore, Double normScore, Double significance, Double identity) {
+ this.analysis = analysis;
+ this.feature = feature;
+ this.rawScore = rawScore;
+ this.normScore = normScore;
+ this.significance = significance;
+ this.identity = identity;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getAnalysisFeatureId()
+ */
+ public int getAnalysisFeatureId() {
+ return this.analysisFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setAnalysisFeatureId(int)
+ */
+ public void setAnalysisFeatureId(int analysisFeatureId) {
+ this.analysisFeatureId = analysisFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getAnalysis()
+ */
+ public Analysis getAnalysis() {
+ return this.analysis;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setAnalysis(org.genedb.db.jpa.Analysis)
+ */
+ public void setAnalysis(Analysis analysis) {
+ this.analysis = analysis;
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getRawscore()
+ */
+ public Double getRawScore() {
+ return this.rawScore;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setRawscore(java.lang.Double)
+ */
+ public void setRawScore(Double rawScore) {
+ this.rawScore = rawScore;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getNormscore()
+ */
+ public Double getNormScore() {
+ return this.normScore;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setNormscore(java.lang.Double)
+ */
+ public void setNormScore(Double normScore) {
+ this.normScore = normScore;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getSignificance()
+ */
+ public Double getSignificance() {
+ return this.significance;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setSignificance(java.lang.Double)
+ */
+ public void setSignificance(Double significance) {
+ this.significance = significance;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#getIdentity()
+ */
+ public Double getIdentity() {
+ return this.identity;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisFeatureI#setIdentity(java.lang.Double)
+ */
+ public void setIdentity(Double identity) {
+ this.identity = identity;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/analysis/AnalysisProp.java b/org/gmod/schema/analysis/AnalysisProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..8770dfd483213de9288b0a8f436ea11b63c1b517
--- /dev/null
+++ b/org/gmod/schema/analysis/AnalysisProp.java
@@ -0,0 +1,104 @@
+package org.gmod.schema.analysis;
+
+
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class AnalysisProp implements Serializable, PropertyI {
+
+ // Fields
+
+
+
+ private int analysisPropId;
+
+
+
+ private Analysis analysis;
+
+
+
+ private CvTerm cvTerm;
+
+
+ private String value;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#getAnalysispropId()
+ */
+ private int getAnalysisPropId() {
+ return this.analysisPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#setAnalysispropId(int)
+ */
+ private void setAnalysisPropId(int analysisPropId) {
+ this.analysisPropId = analysisPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#getAnalysis()
+ */
+ private Analysis getAnalysis() {
+ return this.analysis;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#setAnalysis(org.genedb.db.jpa.Analysis)
+ */
+ private void setAnalysis(Analysis analysis) {
+ this.analysis = analysis;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#getCvterm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#setCvterm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#getValue()
+ */
+ private String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.AnalysisPropI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/Cv.java b/org/gmod/schema/cv/Cv.java
new file mode 100644
index 0000000000000000000000000000000000000000..2f15e4fa622e4fcbbbe62a9e2f41d4e82c309448
--- /dev/null
+++ b/org/gmod/schema/cv/Cv.java
@@ -0,0 +1,111 @@
+package org.gmod.schema.cv;
+
+
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+public class Cv implements Serializable {
+
+ // Fields
+
+
+ private int cvId;
+
+
+ private String name;
+
+
+ private String definition;
+
+
+ private Set<CvTermPath> cvTermPaths = new HashSet<CvTermPath>(0);
+
+
+ private Set<CvTerm> cvTerms = new HashSet<CvTerm>(0);
+
+
+ // Property accessors
+
+ public int getCvId() {
+ return this.cvId;
+ }
+
+ public void setCvId(int cvId) {
+ this.cvId = cvId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#getName()
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#setName(java.lang.String)
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#getDefinition()
+ */
+ public String getDefinition() {
+ return this.definition;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#setDefinition(java.lang.String)
+ */
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#getCvTermPaths()
+ */
+ public Collection<CvTermPath> getCvTermPaths() {
+ return this.cvTermPaths;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#setCvTermPaths(java.util.Set)
+ */
+ public void setCvTermPaths(Set<CvTermPath> cvTermPaths) {
+ this.cvTermPaths = cvTermPaths;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#getCvTerms()
+ */
+ public Collection<CvTerm> getCvTerms() {
+ return this.cvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvI#setCvTerms(java.util.Set)
+ */
+ public void setCvTerms(Set<CvTerm> cvTerms) {
+ this.cvTerms = cvTerms;
+ }
+
+}
+
+
diff --git a/org/gmod/schema/cv/CvTerm.java b/org/gmod/schema/cv/CvTerm.java
new file mode 100644
index 0000000000000000000000000000000000000000..12ff609153b35ded714d694bd00dcea9de39bfd4
--- /dev/null
+++ b/org/gmod/schema/cv/CvTerm.java
@@ -0,0 +1,648 @@
+package org.gmod.schema.cv;
+
+
+import org.gmod.schema.analysis.AnalysisProp;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.organism.OrganismProp;
+import org.gmod.schema.phylogeny.Phylonode;
+import org.gmod.schema.phylogeny.PhylonodeProp;
+import org.gmod.schema.phylogeny.PhylonodeRelationship;
+import org.gmod.schema.phylogeny.Phylotree;
+import org.gmod.schema.pub.Pub;
+import org.gmod.schema.pub.PubProp;
+import org.gmod.schema.pub.PubRelationship;
+import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermProp;
+import org.gmod.schema.sequence.FeatureProp;
+import org.gmod.schema.sequence.FeatureRelationship;
+import org.gmod.schema.sequence.FeatureRelationshipProp;
+import org.gmod.schema.sequence.Synonym;
+
+import java.io.Serializable;
+import java.util.Collection;
+
+
+
+
+
+
+
+
+
+
+
+
+
+public class CvTerm implements Serializable {
+
+ private Collection<Phylotree> phylotrees;
+ private Collection<PhylonodeProp> phylonodeProps;
+ private Collection<PhylonodeRelationship> phylonodeRelationships;
+ private Collection<Phylonode> phylonodes;
+
+
+
+
+ public Collection<Phylotree> getPhylotrees() {
+ return this.phylotrees;
+ }
+
+ public void setPhylotrees(Collection<Phylotree> phylotrees) {
+ this.phylotrees = phylotrees;
+ }
+
+
+ public Collection<PhylonodeProp> getPhylonodeProps() {
+ return this.phylonodeProps;
+ }
+
+ public void setPhylonodeProps(Collection<PhylonodeProp> phylonodeProps) {
+ this.phylonodeProps = phylonodeProps;
+ }
+
+
+
+
+ public Collection<PhylonodeRelationship> getPhylonodeRelationships() {
+ return this.phylonodeRelationships;
+ }
+
+ public void setPhylonodeRelationships(Collection<PhylonodeRelationship> phylonodeRelationships) {
+ this.phylonodeRelationships = phylonodeRelationships;
+ }
+
+
+ public Collection<Phylonode> getPhylonodes() {
+ return this.phylonodes;
+ }
+
+ public void setPhylonodes(Collection<Phylonode> phylonodes) {
+ this.phylonodes = phylonodes;
+ }
+
+
+
+
+
+
+
+
+
+
+
+ // Fields
+
+
+ private int cvTermId;
+
+
+
+ private DbXRef dbXRef;
+
+
+
+ private Cv cv;
+
+
+ private String name;
+
+
+ private String definition;
+
+
+ private int isObsolete;
+
+
+ private int isRelationshipType;
+
+
+ private Collection<AnalysisProp> analysisProps;
+
+
+ private Collection<CvTermProp> cvTermPropsForTypeId;
+
+
+ private Collection<CvTermProp> cvTermPropsForCvTermId;
+
+
+ private Collection<DbXRefProp> dbXRefProps;
+
+
+ private Collection<Synonym> synonyms;
+
+
+ private Collection<CvTermDbXRef> cvTermDbXRefs;
+
+
+ private Collection<CvTermPath> cvTermPathsForTypeId;
+
+
+ private Collection<FeatureCvTermProp> featureCvTermProps;
+
+
+ private Collection<FeatureCvTerm> featureCvTerms;
+
+
+ private Collection<CvTermRelationship> cvTermRelationshipsForTypeId;
+
+
+ private Collection<CvTermRelationship> cvTermRelationshipsForObjectId;
+
+
+ private Collection<PubProp> pubProps;
+
+
+ private Collection<OrganismProp> organismProps;
+
+
+ private Collection<CvTermRelationship> cvTermRelationshipsForSubjectId;
+
+
+ private Collection<CvTermSynonym> cvTermSynonymsForCvTermId;
+
+
+ private Collection<FeatureProp> featureProps;
+
+
+ private Collection<CvTermPath> cvTermPathsForSubjectId;
+
+
+ private Collection<CvTermPath> cvTermPathsForObjectId;
+
+
+ private Collection<CvTermSynonym> cvTermSynonymsForTypeId;
+
+
+ private Collection<Pub> pubs;
+
+
+ private Collection<FeatureRelationshipProp> featureRelationshipProps;
+
+
+ private Collection<Feature> features;
+
+
+ private Collection<PubRelationship> pubRelationships;
+
+
+ private Collection<FeatureRelationship> featureRelationships;
+
+ // Constructors
+
+ /** default constructor */
+ public CvTerm() {
+ // Deliberately empty default constructor
+ }
+
+ /** useful constructor! */
+ public CvTerm(Cv cv, DbXRef dbXRef, String name, String definition) {
+ this.dbXRef = dbXRef;
+ this.cv = cv;
+ this.name = name;
+ this.definition = definition;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermId()
+ */
+ public int getCvTermId() {
+ return this.cvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermId(int)
+ */
+ public void setCvTermId(int cvTermId) {
+ this.cvTermId = cvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getDbXRef()
+ */
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setDbXRef(org.genedb.db.jpa.DbXRef)
+ */
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCv()
+ */
+ public Cv getCv() {
+ return this.cv;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCv(org.gmod.schema.cv.CvI)
+ */
+ public void setCv(Cv cv) {
+ this.cv = cv;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getName()
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setName(java.lang.String)
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getDefinition()
+ */
+ public String getDefinition() {
+ return this.definition;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setDefinition(java.lang.String)
+ */
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getIsObsolete()
+ */
+ public int getIsObsolete() {
+ return this.isObsolete;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setIsObsolete(int)
+ */
+ public void setIsObsolete(int isObsolete) {
+ this.isObsolete = isObsolete;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getIsRelationshipType()
+ */
+ public int getIsRelationshipType() {
+ return this.isRelationshipType;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setIsRelationshipType(int)
+ */
+ public void setIsRelationshipType(int isRelationshipType) {
+ this.isRelationshipType = isRelationshipType;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getAnalsisProps()
+ */
+ private Collection<AnalysisProp> getAnalysisProps() {
+ return this.analysisProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setAnalsisProps(java.util.Set)
+ */
+ private void setAnalysisProps(Collection<AnalysisProp> analysisProps) {
+ this.analysisProps = analysisProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermPropsForTypeId()
+ */
+ private Collection<CvTermProp> getCvTermPropsForTypeId() {
+ return this.cvTermPropsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermPropsForTypeId(java.util.Set)
+ */
+ private void setCvTermPropsForTypeId(Collection<CvTermProp> cvTermPropsForTypeId) {
+ this.cvTermPropsForTypeId = cvTermPropsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermPropsForCvTermId()
+ */
+ private Collection<CvTermProp> getCvTermPropsForCvTermId() {
+ return this.cvTermPropsForCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermPropsForCvTermId(java.util.Set)
+ */
+ private void setCvTermPropsForCvTermId(Collection<CvTermProp> cvTermPropsForCvTermId) {
+ this.cvTermPropsForCvTermId = cvTermPropsForCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getDbXRefProps()
+ */
+ private Collection<DbXRefProp> getDbXRefProps() {
+ return this.dbXRefProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setDbXRefProps(java.util.Set)
+ */
+ private void setDbXRefProps(Collection<DbXRefProp> dbXRefProps) {
+ this.dbXRefProps = dbXRefProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getSynonyms()
+ */
+ private Collection<Synonym> getSynonyms() {
+ return this.synonyms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setSynonyms(java.util.Set)
+ */
+ private void setSynonyms(Collection<Synonym> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermDbXRefs()
+ */
+ private Collection<CvTermDbXRef> getCvTermDbXRefs() {
+ return this.cvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermDbXRefs(java.util.Set)
+ */
+ private void setCvTermDbXRefs(Collection<CvTermDbXRef> cvTermDbXRefs) {
+ this.cvTermDbXRefs = cvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermPathsForTypeId()
+ */
+ private Collection<CvTermPath> getCvTermPathsForTypeId() {
+ return this.cvTermPathsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermPathsForTypeId(java.util.Set)
+ */
+ private void setCvTermPathsForTypeId(Collection<CvTermPath> cvTermPathsForTypeId) {
+ this.cvTermPathsForTypeId = cvTermPathsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatureCvTermProps()
+ */
+ private Collection<FeatureCvTermProp> getFeatureCvTermProps() {
+ return this.featureCvTermProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatureCvTermProps(java.util.Set)
+ */
+ private void setFeatureCvTermProps(Collection<FeatureCvTermProp> featureCvTermProps) {
+ this.featureCvTermProps = featureCvTermProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatureCvTerms()
+ */
+ private Collection<FeatureCvTerm> getFeatureCvTerms() {
+ return this.featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatureCvTerms(java.util.Set)
+ */
+ private void setFeatureCvTerms(Collection<FeatureCvTerm> featureCvTerms) {
+ this.featureCvTerms = featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermRelationshipsForTypeId()
+ */
+ private Collection<CvTermRelationship> getCvTermRelationshipsForTypeId() {
+ return this.cvTermRelationshipsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermRelationshipsForTypeId(java.util.Set)
+ */
+ private void setCvTermRelationshipsForTypeId(Collection<CvTermRelationship> cvTermRelationshipsForTypeId) {
+ this.cvTermRelationshipsForTypeId = cvTermRelationshipsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermRelationshipsForObjectId()
+ */
+ public Collection<CvTermRelationship> getCvTermRelationshipsForObjectId() {
+ return this.cvTermRelationshipsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermRelationshipsForObjectId(java.util.Set)
+ */
+ public void setCvTermRelationshipsForObjectId(Collection<CvTermRelationship> cvTermRelationshipsForObjectId) {
+ this.cvTermRelationshipsForObjectId = cvTermRelationshipsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getPubProps()
+ */
+ private Collection<PubProp> getPubProps() {
+ return this.pubProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setPubProps(java.util.Set)
+ */
+ private void setPubProps(Collection<PubProp> pubProps) {
+ this.pubProps = pubProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getOrganismProps()
+ */
+ private Collection<OrganismProp> getOrganismProps() {
+ return this.organismProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setOrganismProps(java.util.Set)
+ */
+ private void setOrganismProps(Collection<OrganismProp> organismProps) {
+ this.organismProps = organismProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermRelationshipsForSubjectId()
+ */
+ public Collection<CvTermRelationship> getCvTermRelationshipsForSubjectId() {
+ return this.cvTermRelationshipsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermRelationshipsForSubjectId(java.util.Set)
+ */
+ public void setCvTermRelationshipsForSubjectId(Collection<CvTermRelationship> cvTermRelationshipsForSubjectId) {
+ this.cvTermRelationshipsForSubjectId = cvTermRelationshipsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermSynonymsForCvTermId()
+ */
+ private Collection<CvTermSynonym> getCvTermSynonymsForCvTermId() {
+ return this.cvTermSynonymsForCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermSynonymsForCvTermId(java.util.Set)
+ */
+ private void setCvTermSynonymsForCvTermId(Collection<CvTermSynonym> cvTermSynonymsForCvTermId) {
+ this.cvTermSynonymsForCvTermId = cvTermSynonymsForCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatureProps()
+ */
+ private Collection<FeatureProp> getFeatureProps() {
+ return this.featureProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatureProps(java.util.Set)
+ */
+ private void setFeatureProps(Collection<FeatureProp> featureProps) {
+ this.featureProps = featureProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermPathsForSubjectId()
+ */
+ private Collection<CvTermPath> getCvTermPathsForSubjectId() {
+ return this.cvTermPathsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermPathsForSubjectId(java.util.Set)
+ */
+ private void setCvTermPathsForSubjectId(Collection<CvTermPath> cvTermPathsForSubjectId) {
+ this.cvTermPathsForSubjectId = cvTermPathsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermPathsForObjectId()
+ */
+ private Collection<CvTermPath> getCvTermPathsForObjectId() {
+ return this.cvTermPathsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermPathsForObjectId(java.util.Set)
+ */
+ private void setCvTermPathsForObjectId(Collection<CvTermPath> cvTermPathsForObjectId) {
+ this.cvTermPathsForObjectId = cvTermPathsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getCvTermSynonymsForTypeId()
+ */
+ private Collection<CvTermSynonym> getCvTermSynonymsForTypeId() {
+ return this.cvTermSynonymsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setCvTermSynonymsForTypeId(java.util.Set)
+ */
+ private void setCvTermSynonymsForTypeId(Collection<CvTermSynonym> cvTermSynonymsForTypeId) {
+ this.cvTermSynonymsForTypeId = cvTermSynonymsForTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getPubs()
+ */
+ private Collection<Pub> getPubs() {
+ return this.pubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setPubs(java.util.Set)
+ */
+ private void setPubs(Collection<Pub> pubs) {
+ this.pubs = pubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatureRelationshipProps()
+ */
+ private Collection<FeatureRelationshipProp> getFeatureRelationshipProps() {
+ return this.featureRelationshipProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatureRelationshipProps(java.util.Set)
+ */
+ private void setFeatureRelationshipProps(Collection<FeatureRelationshipProp> featureRelationshipProps) {
+ this.featureRelationshipProps = featureRelationshipProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatures()
+ */
+ private Collection<Feature> getFeatures() {
+ return this.features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatures(java.util.Set)
+ */
+ private void setFeatures(Collection<Feature> features) {
+ this.features = features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getPubRelationships()
+ */
+ private Collection<PubRelationship> getPubRelationships() {
+ return this.pubRelationships;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setPubRelationships(java.util.Set)
+ */
+ private void setPubRelationships(Collection<PubRelationship> pubRelationships) {
+ this.pubRelationships = pubRelationships;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#getFeatureRelationships()
+ */
+ private Collection<FeatureRelationship> getFeatureRelationships() {
+ return this.featureRelationships;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermI#setFeatureRelationships(java.util.Set)
+ */
+ private void setFeatureRelationships(Collection<FeatureRelationship> featureRelationships) {
+ this.featureRelationships = featureRelationships;
+ }
+
+
+}
+
diff --git a/org/gmod/schema/cv/CvTermDbXRef.java b/org/gmod/schema/cv/CvTermDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..138bf9ac93dd7154c1d07ea6103c3f283a168afa
--- /dev/null
+++ b/org/gmod/schema/cv/CvTermDbXRef.java
@@ -0,0 +1,103 @@
+package org.gmod.schema.cv;
+
+
+
+import org.gmod.schema.general.DbXRef;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+
+public class CvTermDbXRef implements Serializable {
+
+ // Fields
+
+
+ private int cvTermDbXRefId;
+
+
+
+ private CvTerm cvTerm;
+
+
+
+ private DbXRef dbXRef;
+
+
+ private int isForDefinition;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#getCvTermDbXRefId()
+ */
+ private int getCvTermDbXRefId() {
+ return this.cvTermDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#setCvTermDbXRefId(int)
+ */
+ private void setCvTermDbXRefId(int cvTermDbXRefId) {
+ this.cvTermDbXRefId = cvTermDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#getCvTerm()
+ */
+ private CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#getDbXRef()
+ */
+ private DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#setDbXRef(org.gmod.schema.general.DbXRefI)
+ */
+ private void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#getIsForDefinition()
+ */
+ private int getIsForDefinition() {
+ return this.isForDefinition;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermDbXRefI#setIsForDefinition(int)
+ */
+ private void setIsForDefinition(int isForDefinition) {
+ this.isForDefinition = isForDefinition;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/CvTermPath.java b/org/gmod/schema/cv/CvTermPath.java
new file mode 100644
index 0000000000000000000000000000000000000000..0c21d5c8c475773e864fd2a0c9546c0e91bd8122
--- /dev/null
+++ b/org/gmod/schema/cv/CvTermPath.java
@@ -0,0 +1,139 @@
+package org.gmod.schema.cv;
+
+
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class CvTermPath implements Serializable {
+
+ // Fields
+
+
+ private int cvTermPathId;
+
+
+
+ private CvTerm cvTermBySubjectId;
+
+
+
+
+ private CvTerm cvTermByObjectId;
+
+
+
+
+ private CvTerm cvTermByTypeId;
+
+
+
+
+ private Cv cv;
+
+
+ private Integer pathDistance;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getCvTermPathId()
+ */
+ private int getCvTermPathId() {
+ return this.cvTermPathId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setCvTermPathId(int)
+ */
+ private void setCvTermPathId(int cvTermPathId) {
+ this.cvTermPathId = cvTermPathId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getCvTermBySubjectId()
+ */
+ private CvTerm getCvTermBySubjectId() {
+ return this.cvTermBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setCvTermBySubjectId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermBySubjectId(CvTerm cvTermBySubjectId) {
+ this.cvTermBySubjectId = cvTermBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getCvTermByObjectId()
+ */
+ private CvTerm getCvTermByObjectId() {
+ return this.cvTermByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setCvTermByObjectId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByObjectId(CvTerm cvTermByObjectId) {
+ this.cvTermByObjectId = cvTermByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getCvTermByTypeId()
+ */
+ private CvTerm getCvTermByTypeId() {
+ return this.cvTermByTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setCvTermByTypeId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByTypeId(CvTerm cvTermByTypeId) {
+ this.cvTermByTypeId = cvTermByTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getCv()
+ */
+ private Cv getCv() {
+ return this.cv;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setCv(org.gmod.schema.cv.CvI)
+ */
+ private void setCv(Cv cv) {
+ this.cv = cv;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#getPathDistance()
+ */
+ private Integer getPathDistance() {
+ return this.pathDistance;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPathI#setPathDistance(java.lang.Integer)
+ */
+ private void setPathDistance(Integer pathDistance) {
+ this.pathDistance = pathDistance;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/CvTermProp.java b/org/gmod/schema/cv/CvTermProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..db9eeae4f5b2a3961b0b82141eb4415943c7cd5d
--- /dev/null
+++ b/org/gmod/schema/cv/CvTermProp.java
@@ -0,0 +1,118 @@
+package org.gmod.schema.cv;
+
+
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+
+public class CvTermProp implements Serializable {
+
+ // Fields
+
+
+ private int cvTermPropId;
+
+
+
+ private CvTerm cvTermByCvTermId;
+
+
+
+ private CvTerm cvTermByTypeId;
+
+
+ private String value;
+
+
+ private int rank;
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#getCvTermpropId()
+ */
+ private int getCvTermPropId() {
+ return this.cvTermPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#setCvTermpropId(int)
+ */
+ private void setCvTermPropId(int cvTermPropId) {
+ this.cvTermPropId = cvTermPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#getCvTermByCvTermId()
+ */
+ private CvTerm getCvTermByCvTermId() {
+ return this.cvTermByCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#setCvTermByCvTermId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByCvTermId(CvTerm cvTermByCvTermId) {
+ this.cvTermByCvTermId = cvTermByCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#getCvTermByTypeId()
+ */
+ private CvTerm getCvTermByTypeId() {
+ return this.cvTermByTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#setCvTermByTypeId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByTypeId(CvTerm cvTermByTypeId) {
+ this.cvTermByTypeId = cvTermByTypeId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#getValue()
+ */
+ private String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#getRank()
+ */
+ private int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermPropI#setRank(int)
+ */
+ private void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/CvTermRelationship.java b/org/gmod/schema/cv/CvTermRelationship.java
new file mode 100644
index 0000000000000000000000000000000000000000..c71b35493fbf05c0925ed303c86947a76482be03
--- /dev/null
+++ b/org/gmod/schema/cv/CvTermRelationship.java
@@ -0,0 +1,113 @@
+package org.gmod.schema.cv;
+
+
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class CvTermRelationship implements Serializable {
+
+ // Fields
+
+
+ private int cvTermRelationshipId;
+
+
+
+ private CvTerm cvTermBySubjectId;
+
+
+
+ private CvTerm cvTermByObjectId;
+
+
+
+ private CvTerm cvTermByTypeId;
+
+ // Constructors
+
+ /** default constructor */
+ public CvTermRelationship() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public CvTermRelationship(CvTerm cvTermBySubjectId, CvTerm cvTermByObjectId, CvTerm cvTermByTypeId) {
+ this.cvTermBySubjectId = cvTermBySubjectId;
+ this.cvTermByObjectId = cvTermByObjectId;
+ this.cvTermByTypeId = cvTermByTypeId;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#getCvTermRelationshipId()
+ */
+ private int getCvTermRelationshipId() {
+ return this.cvTermRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#setCvTermRelationshipId(int)
+ */
+ private void setCvTermRelationshipId(int cvTermRelationshipId) {
+ this.cvTermRelationshipId = cvTermRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#getCvTermBySubjectId()
+ */
+ private CvTerm getCvTermBySubjectId() {
+ return this.cvTermBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#setCvTermBySubjectId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermBySubjectId(CvTerm cvTermBySubjectId) {
+ this.cvTermBySubjectId = cvTermBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#getCvTermByObjectId()
+ */
+ private CvTerm getCvTermByObjectId() {
+ return this.cvTermByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#setCvTermByObjectId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByObjectId(CvTerm cvTermByObjectId) {
+ this.cvTermByObjectId = cvTermByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#getCvTermByTypeId()
+ */
+ private CvTerm getCvTermByTypeId() {
+ return this.cvTermByTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermRelationshipI#setCvTermByTypeId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByTypeId(CvTerm cvTermByTypeId) {
+ this.cvTermByTypeId = cvTermByTypeId;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/CvTermSynonym.java b/org/gmod/schema/cv/CvTermSynonym.java
new file mode 100644
index 0000000000000000000000000000000000000000..9401b368c97e9ed33242a707f544dff22c54f142
--- /dev/null
+++ b/org/gmod/schema/cv/CvTermSynonym.java
@@ -0,0 +1,101 @@
+package org.gmod.schema.cv;
+
+
+
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class CvTermSynonym implements Serializable {
+
+ // Fields
+
+
+ private int cvTermSynonymId;
+
+
+
+ private CvTerm cvTermByCvTermId;
+
+
+
+ private CvTerm cvTermByTypeId;
+
+
+ private String synonym;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#getCvTermSynonymId()
+ */
+ private int getCvTermSynonymId() {
+ return this.cvTermSynonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#setCvTermSynonymId(int)
+ */
+ private void setCvTermSynonymId(int cvTermSynonymId) {
+ this.cvTermSynonymId = cvTermSynonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#getCvTermByCvTermId()
+ */
+ private CvTerm getCvTermByCvTermId() {
+ return this.cvTermByCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#setCvTermByCvTermId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByCvTermId(CvTerm cvTermByCvTermId) {
+ this.cvTermByCvTermId = cvTermByCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#getCvTermByTypeId()
+ */
+ private CvTerm getCvTermByTypeId() {
+ return this.cvTermByTypeId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#setCvTermByTypeId(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTermByTypeId(CvTerm cvTermByTypeId) {
+ this.cvTermByTypeId = cvTermByTypeId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#getSynonym()
+ */
+ private String getSynonym() {
+ return this.synonym;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.CvTermSynonymI#setSynonym(java.lang.String)
+ */
+ private void setSynonym(String synonym) {
+ this.synonym = synonym;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/cv/DbXRefProp.java b/org/gmod/schema/cv/DbXRefProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..97ce2ae6968c86bbe6b4d942b9157c0a6e681260
--- /dev/null
+++ b/org/gmod/schema/cv/DbXRefProp.java
@@ -0,0 +1,120 @@
+package org.gmod.schema.cv;
+
+
+
+
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class DbXRefProp implements Serializable, PropertyI {
+
+ // Fields
+
+
+ private int dbXRefPropId;
+
+
+
+ private CvTerm cvTerm;
+
+
+
+ private DbXRef dbXRef;
+
+
+ private String value;
+
+
+ private int rank;
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#getDbXRefpropId()
+ */
+ private int getDbXRefPropId() {
+ return this.dbXRefPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#setDbXRefpropId(int)
+ */
+ private void setDbXRefPropId(int dbXRefPropId) {
+ this.dbXRefPropId = dbXRefPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#getCvTerm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#getDbXRef()
+ */
+ private DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#setDbXRef(org.gmod.schema.general.DbXRefI)
+ */
+ private void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#getValue()
+ */
+ private String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#getRank()
+ */
+ private int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefPropI#setRank(int)
+ */
+ private void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/dao/BaseDaoI.java b/org/gmod/schema/dao/BaseDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..971a8fa642a11607494fdf54164f217e6b40e9c0
--- /dev/null
+++ b/org/gmod/schema/dao/BaseDaoI.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+public interface BaseDaoI {
+
+
+ /**
+ * Save the object to the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is available in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ * @param o the new instance to persist
+ */
+ public abstract void persist(Object o);
+
+ /**
+ * Delete an object from the database
+ * @param o the object to remove
+ *
+ */
+ public abstract void delete(Object o);
+
+ /**
+ * Merge (update) an already persistent object back to the database (at the end of
+ * the current transaction, or depending upon flush mode). This method is defined in
+ * all the DAOs. It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ *
+ * @param o the existing feature to merge
+ */
+ public abstract void merge(Object o);
+
+}
diff --git a/org/gmod/schema/dao/CvDaoI.java b/org/gmod/schema/dao/CvDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..686026f16a702cc3847b3c3ce91b32e9ef90809d
--- /dev/null
+++ b/org/gmod/schema/dao/CvDaoI.java
@@ -0,0 +1,117 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+
+import org.gmod.schema.cv.Cv;
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.utils.CountedName;
+
+import java.util.List;
+
+public interface CvDaoI extends BaseDaoI {
+
+ /**
+ * Get a CV by id
+ *
+ * @param id the cv id (primary key)
+ * @return the corresponding Cv, or null
+ */
+ public abstract Cv getCvById(int id);
+
+ // TODO Should this return a list or just one?
+ /**
+ * Retrieve a controlled vocabulary by its name
+ *
+ * @param name the name to lookup
+ * @return the List<Cv> of matches, or null
+ */
+ public abstract List<Cv> getCvByName(String name);
+
+ /**
+ * Retrieve a CvTerm by id
+ *
+ * @param id then cvterm id (primary key)
+ * @return the corresponding CvTerm, or null
+ */
+ public abstract CvTerm getCvTermById(int id);
+
+
+ // TODO Should this return a list or just one?
+ /**
+ * Retrieve a named CvTerm from a given Cv
+ *
+ * @param cvTermName the name of the cvterm
+ * @param cv the controlled vocabulary this cvterm is part of
+ * @return a (possibly empty) list of matching cvterms
+ */
+ public abstract List<CvTerm> getCvTermByNameInCv(String cvTermName, Cv cv);
+
+
+ /**
+ * Retrieve a CvTerm from the Gene Ontology
+ *
+ * @param value the
+ * @return the corresponding CvTerm, or null
+ */
+ public abstract CvTerm getGoCvTermByAcc(String value);
+
+
+ /**
+ * Retrieve a CvTerm from the Gene Ontology via it's database entry
+ *
+ * @param id the database name eg GO:123456
+ * @return the corresponding CvTerm, or null
+ */
+ public abstract CvTerm getGoCvTermByAccViaDb(final String id);
+
+
+ /**
+ * Retrieve all CvTerms
+ * @return a list of all cvterms
+ */
+ public abstract List<CvTerm> getCvTerms();
+
+ /**
+ * Retrieve a named CvTerm from a given Cv
+ *
+ * @param cvTermName the name of the cvterm
+ * @param name the controlled vocabulary name this cvterm could be part of
+ * @return a (possibly empty) cvterm
+ */
+ public abstract CvTerm getCvTermByNameAndCvName(String cvTermName, String name);
+
+ /**
+ * Get a CvTerm by DbXRef
+ *
+ * @param dbXRef the DbXRef
+ * @return the corresponding CvTerm, or null
+ */
+ public abstract CvTerm getCvTermByDbXRef(DbXRef dbXRef);
+
+ public boolean existsNameInOntology(String name, Cv ontology);
+
+
+ public List<String> getPossibleMatches(String search, Cv cv, int limit);
+
+ public List<CountedName> getAllTermsInCvWithCount(Cv cv);
+
+}
diff --git a/org/gmod/schema/dao/GeneralDaoI.java b/org/gmod/schema/dao/GeneralDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..3a18ae1f412576ab9be804c18fb315a09096a04e
--- /dev/null
+++ b/org/gmod/schema/dao/GeneralDaoI.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+import org.gmod.schema.analysis.AnalysisFeature;
+import org.gmod.schema.general.Db;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.sequence.Feature;
+
+
+
+public interface GeneralDaoI extends BaseDaoI{
+
+ /**
+ * Retrieve a database by name
+ *
+ * @param name the name to lookup
+ * @return the corresponding db, or null
+ */
+ public abstract Db getDbByName(String name);
+
+ /**
+ * Retrieve the db xref corresponding to a given DB and accession number
+ *
+ * @param db the db the dbxref refers to
+ * @param accession the accession "number" the dbxref refers to
+ * @return the dbxref, or null
+ */
+ public abstract DbXRef getDbXRefByDbAndAcc(Db db, String accession);
+
+ /**
+ * Retrieve the analysisfeature corresponding to the given feature
+ *
+ * @param feature the feature whose analysisfeature has to be found
+ * @return the analysisfeature
+ */
+ public abstract AnalysisFeature getAnalysisFeatureFromFeature(Feature feature);
+}
diff --git a/org/gmod/schema/dao/OrganismDaoI.java b/org/gmod/schema/dao/OrganismDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..4edfb6fcbced27fe361bdbb2b0ac4ff13b98a888
--- /dev/null
+++ b/org/gmod/schema/dao/OrganismDaoI.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+import org.gmod.schema.organism.Organism;
+
+import java.util.List;
+
+public interface OrganismDaoI extends BaseDaoI {
+
+ /**
+ * Get the organism corresponding to this id
+ *
+ * @param id the organism id (primary key) to lookup by
+ * @return the corresponding organism, or null
+ */
+ public abstract Organism getOrganismById(int id);
+
+ /**
+ * Get the organism corresponding to this common name
+ *
+ * @param commonName the short name to look up
+ * @return the corresponding organism, or null
+ */
+ public abstract Organism getOrganismByCommonName(String commonName);
+
+ /**
+ * Get a list of the common name of all the organisms.
+ *
+ * @return a (possibly empty) List<String> of all the organisms' common names
+ */
+ public abstract List<String> findAllOrganismCommonNames();
+
+ /**
+ * Get a list of all the organisms
+ *
+ * @return a (possibly empty) List<Organism> of all the organisms'
+ */
+ public abstract List<Organism> getOrganisms();
+
+}
diff --git a/org/gmod/schema/dao/PhylogenyDaoI.java b/org/gmod/schema/dao/PhylogenyDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..e3241eb6231fd650081144f6e9b4d4275c192eee
--- /dev/null
+++ b/org/gmod/schema/dao/PhylogenyDaoI.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.phylogeny.Phylonode;
+import org.gmod.schema.phylogeny.Phylotree;
+
+import java.util.List;
+
+
+
+public interface PhylogenyDaoI extends BaseDaoI {
+
+ public Phylotree getPhyloTreeByName(String name);
+
+ public List<Phylonode> getPhyloNodesByCvTermInTree(CvTerm type, Phylotree tree);
+
+ public List<Phylonode> getAllPhylonodes();
+
+ public List<Phylonode> getPhylonodeByDepthAndParent(double depth,Phylonode parent);
+
+ public List<Phylonode> getPhylonodeByName(String name);
+
+ public List<Phylonode> getPhylonodesByParent(Phylonode parent);
+
+ //public List<Phylonode> getPhylonodeByDepth(double depth);
+}
diff --git a/org/gmod/schema/dao/PubDaoI.java b/org/gmod/schema/dao/PubDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..e196c19beaacd0508ed890359364279671e636e2
--- /dev/null
+++ b/org/gmod/schema/dao/PubDaoI.java
@@ -0,0 +1,65 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+import java.util.List;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.pub.Pub;
+import org.gmod.schema.pub.PubProp;
+import org.gmod.schema.pub.PubDbXRef;
+
+public interface PubDaoI extends BaseDaoI {
+
+ /**
+ * Retrieve the publication with this primary key
+ *
+ * @param id the publication id
+ * @return the corresponding publication, or null
+ */
+ public abstract Pub getPubById(int id);
+
+ /**
+ * Retrieve the publication with this primary key
+ *
+ * @param uniqueName
+ * @return the publication with this unique name, or null
+ */
+ public abstract Pub getPubByUniqueName(String uniqueName);
+
+
+ public Pub getPubByDbXRef(DbXRef dbXRef);
+
+ /**
+ * Get a list of all PubDbXRef's
+ * @return list of PubDbXRef's
+ */
+ public List<PubDbXRef> getPubDbXRef();
+
+ /**
+ * Retrieve the publication property with Pub and Cvterm
+ *
+ * @param pub the Publication
+ * @param cvTerm the cvTerm
+ * @return the publication or null
+ */
+ public abstract List<PubProp> getPubPropByPubAndCvTerm(Pub pub,CvTerm cvTerm);
+}
diff --git a/org/gmod/schema/dao/SchemaDaoI.java b/org/gmod/schema/dao/SchemaDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..484a529c55932b9a6d0c03ae06888bd3d2563fcc
--- /dev/null
+++ b/org/gmod/schema/dao/SchemaDaoI.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+
+import org.gmod.schema.sequence.Feature;
+
+import java.sql.SQLException;
+import java.util.List;
+
+public interface SchemaDaoI extends BaseDaoI {
+
+ /**
+ * Return a list of features with residues.
+ * @return the <code>List</code> of <code>Feature</code> objects
+ * @throws SQLException
+ */
+ public List<Feature> getResidueFeatures() throws SQLException;
+
+
+ /**
+ * For a schema return the type_id's with residues.
+ * @param schema schema/organism name or null
+ * @return the <code>List</code> of type_id's as <code>String</code> objects
+ * @throws SQLException
+ */
+ public List<String> getResidueType(String schema) throws SQLException;
+
+ /**
+ * Get available schemas (as a <code>List</code> of <code>String</code>
+ * objects).
+ * @return the available schemas
+ * @throws SQLException
+ */
+ public List<String> getSchema() throws SQLException;
+
+
+}
diff --git a/org/gmod/schema/dao/SequenceDaoI.java b/org/gmod/schema/dao/SequenceDaoI.java
new file mode 100644
index 0000000000000000000000000000000000000000..b752a05b3270565812b7d3aeec42c3eaca86094e
--- /dev/null
+++ b/org/gmod/schema/dao/SequenceDaoI.java
@@ -0,0 +1,259 @@
+/*
+ * Copyright (c) 2006 Genome Research Limited.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as published
+ * by the Free Software Foundation; either version 2 of the License or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details.
+ *
+ * You should have received a copy of the GNU Library General Public License
+ * along with this program; see the file COPYING.LIB. If not, write to
+ * the Free Software Foundation Inc., 59 Temple Place - Suite 330,
+ * Boston, MA 02111-1307 USA
+ */
+
+package org.gmod.schema.dao;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.organism.Organism;
+import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureCvTermPub;
+import org.gmod.schema.sequence.FeatureDbXRef;
+import org.gmod.schema.sequence.FeatureSynonym;
+import org.gmod.schema.sequence.Synonym;
+import org.gmod.schema.utils.CountedName;
+
+import java.util.List;
+
+public interface SequenceDaoI extends BaseDaoI {
+
+ /**
+ * Return the feature corresponding to this feature_id
+ *
+ * @param id the systematic id
+ * @return the Feature, or null
+ */
+ public Feature getFeatureById(int id);
+
+ /**
+ * Return a list of features with this uniquename
+ *
+ * @param name the uniquename
+ * @return the Feature, or null
+ */
+ public List<Feature> getFeaturesByUniqueName(String name);
+
+ /**
+ *
+ * @param name the uniquename
+ * @param featureType the type of feature to return eg "gene". <b>NB</> String, not a type argument
+ * @return
+ */
+ public Feature getFeatureByUniqueName(String name, String featureType);
+
+ /**
+ * Return a list of features with any current (ie non-obsolete) name or synonym
+ *
+ * @param name the lookup name
+ * @return a (possibly empty) List<Feature> of children with this current name
+ */
+ public List<Feature> getFeaturesByAnyCurrentName(String name);
+
+ /**
+ * Return a list of features with this name or synonym (including obsolete names). The
+ * name can contain an SQL wildcard (%)
+ *
+ * @param name the lookup name
+ * @param featureType the type of feature to return eg "gene"
+ * @return a (possibly empty) List<Feature> of children with this name
+ */
+ public List<Feature> getFeaturesByAnyName(String name, String featureType);
+
+
+ // TODO Document overlap behaviour
+ /**
+ * Return a list of features located on a source Feature, within a given range
+ *
+ * @param min the minimum (interbase) coordinate
+ * @param max the maximum (interbase) coordinate
+ * @param strand
+ * @param parent the source feature
+ * @param type
+ * @return a List<Feature> which ??? this range
+ */
+ public List<Feature> getFeaturesByRange(int min, int max, int strand,
+ Feature parent, String type);
+
+ /**
+ * Return a list of features located on a source Feature
+ *
+ * @param parent the parent feature
+ * @return a (possibly empty) List<Feature> of children located on this parent
+ */
+ public List<Feature> getFeaturesByLocatedOnFeature(Feature parent);
+
+ /**
+ * Return the FeatureCvTerm that links a given Feature and CvTerm, with a given value of 'not'
+ *
+ * @param feature the Feature to test the link for
+ * @param cvTerm the CvTerm to test the link for
+ * @param not test for the not flag in the FeatureCvTerm
+ * @return the Feature, or null
+ */
+ public List<FeatureCvTerm> getFeatureCvTermsByFeatureAndCvTermAndNot(Feature feature,
+ CvTerm cvTerm, boolean not);
+
+ /**
+ * Return a list of FeatureCvterm's for a Feature, or a list
+ * of all FeatureCvTerm's if Feature is null.
+ * @param feature the Feature to retrieve associated FeatureCvTerm's
+ * @return the FeatureCvTerm's
+ */
+ public List<FeatureCvTerm> getFeatureCvTermsByFeature(Feature feature);
+
+ /**
+ * Get a list of all FeatureCvTermDbXRef's for a Feature, or a list
+ * of all FeatureCvTermDbXRef's if Feature is null.
+ * @param feature the Feature to retrieve associated FeatureCvTermDbXRef's
+ * @return the FeatureCvTermDbXRef's
+ */
+ public List<FeatureCvTermDbXRef> getFeatureCvTermDbXRefByFeature(Feature feature);
+
+ /**
+ * Get a list of all FeatureCvTermPub's for a Feature, or a list
+ * of all FeatureCvTermPub's if Feature is null.
+ * @param feature the Feature to retrieve associated FeatureCvTermPub's
+ * @return the FeatureCvTermPub's
+ */
+ public List<FeatureCvTermPub> getFeatureCvTermPubByFeature(Feature feature);
+
+ /**
+ * Return a synonym of the given name and type if it exists
+ *
+ * @param name the name to lookup
+ * @param type the type of the Synonym
+ * @return a Synonym, or null
+ */
+ public Synonym getSynonymByNameAndCvTerm(String name, CvTerm type);
+
+ /**
+ * Return a list of FeatureSynonyms which link a given Feature and Synonym
+ *
+ * @param feature the test Feature
+ * @param synonym the test Synonym
+ * @return a (possibly empty) List<FeatureSynonym>
+ */
+ public List<FeatureSynonym> getFeatureSynonymsByFeatureAndSynonym(
+ Feature feature, Synonym synonym);
+
+ public FeatureDbXRef getFeatureDbXRefByFeatureAndDbXRef(final Feature feature, final DbXRef dbXRef);
+
+ /**
+ * Return all the FeatureDbXRefs for a given feature, <b>specified by name</b>, or all if
+ * <code>null</code> is passed
+ *
+ * @param uniqueName the uniquename of a Feature, or null for all FeatureDbXRefs
+ * @return a (possibly empty) List<FeatureDbXRefI>
+ */
+ public List<FeatureDbXRef> getFeatureDbXRefsByFeatureUniquename(final String uniqueName);
+
+ /**
+ * Return the list of FeatureSynonyms for a given Feature, <b>specified by name</b>, or all if
+ * <code>null</code> is passed
+ *
+ * @param uniqueName the uniquename of a Feature, or null for all
+ * @return a (possibly empty) List<FeatureSynonymI> of matching synonyms
+ */
+ public List<FeatureSynonym> getFeatureSynonymsByFeatureUniquename(final String uniqueName);
+
+ /**
+ * Return the list of all feature_synonyms as Feature.featureSynonyms
+ *
+ * @return a (possibly empty) List<Features> of matching synonyms
+ */
+ public List<Feature> getAllFeatureSynonymsAsFeature();
+
+ /**
+ * Return the list of Features for a given GO number
+ *
+ *
+ * @param go the GO number
+ * @return a (possibly empty) List<Feature> of matching genes
+ */
+ public List<List> getFeatureByGO(final String go);
+
+ /**
+ * Return a list of features that have this particular cvterm
+ *
+ *
+ * @param cvTermName the CvTerm name
+ * @return a (possibly empty) List<Feature> of children
+ */
+ public List<Feature> getFeaturesByCvTermName(String cvTermName);
+
+ /**
+ * Return a list of features that have this particular cvterm
+ *
+ *
+ * @param cvTermName the CvTerm name
+ * @return a (possibly empty) List<Feature> of children
+ */
+ public List<Feature> getFeaturesByCvTermNameAndCvName(String cvTermName, String cvName);
+
+ /**
+ * Return a list of top-level features
+ *
+ *
+ * @return a (possibly empty) List<Feature> of children
+ */
+ public List<Feature> getTopLevelFeatures();
+
+ public List<CountedName> getProducts();
+
+ /**
+ * Return a list of feature uniquename based on cvterm for auto-completion
+ *
+ * @param name the Feature uniquename
+ * @param cvTerm the CvTerm
+ * @param limit the number of maximum results to return
+ * @return a (possibly empty) List<String> of feature uniquename
+ */
+ public List<String> getPossibleMatches(String name,CvTerm cvTerm, int limit);
+
+ /**
+ * Return a list of feature uniquename based on cvterm for auto-completion
+ *
+ * @param name the Feature uniquename
+ * @param orgNames the comma seperated organism common names
+ * @param featureType the type of Features to return e.g gene
+ * @param limit the number of maximum results to return
+ * @return a (possibly empty) List<Feature> of Feature
+ */
+ public List<Feature> getFeaturesByAnyNameAndOrganism(String name,String orgNames,String featureType);
+
+ /**
+ * Return a list of feature based on organism
+ *
+ * @param organism the Organism
+ * @return a (possibly empty) List<String> of feature
+ */
+ public List<Feature> getFeaturesByOrganism(Organism org);
+
+ /**
+ * Return the features corresponding to uniquenames in the list
+ *
+ * @param names the list of uniquenames
+ * @return the list of Features, or null
+ */
+ public List<Feature> getFeaturesByUniqueNames(List<String> names);
+
+}
diff --git a/org/gmod/schema/general/Db.java b/org/gmod/schema/general/Db.java
new file mode 100644
index 0000000000000000000000000000000000000000..eabd4273b541bca47b35e5475fbd6c201073cf59
--- /dev/null
+++ b/org/gmod/schema/general/Db.java
@@ -0,0 +1,136 @@
+package org.gmod.schema.general;
+
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+public class Db implements Serializable {
+
+ // Fields
+
+
+
+ private int dbId;
+
+
+ private String name;
+
+
+ private String description;
+
+
+ private String urlPrefix;
+
+
+ private String url;
+
+
+ private Set<DbXRef> dbXRefs = new HashSet<DbXRef>(0);
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getDbId()
+ */
+ public int getDbId() {
+ return this.dbId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setDbId(int)
+ */
+ public void setDbId(int dbId) {
+ this.dbId = dbId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getName()
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setName(java.lang.String)
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getDescription()
+ */
+ public String getDescription() {
+ return this.description;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setDescription(java.lang.String)
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getUrlPrefix()
+ */
+ public String getUrlPrefix() {
+ return this.urlPrefix;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setUrlPrefix(java.lang.String)
+ */
+ public void setUrlPrefix(String urlPrefix) {
+ this.urlPrefix = urlPrefix;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getUrl()
+ */
+ public String getUrl() {
+ return this.url;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setUrl(java.lang.String)
+ */
+ public void setUrl(String url) {
+ this.url = url;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#getDbXRefs()
+ */
+ public Collection<DbXRef> getDbXRefs() {
+ return this.dbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbI#setDbXRefs(java.util.Set)
+ */
+ public void setDbXRefs(Set<DbXRef> dbXRefs) {
+ this.dbXRefs = dbXRefs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/general/DbXRef.java b/org/gmod/schema/general/DbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..7945f1a2b7dc5122257f1d083221e7d64cf58dfe
--- /dev/null
+++ b/org/gmod/schema/general/DbXRef.java
@@ -0,0 +1,292 @@
+package org.gmod.schema.general;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.cv.CvTermDbXRef;
+import org.gmod.schema.cv.DbXRefProp;
+import org.gmod.schema.organism.OrganismDbXRef;
+import org.gmod.schema.phylogeny.PhylonodeDbXRef;
+import org.gmod.schema.phylogeny.Phylotree;
+import org.gmod.schema.pub.PubDbXRef;
+import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureCvTermDbXRef;
+import org.gmod.schema.sequence.FeatureDbXRef;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+public class DbXRef implements Serializable {
+
+ private Set<PhylonodeDbXRef> phylonodeDbXRefs = new HashSet<PhylonodeDbXRef>(0);
+ private Set<Phylotree> phylotrees = new HashSet<Phylotree>(0);
+
+ public Set<PhylonodeDbXRef> getPhylonodeDbXRefs() {
+ return this.phylonodeDbXRefs;
+ }
+
+ public void setPhylonodeDbXRefs(Set<PhylonodeDbXRef> phylonodeDbXRefs) {
+ this.phylonodeDbXRefs = phylonodeDbXRefs;
+ }
+
+
+ public Set<Phylotree> getPhylotrees() {
+ return this.phylotrees;
+ }
+
+ public void setPhylotrees(Set<Phylotree> phylotrees) {
+ this.phylotrees = phylotrees;
+ }
+
+
+
+ // Fields
+
+
+
+ private int dbXRefId;
+
+
+ private String version;
+
+
+
+ private Db db;
+
+
+ private String accession;
+
+
+ private String description;
+
+
+ private Set<DbXRefProp> dbXRefProps = new HashSet<DbXRefProp>(0);
+
+
+ private Set<FeatureCvTermDbXRef> featureCvTermDbXRefs = new HashSet<FeatureCvTermDbXRef>(0);
+
+
+ private Set<Feature> features = new HashSet<Feature>(0);
+
+
+ private Set<FeatureDbXRef> featureDbXRefs = new HashSet<FeatureDbXRef>(0);
+
+
+ private Set<CvTerm> cvTerms = new HashSet<CvTerm>(0);
+
+
+ private Set<PubDbXRef> pubDbXRefs = new HashSet<PubDbXRef>(0);
+
+
+ private Set<OrganismDbXRef> organismDbXRefs = new HashSet<OrganismDbXRef>(0);
+
+
+ private Set<CvTermDbXRef> cvTermDbXRefs = new HashSet<CvTermDbXRef>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public DbXRef() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public DbXRef(Db db, String accession) {
+ this.version = "1";
+ this.db = db;
+ this.accession = accession;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getDbXRefId()
+ */
+ public int getDbXRefId() {
+ return this.dbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setDbXRefId(int)
+ */
+ public void setDbXRefId(int dbXRefId) {
+ this.dbXRefId = dbXRefId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getVersion()
+ */
+ public String getVersion() {
+ return this.version;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setVersion(java.lang.String)
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getDb()
+ */
+ public Db getDb() {
+ return this.db;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setDb(org.gmod.schema.general.DbI)
+ */
+ public void setDb(Db db) {
+ this.db = db;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getAccession()
+ */
+ public String getAccession() {
+ return this.accession;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setAccession(java.lang.String)
+ */
+ public void setAccession(String accession) {
+ this.accession = accession;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getDescription()
+ */
+ public String getDescription() {
+ return this.description;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setDescription(java.lang.String)
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getDbXRefProps()
+ */
+ private Collection<DbXRefProp> getDbXRefProps() {
+ return this.dbXRefProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setDbXRefProps(java.util.Set)
+ */
+ private void setDbXRefProps(Set<DbXRefProp> dbXRefProps) {
+ this.dbXRefProps = dbXRefProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getFeatureCvTermDbXRefs()
+ */
+ private Collection<FeatureCvTermDbXRef> getFeatureCvTermDbXRefs() {
+ return this.featureCvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setFeatureCvTermDbXRefs(java.util.Set)
+ */
+ private void setFeatureCvTermDbXRefs(Set<FeatureCvTermDbXRef> featureCvTermDbXRefs) {
+ this.featureCvTermDbXRefs = featureCvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getFeatures()
+ */
+ private Collection<Feature> getFeatures() {
+ return this.features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setFeatures(java.util.Set)
+ */
+ private void setFeatures(Set<Feature> features) {
+ this.features = features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getFeatureDbXRefs()
+ */
+ private Collection<FeatureDbXRef> getFeatureDbXRefs() {
+ return this.featureDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setFeatureDbXRefs(java.util.Set)
+ */
+ private void setFeatureDbXRefs(Set<FeatureDbXRef> featureDbXRefs) {
+ this.featureDbXRefs = featureDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getCvTerms()
+ */
+ public Collection<CvTerm> getCvTerms() {
+ return this.cvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setCvTerms(java.util.Set)
+ */
+ private void setCvTerms(Set<CvTerm> cvTerms) {
+ this.cvTerms = cvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getPubDbXRefs()
+ */
+ private Collection<PubDbXRef> getPubDbXRefs() {
+ return this.pubDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setPubDbXRefs(java.util.Set)
+ */
+ private void setPubDbXRefs(Set<PubDbXRef> pubDbXRefs) {
+ this.pubDbXRefs = pubDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getOrganismDbXRefs()
+ */
+ private Collection<OrganismDbXRef> getOrganismDbXRefs() {
+ return this.organismDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setOrganismDbXRefs(java.util.Set)
+ */
+ private void setOrganismDbXRefs(Set<OrganismDbXRef> organismDbXRefs) {
+ this.organismDbXRefs = organismDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#getCvTermDbXRefs()
+ */
+ private Collection<CvTermDbXRef> getCvTermDbXRefs() {
+ return this.cvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.DbXRefI#setCvTermDbXRefs(java.util.Set)
+ */
+ private void setCvTermDbXRefs(Set<CvTermDbXRef> cvTermDbXRefs) {
+ this.cvTermDbXRefs = cvTermDbXRefs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/general/Project.java b/org/gmod/schema/general/Project.java
new file mode 100644
index 0000000000000000000000000000000000000000..f8bfd6a062cac75a931c5114a9220958714927cf
--- /dev/null
+++ b/org/gmod/schema/general/Project.java
@@ -0,0 +1,59 @@
+package org.gmod.schema.general;
+
+
+import java.io.Serializable;
+
+public class Project implements Serializable {
+
+ // Fields
+ private int projectId;
+ private String name;
+ private String description;
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#getProjectId()
+ */
+ private int getProjectId() {
+ return this.projectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#setProjectId(int)
+ */
+ private void setProjectId(int projectId) {
+ this.projectId = projectId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#getName()
+ */
+ private String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#setName(java.lang.String)
+ */
+ private void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#getDescription()
+ */
+ private String getDescription() {
+ return this.description;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.ProjectI#setDescription(java.lang.String)
+ */
+ private void setDescription(String description) {
+ this.description = description;
+ }
+
+}
+
+
diff --git a/org/gmod/schema/general/Tableinfo.java b/org/gmod/schema/general/Tableinfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..665d77fd402e50aec73c424e8d4d991ad9e92bce
--- /dev/null
+++ b/org/gmod/schema/general/Tableinfo.java
@@ -0,0 +1,148 @@
+package org.gmod.schema.general;
+
+
+import java.io.Serializable;
+import java.util.Date;
+
+public class Tableinfo implements Serializable {
+
+ // Fields
+
+ private int tableinfoId;
+ private String name;
+ private String primaryKeyColumn;
+ private int isView;
+ private Integer viewOnTableId;
+ private Integer superclassTableId;
+ private int isUpdateable;
+ private Date modificationDate;
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getTableinfoId()
+ */
+
+
+
+ private int getTableinfoId() {
+ return this.tableinfoId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setTableinfoId(int)
+ */
+ private void setTableinfoId(int tableinfoId) {
+ this.tableinfoId = tableinfoId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getName()
+ */
+ private String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setName(java.lang.String)
+ */
+ private void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getPrimaryKeyColumn()
+ */
+ private String getPrimaryKeyColumn() {
+ return this.primaryKeyColumn;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setPrimaryKeyColumn(java.lang.String)
+ */
+ private void setPrimaryKeyColumn(String primaryKeyColumn) {
+ this.primaryKeyColumn = primaryKeyColumn;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getIsView()
+ */
+ private int getIsView() {
+ return this.isView;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setIsView(int)
+ */
+ private void setIsView(int isView) {
+ this.isView = isView;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getViewOnTableId()
+ */
+ private Integer getViewOnTableId() {
+ return this.viewOnTableId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setViewOnTableId(java.lang.Integer)
+ */
+ private void setViewOnTableId(Integer viewOnTableId) {
+ this.viewOnTableId = viewOnTableId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getSuperclassTableId()
+ */
+ private Integer getSuperclassTableId() {
+ return this.superclassTableId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setSuperclassTableId(java.lang.Integer)
+ */
+ private void setSuperclassTableId(Integer superclassTableId) {
+ this.superclassTableId = superclassTableId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getIsUpdateable()
+ */
+ private int getIsUpdateable() {
+ return this.isUpdateable;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setIsUpdateable(int)
+ */
+ private void setIsUpdateable(int isUpdateable) {
+ this.isUpdateable = isUpdateable;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#getModificationDate()
+ */
+ private Date getModificationDate() {
+ return this.modificationDate;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.TableInfoI#setModificationDate(java.util.Date)
+ */
+ private void setModificationDate(Date modificationDate) {
+ this.modificationDate = modificationDate;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/organism/Organism.java b/org/gmod/schema/organism/Organism.java
new file mode 100644
index 0000000000000000000000000000000000000000..8a539e7000d15dca0008fa467e4d6d64a8ddc6ca
--- /dev/null
+++ b/org/gmod/schema/organism/Organism.java
@@ -0,0 +1,207 @@
+package org.gmod.schema.organism;
+
+
+
+import org.gmod.schema.phylogeny.PhylonodeOrganism;
+import org.gmod.schema.sequence.Feature;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+
+public class Organism implements Serializable {
+
+ private Set<PhylonodeOrganism> phylonodeOrganisms = new HashSet<PhylonodeOrganism>(0);
+
+ public Set<PhylonodeOrganism> getPhylonodeOrganisms() {
+ return this.phylonodeOrganisms;
+ }
+
+ public void setPhylonodeOrganisms(Set<PhylonodeOrganism> phylonodeOrganisms) {
+ this.phylonodeOrganisms = phylonodeOrganisms;
+ }
+
+ // Fields
+
+
+
+ private int organismId;
+
+
+ private String abbreviation;
+
+
+ private String genus;
+
+
+ private String species;
+
+
+ private String commonName;
+
+
+ private String comment;
+
+
+ private Set<OrganismProp> organismProps = new HashSet<OrganismProp>(0);
+
+
+ private Set<Feature> features = new HashSet<Feature>(0);
+
+
+ private Set<OrganismDbXRef> organismDbXRefs = new HashSet<OrganismDbXRef>(0);
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getOrganismId()
+ */
+ public int getOrganismId() {
+ return this.organismId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setOrganismId(int)
+ */
+ public void setOrganismId(int organismId) {
+ this.organismId = organismId;
+ }
+
+ public String getFullName() {
+ return getGenus()+' '+getSpecies();
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getAbbreviation()
+ */
+ public String getAbbreviation() {
+ return this.abbreviation;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setAbbreviation(java.lang.String)
+ */
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getGenus()
+ */
+ public String getGenus() {
+ return this.genus;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setGenus(java.lang.String)
+ */
+ public void setGenus(String genus) {
+ this.genus = genus;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getSpecies()
+ */
+ public String getSpecies() {
+ return this.species;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setSpecies(java.lang.String)
+ */
+ public void setSpecies(String species) {
+ this.species = species;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getCommonName()
+ */
+ public String getCommonName() {
+ return this.commonName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setCommonName(java.lang.String)
+ */
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getComment()
+ */
+ public String getComment() {
+ return this.comment;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setComment(java.lang.String)
+ */
+ public void setComment(String comment) {
+ this.comment = comment;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getOrganismProps()
+ */
+ public Set<OrganismProp> getOrganismProps() {
+ return this.organismProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setOrganismProps(java.util.Set)
+ */
+ private void setOrganismProps(Set<OrganismProp> organismProps) {
+ this.organismProps = organismProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getFeatures()
+ */
+ private Collection<Feature> getFeatures() {
+ return this.features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setFeatures(java.util.Set)
+ */
+ private void setFeatures(Set<Feature> features) {
+ this.features = features;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#getOrganismDbXRefs()
+ */
+ private Collection<OrganismDbXRef> getOrganismDbXRefs() {
+ return this.organismDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismI#setOrganismDbXRefs(java.util.Set)
+ */
+ private void setOrganismDbXRefs(Set<OrganismDbXRef> organismDbXRefs) {
+ this.organismDbXRefs = organismDbXRefs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/organism/OrganismDbXRef.java b/org/gmod/schema/organism/OrganismDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..05ec0768bb664fca0f3dbbab3b639eefd9a9d574
--- /dev/null
+++ b/org/gmod/schema/organism/OrganismDbXRef.java
@@ -0,0 +1,85 @@
+package org.gmod.schema.organism;
+
+import org.gmod.schema.general.DbXRef;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class OrganismDbXRef implements Serializable {
+
+ // Fields
+
+
+
+ private int organismDbXRefId;
+
+
+
+
+ private Organism organism;
+
+
+
+
+ private DbXRef dbXRef;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#getOrganismDbXRefId()
+ */
+ private int getOrganismDbXRefId() {
+ return this.organismDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#setOrganismDbXRefId(int)
+ */
+ private void setOrganismDbXRefId(int organismDbXRefId) {
+ this.organismDbXRefId = organismDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#getOrganism()
+ */
+ private Organism getOrganism() {
+ return this.organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#setOrganism(org.gmod.schema.organism.OrganismI)
+ */
+ private void setOrganism(Organism organism) {
+ this.organism = organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#getDbXRef()
+ */
+ private DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismDbXRefI#setDbXRef(org.gmod.schema.general.DbXRefI)
+ */
+ private void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/organism/OrganismProp.java b/org/gmod/schema/organism/OrganismProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..b8a1d5be595834d199c225d9ed9f37a44d554230
--- /dev/null
+++ b/org/gmod/schema/organism/OrganismProp.java
@@ -0,0 +1,124 @@
+package org.gmod.schema.organism;
+
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class OrganismProp implements Serializable, PropertyI {
+
+ // Fields
+
+
+
+ private int organismPropId;
+
+
+
+
+ private Organism organism;
+
+
+
+
+ private CvTerm cvTerm;
+
+
+ private String value;
+
+
+ private int rank;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#getOrganismPropId()
+ */
+ private int getOrganismPropId() {
+ return this.organismPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#setOrganismPropId(int)
+ */
+ private void setOrganismPropId(int organismPropId) {
+ this.organismPropId = organismPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#getOrganism()
+ */
+ private Organism getOrganism() {
+ return this.organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#setOrganism(org.gmod.schema.organism.OrganismI)
+ */
+ private void setOrganism(Organism organism) {
+ this.organism = organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#getCvTerm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#getValue()
+ */
+ public String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#getRank()
+ */
+ private int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.OrganismPropI#setRank(int)
+ */
+ private void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/Phylonode.java b/org/gmod/schema/phylogeny/Phylonode.java
new file mode 100644
index 0000000000000000000000000000000000000000..8bb2b292d0e8fa90d1b3bcbc251dd2c1ed0e6b89
--- /dev/null
+++ b/org/gmod/schema/phylogeny/Phylonode.java
@@ -0,0 +1,230 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.sequence.Feature;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+
+
+/**
+ * Phylonode generated by hbm2java
+ */
+
+
+public class Phylonode implements java.io.Serializable {
+
+ // Fields
+
+ private int phylonodeId;
+ private Phylotree phylotree;
+ private Phylonode parent;
+ private CvTerm cvTerm;
+ private Feature feature;
+ private int leftIdx;
+ private int rightIdx;
+ private String label;
+ private Double distance;
+ private Set<PhylonodeRelationship> phylonodeRelationshipsForObjectId = new HashSet<PhylonodeRelationship>(0);
+ private Set<PhylonodeOrganism> phylonodeOrganisms = new HashSet<PhylonodeOrganism>(0);
+ private Set<PhylonodePub> phylonodePubs = new HashSet<PhylonodePub>(0);
+ private Set<Phylonode> phylonodes = new HashSet<Phylonode>(0);
+ private Set<PhylonodeRelationship> phylonodeRelationshipsForSubjectId = new HashSet<PhylonodeRelationship>(0);
+ private Set<PhylonodeDbXRef> phylonodeDbXRefs = new HashSet<PhylonodeDbXRef>(0);
+ private Set<PhylonodeProp> phylonodeProps = new HashSet<PhylonodeProp>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public Phylonode() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public Phylonode(int phylonodeId, Phylotree phylotree, int leftIdx, int rightIdx) {
+ this.phylonodeId = phylonodeId;
+ this.phylotree = phylotree;
+ this.leftIdx = leftIdx;
+ this.rightIdx = rightIdx;
+ }
+ /** full constructor */
+ public Phylonode(int phylonodeId, Phylotree phylotree, Phylonode parent, CvTerm cvTerm, Feature feature, int leftIdx, int rightIdx, String label, Double distance, Set<PhylonodeRelationship> phylonodeRelationshipsForObjectId, Set<PhylonodeOrganism> phylonodeOrganisms, Set<PhylonodePub> phylonodePubs, Set<Phylonode> phylonodes, Set<PhylonodeRelationship> phylonodeRelationshipsForSubjectId, Set<PhylonodeDbXRef> phylonodeDbXRefs, Set<PhylonodeProp> phylonodeProps) {
+ this.phylonodeId = phylonodeId;
+ this.phylotree = phylotree;
+ this.parent = parent;
+ this.cvTerm = cvTerm;
+ this.feature = feature;
+ this.leftIdx = leftIdx;
+ this.rightIdx = rightIdx;
+ this.label = label;
+ this.distance = distance;
+ this.phylonodeRelationshipsForObjectId = phylonodeRelationshipsForObjectId;
+ this.phylonodeOrganisms = phylonodeOrganisms;
+ this.phylonodePubs = phylonodePubs;
+ this.phylonodes = phylonodes;
+ this.phylonodeRelationshipsForSubjectId = phylonodeRelationshipsForSubjectId;
+ this.phylonodeDbXRefs = phylonodeDbXRefs;
+ this.phylonodeProps = phylonodeProps;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodeId() {
+ return this.phylonodeId;
+ }
+
+ public void setPhylonodeId(int phylonodeId) {
+ this.phylonodeId = phylonodeId;
+ }
+
+
+
+ public Phylotree getPhylotree() {
+ return this.phylotree;
+ }
+
+ public void setPhylotree(Phylotree phylotree) {
+ this.phylotree = phylotree;
+ }
+
+
+
+ public Phylonode getParent() {
+ return this.parent;
+ }
+
+ public void setParent(Phylonode parent) {
+ this.parent = parent;
+ }
+
+
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+
+ public int getLeftIdx() {
+ return this.leftIdx;
+ }
+
+ public void setLeftIdx(int leftIdx) {
+ this.leftIdx = leftIdx;
+ }
+
+
+ public int getRightIdx() {
+ return this.rightIdx;
+ }
+
+ public void setRightIdx(int rightIdx) {
+ this.rightIdx = rightIdx;
+ }
+
+
+ public String getLabel() {
+ return this.label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+
+ public Double getDistance() {
+ return this.distance;
+ }
+
+ public void setDistance(Double distance) {
+ this.distance = distance;
+ }
+
+ public Collection<PhylonodeRelationship> getPhylonodeRelationshipsForObjectId() {
+ return this.phylonodeRelationshipsForObjectId;
+ }
+
+ public void setPhylonodeRelationshipsForObjectId(Set<PhylonodeRelationship> phylonodeRelationshipsForObjectId) {
+ this.phylonodeRelationshipsForObjectId = phylonodeRelationshipsForObjectId;
+ }
+
+ public Collection<PhylonodeOrganism> getPhylonodeOrganisms() {
+ return this.phylonodeOrganisms;
+ }
+
+ public void setPhylonodeOrganisms(Set<PhylonodeOrganism> phylonodeOrganisms) {
+ this.phylonodeOrganisms = phylonodeOrganisms;
+ }
+
+ public Collection<PhylonodePub> getPhylonodePubs() {
+ return this.phylonodePubs;
+ }
+
+ public void setPhylonodePubs(Set<PhylonodePub> phylonodePubs) {
+ this.phylonodePubs = phylonodePubs;
+ }
+
+ public Collection<Phylonode> getPhylonodes() {
+ return this.phylonodes;
+ }
+
+ public void setPhylonodes(Set<Phylonode> phylonodes) {
+ this.phylonodes = phylonodes;
+ }
+
+ public Collection<PhylonodeRelationship> getPhylonodeRelationshipsForSubjectId() {
+ return this.phylonodeRelationshipsForSubjectId;
+ }
+
+ public void setPhylonodeRelationshipsForSubjectId(Set<PhylonodeRelationship> phylonodeRelationshipsForSubjectId) {
+ this.phylonodeRelationshipsForSubjectId = phylonodeRelationshipsForSubjectId;
+ }
+
+ public Collection<PhylonodeDbXRef> getPhylonodeDbXRefs() {
+ return this.phylonodeDbXRefs;
+ }
+
+ public void setPhylonodeDbXRefs(Set<PhylonodeDbXRef> phylonodeDbXRefs) {
+ this.phylonodeDbXRefs = phylonodeDbXRefs;
+ }
+
+ public Collection<PhylonodeProp> getPhylonodeProps() {
+ return this.phylonodeProps;
+ }
+
+ public void setPhylonodeProps(Set<PhylonodeProp> phylonodeProps) {
+ this.phylonodeProps = phylonodeProps;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylonodeDbXRef.java b/org/gmod/schema/phylogeny/PhylonodeDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..cf18f7569cbefef6fb11c43e19052a2b5829b03b
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylonodeDbXRef.java
@@ -0,0 +1,80 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.general.DbXRef;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylonodeDbXRef generated by hbm2java
+ */
+
+
+public class PhylonodeDbXRef implements java.io.Serializable {
+
+ // Fields
+
+ private int phylonodeDbXRefId;
+ private DbXRef dbXRef;
+ private Phylonode phylonode;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylonodeDbXRef() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PhylonodeDbXRef(int phylonodeDbXRefId, DbXRef dbXRef, Phylonode phylonode) {
+ this.phylonodeDbXRefId = phylonodeDbXRefId;
+ this.dbXRef = dbXRef;
+ this.phylonode = phylonode;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodeDbXRefId() {
+ return this.phylonodeDbXRefId;
+ }
+
+ public void setPhylonodeDbXRefId(int phylonodeDbXRefId) {
+ this.phylonodeDbXRefId = phylonodeDbXRefId;
+ }
+
+
+
+
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+ public Phylonode getPhylonode() {
+ return this.phylonode;
+ }
+
+ public void setPhylonode(Phylonode phylonode) {
+ this.phylonode = phylonode;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylonodeOrganism.java b/org/gmod/schema/phylogeny/PhylonodeOrganism.java
new file mode 100644
index 0000000000000000000000000000000000000000..978e9b6e5fe196d0ad8dbb40968098ff830a6fc7
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylonodeOrganism.java
@@ -0,0 +1,80 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.organism.Organism;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylonodeOrganism generated by hbm2java
+ */
+
+
+public class PhylonodeOrganism implements java.io.Serializable {
+
+ // Fields
+
+ private int phylonodeOrganismId;
+ private Organism organism;
+ private Phylonode phylonode;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylonodeOrganism() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PhylonodeOrganism(int phylonodeOrganismId, Organism organism, Phylonode phylonode) {
+ this.phylonodeOrganismId = phylonodeOrganismId;
+ this.organism = organism;
+ this.phylonode = phylonode;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodeOrganismId() {
+ return this.phylonodeOrganismId;
+ }
+
+ public void setPhylonodeOrganismId(int phylonodeOrganismId) {
+ this.phylonodeOrganismId = phylonodeOrganismId;
+ }
+
+
+
+ public Organism getOrganism() {
+ return this.organism;
+ }
+
+ public void setOrganism(Organism organism) {
+ this.organism = organism;
+ }
+
+
+
+ public Phylonode getPhylonode() {
+ return this.phylonode;
+ }
+
+ public void setPhylonode(Phylonode phylonode) {
+ this.phylonode = phylonode;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylonodeProp.java b/org/gmod/schema/phylogeny/PhylonodeProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..8126743cef9c584d7fb60233e0135263773ff5e1
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylonodeProp.java
@@ -0,0 +1,104 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylonodeProp generated by hbm2java
+ */
+
+
+public class PhylonodeProp implements java.io.Serializable, PropertyI {
+
+ // Fields
+
+ private int phylonodePropId;
+ private CvTerm cvTerm;
+ private Phylonode phylonode;
+ private String value;
+ private int rank;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylonodeProp() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PhylonodeProp(int phylonodePropId, CvTerm cvTerm, Phylonode phylonode, String value, int rank) {
+ this.phylonodePropId = phylonodePropId;
+ this.cvTerm = cvTerm;
+ this.phylonode = phylonode;
+ this.value = value;
+ this.rank = rank;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodePropId() {
+ return this.phylonodePropId;
+ }
+
+ public void setPhylonodePropId(int phylonodePropId) {
+ this.phylonodePropId = phylonodePropId;
+ }
+
+
+
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+
+ public Phylonode getPhylonode() {
+ return this.phylonode;
+ }
+
+ public void setPhylonode(Phylonode phylonode) {
+ this.phylonode = phylonode;
+ }
+
+
+ public String getValue() {
+ return this.value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+
+ public int getRank() {
+ return this.rank;
+ }
+
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylonodePub.java b/org/gmod/schema/phylogeny/PhylonodePub.java
new file mode 100644
index 0000000000000000000000000000000000000000..aabd38ce58112fc94a8808c5505929bec8a31eaf
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylonodePub.java
@@ -0,0 +1,80 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.pub.Pub;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylonodePub generated by hbm2java
+ */
+
+
+public class PhylonodePub implements java.io.Serializable {
+
+ // Fields
+
+ private int phylonodePubId;
+ private Pub pub;
+ private Phylonode phylonode;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylonodePub() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PhylonodePub(int phylonodePubId, Pub pub, Phylonode phylonode) {
+ this.phylonodePubId = phylonodePubId;
+ this.pub = pub;
+ this.phylonode = phylonode;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodePubId() {
+ return this.phylonodePubId;
+ }
+
+ public void setPhylonodePubId(int phylonodePubId) {
+ this.phylonodePubId = phylonodePubId;
+ }
+
+
+
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+ public Phylonode getPhylonode() {
+ return this.phylonode;
+ }
+
+ public void setPhylonode(Phylonode phylonode) {
+ this.phylonode = phylonode;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylonodeRelationship.java b/org/gmod/schema/phylogeny/PhylonodeRelationship.java
new file mode 100644
index 0000000000000000000000000000000000000000..0330c9a217a8002d953004de3e051cc3bec372f5
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylonodeRelationship.java
@@ -0,0 +1,110 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.cv.CvTerm;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylonodeRelationship generated by hbm2java
+ */
+
+
+public class PhylonodeRelationship implements java.io.Serializable {
+
+ // Fields
+
+ private int phylonodeRelationshipId;
+ private Phylonode phylonodeBySubjectId;
+ private Phylonode phylonodeByObjectId;
+ private CvTerm cvTerm;
+ private Integer rank;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylonodeRelationship() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public PhylonodeRelationship(int phylonodeRelationshipId, Phylonode phylonodeBySubjectId, Phylonode phylonodeByObjectId, CvTerm cvTerm) {
+ this.phylonodeRelationshipId = phylonodeRelationshipId;
+ this.phylonodeBySubjectId = phylonodeBySubjectId;
+ this.phylonodeByObjectId = phylonodeByObjectId;
+ this.cvTerm = cvTerm;
+ }
+ /** full constructor */
+ public PhylonodeRelationship(int phylonodeRelationshipId, Phylonode phylonodeBySubjectId, Phylonode phylonodeByObjectId, CvTerm cvTerm, Integer rank) {
+ this.phylonodeRelationshipId = phylonodeRelationshipId;
+ this.phylonodeBySubjectId = phylonodeBySubjectId;
+ this.phylonodeByObjectId = phylonodeByObjectId;
+ this.cvTerm = cvTerm;
+ this.rank = rank;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylonodeRelationshipId() {
+ return this.phylonodeRelationshipId;
+ }
+
+ public void setPhylonodeRelationshipId(int phylonodeRelationshipId) {
+ this.phylonodeRelationshipId = phylonodeRelationshipId;
+ }
+
+
+
+ public Phylonode getPhylonodeBySubjectId() {
+ return this.phylonodeBySubjectId;
+ }
+
+ public void setPhylonodeBySubjectId(Phylonode phylonodeBySubjectId) {
+ this.phylonodeBySubjectId = phylonodeBySubjectId;
+ }
+
+
+
+ public Phylonode getPhylonodeByObjectId() {
+ return this.phylonodeByObjectId;
+ }
+
+ public void setPhylonodeByObjectId(Phylonode phylonodeByObjectId) {
+ this.phylonodeByObjectId = phylonodeByObjectId;
+ }
+
+
+
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+ public Integer getRank() {
+ return this.rank;
+ }
+
+ public void setRank(Integer rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/Phylotree.java b/org/gmod/schema/phylogeny/Phylotree.java
new file mode 100644
index 0000000000000000000000000000000000000000..e7d3ad6124c732326330017b8eca3fa08ca85425
--- /dev/null
+++ b/org/gmod/schema/phylogeny/Phylotree.java
@@ -0,0 +1,131 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+
+/**
+ * Phylotree generated by hbm2java
+ */
+
+
+public class Phylotree implements java.io.Serializable {
+
+ // Fields
+
+ private int phylotreeId;
+ private CvTerm cvTerm;
+ private DbXRef dbXRef;
+ private String name;
+ private String comment;
+ private Set<Phylonode> phylonodes = new HashSet<Phylonode>(0);
+ private Set<PhylotreePub> phylotreePubs = new HashSet<PhylotreePub>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public Phylotree() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public Phylotree(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+ /** full constructor */
+ public Phylotree(CvTerm cvTerm, DbXRef dbXRef, String name, String comment, Set<Phylonode> phylonodes, Set<PhylotreePub> phylotreePubs) {
+ this.cvTerm = cvTerm;
+ this.dbXRef = dbXRef;
+ this.name = name;
+ this.comment = comment;
+ this.phylonodes = phylonodes;
+ this.phylotreePubs = phylotreePubs;
+ }
+
+ // Property accessors
+
+
+ public int getPhylotreeId() {
+ return this.phylotreeId;
+ }
+
+ private void setPhylotreeId(int phylotreeId) {
+ this.phylotreeId = phylotreeId;
+ }
+
+
+
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+ public String getName() {
+ return this.name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ public String getComment() {
+ return this.comment;
+ }
+
+ public void setComment(String comment) {
+ this.comment = comment;
+ }
+
+
+ public Collection<Phylonode> getPhylonodes() {
+ return this.phylonodes;
+ }
+
+ public void setPhylonodes(Set<Phylonode> phylonodes) {
+ this.phylonodes = phylonodes;
+ }
+
+ public Collection<PhylotreePub> getPhylotreePubs() {
+ return this.phylotreePubs;
+ }
+
+ public void setPhylotreePubs(Set<PhylotreePub> phylotreePubs) {
+ this.phylotreePubs = phylotreePubs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/phylogeny/PhylotreePub.java b/org/gmod/schema/phylogeny/PhylotreePub.java
new file mode 100644
index 0000000000000000000000000000000000000000..e5f2dc26e1a6d7aed276c708b993760e378a88f9
--- /dev/null
+++ b/org/gmod/schema/phylogeny/PhylotreePub.java
@@ -0,0 +1,80 @@
+package org.gmod.schema.phylogeny;
+// Generated Aug 31, 2006 4:02:18 PM by Hibernate Tools 3.2.0.beta7
+
+
+import org.gmod.schema.pub.Pub;
+
+
+
+
+
+
+
+
+
+
+/**
+ * PhylotreePub generated by hbm2java
+ */
+
+
+public class PhylotreePub implements java.io.Serializable {
+
+ // Fields
+
+ private int phylotreePubId;
+ private Phylotree phylotree;
+ private Pub pub;
+
+ // Constructors
+
+ /** default constructor */
+ public PhylotreePub() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PhylotreePub(int phylotreePubId, Phylotree phylotree, Pub pub) {
+ this.phylotreePubId = phylotreePubId;
+ this.phylotree = phylotree;
+ this.pub = pub;
+ }
+
+ // Property accessors
+
+
+
+ public int getPhylotreePubId() {
+ return this.phylotreePubId;
+ }
+
+ public void setPhylotreePubId(int phylotreePubId) {
+ this.phylotreePubId = phylotreePubId;
+ }
+
+
+
+ public Phylotree getPhylotree() {
+ return this.phylotree;
+ }
+
+ public void setPhylotree(Phylotree phylotree) {
+ this.phylotree = phylotree;
+ }
+
+
+
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/pub/Pub.java b/org/gmod/schema/pub/Pub.java
new file mode 100644
index 0000000000000000000000000000000000000000..a58817a33f2f59f873fc765d94ec40b1e8ff8b61
--- /dev/null
+++ b/org/gmod/schema/pub/Pub.java
@@ -0,0 +1,555 @@
+package org.gmod.schema.pub;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.phylogeny.PhylonodePub;
+import org.gmod.schema.phylogeny.PhylotreePub;
+import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermPub;
+import org.gmod.schema.sequence.FeatureLocPub;
+import org.gmod.schema.sequence.FeaturePropPub;
+import org.gmod.schema.sequence.FeaturePub;
+import org.gmod.schema.sequence.FeatureRelationshipPropPub;
+import org.gmod.schema.sequence.FeatureRelationshipPub;
+import org.gmod.schema.sequence.FeatureSynonym;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+
+
+
+
+
+
+
+
+
+
+
+
+public class Pub implements Serializable {
+
+
+ private Set<PhylotreePub> phylotreePubs = new HashSet<PhylotreePub>(0);
+ private Set<PhylonodePub> phylonodePubs = new HashSet<PhylonodePub>(0);
+
+
+ public Set<PhylotreePub> getPhylotreePubs() {
+ return this.phylotreePubs;
+ }
+
+ public void setPhylotreePubs(Set<PhylotreePub> phylotreePubs) {
+ this.phylotreePubs = phylotreePubs;
+ }
+
+
+ public Set<PhylonodePub> getPhylonodePubs() {
+ return this.phylonodePubs;
+ }
+
+ public void setPhylonodePubs(Set<PhylonodePub> phylonodePubs) {
+ this.phylonodePubs = phylonodePubs;
+ }
+
+ // Fields
+
+
+
+ private int pubId;
+
+
+
+
+ private CvTerm cvTerm;
+
+
+ private String title;
+
+
+ private String volumeTitle;
+
+
+ private String volume;
+
+
+ private String seriesName;
+
+
+ private String issue;
+
+
+ private String pyear;
+
+
+ private String pages;
+
+
+ private String miniRef;
+
+
+ private String uniqueName;
+
+
+ private Boolean obsolete;
+
+
+ private String publisher;
+
+
+ private String pubPlace;
+
+
+ private Set<PubAuthor> pubAuthors = new HashSet<PubAuthor>(0);
+
+
+ private Set<PubRelationship> pubRelationshipsForObjectId = new HashSet<PubRelationship>(0);
+
+
+ private Set<PubDbXRef> pubDbXRefs = new HashSet<PubDbXRef>(0);
+
+
+ private Set<FeatureCvTerm> featureCvTerms = new HashSet<FeatureCvTerm>(0);
+
+
+ private Set<FeatureRelationshipPub> featureRelationshipPubs = new HashSet<FeatureRelationshipPub>(0);
+
+
+ private Set<FeaturePub> featurePubs = new HashSet<FeaturePub>(0);
+
+
+ private Set<FeaturePropPub> featurePropPubs = new HashSet<FeaturePropPub>(0);
+
+
+ private Set<FeatureSynonym> featureSynonyms = new HashSet<FeatureSynonym>(0);
+
+
+ private Set<FeatureCvTermPub> featureCvTermPubs = new HashSet<FeatureCvTermPub>(0);
+
+
+ private Set<FeatureRelationshipPropPub> featureRelationshipPropPubs = new HashSet<FeatureRelationshipPropPub>(0);
+
+
+ private Set<PubProp> pubProps = new HashSet<PubProp>(0);
+
+
+ private Set<PubRelationship> pubRelationshipsForSubjectId = new HashSet<PubRelationship>(0);
+
+
+ private Set<FeatureLocPub> featureLocPubs = new HashSet<FeatureLocPub>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public Pub() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public Pub(String uniqueName, CvTerm cvTerm) {
+ this.uniqueName = uniqueName;
+ this.cvTerm = cvTerm;
+ }
+
+ public Pub(String uniqueName) {
+ this.uniqueName = uniqueName;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubId()
+ */
+ public int getPubId() {
+ return this.pubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubId(int)
+ */
+ public void setPubId(int pubId) {
+ this.pubId = pubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getCvTerm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getTitle()
+ */
+ public String getTitle() {
+ return this.title;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setTitle(java.lang.String)
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getVolumeTitle()
+ */
+ public String getVolumeTitle() {
+ return this.volumeTitle;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setVolumeTitle(java.lang.String)
+ */
+ public void setVolumeTitle(String volumeTitle) {
+ this.volumeTitle = volumeTitle;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getVolume()
+ */
+ public String getVolume() {
+ return this.volume;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setVolume(java.lang.String)
+ */
+ public void setVolume(String volume) {
+ this.volume = volume;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getSeriesName()
+ */
+ public String getSeriesName() {
+ return this.seriesName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setSeriesName(java.lang.String)
+ */
+ public void setSeriesName(String seriesName) {
+ this.seriesName = seriesName;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getIssue()
+ */
+ public String getIssue() {
+ return this.issue;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setIssue(java.lang.String)
+ */
+ public void setIssue(String issue) {
+ this.issue = issue;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPyear()
+ */
+ public String getPyear() {
+ return this.pyear;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPyear(java.lang.String)
+ */
+ public void setPyear(String pyear) {
+ this.pyear = pyear;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPages()
+ */
+ public String getPages() {
+ return this.pages;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPages(java.lang.String)
+ */
+ public void setPages(String pages) {
+ this.pages = pages;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getMiniRef()
+ */
+ public String getMiniRef() {
+ return this.miniRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setMiniRef(java.lang.String)
+ */
+ public void setMiniRef(String miniRef) {
+ this.miniRef = miniRef;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getUniqueName()
+ */
+ public String getUniqueName() {
+ return this.uniqueName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setUniqueName(java.lang.String)
+ */
+ public void setUniqueName(String uniqueName) {
+ this.uniqueName = uniqueName;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getobsolete()
+ */
+ public Boolean getObsolete() {
+ return this.obsolete;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setobsolete(java.lang.Boolean)
+ */
+ public void setObsolete(Boolean obsolete) {
+ this.obsolete = obsolete;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPublisher()
+ */
+ public String getPublisher() {
+ return this.publisher;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPublisher(java.lang.String)
+ */
+ public void setPublisher(String publisher) {
+ this.publisher = publisher;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubPlace()
+ */
+ public String getPubPlace() {
+ return this.pubPlace;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubPlace(java.lang.String)
+ */
+ public void setPubPlace(String pubPlace) {
+ this.pubPlace = pubPlace;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubAuthors()
+ */
+ public Collection<PubAuthor> getPubAuthors() {
+ return this.pubAuthors;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubAuthors(java.util.Set)
+ */
+ public void setPubAuthors(Set<PubAuthor> pubAuthors) {
+ this.pubAuthors = pubAuthors;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubRelationshipsForObjectId()
+ */
+ public Collection<PubRelationship> getPubRelationshipsForObjectId() {
+ return this.pubRelationshipsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubRelationshipsForObjectId(java.util.Set)
+ */
+ public void setPubRelationshipsForObjectId(Set<PubRelationship> pubRelationshipsForObjectId) {
+ this.pubRelationshipsForObjectId = pubRelationshipsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubDbXRefs()
+ */
+ private Collection<PubDbXRef> getPubDbXRefs() {
+ return this.pubDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubDbXRefs(java.util.Set)
+ */
+ private void setPubDbXRefs(Set<PubDbXRef> pubDbXRefs) {
+ this.pubDbXRefs = pubDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureCvTerms()
+ */
+ private Collection<FeatureCvTerm> getFeatureCvTerms() {
+ return this.featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureCvTerms(java.util.Set)
+ */
+ private void setFeatureCvTerms(Set<FeatureCvTerm> featureCvTerms) {
+ this.featureCvTerms = featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureRelationshipPubs()
+ */
+ private Collection<FeatureRelationshipPub> getFeatureRelationshipPubs() {
+ return this.featureRelationshipPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureRelationshipPubs(java.util.Set)
+ */
+ private void setFeatureRelationshipPubs(Set<FeatureRelationshipPub> featureRelationshipPubs) {
+ this.featureRelationshipPubs = featureRelationshipPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeaturePubs()
+ */
+ private Collection<FeaturePub> getFeaturePubs() {
+ return this.featurePubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeaturePubs(java.util.Set)
+ */
+ private void setFeaturePubs(Set<FeaturePub> featurePubs) {
+ this.featurePubs = featurePubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeaturePropPubs()
+ */
+ private Collection<FeaturePropPub> getFeaturePropPubs() {
+ return this.featurePropPubs;
+ }
+//
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeaturePropPubs(java.util.Set)
+ */
+ private void setFeaturePropPubs(Set<FeaturePropPub> featurePropPubs) {
+ this.featurePropPubs = featurePropPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureSynonyms()
+ */
+ private Collection<FeatureSynonym> getFeatureSynonyms() {
+ return this.featureSynonyms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureSynonyms(java.util.Set)
+ */
+ private void setFeatureSynonyms(Set<FeatureSynonym> featureSynonyms) {
+ this.featureSynonyms = featureSynonyms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureCvTermPubs()
+ */
+ private Collection<FeatureCvTermPub> getFeatureCvTermPubs() {
+ return this.featureCvTermPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureCvTermPubs(java.util.Set)
+ */
+ private void setFeatureCvTermPubs(Set<FeatureCvTermPub> featureCvTermPubs) {
+ this.featureCvTermPubs = featureCvTermPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureRelationshipPropPubs()
+ */
+ private Collection<FeatureRelationshipPropPub> getFeatureRelationshipPropPubs() {
+ return this.featureRelationshipPropPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureRelationshipPropPubs(java.util.Set)
+ */
+ private void setFeatureRelationshipPropPubs(Set<FeatureRelationshipPropPub> featureRelationshipPropPubs) {
+ this.featureRelationshipPropPubs = featureRelationshipPropPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubProps()
+ */
+ private Collection<PubProp> getPubProps() {
+ return this.pubProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubProps(java.util.Set)
+ */
+ private void setPubProps(Set<PubProp> pubProps) {
+ this.pubProps = pubProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getPubRelationshipsForSubjectId()
+ */
+ private Collection<PubRelationship> getPubRelationshipsForSubjectId() {
+ return this.pubRelationshipsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setPubRelationshipsForSubjectId(java.util.Set)
+ */
+ private void setPubRelationshipsForSubjectId(Set<PubRelationship> pubRelationshipsForSubjectId) {
+ this.pubRelationshipsForSubjectId = pubRelationshipsForSubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#getFeatureLocPubs()
+ */
+ private Collection<FeatureLocPub> getFeatureLocPubs() {
+ return this.featureLocPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubI#setFeatureLocPubs(java.util.Set)
+ */
+ private void setFeatureLocPubs(Set<FeatureLocPub> featureLocPubs) {
+ this.featureLocPubs = featureLocPubs;
+ }
+
+}
+
+
diff --git a/org/gmod/schema/pub/PubAuthor.java b/org/gmod/schema/pub/PubAuthor.java
new file mode 100644
index 0000000000000000000000000000000000000000..6edd160bee740297d7b3f49409da156050563e10
--- /dev/null
+++ b/org/gmod/schema/pub/PubAuthor.java
@@ -0,0 +1,155 @@
+package org.gmod.schema.pub;
+
+
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class PubAuthor implements Serializable {
+
+ // Fields
+
+
+
+ private int pubAuthorId;
+
+
+
+ private Pub pub;
+
+
+ private int rank;
+
+
+ private Boolean editor;
+
+
+ private String surname;
+
+
+ private String givenNames;
+
+
+ private String suffix;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getPubAuthorId()
+ */
+ private int getPubAuthorId() {
+ return this.pubAuthorId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setPubAuthorId(int)
+ */
+ private void setPubAuthorId(int pubAuthorId) {
+ this.pubAuthorId = pubAuthorId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getRank()
+ */
+ private int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setRank(int)
+ */
+ private void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getEditor()
+ */
+ private Boolean getEditor() {
+ return this.editor;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setEditor(java.lang.Boolean)
+ */
+ private void setEditor(Boolean editor) {
+ this.editor = editor;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getSurname()
+ */
+ private String getSurname() {
+ return this.surname;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setSurname(java.lang.String)
+ */
+ private void setSurname(String surname) {
+ this.surname = surname;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getGivenNames()
+ */
+ private String getGivenNames() {
+ return this.givenNames;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setGivenNames(java.lang.String)
+ */
+ private void setGivenNames(String givenNames) {
+ this.givenNames = givenNames;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#getSuffix()
+ */
+ private String getSuffix() {
+ return this.suffix;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubAuthorI#setSuffix(java.lang.String)
+ */
+ private void setSuffix(String suffix) {
+ this.suffix = suffix;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/pub/PubDbXRef.java b/org/gmod/schema/pub/PubDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..1db4eda34349dc43dec2a77be75e41f004879489
--- /dev/null
+++ b/org/gmod/schema/pub/PubDbXRef.java
@@ -0,0 +1,117 @@
+package org.gmod.schema.pub;
+
+import org.gmod.schema.general.DbXRef;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class PubDbXRef implements Serializable {
+
+ // Fields
+
+
+
+ private int pubDbXRefId;
+
+
+
+
+ private DbXRef dbXRef;
+
+
+
+
+ private Pub pub;
+
+
+ private boolean current;
+
+ // Constructors
+
+ /** default constructor */
+ public PubDbXRef() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public PubDbXRef(Pub pub, DbXRef dbXRef, boolean current) {
+ this.dbXRef = dbXRef;
+ this.pub = pub;
+ this.current = current;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#getPubDbXRefId()
+ */
+ private int getPubDbXRefId() {
+ return this.pubDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#setPubDbXRefId(int)
+ */
+ private void setPubDbXRefId(int pubDbXRefId) {
+ this.pubDbXRefId = pubDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#getDbXRef()
+ */
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#setDbXRef(org.gmod.schema.general.DbXRefI)
+ */
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#getPub()
+ */
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#setPub(org.gmod.schema.pub.PubI)
+ */
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#isCurrent()
+ */
+ public boolean isCurrent() {
+ return this.current;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubDbXRefI#setCurrent(boolean)
+ */
+ public void setCurrent(boolean current) {
+ this.current = current;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/pub/PubProp.java b/org/gmod/schema/pub/PubProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..3164d86cedfdb157c5d53e97572a3c38efd1daad
--- /dev/null
+++ b/org/gmod/schema/pub/PubProp.java
@@ -0,0 +1,145 @@
+package org.gmod.schema.pub;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+
+public class PubProp implements Serializable, PropertyI {
+
+ // Fields
+
+
+
+ private int pubPropId;
+
+
+
+
+ private CvTerm cvTerm;
+
+
+
+
+ private Pub pub;
+
+
+ private String value;
+
+
+ private Integer rank;
+
+ // Constructors
+
+ /** default constructor */
+ public PubProp() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public PubProp(CvTerm cvTerm, Pub pub, String value) {
+ this.cvTerm = cvTerm;
+ this.pub = pub;
+ this.value = value;
+ }
+ /** full constructor */
+ public PubProp(CvTerm cvTerm, Pub pub, String value, Integer rank) {
+ this.cvTerm = cvTerm;
+ this.pub = pub;
+ this.value = value;
+ this.rank = rank;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#getPubPropId()
+ */
+ private int getPubPropId() {
+ return this.pubPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#setPubPropId(int)
+ */
+ private void setPubPropId(int pubPropId) {
+ this.pubPropId = pubPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#getCvTerm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#getValue()
+ */
+ private String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#getRank()
+ */
+ public Integer getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubPropI#setRank(java.lang.Integer)
+ */
+ private void setRank(Integer rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/pub/PubRelationship.java b/org/gmod/schema/pub/PubRelationship.java
new file mode 100644
index 0000000000000000000000000000000000000000..011a4dba8d0c9429af508e5e9f1ed6bf53006225
--- /dev/null
+++ b/org/gmod/schema/pub/PubRelationship.java
@@ -0,0 +1,104 @@
+package org.gmod.schema.pub;
+
+import org.gmod.schema.cv.CvTerm;
+
+import java.io.Serializable;
+
+
+
+
+
+
+
+
+
+
+
+public class PubRelationship implements Serializable {
+
+ // Fields
+
+
+
+ private int pubRelationshipId;
+
+
+
+
+ private Pub pubBySubjectId;
+
+
+
+
+ private Pub pubByObjectId;
+
+
+
+
+ private CvTerm cvTerm;
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#getPubRelationshipId()
+ */
+ private int getPubRelationshipId() {
+ return this.pubRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#setPubRelationshipId(int)
+ */
+ private void setPubRelationshipId(int pubRelationshipId) {
+ this.pubRelationshipId = pubRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#getPubBySubjectId()
+ */
+ private Pub getPubBySubjectId() {
+ return this.pubBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#setPubBySubjectId(org.gmod.schema.pub.PubI)
+ */
+ private void setPubBySubjectId(Pub pubBySubjectId) {
+ this.pubBySubjectId = pubBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#getPubByObjectId()
+ */
+ private Pub getPubByObjectId() {
+ return this.pubByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#setPubByObjectId(org.gmod.schema.pub.PubI)
+ */
+ private void setPubByObjectId(Pub pubByObjectId) {
+ this.pubByObjectId = pubByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#getCvTerm()
+ */
+ private CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.PubRelationshipI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/Feature.java b/org/gmod/schema/sequence/Feature.java
new file mode 100644
index 0000000000000000000000000000000000000000..ff4a8ed24eb38111a13d83102f2bed2089f8878d
--- /dev/null
+++ b/org/gmod/schema/sequence/Feature.java
@@ -0,0 +1,509 @@
+package org.gmod.schema.sequence;
+
+
+import org.gmod.schema.analysis.AnalysisFeature;
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.general.DbXRef;
+import org.gmod.schema.organism.Organism;
+import org.gmod.schema.phylogeny.Phylonode;
+import org.gmod.schema.utils.CollectionUtils;
+
+
+
+
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.Collection;
+import java.util.Date;
+import java.sql.Timestamp;
+
+public class Feature implements java.io.Serializable {
+
+ private int featureId;
+ private Organism organism;
+ private CvTerm cvTerm;
+ private String name;
+ private String uniqueName;
+ private Integer seqLen = -1;
+ private String md5Checksum;
+ private boolean analysis;
+ private boolean obsolete;
+ private Timestamp timeAccessioned;
+ private Timestamp timeLastModified;
+
+ // -------------------------------------------------------------------------------
+ // Unsorted properties below here
+
+
+ private Collection<Phylonode> phylonodes;
+ private DbXRef dbXRef;
+ private byte residues[];
+ private Collection<FeatureLoc> featureLocsForSrcFeatureId;
+ private Collection<FeatureRelationship> featureRelationshipsForObjectId;
+ private Collection<FeatureRelationship> featureRelationshipsForSubjectId;
+ private Collection<FeatureDbXRef> featureDbXRefs;
+ private Collection<FeatureLoc> featureLocsForFeatureId;
+ private Collection<FeatureCvTerm> featureCvTerms;
+
+ //@Cascade( {CascadeType.ALL, CascadeType.DELETE_ORPHAN} )
+ private Collection<FeatureProp> featureProps;
+ private Collection<FeaturePub> featurePubs;
+ private Collection<AnalysisFeature> analysisFeatures;
+ private Collection<FeatureSynonym> featureSynonyms;
+ private FeatureLoc featureLoc;
+
+ // Constructors
+
+ /** default constructor */
+ public Feature() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public Feature(Organism organism, CvTerm cvTerm, String uniqueName, boolean analysis, boolean obsolete, Timestamp timeAccessioned, Timestamp timeLastModified) {
+ this.organism = organism;
+ this.cvTerm = cvTerm;
+ this.uniqueName = uniqueName;
+ this.analysis = analysis;
+ this.obsolete = obsolete;
+ this.timeAccessioned = timeAccessioned;
+ this.timeLastModified = timeLastModified;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureId()
+ */
+ public int getFeatureId() {
+ return this.featureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureId(int)
+ */
+ public void setFeatureId(int featureId) {
+ this.featureId = featureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getOrganism()
+ */
+ public Organism getOrganism() {
+ return this.organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setOrganism(org.gmod.schema.organism.OrganismI)
+ */
+ public void setOrganism(Organism organism) {
+ this.organism = organism;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getCvTerm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setCvTerm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getDbxref()
+ */
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setDbxref(org.gmod.schema.general.DbXRefI)
+ */
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+
+ /**
+ * Get the human-readable form of the feature eg the gene name
+ *
+ * @return the name, may be null
+ */
+ public String getName() {
+ return this.name;
+ }
+
+
+ /**
+ * Set the human-readable form of the feature eg the gene name
+ *
+ * @param name the human-readable name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ /**
+ * Fetch the unique name (systematic id) for the feature
+ *
+ * @return the unique name, not null
+ */
+ /**
+ * @return
+ */
+ public String getUniqueName() {
+ return this.uniqueName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setUniquename(java.lang.String)
+ */
+ public void setUniqueName(String uniqueName) {
+ this.uniqueName = uniqueName;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getResidues()
+ */
+ public byte[] getResidues() {
+ return this.residues;
+ }
+
+ /**
+ * Fetch a subset of the sequence (may be lazy)
+ *
+ * @param min the lower bound, in interbase coordinates
+ * @param max the upper bound, in interbase coordinates
+ * @return
+ */
+ public byte[] getResidues(int min, int max) {
+ byte[] results = new byte[max - min];
+ System.arraycopy(getResidues(), 0, results, 0, max);
+ return results;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setResidues(java.lang.String)
+ */
+ public void setResidues(byte[] residues) {
+ this.residues = residues;
+ if (residues == null) {
+ seqLen = 0;
+ md5Checksum = "";
+ return;
+ }
+ seqLen = residues.length;
+ this.md5Checksum = calcMD5(this.residues);
+ }
+
+
+ /**
+ * Fetch the length of the sequence. Find it from the parent if necessary
+ *
+ * @return the length
+ */
+ public int getSeqLen() {
+ if (this.seqLen.intValue() == -1 && residues != null) {
+ return getResidues().length;
+ }
+ return this.seqLen.intValue();
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setSeqlen(java.lang.Integer)
+ */
+ public void setSeqLen(Integer seqLen) {
+ if (seqLen == null) {
+ throw new IllegalArgumentException("Length of '"+uniqueName+"' attempted to be set to null");
+ }
+ this.seqLen = seqLen;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getMd5Checksum()
+ */
+ public String getMd5Checksum() {
+ return this.md5Checksum;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setMd5Checksum(java.lang.String)
+ */
+ public void setMd5Checksum(String md5Checksum) {
+ this.md5Checksum = md5Checksum;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#isAnalysis()
+ */
+ public boolean isAnalysis() {
+ return this.analysis;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setAnalysis(boolean)
+ */
+ public void setAnalysis(boolean analysis) {
+ this.analysis = analysis;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#isObsolete()
+ */
+ public boolean isObsolete() {
+ return this.obsolete;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setObsolete(boolean)
+ */
+ public void setObsolete(boolean obsolete) {
+ this.obsolete = obsolete;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getTimeAccessioned()
+ */
+ public Date getTimeAccessioned() {
+ return this.timeAccessioned;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setTimeAccessioned(java.util.Date)
+ */
+ public void setTimeAccessioned(Timestamp timeAccessioned) {
+ this.timeAccessioned = timeAccessioned;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getTimeLastModified()
+ */
+ public Timestamp getTimeLastModified() {
+ return this.timeLastModified;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setTimeLastModified(java.util.Date)
+ */
+ public void setTimeLastModified(Timestamp timeLastModified) {
+ this.timeLastModified = timeLastModified;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeaturelocsForSrcfeatureId()
+ */
+ public Collection<FeatureLoc> getFeatureLocsForSrcFeatureId() {
+ return (featureLocsForSrcFeatureId = CollectionUtils.safeGetter(featureLocsForSrcFeatureId));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeaturelocsForSrcfeatureId(java.util.Set)
+ */
+ public void setFeatureLocsForSrcFeatureId(Collection<FeatureLoc> featureLocsForSrcFeatureId) {
+ this.featureLocsForSrcFeatureId = featureLocsForSrcFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureRelationshipsForObjectId()
+ */
+ public Collection<FeatureRelationship> getFeatureRelationshipsForObjectId() {
+ return (featureRelationshipsForObjectId = CollectionUtils.safeGetter(featureRelationshipsForObjectId));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureRelationshipsForObjectId(java.util.Set)
+ */
+ public void setFeatureRelationshipsForObjectId(Collection<FeatureRelationship> featureRelationshipsForObjectId) {
+ this.featureRelationshipsForObjectId = featureRelationshipsForObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureRelationshipsForSubjectId()
+ */
+ public Collection<FeatureRelationship> getFeatureRelationshipsForSubjectId() {
+ return (featureRelationshipsForSubjectId = CollectionUtils.safeGetter(featureRelationshipsForSubjectId));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureRelationshipsForSubjectId(java.util.Set)
+ */
+ public void setFeatureRelationshipsForSubjectId(Collection<FeatureRelationship> featureRelationshipsForSubjectId) {
+ this.featureRelationshipsForSubjectId = featureRelationshipsForSubjectId;
+ }
+
+ public void addFeatureRelationshipsForSubjectId(FeatureRelationship featureRelationshipForSubjectId) {
+ featureRelationshipForSubjectId.setFeatureBySubjectId(this);
+ this.featureRelationshipsForSubjectId.add(featureRelationshipForSubjectId);
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureDbxrefs()
+ */
+ public Collection<FeatureDbXRef> getFeatureDbXRefs() {
+ return this.featureDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureDbxrefs(java.util.Set)
+ */
+ public void setFeatureDbXRefs(Collection<FeatureDbXRef> featureDbXRefs) {
+ this.featureDbXRefs = featureDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeaturelocsForFeatureId()
+ */
+ public Collection<FeatureLoc> getFeatureLocsForFeatureId() {
+ return (featureLocsForFeatureId = CollectionUtils.safeGetter(featureLocsForFeatureId));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeaturelocsForFeatureId(java.util.Set)
+ */
+ public void addFeatureLocsForFeatureId(FeatureLoc featureLocForFeatureId) {
+ featureLocForFeatureId.setFeatureByFeatureId(this);
+ getFeatureLocsForFeatureId().add(featureLocForFeatureId);
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureCvterms()
+ */
+ public Collection<FeatureCvTerm> getFeatureCvTerms() {
+ return this.featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureCvterms(java.util.Set)
+ */
+ public void setFeatureCvTerms(Collection<FeatureCvTerm> featureCvTerms) {
+ this.featureCvTerms = featureCvTerms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureProps()
+ */
+ public Collection<FeatureProp> getFeatureProps() {
+ return (featureProps = CollectionUtils.safeGetter(featureProps));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureProps(java.util.Set)
+ */
+ public void addFeatureProp(FeatureProp featureProp) {
+ featureProp.setFeature(this);
+ getFeatureProps().add(featureProp);
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeaturePubs()
+ */
+ public Collection<FeaturePub> getFeaturePubs() {
+ return this.featurePubs;
+ }
+
+ public void setFeaturePubs(Collection<FeaturePub> featurePubs) {
+ this.featurePubs = featurePubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getAnalysisfeatures()
+ */
+ public Collection<AnalysisFeature> getAnalysisFeatures() {
+ return this.analysisFeatures;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setAnalysisfeatures(java.util.Set)
+ */
+ public void setAnalysisFeatures(Collection<AnalysisFeature> analysisFeatures) {
+ this.analysisFeatures = analysisFeatures;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#getFeatureSynonyms()
+ */
+ public Collection<FeatureSynonym> getFeatureSynonyms() {
+ return (featureSynonyms = CollectionUtils.safeGetter(featureSynonyms));
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureI#setFeatureSynonyms(java.util.Set)
+ */
+ public void setFeatureSynonyms(Collection<FeatureSynonym> featureSynonyms) {
+ this.featureSynonyms = featureSynonyms;
+ }
+
+ /**
+ * Get the display name for the gene, preferrably the name,
+ * otherwise the display name
+ *
+ * @return the preferred display name, never null
+ */
+ public String getDisplayName() {
+ return (getName() != null) ? getName() : getUniqueName();
+ }
+
+
+ public void setFeatureLocsForFeatureId(Collection<FeatureLoc> featureLocsForFeatureId) {
+ this.featureLocsForFeatureId = featureLocsForFeatureId;
+ }
+
+
+ public void setFeatureProps(Collection<FeatureProp> featureProps) {
+ this.featureProps = featureProps;
+ }
+
+
+ public Collection<Phylonode> getPhylonodes() {
+ return this.phylonodes;
+ }
+
+ public void setPhylonodes(Collection<Phylonode> phylonodes) {
+ this.phylonodes = phylonodes;
+ }
+
+ private String calcMD5(byte[] residue) {
+ try {
+ MessageDigest md5 = MessageDigest.getInstance("MD5");
+// MessageDigest tc1 = md.clone();
+ byte[] md5Bytes = md5.digest(residue);
+
+ StringBuilder hexValue = new StringBuilder();
+ for (int i=0 ; i<md5Bytes.length ; i++) {
+ int val = md5Bytes[i] & 0xff;
+ if (val < 16) hexValue.append("0");
+ hexValue.append(Integer.toHexString(val));
+ }
+ return hexValue.toString();
+
+ }
+ catch (NoSuchAlgorithmException exp) {
+ exp.printStackTrace(); // Shouldn't happen - MD5 is supported algorithm
+ }
+ return null;
+ }
+
+ public FeatureLoc getFeatureLoc()
+ {
+ return featureLoc;
+ }
+
+ public void setFeatureLoc(FeatureLoc featureLoc)
+ {
+ this.featureLoc = featureLoc;
+ }
+
+}
diff --git a/org/gmod/schema/sequence/FeatureCvTerm.java b/org/gmod/schema/sequence/FeatureCvTerm.java
new file mode 100644
index 0000000000000000000000000000000000000000..c4c34210c805305965a79dfee5a5fb6a20a5b2f4
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureCvTerm.java
@@ -0,0 +1,169 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.pub.Pub;
+import org.gmod.schema.utils.Rankable;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+
+public class FeatureCvTerm implements Serializable, Rankable, PropertyI {
+
+ // Fields
+ private int featureCvTermId;
+ private CvTerm cvTerm;
+ private Feature feature;
+ private Pub pub;
+ private boolean not;
+ private int rank;
+ private Collection<FeatureCvTermProp> featureCvTermProps = new HashSet<FeatureCvTermProp>(0);
+ private Collection<FeatureCvTermPub> featureCvTermPubs = new HashSet<FeatureCvTermPub>(0);
+ private Collection<FeatureCvTermDbXRef> featureCvTermDbXRefs = new HashSet<FeatureCvTermDbXRef>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureCvTerm() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public FeatureCvTerm(CvTerm cvTerm, Feature feature, Pub pub, boolean not,int rank) {
+ this.cvTerm = cvTerm;
+ this.feature = feature;
+ this.pub = pub;
+ this.not = not;
+ this.rank = rank;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getFeatureCvTermId()
+ */
+ public int getFeatureCvTermId() {
+ return this.featureCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setFeatureCvTermId(int)
+ */
+ public void setFeatureCvTermId(int featureCvTermId) {
+ this.featureCvTermId = featureCvTermId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getCvterm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setCvterm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getPub()
+ */
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setPub(org.gmod.schema.pub.PubI)
+ */
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#isNot()
+ */
+ public boolean isNot() {
+ return this.not;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setNot(boolean)
+ */
+ public void setNot(boolean not) {
+ this.not = not;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getFeatureCvtermprops()
+ */
+ public Collection<FeatureCvTermProp> getFeatureCvTermProps() {
+ return this.featureCvTermProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setFeatureCvtermprops(java.util.Set)
+ */
+ public void setFeatureCvTermProps(Collection<FeatureCvTermProp> featureCvTermProps) {
+ this.featureCvTermProps = featureCvTermProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getFeatureCvtermPubs()
+ */
+ public Collection<FeatureCvTermPub> getFeatureCvTermPubs() {
+ return this.featureCvTermPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setFeatureCvtermPubs(java.util.Set)
+ */
+ public void setFeatureCvTermPubs(Collection<FeatureCvTermPub> featureCvTermPubs) {
+ this.featureCvTermPubs = featureCvTermPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#getFeatureCvtermDbxrefs()
+ */
+ public Collection<FeatureCvTermDbXRef> getFeatureCvTermDbXRefs() {
+ return this.featureCvTermDbXRefs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermI#setFeatureCvtermDbxrefs(java.util.Set)
+ */
+ public void setFeatureCvTermDbXRefs(Collection<FeatureCvTermDbXRef> featureCvTermDbXRefs) {
+ this.featureCvTermDbXRefs = featureCvTermDbXRefs;
+ }
+
+ public int getRank() {
+ return rank;
+ }
+
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureCvTermDbXRef.java b/org/gmod/schema/sequence/FeatureCvTermDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..14d1db9cb3147487cd01ed7bd5d813ddd95702aa
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureCvTermDbXRef.java
@@ -0,0 +1,76 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.general.DbXRef;
+
+import java.io.Serializable;
+
+public class FeatureCvTermDbXRef implements Serializable {
+
+ // Fields
+ private int featureCvTermDbXRefId;
+ private DbXRef dbXRef;
+ private FeatureCvTerm featureCvTerm;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureCvTermDbXRef() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public FeatureCvTermDbXRef(DbXRef dbXRef, FeatureCvTerm featureCvTerm) {
+ this.dbXRef = dbXRef;
+ this.featureCvTerm = featureCvTerm;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#getFeatureCvTermDbXrefId()
+ */
+ private int getFeatureCvTermDbXRefId() {
+ return this.featureCvTermDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#setFeatureCvTermDbXrefId(int)
+ */
+ private void setFeatureCvTermDbXRefId(int featureCvTermDbXRefId) {
+ this.featureCvTermDbXRefId = featureCvTermDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#getDbxref()
+ */
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#setDbxref(org.gmod.schema.general.DbXRefI)
+ */
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#getFeatureCvterm()
+ */
+ public FeatureCvTerm getFeatureCvTerm() {
+ return this.featureCvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermDbXRefI#setFeatureCvterm(org.gmod.schema.sequence.FeatureCvTermI)
+ */
+ public void setFeatureCvTerm(FeatureCvTerm featureCvTerm) {
+ this.featureCvTerm = featureCvTerm;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureCvTermProp.java b/org/gmod/schema/sequence/FeatureCvTermProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..4af9838b6a12ad2acab09da6245364414d6e0030
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureCvTermProp.java
@@ -0,0 +1,175 @@
+package org.gmod.schema.sequence;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+import org.gmod.schema.utils.Rankable;
+
+import java.io.Serializable;
+
+/**
+ * This represents a key/value pair attached to a FeatureCvTerm. The key is itself a CvTerm, with
+ * a free-text value
+ *
+ * Database constraints: feature_cvtermprop_c1 unique (feature_cvterm_id, type_id, rank)
+ *
+ * @author art
+ */
+/**
+ * @author art
+ *
+ */
+
+
+public class FeatureCvTermProp implements Serializable, PropertyI, Rankable {
+
+ // Fields
+
+
+ /**
+ * Database unique primary key
+ */
+ private int featureCvTermPropId;
+
+
+ /**
+ * The CvTerm that acts as the key in this map of properties
+ */
+ private CvTerm cvTerm;
+
+ /**
+ * The FeatureCvTerm to which this property is attached
+ */
+ private FeatureCvTerm featureCvTerm;
+
+ /**
+ * The value of this property
+ */
+ private String value;
+
+ /**
+ * The rank is used to distinguish multiple
+ * values for the same key eg /foo="value1", /foo="value2" in an EMBL file could be stored as two FeatureCvTerm with
+ * different ranks. The default is 0;
+ */
+ private int rank;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureCvTermProp() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public FeatureCvTermProp(CvTerm cvTerm, FeatureCvTerm featureCvTerm, int rank) {
+ this.cvTerm = cvTerm;
+ this.featureCvTerm = featureCvTerm;
+ this.rank = rank;
+ }
+ /** full constructor */
+ public FeatureCvTermProp(CvTerm cvTerm, FeatureCvTerm featureCvTerm, String value, int rank) {
+ this.cvTerm = cvTerm;
+ this.featureCvTerm = featureCvTerm;
+ this.value = value;
+ this.rank = rank;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPropI#getFeatureCvTermpropId()
+ */
+ private int getFeatureCvTermPropId() {
+ return this.featureCvTermPropId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPropI#setFeatureCvTermpropId(int)
+ */
+ private void setFeatureCvTermPropId(int featureCvTermPropId) {
+ this.featureCvTermPropId = featureCvTermPropId;
+ }
+
+ /**
+ * Accessor for featureCvTerm
+ *
+ * @see featureCvTerm
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /**
+ * Accessor for cvTerm
+ *
+ * @see cvTerm
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /**
+ * Accessor for featureCvTerm
+ *
+ * @see featureCvTerm
+ */
+ public FeatureCvTerm getFeatureCvTerm() {
+ return this.featureCvTerm;
+ }
+
+
+ /**
+ * Accessor for featureCvTerm
+ *
+ * @see featureCvTerm
+ */
+ public void setFeatureCvTerm(FeatureCvTerm featureCvTerm) {
+ this.featureCvTerm = featureCvTerm;
+ }
+
+
+ /**
+ * Accessor for value
+ *
+ * @see value
+ */
+ public String getValue() {
+ return this.value;
+ }
+
+ /**
+ * Accessor for value
+ *
+ * @see value
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /**
+ * Accessor for rank
+ *
+ * @see rank
+ */
+ public int getRank() {
+ return this.rank;
+ }
+
+ /**
+ * Accessor for rank
+ *
+ * @see rank
+ */
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureCvTermPub.java b/org/gmod/schema/sequence/FeatureCvTermPub.java
new file mode 100644
index 0000000000000000000000000000000000000000..3d81a599747bdcd6eb38c71e315581f5492407ad
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureCvTermPub.java
@@ -0,0 +1,78 @@
+package org.gmod.schema.sequence;
+
+
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeatureCvTermPub implements Serializable {
+
+ // Fields
+ private int featureCvTermPubId;
+ private Pub pub;
+ private FeatureCvTerm featureCvTerm;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureCvTermPub() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public FeatureCvTermPub(Pub pub, FeatureCvTerm featureCvTerm) {
+ this.pub = pub;
+ this.featureCvTerm = featureCvTerm;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#getFeatureCvTermPubId()
+ */
+ public int getFeatureCvTermPubId() {
+ return this.featureCvTermPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#setFeatureCvTermPubId(int)
+ */
+ public void setFeatureCvTermPubId(int featureCvTermPubId) {
+ this.featureCvTermPubId = featureCvTermPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#getPub()
+ */
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#getFeatureCvterm()
+ */
+ public FeatureCvTerm getFeatureCvTerm() {
+ return this.featureCvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureCvTermPubI#setFeatureCvterm(org.gmod.schema.sequence.FeatureCvTermI)
+ */
+ public void setFeatureCvTerm(FeatureCvTerm featureCvTerm) {
+ this.featureCvTerm = featureCvTerm;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureDbXRef.java b/org/gmod/schema/sequence/FeatureDbXRef.java
new file mode 100644
index 0000000000000000000000000000000000000000..f43ae4c059657b45bb50a962fdbdb0969bc70b59
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureDbXRef.java
@@ -0,0 +1,93 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.general.DbXRef;
+
+import java.io.Serializable;
+
+public class FeatureDbXRef implements Serializable {
+
+ // Fields
+ private int featureDbXRefId;
+ private DbXRef dbXRef;
+ private Feature feature;
+ private boolean current;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureDbXRef() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public FeatureDbXRef(DbXRef dbXRef, Feature feature, boolean current) {
+ this.dbXRef = dbXRef;
+ this.feature = feature;
+ this.current = current;
+ }
+
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#getFeatureDbXRefId()
+ */
+ public int getFeatureDbXRefId() {
+ return this.featureDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#setFeatureDbXRefId(int)
+ */
+ public void setFeatureDbXRefId(int featureDbXRefId) {
+ this.featureDbXRefId = featureDbXRefId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#getDbxref()
+ */
+ public DbXRef getDbXRef() {
+ return this.dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#setDbxref(org.gmod.schema.general.DbXRefI)
+ */
+ public void setDbXRef(DbXRef dbXRef) {
+ this.dbXRef = dbXRef;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#isCurrent()
+ */
+ public boolean isCurrent() {
+ return this.current;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureDbXRefI#setCurrent(boolean)
+ */
+ public void setCurrent(boolean current) {
+ this.current = current;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureLoc.java b/org/gmod/schema/sequence/FeatureLoc.java
new file mode 100644
index 0000000000000000000000000000000000000000..06699511ea85c83ec97b7085ac83d42a8597e96e
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureLoc.java
@@ -0,0 +1,251 @@
+package org.gmod.schema.sequence;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+public class FeatureLoc implements Serializable {
+
+ // Fields
+ private int featureLocId;
+ private Feature featureBySrcFeatureId;
+ private Feature featureByFeatureId;
+ private Integer fmin;
+ private boolean fminPartial;
+ private Integer fmax;
+ private boolean fmaxPartial;
+ private Short strand;
+ private Integer phase;
+ private String residueInfo;
+ private int locGroup;
+ private int rank;
+ private Set<FeatureLocPub> featureLocPubs = new HashSet<FeatureLocPub>(0);
+
+ // used by artemis
+ private int srcFeatureId;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureLoc() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+
+ private FeatureLoc(Feature featureBySrcFeatureId, boolean fminPartial, boolean fmaxPartial, int locGroup, int rank) {
+ this.featureBySrcFeatureId = featureBySrcFeatureId;
+ this.fminPartial = fminPartial;
+ this.fmaxPartial = fmaxPartial;
+ this.locGroup = locGroup;
+ this.rank = rank;
+ }
+ /** large constructor */
+ public FeatureLoc(Feature featureBySrcfeatureId, Feature featureByFeatureId, Integer fmin, boolean fminPartial, Integer fmax, boolean fmaxPartial, Short strand, Integer phase, int locGroup, int rank) {
+ this.featureBySrcFeatureId = featureBySrcfeatureId;
+ this.featureByFeatureId = featureByFeatureId;
+ this.fmin = fmin;
+ this.fminPartial = fminPartial;
+ this.fmax = fmax;
+ this.fmaxPartial = fmaxPartial;
+ this.strand = strand;
+ this.phase = phase;
+ this.locGroup = locGroup;
+ this.rank = rank;
+ }
+
+
+ // Property accessors
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getFeatureBySrcfeatureId()
+ */
+ public Feature getFeatureBySrcFeatureId() {
+ return this.featureBySrcFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFeatureBySrcfeatureId(org.genedb.db.jpa.Feature)
+ */
+ public void setFeatureBySrcFeatureId(Feature featureBySrcFeatureId) {
+ this.featureBySrcFeatureId = featureBySrcFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getFeatureByFeatureId()
+ */
+ public Feature getFeatureByFeatureId() {
+ return this.featureByFeatureId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFeatureByFeatureId(org.genedb.db.jpa.Feature)
+ */
+ public void setFeatureByFeatureId(Feature featureByFeatureId) {
+ this.featureByFeatureId = featureByFeatureId;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getFmin()
+ */
+ public Integer getFmin() {
+ return this.fmin;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFmin(java.lang.Integer)
+ */
+ public void setFmin(Integer fmin) {
+ this.fmin = fmin;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#isFminPartial()
+ */
+ public boolean isFminPartial() {
+ return this.fminPartial;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFminPartial(boolean)
+ */
+ public void setFminPartial(boolean fminPartial) {
+ this.fminPartial = fminPartial;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getFmax()
+ */
+ public Integer getFmax() {
+ return this.fmax;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFmax(java.lang.Integer)
+ */
+ public void setFmax(Integer fmax) {
+ this.fmax = fmax;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#isFmaxPartial()
+ */
+ public boolean isFmaxPartial() {
+ return this.fmaxPartial;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFmaxPartial(boolean)
+ */
+ public void setFmaxPartial(boolean fmaxPartial) {
+ this.fmaxPartial = fmaxPartial;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getStrand()
+ */
+ public Short getStrand() {
+ return this.strand;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setStrand(java.lang.Short)
+ */
+ public void setStrand(Short strand) {
+ this.strand = strand;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getPhase()
+ */
+ public Integer getPhase() {
+ return this.phase;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setPhase(java.lang.Integer)
+ */
+ public void setPhase(Integer phase) {
+ this.phase = phase;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getResidueInfo()
+ */
+ public String getResidueInfo() {
+ return this.residueInfo;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setResidueInfo(java.lang.String)
+ */
+ public void setResidueInfo(String residueInfo) {
+ this.residueInfo = residueInfo;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getLocgroup()
+ */
+ public int getLocGroup() {
+ return this.locGroup;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setLocgroup(int)
+ */
+ public void setLocGroup(int locGroup) {
+ this.locGroup = locGroup;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getRank()
+ */
+ public int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setRank(int)
+ */
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#getFeaturelocPubs()
+ */
+ public Set<FeatureLocPub> getFeatureLocPubs() {
+ return this.featureLocPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocI#setFeaturelocPubs(java.util.Set)
+ */
+ public void setFeaturelocPubs(Set<FeatureLocPub> featureLocPubs) {
+ this.featureLocPubs = featureLocPubs;
+ }
+
+
+ public int getFeatureLocId() {
+ return this.featureLocId;
+ }
+
+
+ public void setFeatureLocId(int featureLocId) {
+ this.featureLocId = featureLocId;
+ }
+
+ public int getSrcFeatureId() {
+ return srcFeatureId;
+ }
+
+ public void setSrcFeatureId(int srcFeatureId) {
+ this.srcFeatureId = srcFeatureId;
+ }
+
+}
diff --git a/org/gmod/schema/sequence/FeatureLocPub.java b/org/gmod/schema/sequence/FeatureLocPub.java
new file mode 100644
index 0000000000000000000000000000000000000000..0b7bdcf66c77a36995c47ed7f93ebc2c3689753c
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureLocPub.java
@@ -0,0 +1,62 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeatureLocPub implements Serializable {
+
+ // Fields
+ private int featureLocPubId;
+ private FeatureLoc featureLoc;
+ private Pub pub;
+
+ // Property accessors
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#getFeatureLocPubId()
+ */
+ private int getFeatureLocPubId() {
+ return this.featureLocPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#setFeatureLocPubId(int)
+ */
+ private void setFeatureLocPubId(int featureLocPubId) {
+ this.featureLocPubId = featureLocPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#getFeatureloc()
+ */
+ private FeatureLoc getFeatureloc() {
+ return this.featureLoc;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#setFeatureloc(org.gmod.schema.sequence.FeatureLocI)
+ */
+ private void setFeatureloc(FeatureLoc featureloc) {
+ this.featureLoc = featureloc;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureLocPubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureProp.java b/org/gmod/schema/sequence/FeatureProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..f87130d3603ce90bb0a9fefdbd5d699c22d8219f
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureProp.java
@@ -0,0 +1,122 @@
+package org.gmod.schema.sequence;
+
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+
+
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+public class FeatureProp implements Serializable, PropertyI {
+
+ // Fields
+ private int featurePropId;
+ public CvTerm cvTerm;
+ private Feature feature;
+ private String value;
+ private int rank;
+ private Set<FeaturePropPub> featurePropPubs = new HashSet<FeaturePropPub>(0);
+
+ // Constructors
+ /** default constructor */
+ public FeatureProp() {
+ // Deliberately empty default constructor
+ }
+
+ /** useful constructor ! */
+ public FeatureProp(Feature feature, CvTerm cvTerm, String value, int rank) {
+ this.cvTerm = cvTerm;
+ this.feature = feature;
+ this.value = value;
+ this.rank = rank;
+ }
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#getCvterm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#setCvterm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#getValue()
+ */
+ public String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#setValue(java.lang.String)
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#getRank()
+ */
+ public int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#setRank(int)
+ */
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#getFeaturepropPubs()
+ */
+ private Set<FeaturePropPub> getFeaturePropPubs() {
+ return this.featurePropPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropI#setFeaturepropPubs(java.util.Set)
+ */
+ public void setFeaturePropPubs(Set<FeaturePropPub> featurePropPubs) {
+ this.featurePropPubs = featurePropPubs;
+ }
+
+ public int getFeaturePropId() {
+ return this.featurePropId;
+ }
+
+ public void setFeaturePropId(final int featurePropId) {
+ this.featurePropId = featurePropId;
+ }
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeaturePropPub.java b/org/gmod/schema/sequence/FeaturePropPub.java
new file mode 100644
index 0000000000000000000000000000000000000000..c0a35611a1a9f38aa288c72d2dcfdcc6ca702f3a
--- /dev/null
+++ b/org/gmod/schema/sequence/FeaturePropPub.java
@@ -0,0 +1,65 @@
+package org.gmod.schema.sequence;
+
+
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeaturePropPub implements Serializable {
+
+ // Fields
+ private int featurePropPubId;
+ private FeatureProp featureProp;
+ private Pub pub;
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#getFeaturePropPubId()
+ */
+ private int getFeaturePropPubId() {
+ return this.featurePropPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#setFeaturePropPubId(int)
+ */
+ private void setFeaturePropPubId(int featurePropPubId) {
+ this.featurePropPubId = featurePropPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#getFeatureprop()
+ */
+ private FeatureProp getFeatureProp() {
+ return this.featureProp;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#setFeatureprop(org.genedb.db.jpa.FeatureProp)
+ */
+ private void setFeatureProp(FeatureProp featureProp) {
+ this.featureProp = featureProp;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePropPubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeaturePub.java b/org/gmod/schema/sequence/FeaturePub.java
new file mode 100644
index 0000000000000000000000000000000000000000..b99be41a276111547e4847ff16daa11e4f2c4084
--- /dev/null
+++ b/org/gmod/schema/sequence/FeaturePub.java
@@ -0,0 +1,77 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeaturePub implements Serializable {
+
+ // Fields
+ private int featurePubId;
+ private Feature feature;
+ private Pub pub;
+
+ // Constructors
+
+ /** default constructor */
+ public FeaturePub() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public FeaturePub(Feature feature, Pub pub) {
+ this.feature = feature;
+ this.pub = pub;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#getFeaturePubId()
+ */
+ private int getFeaturePubId() {
+ return this.featurePubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#setFeaturePubId(int)
+ */
+ private void setFeaturePubId(int featurePubId) {
+ this.featurePubId = featurePubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#getPub()
+ */
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeaturePubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureRelationship.java b/org/gmod/schema/sequence/FeatureRelationship.java
new file mode 100644
index 0000000000000000000000000000000000000000..739bd78845b8e816002cde51c8750e720e148455
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureRelationship.java
@@ -0,0 +1,160 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.cv.CvTerm;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+public class FeatureRelationship implements Serializable {
+
+ // Fields
+ private int featureRelationshipId;
+ private Feature featureBySubjectId;
+ private Feature featureByObjectId;
+ private CvTerm cvTerm;
+ private String value;
+ private int rank;
+ private Set<FeatureRelationshipProp> featureRelationshipProps = new HashSet<FeatureRelationshipProp>(0);
+ private Set<FeatureRelationshipPub> featureRelationshipPubs = new HashSet<FeatureRelationshipPub>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureRelationship() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public FeatureRelationship(Feature featureBySubjectId, Feature featureByObjectId, CvTerm cvTerm, int rank) {
+ this.featureBySubjectId = featureBySubjectId;
+ this.featureByObjectId = featureByObjectId;
+ this.cvTerm = cvTerm;
+ this.rank = rank;
+ }
+
+
+ // Property accessors
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getFeatureRelationshipId()
+ */
+ public int getFeatureRelationshipId() {
+ return this.featureRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setFeatureRelationshipId(int)
+ */
+ public void setFeatureRelationshipId(int featureRelationshipId) {
+ this.featureRelationshipId = featureRelationshipId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getFeatureBySubjectId()
+ */
+ public Feature getFeatureBySubjectId() {
+ return this.featureBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setFeatureBySubjectId(org.genedb.db.jpa.Feature)
+ */
+ public void setFeatureBySubjectId(Feature featureBySubjectId) {
+ this.featureBySubjectId = featureBySubjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getFeatureByObjectId()
+ */
+ public Feature getFeatureByObjectId() {
+ return this.featureByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setFeatureByObjectId(org.genedb.db.jpa.Feature)
+ */
+ public void setFeatureByObjectId(Feature featureByObjectId) {
+ this.featureByObjectId = featureByObjectId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getCvterm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setCvterm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getValue()
+ */
+ public String getValue() {
+ return this.value;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setValue(java.lang.String)
+ */
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getRank()
+ */
+ public int getRank() {
+ return this.rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setRank(int)
+ */
+ public void setRank(int rank) {
+ this.rank = rank;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getFeatureRelationshipprops()
+ */
+ private Collection<FeatureRelationshipProp> getFeatureRelationshipProps() {
+ return this.featureRelationshipProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setFeatureRelationshipprops(java.util.Set)
+ */
+ private void setFeatureRelationshipProps(Set<FeatureRelationshipProp> featureRelationshipProps) {
+ this.featureRelationshipProps = featureRelationshipProps;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#getFeatureRelationshipPubs()
+ */
+ private Collection<FeatureRelationshipPub> getFeatureRelationshipPubs() {
+ return this.featureRelationshipPubs;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipI#setFeatureRelationshipPubs(java.util.Set)
+ */
+ private void setFeatureRelationshipPubs(Set<FeatureRelationshipPub> featureRelationshipPubs) {
+ this.featureRelationshipPubs = featureRelationshipPubs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureRelationshipProp.java b/org/gmod/schema/sequence/FeatureRelationshipProp.java
new file mode 100644
index 0000000000000000000000000000000000000000..6aaeab90dcf4e775041eec57a383ecc3ac3447fb
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureRelationshipProp.java
@@ -0,0 +1,78 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.utils.propinterface.PropertyI;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+public class FeatureRelationshipProp implements Serializable, PropertyI {
+
+ // Fields
+ private int featureRelationshipPropId;
+ private CvTerm cvTerm;
+ private FeatureRelationship featureRelationship;
+ private String value;
+ private int rank;
+ private Set<FeatureRelationshipPropPub> featureRelationshipPropPubs = new HashSet<FeatureRelationshipPropPub>(0);
+
+ // Property accessors
+
+ private int getFeatureRelationshipPropId() {
+ return this.featureRelationshipPropId;
+ }
+
+ private void setFeatureRelationshipPropId(int featureRelationshipPropId) {
+ this.featureRelationshipPropId = featureRelationshipPropId;
+ }
+
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ private void setCvTerm(CvTerm cvTerm) {
+ this.cvTerm = cvTerm;
+ }
+
+ private FeatureRelationship getFeatureRelationship() {
+ return this.featureRelationship;
+ }
+
+ private void setFeatureRelationship(FeatureRelationship featureRelationship) {
+ this.featureRelationship = featureRelationship;
+ }
+
+
+ private String getValue() {
+ return this.value;
+ }
+
+ private void setValue(String value) {
+ this.value = value;
+ }
+
+
+ private int getRank() {
+ return this.rank;
+ }
+
+ private void setRank(int rank) {
+ this.rank = rank;
+ }
+
+ private Collection<FeatureRelationshipPropPub> getFeatureRelationshipPropPubs() {
+ return this.featureRelationshipPropPubs;
+ }
+
+ private void setFeatureRelationshipPropPubs(Set<FeatureRelationshipPropPub> featureRelationshipPropPubs) {
+ this.featureRelationshipPropPubs = featureRelationshipPropPubs;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureRelationshipPropPub.java b/org/gmod/schema/sequence/FeatureRelationshipPropPub.java
new file mode 100644
index 0000000000000000000000000000000000000000..bac84e251a75337f933ad624e6f301d880463f71
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureRelationshipPropPub.java
@@ -0,0 +1,63 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeatureRelationshipPropPub implements Serializable {
+
+ // Fields
+ private int featureRelationshipPropPubId;
+ private FeatureRelationshipProp featureRelationshipProp;
+ private Pub pub;
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#getFeatureRelationshipPropPubId()
+ */
+ private int getFeatureRelationshipPropPubId() {
+ return this.featureRelationshipPropPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#setFeatureRelationshipPropPubId(int)
+ */
+ private void setFeatureRelationshipPropPubId(int featureRelationshipPropPubId) {
+ this.featureRelationshipPropPubId = featureRelationshipPropPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#getFeatureRelationshipprop()
+ */
+ private FeatureRelationshipProp getFeatureRelationshipProp() {
+ return this.featureRelationshipProp;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#setFeatureRelationshipprop(org.genedb.db.jpa.FeatureRelationshipProp)
+ */
+ private void setFeatureRelationshipProp(FeatureRelationshipProp featureRelationshipProp) {
+ this.featureRelationshipProp = featureRelationshipProp;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPropPubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureRelationshipPub.java b/org/gmod/schema/sequence/FeatureRelationshipPub.java
new file mode 100644
index 0000000000000000000000000000000000000000..0f420b713c6e0a14757bc7df7ee85a8d208e31df
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureRelationshipPub.java
@@ -0,0 +1,63 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeatureRelationshipPub implements Serializable {
+
+ // Fields
+ private int featureRelationshipPubId;
+ private Pub pub;
+ private FeatureRelationship featureRelationship;
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#getFeatureRelationshipPubId()
+ */
+ private int getFeatureRelationshipPubId() {
+ return this.featureRelationshipPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#setFeatureRelationshipPubId(int)
+ */
+ private void setFeatureRelationshipPubId(int featureRelationshipPubId) {
+ this.featureRelationshipPubId = featureRelationshipPubId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#getPub()
+ */
+ private Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#setPub(org.gmod.schema.pub.PubI)
+ */
+ private void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#getFeatureRelationship()
+ */
+ private FeatureRelationship getFeatureRelationship() {
+ return this.featureRelationship;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureRelationshipPubI#setFeatureRelationship(org.genedb.db.jpa.FeatureRelationship)
+ */
+ private void setFeatureRelationship(FeatureRelationship featureRelationship) {
+ this.featureRelationship = featureRelationship;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/FeatureSynonym.java b/org/gmod/schema/sequence/FeatureSynonym.java
new file mode 100644
index 0000000000000000000000000000000000000000..4374656e10af82a053439dceaaee8b2939bc5582
--- /dev/null
+++ b/org/gmod/schema/sequence/FeatureSynonym.java
@@ -0,0 +1,127 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.pub.Pub;
+
+import java.io.Serializable;
+
+public class FeatureSynonym implements Serializable {
+
+ // Fields
+ private int featureSynonymId;
+ private Synonym synonym;
+ private Feature feature;
+ private Pub pub;
+ private boolean current;
+ private boolean internal;
+
+ // Constructors
+
+ /** default constructor */
+ public FeatureSynonym() {
+ // Deliberately empty default constructor
+ }
+
+ /** full constructor */
+ public FeatureSynonym(Synonym synonym, Feature feature, Pub pub, boolean current, boolean internal) {
+ this.synonym = synonym;
+ this.feature = feature;
+ this.pub = pub;
+ this.current = current;
+ this.internal = internal;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#getFeatureSynonymId()
+ */
+ public int getFeatureSynonymId() {
+ return this.featureSynonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setFeatureSynonymId(int)
+ */
+ public void setFeatureSynonymId(int featureSynonymId) {
+ this.featureSynonymId = featureSynonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#getSynonym()
+ */
+ public Synonym getSynonym() {
+ return this.synonym;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setSynonym(org.gmod.schema.sequence.SynonymI)
+ */
+ public void setSynonym(Synonym synonym) {
+ this.synonym = synonym;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#getFeature()
+ */
+ public Feature getFeature() {
+ return this.feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setFeature(org.genedb.db.jpa.Feature)
+ */
+ public void setFeature(Feature feature) {
+ this.feature = feature;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#getPub()
+ */
+ public Pub getPub() {
+ return this.pub;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setPub(org.gmod.schema.pub.PubI)
+ */
+ public void setPub(Pub pub) {
+ this.pub = pub;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#isCurrent()
+ */
+ public boolean isCurrent() {
+ return this.current;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setCurrent(boolean)
+ */
+ public void setCurrent(boolean current) {
+ this.current = current;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#isInternal()
+ */
+ public boolean isInternal() {
+ return this.internal;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.FeatureSynonymI#setInternal(boolean)
+ */
+ public void setInternal(boolean internal) {
+ this.internal = internal;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/sequence/Synonym.java b/org/gmod/schema/sequence/Synonym.java
new file mode 100644
index 0000000000000000000000000000000000000000..b68d85012bc412c2e3847fa3aa2566b481187a99
--- /dev/null
+++ b/org/gmod/schema/sequence/Synonym.java
@@ -0,0 +1,113 @@
+package org.gmod.schema.sequence;
+
+import org.gmod.schema.cv.CvTerm;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+public class Synonym implements Serializable {
+
+ // Fields
+ private int synonymId;
+ private CvTerm cvTerm;
+ private String name;
+ private String synonymSgml;
+ private Set<FeatureSynonym> featureSynonyms = new HashSet<FeatureSynonym>(0);
+
+ // Constructors
+
+ /** default constructor */
+ public Synonym() {
+ // Deliberately empty default constructor
+ }
+
+ /** minimal constructor */
+ public Synonym(CvTerm cvTerm, String name, String synonymSgml) {
+ this.cvTerm = cvTerm;
+ this.name = name;
+ this.synonymSgml = synonymSgml;
+ }
+
+
+ // Property accessors
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#getSynonymId()
+ */
+ public int getSynonymId() {
+ return this.synonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#setSynonymId(int)
+ */
+ public void setSynonymId(int synonymId) {
+ this.synonymId = synonymId;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#getCvterm()
+ */
+ public CvTerm getCvTerm() {
+ return this.cvTerm;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#setCvterm(org.gmod.schema.cv.CvTermI)
+ */
+ public void setCvTerm(CvTerm cvterm) {
+ this.cvTerm = cvterm;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#getName()
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#setName(java.lang.String)
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#getSynonymSgml()
+ */
+ private String getSynonymSgml() {
+ return this.synonymSgml;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#setSynonymSgml(java.lang.String)
+ */
+ public void setSynonymSgml(String synonymSgml) {
+ this.synonymSgml = synonymSgml;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#getFeatureSynonyms()
+ */
+ private Collection<FeatureSynonym> getFeatureSynonyms() {
+ return this.featureSynonyms;
+ }
+
+ /* (non-Javadoc)
+ * @see org.genedb.db.jpa.SynonymI#setFeatureSynonyms(java.util.Set)
+ */
+ private void setFeatureSynonyms(Set<FeatureSynonym> featureSynonyms) {
+ this.featureSynonyms = featureSynonyms;
+ }
+
+
+
+
+}
+
+
diff --git a/org/gmod/schema/utils/CollectionUtils.java b/org/gmod/schema/utils/CollectionUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..79430802e83a32be9c285bfc8a087ac69e53cd51
--- /dev/null
+++ b/org/gmod/schema/utils/CollectionUtils.java
@@ -0,0 +1,27 @@
+package org.gmod.schema.utils;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+/**
+ * Static utility class for miscellaneous collection handling
+ *
+ * @author art
+ */
+public class CollectionUtils {
+
+ /**
+ *
+ *
+ * @param <T>
+ * @param collection
+ * @return the original collection, or an empty collection
+ */
+ public static <T> Collection<T> safeGetter(Collection<T> collection) {
+ if (collection != null) {
+ return collection;
+ }
+ return new HashSet<T>(0);
+ }
+
+}
diff --git a/org/gmod/schema/utils/CountedName.java b/org/gmod/schema/utils/CountedName.java
new file mode 100644
index 0000000000000000000000000000000000000000..ed3477cbe101f668ba0e4a62dfdc397d29527157
--- /dev/null
+++ b/org/gmod/schema/utils/CountedName.java
@@ -0,0 +1,55 @@
+package org.gmod.schema.utils;
+
+/**
+ * Class to store terms, eg products, and how many occurences there are
+ *
+ * @author cp2
+ */
+public class CountedName {
+
+ /**
+ *
+ */
+ private String name;
+
+ /**
+ *
+ */
+ private int count;
+
+
+
+ public CountedName(String name, int count) {
+ this.name = name;
+ this.count = count;
+ }
+
+ /**
+ * @return
+ */
+ public int getCount() {
+ return count;
+ }
+
+ /**
+ * @param count
+ */
+ public void setCount(int count) {
+ this.count = count;
+ }
+
+ /**
+ * @return
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+}
diff --git a/org/gmod/schema/utils/PeptideProperties.java b/org/gmod/schema/utils/PeptideProperties.java
new file mode 100644
index 0000000000000000000000000000000000000000..5fffa5af78ef157ff61fb9e588bacad1f7c42483
--- /dev/null
+++ b/org/gmod/schema/utils/PeptideProperties.java
@@ -0,0 +1,76 @@
+package org.gmod.schema.utils;
+
+public class PeptideProperties {
+
+ private String mass;
+
+ private String aminoAcids;
+
+ private String isoelectricPoint;
+
+ private String charge;
+
+ private String signalPeptide;
+
+ private String transmembraneDomain;
+
+ private String gpiAnchor;
+
+ public String getAminoAcids() {
+ return aminoAcids;
+ }
+
+ public void setAminoAcids(String aminoAcids) {
+ this.aminoAcids = aminoAcids;
+ }
+
+ public String getCharge() {
+ return charge;
+ }
+
+ public void setCharge(String charge) {
+ this.charge = charge;
+ }
+
+ public String getGpiAnchor() {
+ return gpiAnchor;
+ }
+
+ public void setGpiAnchor(String gpiAnchor) {
+ this.gpiAnchor = gpiAnchor;
+ }
+
+ public String getIsoelectricPoint() {
+ return isoelectricPoint;
+ }
+
+ public void setIsoelectricPoint(String isoelectricPoint) {
+ this.isoelectricPoint = isoelectricPoint;
+ }
+
+ public String getMass() {
+ return mass;
+ }
+
+ public void setMass(String mass) {
+ this.mass = mass;
+ }
+
+ public String getSignalPeptide() {
+ return signalPeptide;
+ }
+
+ public void setSignalPeptide(String signalPeptide) {
+ this.signalPeptide = signalPeptide;
+ }
+
+ public String getTransmembraneDomain() {
+ return transmembraneDomain;
+ }
+
+ public void setTransmembraneDomain(String transmembraneDomain) {
+ this.transmembraneDomain = transmembraneDomain;
+ }
+
+
+}
diff --git a/org/gmod/schema/utils/Rankable.java b/org/gmod/schema/utils/Rankable.java
new file mode 100644
index 0000000000000000000000000000000000000000..ca36d2e20fdc12f68fd97188d1314364be859228
--- /dev/null
+++ b/org/gmod/schema/utils/Rankable.java
@@ -0,0 +1,16 @@
+package org.gmod.schema.utils;
+
+/**
+ * These domain objects use rank to define an order
+ *
+ * @author art
+ */
+public abstract interface Rankable {
+
+ /**
+ * Retrieve the rank, ie order, of this object. Ranks start at zero
+ *
+ * @return the rank
+ */
+ public abstract int getRank();
+}
diff --git a/org/gmod/schema/utils/propinterface/PropertyI.java b/org/gmod/schema/utils/propinterface/PropertyI.java
new file mode 100644
index 0000000000000000000000000000000000000000..6b55fa2819ca237754b664bd3121a37442caba14
--- /dev/null
+++ b/org/gmod/schema/utils/propinterface/PropertyI.java
@@ -0,0 +1,13 @@
+package org.gmod.schema.utils.propinterface;
+
+import org.gmod.schema.cv.CvTerm;
+
+/**
+ *
+ * @author cp2
+ */
+public interface PropertyI {
+
+ public abstract CvTerm getCvTerm();
+
+}