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org.gmod.schema

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11541 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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1 parent 4bf6931 commit 8b57cac9c615d3323f3688d47d891f009406772b tjc committed Aug 13, 2009
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  1. +242 −0 org/gmod/schema/analysis/Analysis.java
  2. +176 −0 org/gmod/schema/analysis/AnalysisFeature.java
  3. +104 −0 org/gmod/schema/analysis/AnalysisProp.java
  4. +111 −0 org/gmod/schema/cv/Cv.java
  5. +648 −0 org/gmod/schema/cv/CvTerm.java
  6. +103 −0 org/gmod/schema/cv/CvTermDbXRef.java
  7. +139 −0 org/gmod/schema/cv/CvTermPath.java
  8. +118 −0 org/gmod/schema/cv/CvTermProp.java
  9. +113 −0 org/gmod/schema/cv/CvTermRelationship.java
  10. +101 −0 org/gmod/schema/cv/CvTermSynonym.java
  11. +120 −0 org/gmod/schema/cv/DbXRefProp.java
  12. +51 −0 org/gmod/schema/dao/BaseDaoI.java
  13. +117 −0 org/gmod/schema/dao/CvDaoI.java
  14. +55 −0 org/gmod/schema/dao/GeneralDaoI.java
  15. +58 −0 org/gmod/schema/dao/OrganismDaoI.java
  16. +45 −0 org/gmod/schema/dao/PhylogenyDaoI.java
  17. +65 −0 org/gmod/schema/dao/PubDaoI.java
  18. +55 −0 org/gmod/schema/dao/SchemaDaoI.java
  19. +259 −0 org/gmod/schema/dao/SequenceDaoI.java
  20. +136 −0 org/gmod/schema/general/Db.java
  21. +292 −0 org/gmod/schema/general/DbXRef.java
  22. +59 −0 org/gmod/schema/general/Project.java
  23. +148 −0 org/gmod/schema/general/Tableinfo.java
  24. +207 −0 org/gmod/schema/organism/Organism.java
  25. +85 −0 org/gmod/schema/organism/OrganismDbXRef.java
  26. +124 −0 org/gmod/schema/organism/OrganismProp.java
  27. +230 −0 org/gmod/schema/phylogeny/Phylonode.java
  28. +80 −0 org/gmod/schema/phylogeny/PhylonodeDbXRef.java
  29. +80 −0 org/gmod/schema/phylogeny/PhylonodeOrganism.java
  30. +104 −0 org/gmod/schema/phylogeny/PhylonodeProp.java
  31. +80 −0 org/gmod/schema/phylogeny/PhylonodePub.java
  32. +110 −0 org/gmod/schema/phylogeny/PhylonodeRelationship.java
  33. +131 −0 org/gmod/schema/phylogeny/Phylotree.java
  34. +80 −0 org/gmod/schema/phylogeny/PhylotreePub.java
  35. +555 −0 org/gmod/schema/pub/Pub.java
  36. +155 −0 org/gmod/schema/pub/PubAuthor.java
  37. +117 −0 org/gmod/schema/pub/PubDbXRef.java
  38. +145 −0 org/gmod/schema/pub/PubProp.java
  39. +104 −0 org/gmod/schema/pub/PubRelationship.java
  40. +509 −0 org/gmod/schema/sequence/Feature.java
  41. +169 −0 org/gmod/schema/sequence/FeatureCvTerm.java
  42. +76 −0 org/gmod/schema/sequence/FeatureCvTermDbXRef.java
  43. +175 −0 org/gmod/schema/sequence/FeatureCvTermProp.java
  44. +78 −0 org/gmod/schema/sequence/FeatureCvTermPub.java
  45. +93 −0 org/gmod/schema/sequence/FeatureDbXRef.java
  46. +251 −0 org/gmod/schema/sequence/FeatureLoc.java
  47. +62 −0 org/gmod/schema/sequence/FeatureLocPub.java
  48. +122 −0 org/gmod/schema/sequence/FeatureProp.java
  49. +65 −0 org/gmod/schema/sequence/FeaturePropPub.java
  50. +77 −0 org/gmod/schema/sequence/FeaturePub.java
  51. +160 −0 org/gmod/schema/sequence/FeatureRelationship.java
  52. +78 −0 org/gmod/schema/sequence/FeatureRelationshipProp.java
  53. +63 −0 org/gmod/schema/sequence/FeatureRelationshipPropPub.java
  54. +63 −0 org/gmod/schema/sequence/FeatureRelationshipPub.java
  55. +127 −0 org/gmod/schema/sequence/FeatureSynonym.java
  56. +113 −0 org/gmod/schema/sequence/Synonym.java
  57. +27 −0 org/gmod/schema/utils/CollectionUtils.java
  58. +55 −0 org/gmod/schema/utils/CountedName.java
  59. +76 −0 org/gmod/schema/utils/PeptideProperties.java
  60. +16 −0 org/gmod/schema/utils/Rankable.java
  61. +13 −0 org/gmod/schema/utils/propinterface/PropertyI.java
View
242 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;
+ }
+
+
+
+
+}
+
+
View
176 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;
+ }
+
+
+
+
+}
+
+
View
104 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;
+ }
+
+
+
+
+}
+
+
View
111 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;
+ }
+
+}
+
+
View
648 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;
+ }
+
+
+}
+
View
103 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;
+ }
+
+
+
+
+}
+
+
View
139 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;
+ }
+
+
+
+
+}
+
+
View
118 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;
+ }
+
+
+
+
+}
+
+
View
113 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;
+ }
+
+
+
+
+}
+
+
View
101 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;
+ }
+
+
+
+
+}
+
+
View
120 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;
+ }
+
+
+
+
+}
+
+
View
51 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);
+
+}
View
117 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);
+
+}
View
55 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);
+}
View
58 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();
+
+}
View
45 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);
+}
View
65 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);
+}
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55 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;
+
+
+}
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259 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 PARTICU