Changeset 2208

Timestamp:

May 2, 2006, 3:45:04 PM (17 years ago)

Author:

dominic

Message:

 

Location:

branches/dominic_annotations/src/core/net/sf/basedb/core/data

Files:

• AnnotationTypeCategoryData.java (added)
• AnnotationTypeData.java (modified) (2 diffs)
• ParameterValueData.java (modified) (1 diff)
• UnitData.java (added)
• UnitParameterValueData.java (added)
• hibernate-properties-HybridizationData.xml (modified) (1 diff)

branches/dominic_annotations/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

@@ -39 +39 @@
   @base.modified $Date$
   @hibernate.class table="`AnnotationTypes`" lazy="false"
+  @modified by Dominic Oyeniran
 */
 public class AnnotationTypeData
@@ -204 +205 @@
     this.enumerationValues = enumerationValues;
   }
-
+  /*
+   * Newly added properties(fields) and mappings addedd by Dominic Oyeniran
+   * for adherence to Nutri-Base Specifications and Requirements.
+   * 
+   */
+  
+  private Set<AnnotationTypeCategoryData> category;
+  /**
+    Many to many from  AnnotationTypes to AnnotationTypeCategory. 
+    This is the inverse end
+    @hibernate.set table="'CategorisedAnnotationTypes'" lazy="true"
+    @hibernate.collection-key column="'annotationtype_id'"
+    @hibernate.collection-many-to-many column="'category_id'"
+      class="net.sf.basedb.core.data.AnnotationTypeCategoryData"
+   */
+  
+  public Set<AnnotationTypeCategoryData> getCategory() {
+    if ( category==null)
+    {
+      category= new HashSet<AnnotationTypeCategoryData>();
+    }
+    return category;
+  }
+  /*
+   the set method() without scope resolution is private and this is done so that 
+   hibernate can keep track of the objects it creates in the collection 
+   and also can 'only' return this object thru the get method().
+   */
+  void setCategory(Set<AnnotationTypeCategoryData> category) {
+    this.category = category;
+  }
+  
+  private String accessionNumber;
+  public static final int MAX_ACCESSION_NUMBER_LENGTH = 255;
+  /**
+   Accession Number: The identifier devised to track a record by an authority. 
+   For example NM_12343 is the accession number for the record XXXX in authority = RefSeq
+   @hibernate.property column="'accession_number'" type=string" length="255" not-null="false"
+   */
+  
+  public String getAccessionNumber() {
+    return accessionNumber;
+  }
+  public void setAccessionNumber(String accessionNumber) {
+    this.accessionNumber = accessionNumber;
+  }
+  
+  private String authority;
+  public static final int MAX_AUTHORITY_LENGTH = 255;
+  /**
+   Authority: the origin or source for the controlled vocabulary 
+   allocated to this annotationtype. For example, CellType Ontology 
+   available from OBO.
+   @hibernate.property column="'authority'" type="string" length="255" not-null="false" 
+  */
+  
+  public String getAuthority() {
+    return authority;
+  }
+  public void setAuthority(String authority) {
+    this.authority = authority;
+  }
+  
+  private float authorityVersion;
+  /**
+   Authority version: this could be either the build number for ensembl 
+   annotation releases or the version of the authority used to annotate 
+   a document. for example MO version 1.2
+   @hibernate.property column="'authority_version'" type="float" not-null="false"
+   */
+  
+  public float getAuthorityVersion() {
+    return authorityVersion;
+  }
+  public void setAuthorityVersion(float authorityVersion) {
+    this.authorityVersion = authorityVersion;
+  }
+
+  // This may be changed to a CuratableData interface class like the RemovableData interface class
+  // can then be implemented by other classes.
+  private boolean curated;
+  /**
+    This flag specify if a newly added annotationtype 
+    has been curated and valid for public use or not
+    @hibernate.property column="'curated'" type="boolean" not-null="false" 
+   */
+  public boolean isCurated() {
+    return curated;
+  }
+  public void setCurated(boolean curated) {
+    this.curated = curated;
+  }
+
+  private ParameterValueData<?> unitValues;
+  /**
+  The allowed values if this annotationtype has a unit enumeration.
+  @hibernate.many-to-one column="`unitenumvalues_id`" not-null="false" cascade="all" unique="true"
+  */
+  public ParameterValueData<?> getUnitValues() {
+    return unitValues;
+  }
+  public void setUnitValues(ParameterValueData<?> unitValues) {
+    this.unitValues = unitValues;
+  }
+  
 }

branches/dominic_annotations/src/core/net/sf/basedb/core/data/ParameterValueData.java

@@ -85 +85 @@
     current.add((T) value);
   }
+  
 }

branches/dominic_annotations/src/core/net/sf/basedb/core/data/hibernate-properties-HybridizationData.xml

@@ -1 @@
-<!--
+<!-- 
   $Id$
-
+  New
   BioArray Software Environment (BASE) - http://base.thep.lu.se/
   Copyright (C) 2002-2004 Lao Saal, Carl Troein,