Changeset 2208


Ignore:
Timestamp:
May 2, 2006, 3:45:04 PM (16 years ago)
Author:
dominic
Message:
 
Location:
branches/dominic_annotations/src/core/net/sf/basedb/core/data
Files:
3 added
3 edited

Legend:

Unmodified
Added
Removed
  • branches/dominic_annotations/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

    r871 r2208  
    3939  @base.modified $Date$
    4040  @hibernate.class table="`AnnotationTypes`" lazy="false"
     41  @modified by Dominic Oyeniran
    4142*/
    4243public class AnnotationTypeData
     
    204205    this.enumerationValues = enumerationValues;
    205206  }
    206 
     207  /*
     208   * Newly added properties(fields) and mappings addedd by Dominic Oyeniran
     209   * for adherence to Nutri-Base Specifications and Requirements.
     210   *
     211   */
     212 
     213  private Set<AnnotationTypeCategoryData> category;
     214  /**
     215    Many to many from  AnnotationTypes to AnnotationTypeCategory.
     216    This is the inverse end
     217    @hibernate.set table="'CategorisedAnnotationTypes'" lazy="true"
     218    @hibernate.collection-key column="'annotationtype_id'"
     219    @hibernate.collection-many-to-many column="'category_id'"
     220      class="net.sf.basedb.core.data.AnnotationTypeCategoryData"
     221   */
     222 
     223  public Set<AnnotationTypeCategoryData> getCategory() {
     224    if ( category==null)
     225    {
     226      category= new HashSet<AnnotationTypeCategoryData>();
     227    }
     228    return category;
     229  }
     230  /*
     231   the set method() without scope resolution is private and this is done so that
     232   hibernate can keep track of the objects it creates in the collection
     233   and also can 'only' return this object thru the get method().
     234   */
     235  void setCategory(Set<AnnotationTypeCategoryData> category) {
     236    this.category = category;
     237  }
     238 
     239  private String accessionNumber;
     240  public static final int MAX_ACCESSION_NUMBER_LENGTH = 255;
     241  /**
     242   Accession Number: The identifier devised to track a record by an authority.
     243   For example NM_12343 is the accession number for the record XXXX in authority = RefSeq
     244   @hibernate.property column="'accession_number'" type=string" length="255" not-null="false"
     245   */
     246 
     247  public String getAccessionNumber() {
     248    return accessionNumber;
     249  }
     250  public void setAccessionNumber(String accessionNumber) {
     251    this.accessionNumber = accessionNumber;
     252  }
     253 
     254  private String authority;
     255  public static final int MAX_AUTHORITY_LENGTH = 255;
     256  /**
     257   Authority: the origin or source for the controlled vocabulary
     258   allocated to this annotationtype. For example, CellType Ontology
     259   available from OBO.
     260   @hibernate.property column="'authority'" type="string" length="255" not-null="false"
     261  */
     262 
     263  public String getAuthority() {
     264    return authority;
     265  }
     266  public void setAuthority(String authority) {
     267    this.authority = authority;
     268  }
     269 
     270  private float authorityVersion;
     271  /**
     272   Authority version: this could be either the build number for ensembl
     273   annotation releases or the version of the authority used to annotate
     274   a document. for example MO version 1.2
     275   @hibernate.property column="'authority_version'" type="float" not-null="false"
     276   */
     277 
     278  public float getAuthorityVersion() {
     279    return authorityVersion;
     280  }
     281  public void setAuthorityVersion(float authorityVersion) {
     282    this.authorityVersion = authorityVersion;
     283  }
     284
     285  // This may be changed to a CuratableData interface class like the RemovableData interface class
     286  // can then be implemented by other classes.
     287  private boolean curated;
     288  /**
     289    This flag specify if a newly added annotationtype
     290    has been curated and valid for public use or not
     291    @hibernate.property column="'curated'" type="boolean" not-null="false"
     292   */
     293  public boolean isCurated() {
     294    return curated;
     295  }
     296  public void setCurated(boolean curated) {
     297    this.curated = curated;
     298  }
     299
     300  private ParameterValueData<?> unitValues;
     301  /**
     302  The allowed values if this annotationtype has a unit enumeration.
     303  @hibernate.many-to-one column="`unitenumvalues_id`" not-null="false" cascade="all" unique="true"
     304  */
     305  public ParameterValueData<?> getUnitValues() {
     306    return unitValues;
     307  }
     308  public void setUnitValues(ParameterValueData<?> unitValues) {
     309    this.unitValues = unitValues;
     310  }
     311 
    207312}
  • branches/dominic_annotations/src/core/net/sf/basedb/core/data/ParameterValueData.java

    r1415 r2208  
    8585    current.add((T) value);
    8686  }
     87 
    8788}
  • branches/dominic_annotations/src/core/net/sf/basedb/core/data/hibernate-properties-HybridizationData.xml

    r2053 r2208  
    1 <!--
     1<!-- 
    22  $Id$
    3 
     3  New
    44  BioArray Software Environment (BASE) - http://base.thep.lu.se/
    55  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
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