Changeset 2962


Ignore:
Timestamp:
Nov 27, 2006, 3:02:39 PM (15 years ago)
Author:
Nicklas Nordborg
Message:

References #412: Fix build.xml to make it more developer-friendly

Fixed lots of incorrect links between the generated javadoc and other written documentation.

Location:
trunk
Files:
173 edited

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r2959 r2962  
    129129    name="dist"
    130130    depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,installprg.jar,
    131       jobagent.jar,migrate.jar,copy.config,copy.jar,doc.dist"
     131      jobagent.jar,migrate.jar,copy.config,copy.jar,doc,doc.dist"
    132132    description="Create everything needed for distribution"
    133133    >
     
    141141    <copy todir="${dist}/bin" description="Scripts, etc.">
    142142      <fileset dir="bin" />
     143    </copy>
     144    <copy todir="${dist}" description="License and creadits">
     145      <fileset file="base2.license.txt" />
     146      <fileset file="credits.txt" />
    143147    </copy>
    144148  </target>
     
    960964      <fileset dir="doc" includes="development/**/*" />
    961965      <fileset dir="doc" includes="licenses/**/*" />
     966      <fileset dir="doc" includes="specifications/**/*" />
    962967      <fileset dir="doc" includes="user/**/*" />
    963       <fileset dir="doc" includes="*.*" excludes="index.html" />
     968      <fileset dir="doc" includes="*.*" />
    964969    </copy>
    965970  </target>
  • trunk/doc/admin/base.config.html

    r2936 r2962  
    7979    <li><code>org.hibernate.dialect.PostgreSQLDialect</code> for Postgres</li>
    8080    </ul>
    81     Other dialects may wirk but are not supported.
     81    Other dialects may work but are not supported.
    8282  </dd>
    8383 
  • trunk/doc/admin/extended-properties.html

    r2959 r2962  
    190190      A more detailed information about the attributes is available in
    191191      the <a
    192       href="../api/develop/net/sf/basedb/core/data/ExtendableData.html">javadoc
     192      href="../api/net/sf/basedb/core/data/ExtendableData.html">javadoc
    193193      for the ExtendableData class</a>.
    194194    </p>
  • trunk/doc/admin/jobagent.html

    r2648 r2962  
    127127    as job agents. The setting <code>jobqueue.internal.enabled</code>
    128128    should be changed to <code>false</code> for the web server. This setting
    129     is found in the <code>www/WEB-INF/classes/base.config.file</code>. After
     129    is found in the <code>www/WEB-INF/classes/base.config</code> file. After
    130130    you have changed the setting the web server must be restarted.
    131131  </dd>
     
    192192  <dt>3. Edit the <code>jobagent.properties</code> file</dt>
    193193  <dd>
    194     The <code>bin/jobagent.properties</code> file contains settings for
     194    The <code>www/WEB-INF/classes/jobagent.properties</code> file contains settings for
    195195    the job agent. The most important ones to specify value for are:
    196196   
  • trunk/doc/development/coding/batch/index.html

    r2304 r2962  
    5555    <b>See also</b>
    5656    <ul>
    57     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     57    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5858    <li><a href="../../overview/core/index.html">An overview of the core API</a>
    5959    </ul>
  • trunk/doc/development/coding/data/index.html

    r2304 r2962  
    8282    <li><a href="AnyData.txt">AnyData.txt - a template class file for <code>CommonData</code> object</a>
    8383    <li><a href="ChildData.txt">ChildData.txt - a template class file for child items</a>
    84     <li><a href="../../../api/develop/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
     84    <li><a href="../../../api/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
    8585    <li><a href="../../overview/data/index.html">An overview of the database schema and data layer API</a>
    8686    </ul>
  • trunk/doc/development/coding/item/index.html

    r2898 r2962  
    8484    <li><a href="../../overview/core/datavalidation.html">Core API overview - Data validation</a>
    8585    <li><a href="../../overview/core/transactions.html">Core API overview - Transaction handling</a>
    86     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     86    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    8787    </ul>
    8888    </p>
  • trunk/doc/development/index.html

    r2959 r2962  
    4646    <ol>
    4747    <li><a href="#startingpoints">Where to start</a>
    48     <li><a href="api/index.html">API Javadoc</a>
     48    <li><a href="../api/index.html">API Javadoc</a>
    4949    <li><a href="#specifications">Specifications</a>
    5050    <li><a href="#overview">Implementation overview</a>
     
    7575
    7676  <p>
    77     <a href="api/index.html">API Javadoc is here.</a>
     77    <a href="../api/index.html">API Javadoc is here.</a>
    7878  </p>
    7979 
  • trunk/doc/development/overview/core/accesspermissions.html

    r2304 r2962  
    7979 
    8080  <p>
    81     The <code>Keyring</code> [<a href="../../../api/develop/net/sf/basedb/core/Keyring.html">API</a>]
     81    The <code>Keyring</code> [<a href="../../../api/net/sf/basedb/core/Keyring.html">API</a>]
    8282    class is the core class that is responsible
    8383    for handling most permission checks in BASE. A keyring object
     
    8888  <ul>
    8989  <li>Which roles the user is a member of and the permissions granted to those roles
    90     (RoleKey [<a href="../../../api/develop/net/sf/basedb/core/RoleKey.html">API</a>])
     90    (RoleKey [<a href="../../../api/net/sf/basedb/core/RoleKey.html">API</a>])
    9191  <li>Which groups the user is a member of, including following groups-within-groups,
    9292    and the permissions granted to those groups (ItemKey
    93      [<a href="../../../api/develop/net/sf/basedb/core/ItemKey.html">API</a>])
     93     [<a href="../../../api/net/sf/basedb/core/ItemKey.html">API</a>])
    9494  <li>The permissions granted to the user directly (ItemKey)
    9595  <li>If a project is active, the permissions within that project (ProjectKey
    96    [<a href="../../../api/develop/net/sf/basedb/core/ProjectKey.html">API</a>])
    97   <li>Which <code>Project</code>:s  [<a href="../../../api/develop/net/sf/basedb/core/Project.html">API</a>]
     96   [<a href="../../../api/net/sf/basedb/core/ProjectKey.html">API</a>])
     97  <li>Which <code>Project</code>:s  [<a href="../../../api/net/sf/basedb/core/Project.html">API</a>]
    9898    the user has access to
    9999  <li>Which other users are members of at least one of the groups the logged in
     
    122122
    123123  <p>
    124     The <code>Permission</code> [<a href="../../../api/develop/net/sf/basedb/core/Permission.html">API</a>]
     124    The <code>Permission</code> [<a href="../../../api/net/sf/basedb/core/Permission.html">API</a>]
    125125    enumeration defines the permissions available in BASE.
    126126    Each permission is represented by an integer value (<code>grantValue()</code>)
     
    151151 
    152152  <p>
    153     Each <code>BasicItem</code> [<a href="../../../api/develop/net/sf/basedb/core/BasicItem.html">API</a>]
     153    Each <code>BasicItem</code> [<a href="../../../api/net/sf/basedb/core/BasicItem.html">API</a>]
    154154    has an internal <code>permissions</code> variable
    155155    which holds the logged in users permission to manipulate the item. This value
     
    160160  </p>
    161161  <p>
    162     Since it is the <code>DbControl</code> [<a href="../../../api/develop/net/sf/basedb/core/DbControl.html">API</a>]
     162    Since it is the <code>DbControl</code> [<a href="../../../api/net/sf/basedb/core/DbControl.html">API</a>]
    163163    that is responsible for creating, loading, saving,
    164164    deleting, etc. items from the database, it is also the <code>DbControl</code> that is
     
    174174    in <code>BasicItem</code> will use the <code>SessionControl.getRolePermissions()</code>
    175175    to find the permissions the logged in user has been granted based on role
    176     membership. The <code>OwnedItem</code> [<a href="../../../api/develop/net/sf/basedb/core/OwnedItem.html">API</a>]
     176    membership. The <code>OwnedItem</code> [<a href="../../../api/net/sf/basedb/core/OwnedItem.html">API</a>]
    177177    class grants additional permissions
    178178    if the logged in user is the owner of an item, and the <code>SharedItem</code>
    179     [<a href="../../../api/develop/net/sf/basedb/core/SharedItem.html">API</a>]
     179    [<a href="../../../api/net/sf/basedb/core/SharedItem.html">API</a>]
    180180    class grants additional permission if the logged in user has an item or project
    181181    key with permissions for the item. The <code>ChildItem</code> implementation
     
    187187    Subclasses that need to grant or deny additional
    188188    permissions must override the <code>initPermissions()</code> method.
    189     For example the <code>News</code> [<a href="../../../api/develop/net/sf/basedb/core/News.html">API</a>]
     189    For example the <code>News</code> [<a href="../../../api/net/sf/basedb/core/News.html">API</a>]
    190190    class will grant read access to everyone
    191191    (even if no user is logged in) if the current date is between the start and end
    192     date of the news item. The <code>Role</code> [<a href="../../../api/develop/net/sf/basedb/core/Role.html">API</a>]
    193     and <code>Group</code> [<a href="../../../api/develop/net/sf/basedb/core/Group.html">API</a>]
     192    date of the news item. The <code>Role</code> [<a href="../../../api/net/sf/basedb/core/Role.html">API</a>]
     193    and <code>Group</code> [<a href="../../../api/net/sf/basedb/core/Group.html">API</a>]
    194194    classes are other exemples which grant read permission if the logged in user
    195195    is a member of the role or group.
     
    229229
    230230  <p>
    231     The various subclasses to the <code>Key</code> [<a href="../../../api/develop/net/sf/basedb/core/Key.html">API</a>]
     231    The various subclasses to the <code>Key</code> [<a href="../../../api/net/sf/basedb/core/Key.html">API</a>]
    232232    class are used to  store the actual permissions in the database. There are three subclasses:
    233233  </p>
    234234 
    235235  <ul>
    236   <li>RoleKey [<a href="../../../api/develop/net/sf/basedb/core/RoleKey.html">API</a>]: Used to grant permissions to roles.
    237   <li>ItemKey [<a href="../../../api/develop/net/sf/basedb/core/ItemKey.html">API</a>]: Used to grant permissions to users/groups.
    238   <li>ProjectKey [<a href="../../../api/develop/net/sf/basedb/core/ProjectKey.html">API</a>]: Used to grant permission to projects.
     236  <li>RoleKey [<a href="../../../api/net/sf/basedb/core/RoleKey.html">API</a>]: Used to grant permissions to roles.
     237  <li>ItemKey [<a href="../../../api/net/sf/basedb/core/ItemKey.html">API</a>]: Used to grant permissions to users/groups.
     238  <li>ProjectKey [<a href="../../../api/net/sf/basedb/core/ProjectKey.html">API</a>]: Used to grant permission to projects.
    239239  </ul>
    240240
     
    273273    existing item keys. The item key has no <code>set</code> methods to change
    274274    the permissions. Instead you have to use the helper classes,
    275     <code>UserPermissions</code> [<a href="../../../api/develop/net/sf/basedb/core/UserPermissions.html">API</a>]
    276     and <code>GroupPermissions</code> [<a href="../../../api/develop/net/sf/basedb/core/GroupPermissions.html">API</a>].
     275    <code>UserPermissions</code> [<a href="../../../api/net/sf/basedb/core/UserPermissions.html">API</a>]
     276    and <code>GroupPermissions</code> [<a href="../../../api/net/sf/basedb/core/GroupPermissions.html">API</a>].
    277277  </p>
    278278 
     
    282282    they share items to projects instead of to user and groups.
    283283    To set the permissions you use a <code>ProjectPermissions</code>
    284     [<a href="../../../api/develop/net/sf/basedb/core/ProjectPermissions.html">API</a>]
     284    [<a href="../../../api/net/sf/basedb/core/ProjectPermissions.html">API</a>]
    285285    object.
    286286  </p>
     
    309309  <p>
    310310    The <code>MultiPermissions</code>
    311     [<a href="../../../api/develop/net/sf/basedb/core/MultiPermissions.html">API</a>]
     311    [<a href="../../../api/net/sf/basedb/core/MultiPermissions.html">API</a>]
    312312    class is not shown in the diagram. It is a useful helper class to modify
    313313    lots of permissions to multiple items at the same time, while keeping those that
  • trunk/doc/development/overview/core/authentication.html

    r2304 r2962  
    6060    <ul>
    6161    <li><a href="../data/authentication.html">Data layer API and database schema</a>
    62     <li><a href="../../../api/develop/net/sf/basedb/core/Application.html">Application.java API</a>
    63     <li><a href="../../../api/develop/net/sf/basedb/core/SessionControl.html">SessionControl.java API</a>
    64     <li><a href="../../../api/develop/net/sf/basedb/core/authentication/Authenticator.html">Authenticator.java API</a>
     62    <li><a href="../../../api/net/sf/basedb/core/Application.html">Application.java API</a>
     63    <li><a href="../../../api/net/sf/basedb/core/SessionControl.html">SessionControl.java API</a>
     64    <li><a href="../../../api/net/sf/basedb/core/authentication/Authenticator.html">Authenticator.java API</a>
    6565    </ul>
    6666   
  • trunk/doc/development/overview/core/index.html

    r2304 r2962  
    6565    <li><a href="../../coding/batch/index.html">Coding rules and guidelines for batch classes</a>
    6666    <li><a href="../query/index.html">Overview of queries and the Query API</a>
    67     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     67    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    6868    </ul>
    6969   
  • trunk/doc/development/overview/data/annotations.html

    r2875 r2962  
    6262  <h3>AnnotationSets</h3>
    6363  <p>
    64     The <code>AnnotationSetData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationSetData.html">API</a>]
     64    The <code>AnnotationSetData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationSetData.html">API</a>]
    6565    class holds all annotations for a single item. An item must implement the
    66     <code>AnnotatableData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatableData.html">API</a>]
     66    <code>AnnotatableData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotatableData.html">API</a>]
    6767    interface which defines the <code>annotationSet</code> property for that item.
    6868  </p>
     
    8686  <h3>Annotations</h3>
    8787  <p>
    88     The <code>AnnotationData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationData.html">API</a>]
     88    The <code>AnnotationData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationData.html">API</a>]
    8989    class is the placeholder for an annotation. It must have a type and belong to an
    9090    annotation set. The actual annotation values are stored as <code>ParameterValueData</code>
     
    9494  <h3>AnnotationTypes</h3>
    9595  <p>
    96     The <code>AnnotationTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationTypeData.html">API</a>]
     96    The <code>AnnotationTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationTypeData.html">API</a>]
    9797    class defines the various annotations. It must have a <code>valueType</code> property which cannot
    9898    be changed. The value of this property controls which <code>ParameterValueData</code> subclass
     
    134134  <h3>AnnotationTypeCategories</h3>
    135135  <p>
    136     The <code>AnnotationTypeCategory</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationTypeCategoryData.html">API</a>]
     136    The <code>AnnotationTypeCategory</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationTypeCategoryData.html">API</a>]
    137137    class defined categories that are used to group annotation types that are
    138138    related to each other. This information is mainly useful for client applications
  • trunk/doc/development/overview/data/authentication.html

    r2722 r2962  
    6565  <h3>Users and passwords</h3>
    6666  <p>
    67   The <code>UserData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/UserData.html">API</a>]
     67  The <code>UserData</code> [<a href="../../../api/net/sf/basedb/core/data/UserData.html">API</a>]
    6868  class holds information about users. We keep the passwords in
    6969  a separate table and use proxies to avoid loading password data each time a user is loaded
    7070  to minimize security risks. It is only if the password needs to be changed that the
    71   <code>PasswordData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PasswordData.html">API</a>]
     71  <code>PasswordData</code> [<a href="../../../api/net/sf/basedb/core/data/PasswordData.html">API</a>]
    7272  object is loaded. The one-to-one mapping between user and
    7373  password is controlled by the password class, but a cascade attribute on the user class
     
    7777  <h3>Groups, roles and projects</h3>
    7878  <p>
    79   The <code>GroupData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/GroupData.html">API</a>],
    80   <code>RoleData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/RoleData.html">API</a>] and
    81   <code>ProjectData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ProjectData.html">API</a>]
     79  The <code>GroupData</code> [<a href="../../../api/net/sf/basedb/core/data/GroupData.html">API</a>],
     80  <code>RoleData</code> [<a href="../../../api/net/sf/basedb/core/data/RoleData.html">API</a>] and
     81  <code>ProjectData</code> [<a href="../../../api/net/sf/basedb/core/data/ProjectData.html">API</a>]
    8282  classes holds information about groups, roles and projects respectively. The connection
    8383  to users are controlled by each of the classes.
     
    8787  <p>
    8888  The <code>PluginDefinitionData</code>
    89   [<a href="../../../api/develop/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>] class
     89  [<a href="../../../api/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>] class
    9090  holds information about plugins. If the plugin is defind to use perminssions, the default
    9191  is to deny everything. The mapping to role key is used to grant/deny permissions to the plugin.
     
    9595  <h3>Keys</h3>
    9696  <p>
    97   The <code>KeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/KeyData.html">API</a>]
     97  The <code>KeyData</code> [<a href="../../../api/net/sf/basedb/core/data/KeyData.html">API</a>]
    9898  class and it's subclasses <code>ItemKeyData</code>
    99   [<a href="../../../api/develop/net/sf/basedb/core/data/ItemKeyData.html">API</a>],
    100   <code>ProjectKeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ProjectKeyData.html">API</a>]
    101   and <code>RoleKeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/RoleKeyData.html">API</a>],
     99  [<a href="../../../api/net/sf/basedb/core/data/ItemKeyData.html">API</a>],
     100  <code>ProjectKeyData</code> [<a href="../../../api/net/sf/basedb/core/data/ProjectKeyData.html">API</a>]
     101  and <code>RoleKeyData</code> [<a href="../../../api/net/sf/basedb/core/data/RoleKeyData.html">API</a>],
    102102  are used to store information
    103103  about access permissions to items. To get permission to manipulate an item
  • trunk/doc/development/overview/data/basic.html

    r2304 r2962  
    8585
    8686<dl>
    87 <dt>BasicData [<a href="../../../api/develop/net/sf/basedb/core/data/BasicData.html">API</a>]<dt>
     87<dt>BasicData [<a href="../../../api/net/sf/basedb/core/data/BasicData.html">API</a>]<dt>
    8888  <dd>
    8989  The root class. It overrides the <code>equals()</code>, <code>hashCode()</code>
     
    9292  </dd>
    9393
    94 <dt>OwnedData [<a href="../../../api/develop/net/sf/basedb/core/data/OwnedData.html">API</a>]</dt>
     94<dt>OwnedData [<a href="../../../api/net/sf/basedb/core/data/OwnedData.html">API</a>]</dt>
    9595  <dd>
    9696  This class extends the <code>BasicData</code> class and adds an <code>owner</code>
     
    9898  </dd>
    9999
    100 <dt>SharedData [<a href="../../../api/develop/net/sf/basedb/core/data/SharedData.html">API</a>]</dt>
     100<dt>SharedData [<a href="../../../api/net/sf/basedb/core/data/SharedData.html">API</a>]</dt>
    101101  <dd>
    102102  This class extends the <code>OwnerData</code> class and adds methods for
     
    106106  </dd>
    107107
    108 <dt>CommonData [<a href="../../../api/develop/net/sf/basedb/core/data/CommonData.html">API</a>]</dt>
     108<dt>CommonData [<a href="../../../api/net/sf/basedb/core/data/CommonData.html">API</a>]</dt>
    109109  <dd>
    110110  This is a convenience class for items that extends the <code>SharedData</code>
     
    114114  </dd>
    115115
    116 <dt>AnnotatedData [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatedData.html">API</a>]</dt>
     116<dt>AnnotatedData [<a href="../../../api/net/sf/basedb/core/data/AnnotatedData.html">API</a>]</dt>
    117117  <dd>
    118118  This is a convenience class for items that can be annotated. Annotations are held
     
    127127
    128128<dl>
    129   <dt>IdentifiableData [<a href="../../../api/develop/net/sf/basedb/core/data/IdentifiableData.html">API</a>]</dt>
     129  <dt>IdentifiableData [<a href="../../../api/net/sf/basedb/core/data/IdentifiableData.html">API</a>]</dt>
    130130  <dd>
    131131    All items are identifiable, which means that they have a unique <code>id</code>. The
     
    136136  </dd>
    137137 
    138   <dt>OwnableData [<a href="../../../api/develop/net/sf/basedb/core/data/OwnableData.html">API</a>]</dt>
     138  <dt>OwnableData [<a href="../../../api/net/sf/basedb/core/data/OwnableData.html">API</a>]</dt>
    139139  <dd>
    140140    An ownable item is an item which has an <code>owner</code>. The owner is
     
    142142  </dd>
    143143 
    144   <dt>ShareableData [<a href="../../../api/develop/net/sf/basedb/core/data/ShareableData.html">API</a>]</dt>
     144  <dt>ShareableData [<a href="../../../api/net/sf/basedb/core/data/ShareableData.html">API</a>]</dt>
    145145  <dd>
    146146    A shareable item is an item which can be shared to other users, groups or projects.
     
    149149  </dd>
    150150 
    151   <dt>NameableData [<a href="../../../api/develop/net/sf/basedb/core/data/NameableData.html">API</a>]</dt>
     151  <dt>NameableData [<a href="../../../api/net/sf/basedb/core/data/NameableData.html">API</a>]</dt>
    152152  <dd>
    153153    A nameable item is an item that has a <code>name</code> and, optionally, a <code>description</code>.
    154154  </dd>
    155155 
    156   <dt>RemovableData [<a href="../../../api/develop/net/sf/basedb/core/data/RemovableData.html">API</a>]</dt>
     156  <dt>RemovableData [<a href="../../../api/net/sf/basedb/core/data/RemovableData.html">API</a>]</dt>
    157157  <dd>
    158158    A removable item is an item that can be flagged as removed. This doesn't remove the
     
    162162  </dd>
    163163 
    164   <dt>SystemData [<a href="../../../api/develop/net/sf/basedb/core/data/SystemData.html">API</a>]</dt>
     164  <dt>SystemData [<a href="../../../api/net/sf/basedb/core/data/SystemData.html">API</a>]</dt>
    165165  <dd>
    166166    A system item is an item which has an additional id in the form of string. A system id
     
    172172  </dd>
    173173
    174   <dt>FileAttachableData [<a href="../../../api/develop/net/sf/basedb/core/data/FileAttachableData.html">API</a>]</dt>
     174  <dt>FileAttachableData [<a href="../../../api/net/sf/basedb/core/data/FileAttachableData.html">API</a>]</dt>
    175175  <dd>
    176176    This interface is used by items that can have an optional file attached to them, for
     
    178178  </dd>
    179179
    180   <dt>DiskConsumableData [<a href="../../../api/develop/net/sf/basedb/core/data/DiskConsumableData.html">API</a>]</dt>
     180  <dt>DiskConsumableData [<a href="../../../api/net/sf/basedb/core/data/DiskConsumableData.html">API</a>]</dt>
    181181  <dd>
    182182    This interface is used by items which occupies a lot of disk space and must
     
    185185  </dd>
    186186
    187   <dt>AnnotatableData [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatableData.html">API</a>]</dt>
     187  <dt>AnnotatableData [<a href="../../../api/net/sf/basedb/core/data/AnnotatableData.html">API</a>]</dt>
    188188  <dd>
    189189    This interface is used by items which can be annotated. Annotations are
     
    192192  </dd>
    193193
    194   <dt>ExtendableData [<a href="../../../api/develop/net/sf/basedb/core/data/ExtendableData.html">API</a>]</dt>
     194  <dt>ExtendableData [<a href="../../../api/net/sf/basedb/core/data/ExtendableData.html">API</a>]</dt>
    195195  <dd>
    196196    This interface is used by items which can have extra administrator-defined columns.
     
    199199  </dd>
    200200 
    201   <dt>BatchableData [<a href="../../../api/develop/net/sf/basedb/core/data/BatchableData.html">API</a>]</dt>
     201  <dt>BatchableData [<a href="../../../api/net/sf/basedb/core/data/BatchableData.html">API</a>]</dt>
    202202  <dd>
    203203    This interface is a tagging interface which is used by items that needs batch
  • trunk/doc/development/overview/data/biomaterial.html

    r2304 r2962  
    6363  <p>
    6464    There are four types of biomaterials.
    65     <code>BioSourceData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/BioSourceData.html">API</a>],
    66     <code>SampleData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/SampleData.html">API</a>],
    67     <code>ExtractData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ExtractData.html">API</a>]
     65    <code>BioSourceData</code> [<a href="../../../api/net/sf/basedb/core/data/BioSourceData.html">API</a>],
     66    <code>SampleData</code> [<a href="../../../api/net/sf/basedb/core/data/SampleData.html">API</a>],
     67    <code>ExtractData</code> [<a href="../../../api/net/sf/basedb/core/data/ExtractData.html">API</a>]
    6868    and
    69     <code>LabeledExtractData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/LabeledExtractData.html">API</a>],
     69    <code>LabeledExtractData</code> [<a href="../../../api/net/sf/basedb/core/data/LabeledExtractData.html">API</a>],
    7070  </p>
    7171 
    7272  <p>
    7373    All four types of biomaterials are derived from the base class <code>BioMaterialData</code>
    74     [<a href="../../../api/develop/net/sf/basedb/core/data/BioMaterialData.html">API</a>].
     74    [<a href="../../../api/net/sf/basedb/core/data/BioMaterialData.html">API</a>].
    7575    The reason for this is that they all share common functionality such as
    7676    pooling and events. By using a common base class we do not have to create
     
    8585  <p>
    8686    The <code>MeasuredBioMaterialData</code>
    87     [<a href="../../../api/develop/net/sf/basedb/core/data/MeasuredBioMaterialData.html">API</a>]
     87    [<a href="../../../api/net/sf/basedb/core/data/MeasuredBioMaterialData.html">API</a>]
    8888    class is used as a base class for the other three biomaterial types. It introduces
    8989    quantity measurements and can store original and remaining quantities. They are both optional.
     
    132132    An event represents something that happened to one or more biomaterials,
    133133    for example the creation of another biomaterial. The <code>BioMaterialEventData</code>
    134     [<a href="../../../api/develop/net/sf/basedb/core/data/BioMaterialEventData.html">API</a>]
     134    [<a href="../../../api/net/sf/basedb/core/data/BioMaterialEventData.html">API</a>]
    135135    holds information about entry and event dates, protocols used, the user who is responsible,
    136136    etc.
  • trunk/doc/development/overview/data/experiments.html

    r2709 r2962  
    6666  <p>
    6767    The <code>ExperimentData</code>
    68     [<a href="../../../api/develop/net/sf/basedb/core/data/ExperimentData.html">API</a>]
     68    [<a href="../../../api/net/sf/basedb/core/data/ExperimentData.html">API</a>]
    6969    class is used to collect information about a single experiment. It links
    7070    to any number of <code>RawBioAssayData</code>
    71     [<a href="../../../api/develop/net/sf/basedb/core/data/RawBioAssayData.html">API</a>]
     71    [<a href="../../../api/net/sf/basedb/core/data/RawBioAssayData.html">API</a>]
    7272    items, which must all be of the same <code>RawDataType</code>
    73     [<a href="../../../api/develop/net/sf/basedb/core/RawDataType.html">API</a>].
     73    [<a href="../../../api/net/sf/basedb/core/RawDataType.html">API</a>].
    7474  </p>
    7575  <p>
     
    8686  <p>
    8787    Each line of analysis starts with the creation of a root <code>BioAssaySetData</code>
    88     [<a href="../../../api/develop/net/sf/basedb/core/data/BioAssaySetData.html">API</a>],
     88    [<a href="../../../api/net/sf/basedb/core/data/BioAssaySetData.html">API</a>],
    8989    which holds the intensities calculated from the raw data. A bioassayset can hold
    9090    one intensity for each channel. The number of channels is defined by the raw data type.
    9191    For each raw bioassay used a <code>BioAssayData</code>
    92     [<a href="../../../api/develop/net/sf/basedb/core/data/BioAssayData.html">API</a>]
     92    [<a href="../../../api/net/sf/basedb/core/data/BioAssayData.html">API</a>]
    9393    is created.
    9494  </p>
     
    9696    Information about the process that calculated the intensities are stored in
    9797    a <code>TransformationData</code>
    98     [<a href="../../../api/develop/net/sf/basedb/core/data/TransformationData.html">API</a>]
     98    [<a href="../../../api/net/sf/basedb/core/data/TransformationData.html">API</a>]
    9999    object. The root transformation links with the raw bioassays that are used in this
    100100    line of analysis and to a <code>Job</code>
    101     [<a href="../../../api/develop/net/sf/basedb/core/data/JobData.html">API</a>]
     101    [<a href="../../../api/net/sf/basedb/core/data/JobData.html">API</a>]
    102102    which holds the plugin and parameters used in the calculation. A typical plugin
    103103    may calculate the intensities by subtracting the mean background from the
     
    120120    The above processes requires a flexible storage solution for the data.
    121121    The <code>VirtualDbData</code>
    122     [<a href="../../../api/develop/net/sf/basedb/core/data/DynamicTablesData.html">API</a>]
     122    [<a href="../../../api/net/sf/basedb/core/data/DynamicTablesData.html">API</a>]
    123123    object represents a set of tables
    124124    that are created in the dynamic part of the database. In MySQL the dynamic
     
    129129  <p>
    130130    The <code>DataCubeData</code>
    131     [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeData.html">API</a>]
     131    [<a href="../../../api/net/sf/basedb/core/data/DataCubeData.html">API</a>]
    132132    is the main item used in the analysis. A coordinate in the cube is given by
    133133    a layer, a column and a position, represented by <code>DataCubeLayerData</code>
    134     [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeLayerData.html">API</a>]
     134    [<a href="../../../api/net/sf/basedb/core/data/DataCubeLayerData.html">API</a>]
    135135    and <code>DataCubeColumnData</code>
    136     [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeColumnData.html">API</a>]
     136    [<a href="../../../api/net/sf/basedb/core/data/DataCubeColumnData.html">API</a>]
    137137    object. The position has no separate object. At each coordinate we can store the
    138138    intensities and extra values related to the intensities.
     
    145145    doesn't modify the data can reuse the same layer if the new bioassayset is linked
    146146    to a <code>DataCubeFilterData</code>
    147     [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeFilterData.html">API</a>]
     147    [<a href="../../../api/net/sf/basedb/core/data/DataCubeFilterData.html">API</a>]
    148148    item. The filter tells which coordinates should remain in the bioassayset.
    149149  </p>
     
    166166    In this case we must create a new cube and add mapping information to
    167167    a <code>DataCubeMappingData</code>
    168     [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeMappingData.html">API</a>]
     168    [<a href="../../../api/net/sf/basedb/core/data/DataCubeMappingData.html">API</a>]
    169169    The mapping is a many-to-many mapping between coordinates in the source and destination
    170170    cubes. This allows us to track the source coordinates that were used to calculate
  • trunk/doc/development/overview/data/index.html

    r2304 r2962  
    5252    </p>
    5353    <ul>
    54     <li><a href="../../../api/develop/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
     54    <li><a href="../../../api/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
    5555    <li><a href="../../coding/data/index.html">Coding rules and guidelines for the data layer</a>
    5656    </ul>
  • trunk/doc/development/overview/data/misc.html

    r2382 r2962  
    5555  <h3>News</h3>
    5656  <p>
    57     The <code>NewsData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/NewsData.html">API</a>]
     57    The <code>NewsData</code> [<a href="../../../api/net/sf/basedb/core/data/NewsData.html">API</a>]
    5858    class holds information about news. It has three dates:
    5959    <code>startDate</code>, <code>newsDate</code> and <code>endDate</code>. The
     
    6666  <h3>Filters</h3>
    6767  Filters have been replace by <code>ItemContext</code>:s
    68   [<a href="../../../api/develop/net/sf/basedb/core/ItemContext.html">API</a>].
     68  [<a href="../../../api/net/sf/basedb/core/ItemContext.html">API</a>].
    6969  <p>
    7070  TODO - write documentation and add to UML image
     
    7575    Messages are mainly used for the system to notify a user when something, ie. a job
    7676    has been completed. A <code>MessageData</code>
    77     [<a href="../../../api/develop/net/sf/basedb/core/data/MessageData.html">API</a>]
     77    [<a href="../../../api/net/sf/basedb/core/data/MessageData.html">API</a>]
    7878    holds information about the message. Information about the sender is kept in
    7979    the <code>from</code> and <code>fromId</code> properties. We didn't want to create
     
    9292  <p>
    9393    The <code>AnyToAnyData</code>
    94     [<a href="../../../api/develop/net/sf/basedb/core/data/AnyToAnyData.html">API</a>]
     94    [<a href="../../../api/net/sf/basedb/core/data/AnyToAnyData.html">API</a>]
    9595    class allows us to create links between any two items. A link has a direction and name.
    9696    It starts at the <b>from</b> item leading to the <b>to</b> item. The link has a name
  • trunk/doc/development/overview/data/parameters.html

    r2304 r2962  
    6464  <h3>ParameterValueData</h3>
    6565  <p>
    66   The <code>ParameterValueData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ParameterValueData.html">API</a>]
     66  The <code>ParameterValueData</code> [<a href="../../../api/net/sf/basedb/core/data/ParameterValueData.html">API</a>]
    6767  class is an abstract base class that can hold multiple values. It should be used when declaring the generic for
    6868  collection classes. That way a collection can hold mixed type of parameter value classes. The values will be saved as
     
    107107  <p>
    108108  Every type that can be saved have its own subclass. Except for the item classes that all share the same subclass, a subclass
    109   that can hold <code>BasicItem</code>s [<a href="../../../api/develop/net/sf/basedb/core/BasicItem.html">API</a>] derives.
     109  that can hold <code>BasicItem</code>s [<a href="../../../api/net/sf/basedb/core/BasicItem.html">API</a>] derives.
    110110  </p>
    111111</body>
  • trunk/doc/development/overview/data/plates.html

    r2304 r2962  
    6262  <h3>Plates</h3>
    6363  <p>
    64     <code>PlateData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PlateData.html">API</a>]
     64    <code>PlateData</code> [<a href="../../../api/net/sf/basedb/core/data/PlateData.html">API</a>]
    6565    is the main class holding information about a single plate.
    6666    However it all starts with the <code>PlateGeometryData</code>
    67     [<a href="../../../api/develop/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
     67    [<a href="../../../api/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
    6868    which defines how many rows and columns there are on a plate. Since this information is used
    6969    to create wells, and various other checks it is not possible to change the number of
     
    7373  <p>
    7474    All plates must have a <code>PlateTypeData</code>
    75     [<a href="../../../api/develop/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
     75    [<a href="../../../api/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
    7676    which defines the geometry and a set of event types (see below).
    7777  </p>
     
    8989  <p>
    9090    A plate can be created either from scratch or by a <code>PlateMappingData</code>
    91     [<a href="../../../api/develop/net/sf/basedb/core/data/PlateMappingData.html">API</a>].
     91    [<a href="../../../api/net/sf/basedb/core/data/PlateMappingData.html">API</a>].
    9292    In the first case it is possible to specify a reporter for each well on the plate.
    9393    In the second case the mapping code creates all the wells and links them to
     
    101101  <p>
    102102    The plate type defines a set of <code>PlateEventTypeData</code>
    103     [<a href="../../../api/develop/net/sf/basedb/core/data/PlateEventTypeData.html">API</a>]
     103    [<a href="../../../api/net/sf/basedb/core/data/PlateEventTypeData.html">API</a>]
    104104    objects. For a plate of a certain type, it is possible to attach
    105105    exactly one event of each event type. The event type defines an optional protocol type,
  • trunk/doc/development/overview/data/plugins.html

    r2709 r2962  
    6161  <h3>PluginDefinitionData</h3>
    6262  <p>
    63     The <code>PluginDefinitionData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>]
     63    The <code>PluginDefinitionData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>]
    6464    holds information of the installed plugin classes. This information is saved when the plugin is installed, it's then used by the
    6565    system to load and run the plugin.
     
    6868  <h3>PluginConfigurationData</h3>
    6969  <p>
    70     <code>PluginConfigurationData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginConfigurationData.html">API</a>]
     70    <code>PluginConfigurationData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginConfigurationData.html">API</a>]
    7171    is used for storing configuration values related to a plugin. A plugin may have many
    7272    different configurations. The flags <code>supportsConfigurations</code> and
     
    8787  <h3>PluginTypeData</h3>
    8888  <p>
    89     The <code>PluginTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginTypeData.html">API</a>]
     89    The <code>PluginTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginTypeData.html">API</a>]
    9090    is used to register information about the additional interfaces a plugin implements. This
    9191    may allow a plugins to be used only in certain contexts. For example, we define
     
    9898  <h3>JobData</h3>
    9999  <p>
    100     The <code>JobData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/JobData.html">API</a>]
     100    The <code>JobData</code> [<a href="../../../api/net/sf/basedb/core/data/JobData.html">API</a>]
    101101    class holds information about one execution of a plugin. The job can be in different states:
    102102    <ul>
     
    112112  <h3>JobAgentData and JobAgentSettingsData</h3>
    113113  <p>
    114     A <code>JobAgentData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/JobAgentData.html">API</a>]
     114    A <code>JobAgentData</code> [<a href="../../../api/net/sf/basedb/core/data/JobAgentData.html">API</a>]
    115115    holds information about a job agent. A job agent is a program running on the same
    116116    or a different server that is regularly checking for jobs that are waiting
    117117    to be executed. The <code>JobAgentSettingsData</code>
    118     [<a href="../../../api/develop/net/sf/basedb/core/data/JobAgentSettingsData.html">API</a>]
     118    [<a href="../../../api/net/sf/basedb/core/data/JobAgentSettingsData.html">API</a>]
    119119    class links to the plugins the job agent is able to execute. The job agent will
    120120    only execute jobs that are owner by users or projects that the job agent has been
  • trunk/doc/development/overview/data/reporters.html

    r2712 r2962  
    6262  <h3>Reporters</h3>
    6363  <p>
    64   The <code>ReporterData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ReporterData.html">API</a>]
     64  The <code>ReporterData</code> [<a href="../../../api/net/sf/basedb/core/data/ReporterData.html">API</a>]
    6565  class holds information about reporters. The <code>externalId</code>
    6666  is a unique name for the reporter. In the default setup this
    6767  table contains nothing more than the external ID, gene name and symbol.
    6868  This class doesn't have an item class in the core, instead
    69   it has an utility class <code>Reporter</code> [<a href="../../../api/develop/net/sf/basedb/core/Reporter.html">API</a>]
    70   and is saved with <code>ReporterBatcher</code> [<a href="../../../api/develop/net/sf/basedb/core/ReporterBatcher.html">API</a>].
     69  it has an utility class <code>Reporter</code> [<a href="../../../api/net/sf/basedb/core/Reporter.html">API</a>]
     70  and is saved with <code>ReporterBatcher</code> [<a href="../../../api/net/sf/basedb/core/ReporterBatcher.html">API</a>].
    7171  </p>
    7272  <p>
     
    7575  into this table. The name and type of the columns must also be
    7676  described in an XML configuration file. The format of this file
    77   is described by the <code>ExtendableData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ExtendableData.html">API</a>].
     77  is described by the <code>ExtendableData</code> [<a href="../../../api/net/sf/basedb/core/data/ExtendableData.html">API</a>].
    7878  Here is an example:
    7979  </p>
     
    9797  <h3>ReporterTypes</h3>
    9898  <p>
    99   The <code>ReporterTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ReporterTypeData.html">API</a>]
     99  The <code>ReporterTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/ReporterTypeData.html">API</a>]
    100100  class holds reporter type information. A reporter may have, but is
    101101  not required to have a type. The main reason for a reporter to have a
  • trunk/doc/development/overview/dynamic/create.html

    r2304 r2962  
    5555    <ul>
    5656    <li><a href="../data/experiments.html">Data layer API and database schema</a>
    57     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     57    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5858    </ul>
    5959   
  • trunk/doc/development/overview/dynamic/datacube.html

    r2304 r2962  
    5454    </p>
    5555    <ul>
    56     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     56    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5757    </ul>
    5858   
  • trunk/doc/development/overview/dynamic/extravalues.html

    r2304 r2962  
    5454    <ul>
    5555    <li><a href="datacube.html">Understanding the data cube</a>
    56     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     56    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5757    </ul>
    5858   
  • trunk/doc/development/overview/dynamic/filter.html

    r2498 r2962  
    5454    <ul>
    5555    <li><a href="datacube.html">Understanding the data cube</a>
    56     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     56    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5757    </ul>
    5858   
  • trunk/doc/development/overview/dynamic/index.html

    r2304 r2962  
    6565    <ul>
    6666    <li><a href="../data/experiments.html">Data layer API and database schema</a>
    67     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     67    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    6868    </ul>
    6969   
  • trunk/doc/development/overview/dynamic/insert.html

    r2304 r2962  
    5555    <ul>
    5656    <li><a href="query.html">Querying the dynamic tables</a>
    57     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     57    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5858    </ul>
    5959   
  • trunk/doc/development/overview/dynamic/intensities.html

    r2304 r2962  
    5454    <ul>
    5555    <li><a href="datacube.html">Understanding the data cube</a>
    56     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     56    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5757    </ul>
    5858   
  • trunk/doc/development/overview/dynamic/merge.html

    r2304 r2962  
    5454    <ul>
    5555    <li><a href="datacube.html">Understanding the data cube</a>
    56     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     56    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5757    </ul>
    5858   
  • trunk/doc/development/overview/dynamic/query.html

    r2304 r2962  
    6060    <ul>
    6161    <li><a href="../query/index.html">Query API overview</a>
    62     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     62    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    6363    </ul>
    6464   
  • trunk/doc/development/overview/dynamic/rootbioassayset.html

    r2498 r2962  
    6060    <ul>
    6161    <li><a href="datacube.html">Understanding the data cube</a>
    62     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     62    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    6363    </ul>
    6464   
  • trunk/doc/development/overview/exceptions/index.html

    r2304 r2962  
    4949    </p>
    5050    <ul>
    51     <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     51    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
    5252    </ul>
    5353   
  • trunk/doc/development/overview/query/elements.html

    r2304 r2962  
    5555    <ul>
    5656    <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
    57     <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     57    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
    5858    </ul>
    5959   
  • trunk/doc/development/overview/query/index.html

    r2304 r2962  
    6363    <ul>
    6464    <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
    65     <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     65    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
    6666    </ul>
    6767   
  • trunk/doc/development/overview/query/overview.html

    r2304 r2962  
    6363    <li><a href="../core/batchprocessing.html">Batch processing</code>
    6464    <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
    65     <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     65    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
    6666    </ul>
    6767   
  • trunk/doc/development/overview/query/result.html

    r2304 r2962  
    5555    <ul>
    5656    <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
    57     <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     57    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
    5858    </ul>
    5959   
  • trunk/doc/development/overview/utility/index.html

    r2304 r2962  
    4949    </p>
    5050    <ul>
    51     <li><a href="../../../api/develop/net/sf/basedb/util/package-summary.html">Javadoc for the net.sf.basedb.util package</a>
     51    <li><a href="../../../api/net/sf/basedb/util/package-summary.html">Javadoc for the net.sf.basedb.util package</a>
    5252    </ul>
    5353   
  • trunk/doc/development/overview/web/index.html

    r2304 r2962  
    4949    </p>
    5050    <ul>
    51     <li><a href="../../../api/develop/net/sf/basedb/clients/web/package-summary.html">Javadoc for the net.sf.basedb.clients.web package</a>
     51    <li><a href="../../../api/net/sf/basedb/clients/web/package-summary.html">Javadoc for the net.sf.basedb.clients.web package</a>
    5252    </ul>
    5353   
  • trunk/doc/index.html

    r2623 r2962  
    2727<html>
    2828  <head>
    29     <title>BASE 2.0 - Development site</title>
     29    <title>BASE 2 - Documentation</title>
    3030  <link rel=stylesheet type="text/css" href="styles.css">
    31   <meta http-equiv="refresh" content="0;url=http://base.thep.lu.se">
    32   </head>
     31 </head>
    3332<body>
    3433
    35 <a href="http://base.thep.lu.se">The BASE project site</a>
     34<div class="navigation">
     35  BASE 2 - Documentation
     36</div>
     37
     38  <h1>BASE 2 - Documentation</h1>
     39
     40  <div class="abstract">
     41   
     42    <b>Contents</b><br>
     43    <ul>
     44    <li><a href="installation.html">Installation instructions</a></li>
     45    <li><a href="admin/index.html">Administrator documentation</a></li>
     46    <li><a href="development/index.html">Developers documentation</a></li>
     47    <li><a href="user/index.html">User documentation</a></li>
     48    </ul>
     49  </div>
    3650
    3751</body>
  • trunk/doc/specifications/core/defaultdata.html

    r2304 r2962  
    111111    <ul>
    112112    <li>One role key for each item type. For permissions
    113     see the <a href="../../api/develop/net/sf/basedb/core/doc-files/item_permissions.html">
     113    see the <a href="../../api/net/sf/basedb/core/doc-files/item_permissions.html">
    114114    Item permissions</a> document
    115115    </ul>
  • trunk/src/core/net/sf/basedb/core/BasicItem.java

    r2898 r2962  
    384384    @throws BaseException If there is an error
    385385    @see Validatable
    386     @see <a href="../../../../../../development/overview/core/datavalidation.html">Core API overview - Data validation</a>
    387     @see <a href="../../../../../../development/coding/item/index.html#validation">Coding rules and guidelines for item classes</a>
     386    @see <a href="../../../../../development/overview/core/datavalidation.html">Core API overview - Data validation</a>
     387    @see <a href="../../../../../development/coding/item/index.html#validation">Coding rules and guidelines for item classes</a>
    388388  */
    389389  void validate()
     
    400400    @throws BaseException If there is an error
    401401    @see Transactional
    402     @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    403     @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     402    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
     403    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
    404404  */
    405405  void onBeforeCommit(Transactional.Action action)
     
    432432    @throws BaseException If there is an error
    433433    @see Transactional
    434     @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    435     @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     434    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
     435    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
    436436  */
    437437  void onAfterInsert()
     
    449449
    450450    @see Transactional
    451     @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    452     @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     451    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
     452    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
    453453  */
    454454  void onAfterCommit(Transactional.Action action)
     
    465465
    466466    @see Transactional
    467     @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    468     @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     467    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
     468    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
    469469  */
    470470  void onRollback(Transactional.Action action)
  • trunk/src/core/net/sf/basedb/core/Batcher.java

    r2304 r2962  
    3030  @author Nicklas
    3131  @version 2.0
    32   @see <a href="../../../../../../development/overview/core/batchprocessing.html">Batch processing overview</a>
     32  @see <a href="../../../../../development/overview/core/batchprocessing.html">Batch processing overview</a>
    3333  @base.modified $Date$
    3434*/
  • trunk/src/core/net/sf/basedb/core/ContextKey.java

    r2610 r2962  
    2828  @author Nicklas
    2929  @version 2.0
    30   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     30  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3131  @base.modified $Date$
    3232*/
  • trunk/src/core/net/sf/basedb/core/DataCube.java

    r2610 r2962  
    6868  @version 2.0
    6969  @base.modified $Date$
    70   @see <a href="../../../../../../development/overview/dynamic/index.html">Dynamic API overview</a>
     70  @see <a href="../../../../../development/overview/dynamic/index.html">Dynamic API overview</a>
    7171*/
    7272public class DataCube
  • trunk/src/core/net/sf/basedb/core/MappingBatcher.java

    r2669 r2962  
    4040  implemented).
    4141  <p>
    42   Code example: {@link <a href="../../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
     42  Code example: {@link <a href="../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
    4343
    4444  @author Nicklas
  • trunk/src/core/net/sf/basedb/core/PositionBatcher.java

    r2669 r2962  
    4040  Normally this means linking a position to a reporter.
    4141  <p>
    42   Code example: {@link <a href="../../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
     42  Code example: {@link <a href="../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
    4343
    4444  @author Nicklas
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilter.java

    r2304 r2962  
    4545  @author Nicklas
    4646  @version 2.0
    47   @see <a href="../../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
     47  @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
    4848  @base.modified $Date$
    4949*/
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterFactory.java

    r2722 r2962  
    4444  @author Nicklas
    4545  @version 2.0
    46   @see <a href="../../../../../../development/overview/query/overview.html#factory">Query API overview - filter factory</a>
     46  @see <a href="../../../../../development/overview/query/overview.html#factory">Query API overview - filter factory</a>
    4747  @base.modified $Date$
    4848*/
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterManager.java

    r2304 r2962  
    3434  @author Nicklas
    3535  @version 2.0
    36   @see <a href="../../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
     36  @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
    3737  @base.modified $Date$
    3838*/
  • trunk/src/core/net/sf/basedb/core/Validatable.java

    r2304 r2962  
    2727  This interface is a tagging interface for items that needs case 2
    2828  validation. See <a
    29   href="../../../../../../development/overview/core/datavalidation,html">Core API overview -
     29  href="../../../../../development/overview/core/datavalidation,html">Core API overview -
    3030  Data validation</a> and <a
    31   href="../../../../../../development/coding/item/index.html#validation">Coding rules and
     31  href="../../../../../development/coding/item/index.html#validation">Coding rules and
    3232  guidelines for item classes</a>
    3333  <p>
  • trunk/src/core/net/sf/basedb/core/data/AnnotatableData.java

    r2304 r2962  
    5757  @see AnnotationTypeData
    5858  @see net.sf.basedb.core.Annotatable
    59   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
     59  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
    6060*/
    6161public interface AnnotatableData
  • trunk/src/core/net/sf/basedb/core/data/AnnotatedData.java

    r2304 r2962  
    3333  @see AnnotatableData
    3434  @see net.sf.basedb.core.AnnotatedItem
    35   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotation overview</a>
     35  @see <a href="../../../../../../development/overview/data/annotations.html">Annotation overview</a>
    3636*/
    3737public abstract class AnnotatedData
  • trunk/src/core/net/sf/basedb/core/data/AnnotationData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Annotation
    34   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
     34  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
    3535  @hibernate.class table="`Annotations`" lazy="false"
    3636 */
  • trunk/src/core/net/sf/basedb/core/data/AnnotationSetData.java

    r2304 r2962  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.AnnotationSet
    37   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
     37  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
    3838  @hibernate.class table="`AnnotationSets`" lazy="true" batch-size="10"
    3939 */
  • trunk/src/core/net/sf/basedb/core/data/AnnotationTypeCategoryData.java

    r2517 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.AnnotationTypeCategory
    33   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
     33  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
    3434  @base.modified $Date: 2006-04-18 10:48:02 +0100 (Tue, 18 Apr 2006) $
    3535  @hibernate.class table="`AnnotationTypeCategories`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

    r2933 r2962  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.AnnotationType
    37   @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
     37  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`AnnotationTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/AnyToAnyData.java

    r2382 r2962  
    3232  @see net.sf.basedb.core.AnyToAny
    3333  @base.modified $Date$
    34   @see <a href="../../../../../../../development/overview/data/misc.html">Misc overview</a>
     34  @see <a href="../../../../../../development/overview/data/misc.html">Misc overview</a>
    3535  @hibernate.class table="`AnyToAny`" lazy="false"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/ArrayBatchData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ArrayBatch
    35   @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     35  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`ArrayBatches`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignBlockData.java

    r2809 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ArrayDesignBlock
    35   @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     35  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`ArrayDesignBlocks`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignData.java

    r2809 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ArrayDesign
    35   @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     35  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`ArrayDesigns`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignPlateData.java

    r2304 r2962  
    3131  @see net.sf.basedb.core.ArrayDesign
    3232  @see net.sf.basedb.core.Plate
    33   @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     33  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`ArrayDesignPlates`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ArraySlideData.java

    r2304 r2962  
    3030 @version 2.0
    3131 @see net.sf.basedb.core.ArraySlide
    32  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     32 @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3333 @base.modified $Date$
    3434 @hibernate.class table="`ArraySlides`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/BasicData.java

    r2304 r2962  
    4444  @author Nicklas
    4545  @version 2.0
    46   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     46  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    4747*/
    4848public abstract class BasicData
  • trunk/src/core/net/sf/basedb/core/data/BatchableData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.BasicBatcher
    35   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    36   @see <a href="../../../../../../../development/overview/core/index.html#batch">Batch processing</a>
     35  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     36  @see <a href="../../../../../../development/overview/core/index.html#batch">Batch processing</a>
    3737*/
    3838public interface BatchableData
  • trunk/src/core/net/sf/basedb/core/data/BioAssayData.java

    r2892 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.BioAssay
    35   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     35  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`BioAssays`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioAssaySetData.java

    r2892 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.BioAssaySet
    36   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     36  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`BioAssaySets`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.BioMaterial
    32   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     32  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`BioMaterials`" lazy="false" discriminator-value="-1"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialEventData.java

    r2479 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.BioMaterialEvent
    36   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     36  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`BioMaterialEvents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/BioSourceData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.BioSource
    33   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     33  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.subclass discriminator-value="1"
  • trunk/src/core/net/sf/basedb/core/data/BooleanParameterValueData.java

    r2304 r2962  
    3232  @author Nicklas, Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="7"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ClientData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Client
    34   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     34  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3535  @hibernate.class table="`Clients`" lazy="false"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/ClientDefaultSettingData.java

    r2304 r2962  
    2727  @author enell
    2828  @see net.sf.basedb.core.ClientDefaultSetting
    29   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3030  @hibernate.class table="`ClienDefaultSettings`" lazy="false"
    3131*/
  • trunk/src/core/net/sf/basedb/core/data/CommonData.java

    r2304 r2962  
    3232  @author Nicklas
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     34  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    3535*/
    3636public abstract class CommonData
  • trunk/src/core/net/sf/basedb/core/data/ContextData.java

    r2304 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.ItemContext
    36   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     36  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Contexts`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ContextIndex.java

    r2864 r2962  
    3030  @author Nicklas
    3131  @version 2.0
    32   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     32  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3333  @base.modified $Date$
    3434*/
  • trunk/src/core/net/sf/basedb/core/data/DataCubeColumnData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.DataCubeColumn
    32   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     32  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`DataCubeColumns`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeData.java

    r2387 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.DataCube
    34   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     34  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`DataCubes`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeExtraValueData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.DataCubeExtraValue
    32   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     32  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`DataCubeExtraValues`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeFilterData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.DataCubeFilter
    32   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     32  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`DataCubeFilters`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeLayerData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.DataCubeLayer
    32   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     32  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`DataCubeLayers`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DateParameterValueData.java

    r2304 r2962  
    3333  @author Samuel
    3434  @version 2.0
    35   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     35  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3636  @hibernate.subclass discriminator-value="8"
    3737  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/DirectoryData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.Directory
    35   @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
     35  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`Directories`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/DiskConsumableData.java

    r2304 r2962  
    6161  @see DiskUsageData
    6262  @see net.sf.basedb.core.DiskConsumable
    63   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     63  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    6464*/
    6565public interface DiskConsumableData
  • trunk/src/core/net/sf/basedb/core/data/DiskUsageData.java

    r2929 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.DiskUsage
    34   @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
     34  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`DiskUsage`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DoubleParameterValueData.java

    r2305 r2962  
    3232  @author Nicklas, Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="4"
    3636  @base.modified $Date: 2005-07-05 15:51:30 +0200 (ti, 05 jul 2005) $
  • trunk/src/core/net/sf/basedb/core/data/ExperimentData.java

    r2694 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Experiment
    36   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     36  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Experiments`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ExtraValueData.java

    r2664 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ExtraValue
    33   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     33  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3434  @hibernate.class table="`ExtraValues`" lazy="false"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ExtraValueTypeData.java

    r2733 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ExtraValueType
    33   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     33  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3434  @hibernate.class table="`ExtraValueTypes`" lazy="true"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ExtractData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Extract
    32   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     32  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.subclass discriminator-value="3" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/FeatureData.java

    r2497 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Feature
    32   @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
     32  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`Features`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/FileAttachableData.java

    r2304 r2962  
    5252  @version 2.0
    5353  @see BasicData
    54   @see <a href="../../../../../../../development/overview/data/files.html">File and directory overview</a>
    55   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     54  @see <a href="../../../../../../development/overview/data/files.html">File and directory overview</a>
     55  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    5656*/
    5757public interface FileAttachableData
  • trunk/src/core/net/sf/basedb/core/data/FileData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.File
    32   @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
     32  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`Files`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/FileTypeData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.File
    32   @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
     32  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`FileTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/FloatParameterValueData.java

    r2304 r2962  
    3232  @author Nicklas, Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="3"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/FormulaData.java

    r2733 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Formula
    36   @see <a href="../../../../../../../development/overview/data/experiments.html">Session and client overview</a>
     36  @see <a href="../../../../../../development/overview/data/experiments.html">Session and client overview</a>
    3737  @hibernate.class table="`Formulas`" lazy="false"
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/GlobalDefaultSettingData.java

    r2304 r2962  
    2727  @author enell
    2828  @see net.sf.basedb.core.GlobalDefaultSetting
    29   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3030  @hibernate.class table="`GlobalDefaultSettings`" lazy="false"
    3131*/
  • trunk/src/core/net/sf/basedb/core/data/GroupData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.Group
    35   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`Groups`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/GuiContextData.java

    r2304 r2962  
    3434  @author Nicklas
    3535  @version 2.0
    36   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins ovreview</a>
     36  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins ovreview</a>
    3737  @base.modified $Date$
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/HardwareData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Hardware
    32   @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
     32  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`Hardware`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/HardwareTypeData.java

    r2495 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.HardwareType
    34   @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
     34  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`HardwareTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/HelpData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Help
    32   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     32  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`HelpTexts`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/HybridizationData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Hybridization
    34   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     34  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Hybridizations`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/IdentifiableData.java

    r2304 r2962  
    4646  @version 2.0
    4747  @see BasicData
    48   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     48  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    4949*/
    5050public interface IdentifiableData
  • trunk/src/core/net/sf/basedb/core/data/ImageData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Image
    33   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     33  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`Images`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/IntegerParameterValueData.java

    r2304 r2962  
    3232  @author Nicklas, Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="1"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ItemKeyData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ItemKey
    35   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.subclass discriminator-value="1"
  • trunk/src/core/net/sf/basedb/core/data/ItemParameterValueData.java

    r2304 r2962  
    3434  @author Nicklas, Samuel
    3535  @version 2.0
    36   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     36  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3737  @hibernate.subclass discriminator-value="10"
    3838  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/JobAgentData.java

    r2627 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.JobAgent
    35   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
     35  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`JobAgents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/JobAgentSettingsData.java

    r2627 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.JobAgentSettings
    33   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
     33  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`JobAgentSettings`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/JobData.java

    r2745 r2962  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.Job
    37   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
     37  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`Jobs`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/KeyData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Key
    33   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     33  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`Keys`" lazy="true" discriminator-value="-1"
  • trunk/src/core/net/sf/basedb/core/data/LabelData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Label
    32   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     32  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3333  @hibernate.class table="`Labels`" lazy="false"
    3434  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/LabeledExtractData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.LabeledExtract
    32   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     32  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.subclass discriminator-value="4" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/LongParameterValueData.java

    r2305 r2962  
    3232  @author Nicklas, Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="2"
    3636  @base.modified $Date: 2005-07-14 09:57:11 +0200 (to, 14 jul 2005) $
  • trunk/src/core/net/sf/basedb/core/data/MappingCoordinate.java

    r2304 r2962  
    3636  @version 2.0
    3737  @see PlateMappingData
    38   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     38  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3939  @base.modified $Date$
    4040*/
  • trunk/src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.MeasuredBioMaterial
    35   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     35  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.subclass discriminator-value="-1" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/MessageData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Message
    34   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
     34  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
    3535  @hibernate.class table="`Messages`" lazy="false"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/MimeTypeData.java

    r2691 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.MimeType
    32   @see <a href="../../../../../../../development/overview/data/files.html">File and directory overview</a>
     32  @see <a href="../../../../../../development/overview/data/files.html">File and directory overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`MimeTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/NameableData.java

    r2304 r2962  
    6161  @version 2.0
    6262  @see CommonData
    63   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     63  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    6464*/
    6565public interface NameableData
  • trunk/src/core/net/sf/basedb/core/data/NewsData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.News
    34   @see <a href="../../../../../../../development/overview/data/misc.html">Misc overview</a>
     34  @see <a href="../../../../../../development/overview/data/misc.html">Misc overview</a>
    3535  @hibernate.class table="`News`" lazy="false"
    3636 */
  • trunk/src/core/net/sf/basedb/core/data/OwnableData.java

    r2304 r2962  
    5353  @see OwnedData
    5454  @see net.sf.basedb.core.Ownable
    55   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    56   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     55  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     56  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    5757*/
    5858public interface OwnableData
  • trunk/src/core/net/sf/basedb/core/data/OwnedData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.OwnedItem
    34   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    35   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     34  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    3636*/
    3737public abstract class OwnedData
  • trunk/src/core/net/sf/basedb/core/data/ParameterValueData.java

    r2787 r2962  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3434  @hibernate.class table="`ParameterValues`" discriminator-value="-1" lazy="true" batch-size="10"
    3535  @hibernate.discriminator column="`discriminator`" type="int"
  • trunk/src/core/net/sf/basedb/core/data/PasswordData.java

    r2304 r2962  
    3232  @author Nicklas
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     34  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3535  @hibernate.class table="`Passwords`" lazy="true"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/PlateCoordinate.java

    r2304 r2962  
    3636  @version 2.0
    3737  @see PlateData
    38   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     38  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3939  @base.modified $Date$
    4040*/
  • trunk/src/core/net/sf/basedb/core/data/PlateData.java

    r2304 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Plate
    36   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     36  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Plates`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateEventData.java

    r2479 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PlateEvent
    34   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     34  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`PlateEvents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateEventTypeData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PlateEventType
    34   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     34  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`PlateEventTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateGeometryData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.PlateGeometry
    32   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     32  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`PlateGeometries`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateMappingData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.PlateMapping
    35   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     35  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`PlateMappings`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/PlateTypeData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PlateType
    34   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     34  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`PlateTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PluginConfigurationData.java

    r2709 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.PluginConfiguration
    36   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
     36  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
    3737  @hibernate.class table="`PluginConfigurations`" lazy="false"
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/PluginDefinitionData.java

    r2854 r2962  
    3737  @version 2.0
    3838  @see net.sf.basedb.core.PluginDefinition
    39   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
     39  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
    4040  @hibernate.class table="`PluginDefinitions`" lazy="false"
    4141*/
  • trunk/src/core/net/sf/basedb/core/data/PluginPermission.java

    r2722 r2962  
    2828  @author Martin
    2929  @version 2.1
    30   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     30  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3131*/
    3232public class PluginPermission
  • trunk/src/core/net/sf/basedb/core/data/PluginTypeData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PluginType
    34   @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
     34  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
    3535  @hibernate.class table="`PluginTypes`" lazy="false"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ProjectData.java

    r2941 r2962  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Project
    36   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     36  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Projects`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ProjectKeyData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ProjectKey
    35   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.subclass discriminator-value="2"
  • trunk/src/core/net/sf/basedb/core/data/PropertyFilterData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ItemContext
    33   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     33  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3434  @base.modified $Date$
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/ProtocolData.java

    r2875 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Protocol
    33   @see <a href="../../../../../../../development/overview/data/protocols.html">Protocol overview</a>
     33  @see <a href="../../../../../../development/overview/data/protocols.html">Protocol overview</a>
    3434  @hibernate.class table="`Protocols`" lazy="true"
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/ProtocolTypeData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ProtocolType
    33   @see <a href="../../../../../../../development/overview/data/protocols.html">Protocol overview</a>
     33  @see <a href="../../../../../../development/overview/data/protocols.html">Protocol overview</a>
    3434  @hibernate.class table="`ProtocolTypes`" lazy="false"
    3535 
  • trunk/src/core/net/sf/basedb/core/data/QuotaData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.Quota
    35   @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
     35  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
    3636  @hibernate.class table="`Quota`" lazy="true"
    3737  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/QuotaIndex.java

    r2864 r2962  
    3535  @author enell
    3636  @version 2.0
    37   @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
     37  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
    3838  @base.modified $Date$
    3939*/
  • trunk/src/core/net/sf/basedb/core/data/QuotaTypeData.java

    r2304 r2962  
    2929  @author enell
    3030  @version 2.0
    31   @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
     31  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`QuotaTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/RawBioAssayData.java

    r2419 r2962  
    3636  @version 2.0
    3737  @see net.sf.basedb.core.RawBioAssay
    38   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     38  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    3939  @base.modified $Date$
    4040  @hibernate.class table="`RawBioAssays`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/RawData.java

    r2814 r2962  
    3737  @see net.sf.basedb.core.RawDataBatcher
    3838  @see net.sf.basedb.core.RawDataUtil
    39   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     39  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    4040  @base.modified $Date$
    4141*/
  • trunk/src/core/net/sf/basedb/core/data/RemovableData.java

    r2304 r2962  
    5959  @author Nicklas
    6060  @version 2.0
    61   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     61  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    6262*/
    6363public interface RemovableData
  • trunk/src/core/net/sf/basedb/core/data/ReporterData.java

    r2304 r2962  
    4747  @see net.sf.basedb.core.ReporterBatcher
    4848  @see net.sf.basedb.core.ExtendedProperties
    49   @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
     49  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
    5050  @hibernate.class table="`Reporters`" lazy="false"
    5151*/
  • trunk/src/core/net/sf/basedb/core/data/ReporterListData.java

    r2428 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ReporterList
    35   @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
     35  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
    3636  @hibernate.class table="`ReporterLists`" lazy="true"
    3737*/
  • trunk/src/core/net/sf/basedb/core/data/ReporterListScoreData.java

    r2864 r2962  
    3636  @version 2.0
    3737  @see net.sf.basedb.core.ReporterList
    38   @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
     38  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
    3939*/
    4040@SuppressWarnings({"serial"})
  • trunk/src/core/net/sf/basedb/core/data/ReporterTypeData.java

    r2304 r2962  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.data.ReporterData
    37   @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
     37  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
    3838  @hibernate.class table="`ReporterTypes`" lazy="true"
    3939*/
  • trunk/src/core/net/sf/basedb/core/data/RoleData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.Role
    35   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`Roles`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/RoleKeyData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.RoleKey
    35   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.subclass discriminator-value="3"
  • trunk/src/core/net/sf/basedb/core/data/SampleData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Sample
    32   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     32  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.subclass discriminator-value="2" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ScanData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Scan
    34   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     34  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Scans`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/SessionData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Session
    34   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     34  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3535  @hibernate.class table="`Sessions`" lazy="false"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/SettingData.java

    r2786 r2962  
    2828  @version 2.0
    2929  @see net.sf.basedb.core.Setting
    30   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     30  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3131*/
    3232public abstract class SettingData
  • trunk/src/core/net/sf/basedb/core/data/ShareableData.java

    r2304 r2962  
    7171  @see SharedData
    7272  @see net.sf.basedb.core.Shareable
    73   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    74   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     73  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     74  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    7575*/
    7676public interface ShareableData
  • trunk/src/core/net/sf/basedb/core/data/SharedData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.SharedItem
    34   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    35   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     34  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     35  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    3636*/
    3737public abstract class SharedData
  • trunk/src/core/net/sf/basedb/core/data/SoftwareData.java

    r2304 r2962  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Software
    31   @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
     31  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`Software`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/SoftwareTypeData.java

    r2304 r2962  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.SoftwareType
    34   @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
     34  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`SoftwareTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/SpotImagesData.java

    r2304 r2962  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.SpotImages
    33   @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
     33  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`SpotImages`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/StringParameterValueData.java

    r2304 r2962  
    3232  @author Nicklas
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="5"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/SystemData.java

    r2304 r2962  
    6060  @author Nicklas
    6161  @version 2.0
    62   @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
     62  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
    6363*/
    6464public interface SystemData
  • trunk/src/core/net/sf/basedb/core/data/TextParameterValueData.java

    r2304 r2962  
    3232  @author Samuel
    3333  @version 2.0
    34   @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
     34  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
    3535  @hibernate.subclass discriminator-value="6"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/TransformationData.java

    r2304 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.Transformation
    35   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     35  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`Transformations`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/UsedQuantity.java

    r2304 r2962  
    3333  @author Nicklas
    3434  @version 2.0
    35   @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
     35  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
    3636  @base.modified $Date$
    3737*/
  • trunk/src/core/net/sf/basedb/core/data/UserClientSettingData.java

    r2304 r2962  
    2727  @author enell
    2828  @see net.sf.basedb.core.UserClientSetting
    29   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3030  @hibernate.class table="`UserClientSettings`" lazy="false"
    3131 */
  • trunk/src/core/net/sf/basedb/core/data/UserData.java

    r2304 r2962  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.User
    37   @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
     37  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`Users`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/UserDefaultSettingData.java

    r2304 r2962  
    2727  @author enell
    2828  @see net.sf.basedb.core.UserDefaultSetting
    29   @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
    3030  @hibernate.class table="`UserDefaultSettings`" lazy="false"
    3131*/
  • trunk/src/core/net/sf/basedb/core/data/VirtualDbData.java

    r2387 r2962  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.VirtualDb
    35   @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
     35  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`VirtualDbs`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/WellData.java

    r2304 r2962  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.Well
    32   @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
     32  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`Wells`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/query/Query.java

    r2669 r2962  
    6060  @author Nicklas
    6161  @version 2.0
    62   @see <a href="../../../../../../../development/overview/query/index.html">Query API documentation</a>
     62  @see <a href="../../../../../../development/overview/query/index.html">Query API documentation</a>
    6363  @see net.sf.basedb.core.AbstractQuery
    6464  @base.modified $Date$
Note: See TracChangeset for help on using the changeset viewer.