Changeset 2962

Timestamp:

Nov 27, 2006, 3:02:39 PM (16 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:

• build.xml (modified) (3 diffs)
• doc/admin/base.config.html (modified) (1 diff)
• doc/admin/extended-properties.html (modified) (1 diff)
• doc/admin/jobagent.html (modified) (2 diffs)
• doc/development/coding/batch/index.html (modified) (1 diff)
• doc/development/coding/data/index.html (modified) (1 diff)
• doc/development/coding/item/index.html (modified) (1 diff)
• doc/development/index.html (modified) (2 diffs)
• doc/development/overview/core/accesspermissions.html (modified) (11 diffs)
• doc/development/overview/core/authentication.html (modified) (1 diff)
• doc/development/overview/core/index.html (modified) (1 diff)
• doc/development/overview/data/annotations.html (modified) (4 diffs)
• doc/development/overview/data/authentication.html (modified) (4 diffs)
• doc/development/overview/data/basic.html (modified) (15 diffs)
• doc/development/overview/data/biomaterial.html (modified) (3 diffs)
• doc/development/overview/data/experiments.html (modified) (7 diffs)
• doc/development/overview/data/index.html (modified) (1 diff)
• doc/development/overview/data/misc.html (modified) (4 diffs)
• doc/development/overview/data/parameters.html (modified) (2 diffs)
• doc/development/overview/data/plates.html (modified) (4 diffs)
• doc/development/overview/data/plugins.html (modified) (5 diffs)
• doc/development/overview/data/reporters.html (modified) (3 diffs)
• doc/development/overview/dynamic/create.html (modified) (1 diff)
• doc/development/overview/dynamic/datacube.html (modified) (1 diff)
• doc/development/overview/dynamic/extravalues.html (modified) (1 diff)
• doc/development/overview/dynamic/filter.html (modified) (1 diff)
• doc/development/overview/dynamic/index.html (modified) (1 diff)
• doc/development/overview/dynamic/insert.html (modified) (1 diff)
• doc/development/overview/dynamic/intensities.html (modified) (1 diff)
• doc/development/overview/dynamic/merge.html (modified) (1 diff)
• doc/development/overview/dynamic/query.html (modified) (1 diff)
• doc/development/overview/dynamic/rootbioassayset.html (modified) (1 diff)
• doc/development/overview/exceptions/index.html (modified) (1 diff)
• doc/development/overview/query/elements.html (modified) (1 diff)
• doc/development/overview/query/index.html (modified) (1 diff)
• doc/development/overview/query/overview.html (modified) (1 diff)
• doc/development/overview/query/result.html (modified) (1 diff)
• doc/development/overview/utility/index.html (modified) (1 diff)
• doc/development/overview/web/index.html (modified) (1 diff)
• doc/index.html (modified) (1 diff)
• doc/specifications/core/defaultdata.html (modified) (1 diff)
• src/core/net/sf/basedb/core/BasicItem.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/Batcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ContextKey.java (modified) (1 diff)
• src/core/net/sf/basedb/core/DataCube.java (modified) (1 diff)
• src/core/net/sf/basedb/core/MappingBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PositionBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/QueryRuntimeFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/core/QueryRuntimeFilterFactory.java (modified) (1 diff)
• src/core/net/sf/basedb/core/QueryRuntimeFilterManager.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Validatable.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotatableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotatedData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotationData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotationSetData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotationTypeCategoryData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnnotationTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/AnyToAnyData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ArrayBatchData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ArrayDesignBlockData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ArrayDesignData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ArrayDesignPlateData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ArraySlideData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BasicData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BatchableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioAssayData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioAssaySetData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioMaterialData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioMaterialEventData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioSourceData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BooleanParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ClientData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ClientDefaultSettingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/CommonData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ContextData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ContextIndex.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataCubeColumnData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataCubeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataCubeExtraValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataCubeFilterData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DataCubeLayerData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DateParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DirectoryData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DiskConsumableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DiskUsageData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/DoubleParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ExperimentData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ExtraValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ExtraValueTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ExtractData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FeatureData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FileAttachableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FileData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FileTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FloatParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FormulaData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/GlobalDefaultSettingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/GroupData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/GuiContextData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/HardwareData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/HardwareTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/HelpData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/HybridizationData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/IdentifiableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ImageData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/IntegerParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ItemKeyData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ItemParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/JobAgentData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/JobAgentSettingsData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/JobData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/KeyData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/LabelData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/LabeledExtractData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/LongParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/MappingCoordinate.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/MessageData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/MimeTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/NameableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/NewsData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/OwnableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/OwnedData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PasswordData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateCoordinate.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateEventData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateEventTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateGeometryData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateMappingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PlateTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PluginConfigurationData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PluginDefinitionData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PluginPermission.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PluginTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ProjectData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ProjectKeyData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/PropertyFilterData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ProtocolData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ProtocolTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/QuotaData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/QuotaIndex.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/QuotaTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RawBioAssayData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RawData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RemovableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterListData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterListScoreData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RoleData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RoleKeyData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SampleData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ScanData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SessionData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SettingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ShareableData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SharedData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SoftwareData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SoftwareTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SpotImagesData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/StringParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/SystemData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/TextParameterValueData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/TransformationData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/UsedQuantity.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/UserClientSettingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/UserData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/UserDefaultSettingData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/VirtualDbData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/WellData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/query/Query.java (modified) (1 diff)

trunk/build.xml

@@ -129 +129 @@
     name="dist"
     depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,installprg.jar,
-      jobagent.jar,migrate.jar,copy.config,copy.jar,doc.dist"
+      jobagent.jar,migrate.jar,copy.config,copy.jar,doc,doc.dist"
     description="Create everything needed for distribution"
     >
@@ -141 +141 @@
     <copy todir="${dist}/bin" description="Scripts, etc.">
       <fileset dir="bin" />
+    </copy>
+    <copy todir="${dist}" description="License and creadits">
+      <fileset file="base2.license.txt" />
+      <fileset file="credits.txt" />
     </copy>
   </target>
@@ -960 +964 @@
       <fileset dir="doc" includes="development/**/*" />
       <fileset dir="doc" includes="licenses/**/*" />
+      <fileset dir="doc" includes="specifications/**/*" />
       <fileset dir="doc" includes="user/**/*" />
-      <fileset dir="doc" includes="*.*" excludes="index.html" />
+      <fileset dir="doc" includes="*.*" />
     </copy>
   </target>

trunk/doc/admin/base.config.html

@@ -79 +79 @@
     <li><code>org.hibernate.dialect.PostgreSQLDialect</code> for Postgres</li>
     </ul>
-    Other dialects may wirk but are not supported.
+    Other dialects may work but are not supported.
   </dd>
   

trunk/doc/admin/extended-properties.html

@@ -190 +190 @@
       A more detailed information about the attributes is available in
       the <a
-      href="../api/develop/net/sf/basedb/core/data/ExtendableData.html">javadoc
+      href="../api/net/sf/basedb/core/data/ExtendableData.html">javadoc
       for the ExtendableData class</a>.
     </p>

trunk/doc/admin/jobagent.html

@@ -127 +127 @@
     as job agents. The setting <code>jobqueue.internal.enabled</code>
     should be changed to <code>false</code> for the web server. This setting
-    is found in the <code>www/WEB-INF/classes/base.config.file</code>. After
+    is found in the <code>www/WEB-INF/classes/base.config</code> file. After
     you have changed the setting the web server must be restarted.
   </dd>
@@ -192 +192 @@
   <dt>3. Edit the <code>jobagent.properties</code> file</dt>
   <dd>
-    The <code>bin/jobagent.properties</code> file contains settings for
+    The <code>www/WEB-INF/classes/jobagent.properties</code> file contains settings for
     the job agent. The most important ones to specify value for are:
     

trunk/doc/development/coding/batch/index.html

@@ -55 +55 @@
     <b>See also</b>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     <li><a href="../../overview/core/index.html">An overview of the core API</a>
     </ul>

trunk/doc/development/coding/data/index.html

@@ -82 +82 @@
     <li><a href="AnyData.txt">AnyData.txt - a template class file for <code>CommonData</code> object</a>
     <li><a href="ChildData.txt">ChildData.txt - a template class file for child items</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
+    <li><a href="../../../api/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
     <li><a href="../../overview/data/index.html">An overview of the database schema and data layer API</a>
     </ul>

trunk/doc/development/coding/item/index.html

@@ -84 +84 @@
     <li><a href="../../overview/core/datavalidation.html">Core API overview - Data validation</a>
     <li><a href="../../overview/core/transactions.html">Core API overview - Transaction handling</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     </p>

trunk/doc/development/index.html

@@ -46 +46 @@
     <ol>
     <li><a href="#startingpoints">Where to start</a>
-    <li><a href="api/index.html">API Javadoc</a>
+    <li><a href="../api/index.html">API Javadoc</a>
     <li><a href="#specifications">Specifications</a>
     <li><a href="#overview">Implementation overview</a>
@@ -75 +75 @@
 
   <p>
-    <a href="api/index.html">API Javadoc is here.</a>
+    <a href="../api/index.html">API Javadoc is here.</a>
   </p>
   

trunk/doc/development/overview/core/accesspermissions.html

@@ -79 +79 @@
   
   <p>
-    The <code>Keyring</code> [<a href="../../../api/develop/net/sf/basedb/core/Keyring.html">API</a>] 
+    The <code>Keyring</code> [<a href="../../../api/net/sf/basedb/core/Keyring.html">API</a>] 
     class is the core class that is responsible
     for handling most permission checks in BASE. A keyring object
@@ -88 +88 @@
   <ul>
   <li>Which roles the user is a member of and the permissions granted to those roles 
-    (RoleKey [<a href="../../../api/develop/net/sf/basedb/core/RoleKey.html">API</a>])
+    (RoleKey [<a href="../../../api/net/sf/basedb/core/RoleKey.html">API</a>])
   <li>Which groups the user is a member of, including following groups-within-groups,
     and the permissions granted to those groups (ItemKey
-     [<a href="../../../api/develop/net/sf/basedb/core/ItemKey.html">API</a>])
+     [<a href="../../../api/net/sf/basedb/core/ItemKey.html">API</a>])
   <li>The permissions granted to the user directly (ItemKey)
   <li>If a project is active, the permissions within that project (ProjectKey
-   [<a href="../../../api/develop/net/sf/basedb/core/ProjectKey.html">API</a>])
-  <li>Which <code>Project</code>:s  [<a href="../../../api/develop/net/sf/basedb/core/Project.html">API</a>]
+   [<a href="../../../api/net/sf/basedb/core/ProjectKey.html">API</a>])
+  <li>Which <code>Project</code>:s  [<a href="../../../api/net/sf/basedb/core/Project.html">API</a>]
     the user has access to
   <li>Which other users are members of at least one of the groups the logged in
@@ -122 +122 @@
 
   <p>
-    The <code>Permission</code> [<a href="../../../api/develop/net/sf/basedb/core/Permission.html">API</a>]
+    The <code>Permission</code> [<a href="../../../api/net/sf/basedb/core/Permission.html">API</a>]
     enumeration defines the permissions available in BASE.
     Each permission is represented by an integer value (<code>grantValue()</code>)
@@ -151 +151 @@
   
   <p>
-    Each <code>BasicItem</code> [<a href="../../../api/develop/net/sf/basedb/core/BasicItem.html">API</a>]
+    Each <code>BasicItem</code> [<a href="../../../api/net/sf/basedb/core/BasicItem.html">API</a>]
     has an internal <code>permissions</code> variable
     which holds the logged in users permission to manipulate the item. This value
@@ -160 +160 @@
   </p>
   <p>
-    Since it is the <code>DbControl</code> [<a href="../../../api/develop/net/sf/basedb/core/DbControl.html">API</a>]
+    Since it is the <code>DbControl</code> [<a href="../../../api/net/sf/basedb/core/DbControl.html">API</a>]
     that is responsible for creating, loading, saving,
     deleting, etc. items from the database, it is also the <code>DbControl</code> that is
@@ -174 +174 @@
     in <code>BasicItem</code> will use the <code>SessionControl.getRolePermissions()</code>
     to find the permissions the logged in user has been granted based on role
-    membership. The <code>OwnedItem</code> [<a href="../../../api/develop/net/sf/basedb/core/OwnedItem.html">API</a>]
+    membership. The <code>OwnedItem</code> [<a href="../../../api/net/sf/basedb/core/OwnedItem.html">API</a>]
     class grants additional permissions
     if the logged in user is the owner of an item, and the <code>SharedItem</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/SharedItem.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/SharedItem.html">API</a>]
     class grants additional permission if the logged in user has an item or project 
     key with permissions for the item. The <code>ChildItem</code> implementation 
@@ -187 +187 @@
     Subclasses that need to grant or deny additional
     permissions must override the <code>initPermissions()</code> method.
-    For example the <code>News</code> [<a href="../../../api/develop/net/sf/basedb/core/News.html">API</a>]
+    For example the <code>News</code> [<a href="../../../api/net/sf/basedb/core/News.html">API</a>]
     class will grant read access to everyone
     (even if no user is logged in) if the current date is between the start and end
-    date of the news item. The <code>Role</code> [<a href="../../../api/develop/net/sf/basedb/core/Role.html">API</a>]
-    and <code>Group</code> [<a href="../../../api/develop/net/sf/basedb/core/Group.html">API</a>]
+    date of the news item. The <code>Role</code> [<a href="../../../api/net/sf/basedb/core/Role.html">API</a>]
+    and <code>Group</code> [<a href="../../../api/net/sf/basedb/core/Group.html">API</a>]
     classes are other exemples which grant read permission if the logged in user
     is a member of the role or group.
@@ -229 +229 @@
 
   <p>
-    The various subclasses to the <code>Key</code> [<a href="../../../api/develop/net/sf/basedb/core/Key.html">API</a>]
+    The various subclasses to the <code>Key</code> [<a href="../../../api/net/sf/basedb/core/Key.html">API</a>]
     class are used to  store the actual permissions in the database. There are three subclasses:
   </p>
   
   <ul>
-  <li>RoleKey [<a href="../../../api/develop/net/sf/basedb/core/RoleKey.html">API</a>]: Used to grant permissions to roles.
-  <li>ItemKey [<a href="../../../api/develop/net/sf/basedb/core/ItemKey.html">API</a>]: Used to grant permissions to users/groups.
-  <li>ProjectKey [<a href="../../../api/develop/net/sf/basedb/core/ProjectKey.html">API</a>]: Used to grant permission to projects.
+  <li>RoleKey [<a href="../../../api/net/sf/basedb/core/RoleKey.html">API</a>]: Used to grant permissions to roles.
+  <li>ItemKey [<a href="../../../api/net/sf/basedb/core/ItemKey.html">API</a>]: Used to grant permissions to users/groups.
+  <li>ProjectKey [<a href="../../../api/net/sf/basedb/core/ProjectKey.html">API</a>]: Used to grant permission to projects.
   </ul>
 
@@ -273 +273 @@
     existing item keys. The item key has no <code>set</code> methods to change
     the permissions. Instead you have to use the helper classes,
-    <code>UserPermissions</code> [<a href="../../../api/develop/net/sf/basedb/core/UserPermissions.html">API</a>]
-    and <code>GroupPermissions</code> [<a href="../../../api/develop/net/sf/basedb/core/GroupPermissions.html">API</a>].
+    <code>UserPermissions</code> [<a href="../../../api/net/sf/basedb/core/UserPermissions.html">API</a>]
+    and <code>GroupPermissions</code> [<a href="../../../api/net/sf/basedb/core/GroupPermissions.html">API</a>].
   </p>
   
@@ -282 +282 @@
     they share items to projects instead of to user and groups. 
     To set the permissions you use a <code>ProjectPermissions</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/ProjectPermissions.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/ProjectPermissions.html">API</a>]
     object.
   </p>
@@ -309 +309 @@
   <p>
     The <code>MultiPermissions</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/MultiPermissions.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/MultiPermissions.html">API</a>]
     class is not shown in the diagram. It is a useful helper class to modify
     lots of permissions to multiple items at the same time, while keeping those that

trunk/doc/development/overview/core/authentication.html

@@ -60 +60 @@
     <ul>
     <li><a href="../data/authentication.html">Data layer API and database schema</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/Application.html">Application.java API</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/SessionControl.html">SessionControl.java API</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/authentication/Authenticator.html">Authenticator.java API</a>
+    <li><a href="../../../api/net/sf/basedb/core/Application.html">Application.java API</a>
+    <li><a href="../../../api/net/sf/basedb/core/SessionControl.html">SessionControl.java API</a>
+    <li><a href="../../../api/net/sf/basedb/core/authentication/Authenticator.html">Authenticator.java API</a>
     </ul>
     

trunk/doc/development/overview/core/index.html

@@ -65 +65 @@
     <li><a href="../../coding/batch/index.html">Coding rules and guidelines for batch classes</a>
     <li><a href="../query/index.html">Overview of queries and the Query API</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/data/annotations.html

@@ -62 +62 @@
   <h3>AnnotationSets</h3>
   <p>
-    The <code>AnnotationSetData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationSetData.html">API</a>]
+    The <code>AnnotationSetData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationSetData.html">API</a>]
     class holds all annotations for a single item. An item must implement the
-    <code>AnnotatableData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatableData.html">API</a>]
+    <code>AnnotatableData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotatableData.html">API</a>]
     interface which defines the <code>annotationSet</code> property for that item.
   </p>
@@ -86 +86 @@
   <h3>Annotations</h3>
   <p>
-    The <code>AnnotationData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationData.html">API</a>]
+    The <code>AnnotationData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationData.html">API</a>]
     class is the placeholder for an annotation. It must have a type and belong to an
     annotation set. The actual annotation values are stored as <code>ParameterValueData</code>
@@ -94 +94 @@
   <h3>AnnotationTypes</h3>
   <p>
-    The <code>AnnotationTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationTypeData.html">API</a>]
+    The <code>AnnotationTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationTypeData.html">API</a>]
     class defines the various annotations. It must have a <code>valueType</code> property which cannot
     be changed. The value of this property controls which <code>ParameterValueData</code> subclass
@@ -134 +134 @@
   <h3>AnnotationTypeCategories</h3>
   <p>
-    The <code>AnnotationTypeCategory</code> [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotationTypeCategoryData.html">API</a>]
+    The <code>AnnotationTypeCategory</code> [<a href="../../../api/net/sf/basedb/core/data/AnnotationTypeCategoryData.html">API</a>]
     class defined categories that are used to group annotation types that are
     related to each other. This information is mainly useful for client applications

trunk/doc/development/overview/data/authentication.html

@@ -65 +65 @@
   <h3>Users and passwords</h3>
   <p>
-  The <code>UserData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/UserData.html">API</a>] 
+  The <code>UserData</code> [<a href="../../../api/net/sf/basedb/core/data/UserData.html">API</a>] 
   class holds information about users. We keep the passwords in 
   a separate table and use proxies to avoid loading password data each time a user is loaded
   to minimize security risks. It is only if the password needs to be changed that the 
-  <code>PasswordData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PasswordData.html">API</a>]
+  <code>PasswordData</code> [<a href="../../../api/net/sf/basedb/core/data/PasswordData.html">API</a>]
   object is loaded. The one-to-one mapping between user and 
   password is controlled by the password class, but a cascade attribute on the user class
@@ -77 +77 @@
   <h3>Groups, roles and projects</h3>
   <p>
-  The <code>GroupData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/GroupData.html">API</a>], 
-  <code>RoleData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/RoleData.html">API</a>] and 
-  <code>ProjectData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ProjectData.html">API</a>]
+  The <code>GroupData</code> [<a href="../../../api/net/sf/basedb/core/data/GroupData.html">API</a>], 
+  <code>RoleData</code> [<a href="../../../api/net/sf/basedb/core/data/RoleData.html">API</a>] and 
+  <code>ProjectData</code> [<a href="../../../api/net/sf/basedb/core/data/ProjectData.html">API</a>]
   classes holds information about groups, roles and projects respectively. The connection
   to users are controlled by each of the classes.
@@ -87 +87 @@
   <p>
   The <code>PluginDefinitionData</code> 
-  [<a href="../../../api/develop/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>] class
+  [<a href="../../../api/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>] class
   holds information about plugins. If the plugin is defind to use perminssions, the default
   is to deny everything. The mapping to role key is used to grant/deny permissions to the plugin.
@@ -95 +95 @@
   <h3>Keys</h3>
   <p>
-  The <code>KeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/KeyData.html">API</a>]
+  The <code>KeyData</code> [<a href="../../../api/net/sf/basedb/core/data/KeyData.html">API</a>]
   class and it's subclasses <code>ItemKeyData</code> 
-  [<a href="../../../api/develop/net/sf/basedb/core/data/ItemKeyData.html">API</a>], 
-  <code>ProjectKeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ProjectKeyData.html">API</a>]
-  and <code>RoleKeyData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/RoleKeyData.html">API</a>], 
+  [<a href="../../../api/net/sf/basedb/core/data/ItemKeyData.html">API</a>], 
+  <code>ProjectKeyData</code> [<a href="../../../api/net/sf/basedb/core/data/ProjectKeyData.html">API</a>]
+  and <code>RoleKeyData</code> [<a href="../../../api/net/sf/basedb/core/data/RoleKeyData.html">API</a>], 
   are used to store information 
   about access permissions to items. To get permission to manipulate an item

trunk/doc/development/overview/data/basic.html

@@ -85 +85 @@
 
 <dl>
-<dt>BasicData [<a href="../../../api/develop/net/sf/basedb/core/data/BasicData.html">API</a>]<dt>
+<dt>BasicData [<a href="../../../api/net/sf/basedb/core/data/BasicData.html">API</a>]<dt>
   <dd>
   The root class. It overrides the <code>equals()</code>, <code>hashCode()</code>
@@ -92 +92 @@
   </dd>
 
-<dt>OwnedData [<a href="../../../api/develop/net/sf/basedb/core/data/OwnedData.html">API</a>]</dt>
+<dt>OwnedData [<a href="../../../api/net/sf/basedb/core/data/OwnedData.html">API</a>]</dt>
   <dd>
   This class extends the <code>BasicData</code> class and adds an <code>owner</code>
@@ -98 +98 @@
   </dd>
 
-<dt>SharedData [<a href="../../../api/develop/net/sf/basedb/core/data/SharedData.html">API</a>]</dt>
+<dt>SharedData [<a href="../../../api/net/sf/basedb/core/data/SharedData.html">API</a>]</dt>
   <dd>
   This class extends the <code>OwnerData</code> class and adds methods for
@@ -106 +106 @@
   </dd>
 
-<dt>CommonData [<a href="../../../api/develop/net/sf/basedb/core/data/CommonData.html">API</a>]</dt>
+<dt>CommonData [<a href="../../../api/net/sf/basedb/core/data/CommonData.html">API</a>]</dt>
   <dd>
   This is a convenience class for items that extends the <code>SharedData</code>
@@ -114 +114 @@
   </dd>
 
-<dt>AnnotatedData [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatedData.html">API</a>]</dt>
+<dt>AnnotatedData [<a href="../../../api/net/sf/basedb/core/data/AnnotatedData.html">API</a>]</dt>
   <dd>
   This is a convenience class for items that can be annotated. Annotations are held
@@ -127 +127 @@
 
 <dl>
-  <dt>IdentifiableData [<a href="../../../api/develop/net/sf/basedb/core/data/IdentifiableData.html">API</a>]</dt>
+  <dt>IdentifiableData [<a href="../../../api/net/sf/basedb/core/data/IdentifiableData.html">API</a>]</dt>
   <dd>
     All items are identifiable, which means that they have a unique <code>id</code>. The
@@ -136 +136 @@
   </dd>
   
-  <dt>OwnableData [<a href="../../../api/develop/net/sf/basedb/core/data/OwnableData.html">API</a>]</dt>
+  <dt>OwnableData [<a href="../../../api/net/sf/basedb/core/data/OwnableData.html">API</a>]</dt>
   <dd>
     An ownable item is an item which has an <code>owner</code>. The owner is 
@@ -142 +142 @@
   </dd>
   
-  <dt>ShareableData [<a href="../../../api/develop/net/sf/basedb/core/data/ShareableData.html">API</a>]</dt>
+  <dt>ShareableData [<a href="../../../api/net/sf/basedb/core/data/ShareableData.html">API</a>]</dt>
   <dd>
     A shareable item is an item which can be shared to other users, groups or projects.
@@ -149 +149 @@
   </dd>
   
-  <dt>NameableData [<a href="../../../api/develop/net/sf/basedb/core/data/NameableData.html">API</a>]</dt>
+  <dt>NameableData [<a href="../../../api/net/sf/basedb/core/data/NameableData.html">API</a>]</dt>
   <dd>
     A nameable item is an item that has a <code>name</code> and, optionally, a <code>description</code>.
   </dd>
   
-  <dt>RemovableData [<a href="../../../api/develop/net/sf/basedb/core/data/RemovableData.html">API</a>]</dt>
+  <dt>RemovableData [<a href="../../../api/net/sf/basedb/core/data/RemovableData.html">API</a>]</dt>
   <dd>
     A removable item is an item that can be flagged as removed. This doesn't remove the 
@@ -162 +162 @@
   </dd>
   
-  <dt>SystemData [<a href="../../../api/develop/net/sf/basedb/core/data/SystemData.html">API</a>]</dt>
+  <dt>SystemData [<a href="../../../api/net/sf/basedb/core/data/SystemData.html">API</a>]</dt>
   <dd>
     A system item is an item which has an additional id in the form of string. A system id 
@@ -172 +172 @@
   </dd>
 
-  <dt>FileAttachableData [<a href="../../../api/develop/net/sf/basedb/core/data/FileAttachableData.html">API</a>]</dt>
+  <dt>FileAttachableData [<a href="../../../api/net/sf/basedb/core/data/FileAttachableData.html">API</a>]</dt>
   <dd>
     This interface is used by items that can have an optional file attached to them, for
@@ -178 +178 @@
   </dd>
 
-  <dt>DiskConsumableData [<a href="../../../api/develop/net/sf/basedb/core/data/DiskConsumableData.html">API</a>]</dt>
+  <dt>DiskConsumableData [<a href="../../../api/net/sf/basedb/core/data/DiskConsumableData.html">API</a>]</dt>
   <dd>
     This interface is used by items which occupies a lot of disk space and must
@@ -185 +185 @@
   </dd>
 
-  <dt>AnnotatableData [<a href="../../../api/develop/net/sf/basedb/core/data/AnnotatableData.html">API</a>]</dt>
+  <dt>AnnotatableData [<a href="../../../api/net/sf/basedb/core/data/AnnotatableData.html">API</a>]</dt>
   <dd>
     This interface is used by items which can be annotated. Annotations are 
@@ -192 +192 @@
   </dd>
 
-  <dt>ExtendableData [<a href="../../../api/develop/net/sf/basedb/core/data/ExtendableData.html">API</a>]</dt>
+  <dt>ExtendableData [<a href="../../../api/net/sf/basedb/core/data/ExtendableData.html">API</a>]</dt>
   <dd>
     This interface is used by items which can have extra administrator-defined columns.
@@ -199 +199 @@
   </dd>
   
-  <dt>BatchableData [<a href="../../../api/develop/net/sf/basedb/core/data/BatchableData.html">API</a>]</dt>
+  <dt>BatchableData [<a href="../../../api/net/sf/basedb/core/data/BatchableData.html">API</a>]</dt>
   <dd>
     This interface is a tagging interface which is used by items that needs batch 

trunk/doc/development/overview/data/biomaterial.html

@@ -63 +63 @@
   <p>
     There are four types of biomaterials. 
-    <code>BioSourceData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/BioSourceData.html">API</a>],
-    <code>SampleData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/SampleData.html">API</a>],
-    <code>ExtractData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ExtractData.html">API</a>] 
+    <code>BioSourceData</code> [<a href="../../../api/net/sf/basedb/core/data/BioSourceData.html">API</a>],
+    <code>SampleData</code> [<a href="../../../api/net/sf/basedb/core/data/SampleData.html">API</a>],
+    <code>ExtractData</code> [<a href="../../../api/net/sf/basedb/core/data/ExtractData.html">API</a>] 
     and 
-    <code>LabeledExtractData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/LabeledExtractData.html">API</a>],
+    <code>LabeledExtractData</code> [<a href="../../../api/net/sf/basedb/core/data/LabeledExtractData.html">API</a>],
   </p>
   
   <p>
     All four types of biomaterials are derived from the base class <code>BioMaterialData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/BioMaterialData.html">API</a>].
+    [<a href="../../../api/net/sf/basedb/core/data/BioMaterialData.html">API</a>].
     The reason for this is that they all share common functionality such as 
     pooling and events. By using a common base class we do not have to create 
@@ -85 +85 @@
   <p>
     The <code>MeasuredBioMaterialData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/MeasuredBioMaterialData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/MeasuredBioMaterialData.html">API</a>]
     class is used as a base class for the other three biomaterial types. It introduces
     quantity measurements and can store original and remaining quantities. They are both optional.
@@ -132 +132 @@
     An event represents something that happened to one or more biomaterials,
     for example the creation of another biomaterial. The <code>BioMaterialEventData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/BioMaterialEventData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/BioMaterialEventData.html">API</a>]
     holds information about entry and event dates, protocols used, the user who is responsible, 
     etc.

trunk/doc/development/overview/data/experiments.html

@@ -66 +66 @@
   <p>
     The <code>ExperimentData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/ExperimentData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/ExperimentData.html">API</a>]
     class is used to collect information about a single experiment. It links
     to any number of <code>RawBioAssayData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/RawBioAssayData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/RawBioAssayData.html">API</a>]
     items, which must all be of the same <code>RawDataType</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/RawDataType.html">API</a>].
+    [<a href="../../../api/net/sf/basedb/core/RawDataType.html">API</a>].
   </p>
   <p>
@@ -86 +86 @@
   <p>
     Each line of analysis starts with the creation of a root <code>BioAssaySetData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/BioAssaySetData.html">API</a>],
+    [<a href="../../../api/net/sf/basedb/core/data/BioAssaySetData.html">API</a>],
     which holds the intensities calculated from the raw data. A bioassayset can hold
     one intensity for each channel. The number of channels is defined by the raw data type.
     For each raw bioassay used a <code>BioAssayData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/BioAssayData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/BioAssayData.html">API</a>]
     is created.
   </p>
@@ -96 +96 @@
     Information about the process that calculated the intensities are stored in
     a <code>TransformationData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/TransformationData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/TransformationData.html">API</a>]
     object. The root transformation links with the raw bioassays that are used in this
     line of analysis and to a <code>Job</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/JobData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/JobData.html">API</a>]
     which holds the plugin and parameters used in the calculation. A typical plugin
     may calculate the intensities by subtracting the mean background from the 
@@ -120 +120 @@
     The above processes requires a flexible storage solution for the data.
     The <code>VirtualDbData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DynamicTablesData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DynamicTablesData.html">API</a>]
     object represents a set of tables
     that are created in the dynamic part of the database. In MySQL the dynamic
@@ -129 +129 @@
   <p>
     The <code>DataCubeData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DataCubeData.html">API</a>]
     is the main item used in the analysis. A coordinate in the cube is given by
     a layer, a column and a position, represented by <code>DataCubeLayerData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeLayerData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DataCubeLayerData.html">API</a>]
     and <code>DataCubeColumnData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeColumnData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DataCubeColumnData.html">API</a>]
     object. The position has no separate object. At each coordinate we can store the 
     intensities and extra values related to the intensities.
@@ -145 +145 @@
     doesn't modify the data can reuse the same layer if the new bioassayset is linked
     to a <code>DataCubeFilterData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeFilterData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DataCubeFilterData.html">API</a>]
     item. The filter tells which coordinates should remain in the bioassayset.
   </p>
@@ -166 +166 @@
     In this case we must create a new cube and add mapping information to
     a <code>DataCubeMappingData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/DataCubeMappingData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/DataCubeMappingData.html">API</a>]
     The mapping is a many-to-many mapping between coordinates in the source and destination
     cubes. This allows us to track the source coordinates that were used to calculate

trunk/doc/development/overview/data/index.html

@@ -52 +52 @@
     </p>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
+    <li><a href="../../../api/net/sf/basedb/core/data/package-summary.html">Javadoc for the net.sf.basedb.core.data package</a>
     <li><a href="../../coding/data/index.html">Coding rules and guidelines for the data layer</a>
     </ul>

trunk/doc/development/overview/data/misc.html

@@ -55 +55 @@
   <h3>News</h3>
   <p>
-    The <code>NewsData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/NewsData.html">API</a>]
+    The <code>NewsData</code> [<a href="../../../api/net/sf/basedb/core/data/NewsData.html">API</a>]
     class holds information about news. It has three dates: 
     <code>startDate</code>, <code>newsDate</code> and <code>endDate</code>. The
@@ -66 +66 @@
   <h3>Filters</h3>
   Filters have been replace by <code>ItemContext</code>:s 
-  [<a href="../../../api/develop/net/sf/basedb/core/ItemContext.html">API</a>].
+  [<a href="../../../api/net/sf/basedb/core/ItemContext.html">API</a>].
   <p>
   TODO - write documentation and add to UML image
@@ -75 +75 @@
     Messages are mainly used for the system to notify a user when something, ie. a job
     has been completed. A <code>MessageData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/MessageData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/MessageData.html">API</a>]
     holds information about the message. Information about the sender is kept in
     the <code>from</code> and <code>fromId</code> properties. We didn't want to create
@@ -92 +92 @@
   <p>
     The <code>AnyToAnyData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/AnyToAnyData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/AnyToAnyData.html">API</a>]
     class allows us to create links between any two items. A link has a direction and name. 
     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

@@ -64 +64 @@
   <h3>ParameterValueData</h3>
   <p>
-  The <code>ParameterValueData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ParameterValueData.html">API</a>]
+  The <code>ParameterValueData</code> [<a href="../../../api/net/sf/basedb/core/data/ParameterValueData.html">API</a>]
   class is an abstract base class that can hold multiple values. It should be used when declaring the generic for
   collection classes. That way a collection can hold mixed type of parameter value classes. The values will be saved as
@@ -107 +107 @@
   <p>
   Every type that can be saved have its own subclass. Except for the item classes that all share the same subclass, a subclass
-  that can hold <code>BasicItem</code>s [<a href="../../../api/develop/net/sf/basedb/core/BasicItem.html">API</a>] derives.
+  that can hold <code>BasicItem</code>s [<a href="../../../api/net/sf/basedb/core/BasicItem.html">API</a>] derives.
   </p>
 </body>

trunk/doc/development/overview/data/plates.html

@@ -62 +62 @@
   <h3>Plates</h3>
   <p>
-    <code>PlateData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PlateData.html">API</a>]
+    <code>PlateData</code> [<a href="../../../api/net/sf/basedb/core/data/PlateData.html">API</a>]
     is the main class holding information about a single plate.
     However it all starts with the <code>PlateGeometryData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
     which defines how many rows and columns there are on a plate. Since this information is used
     to create wells, and various other checks it is not possible to change the number of
@@ -73 +73 @@
   <p>
     All plates must have a <code>PlateTypeData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/PlateGeometryData.html">API</a>]
     which defines the geometry and a set of event types (see below).
   </p>
@@ -89 +89 @@
   <p>
     A plate can be created either from scratch or by a <code>PlateMappingData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/PlateMappingData.html">API</a>]. 
+    [<a href="../../../api/net/sf/basedb/core/data/PlateMappingData.html">API</a>]. 
     In the first case it is possible to specify a reporter for each well on the plate.
     In the second case the mapping code creates all the wells and links them to
@@ -101 +101 @@
   <p>
     The plate type defines a set of <code>PlateEventTypeData</code>
-    [<a href="../../../api/develop/net/sf/basedb/core/data/PlateEventTypeData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/PlateEventTypeData.html">API</a>]
     objects. For a plate of a certain type, it is possible to attach
     exactly one event of each event type. The event type defines an optional protocol type,

trunk/doc/development/overview/data/plugins.html

@@ -61 +61 @@
   <h3>PluginDefinitionData</h3>
   <p>
-    The <code>PluginDefinitionData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>]
+    The <code>PluginDefinitionData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginDefinitionData.html">API</a>]
     holds information of the installed plugin classes. This information is saved when the plugin is installed, it's then used by the
     system to load and run the plugin.
@@ -68 +68 @@
   <h3>PluginConfigurationData</h3>
   <p>
-    <code>PluginConfigurationData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginConfigurationData.html">API</a>]
+    <code>PluginConfigurationData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginConfigurationData.html">API</a>]
     is used for storing configuration values related to a plugin. A plugin may have many
     different configurations. The flags <code>supportsConfigurations</code> and
@@ -87 +87 @@
   <h3>PluginTypeData</h3>
   <p>
-    The <code>PluginTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/PluginTypeData.html">API</a>]
+    The <code>PluginTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/PluginTypeData.html">API</a>]
     is used to register information about the additional interfaces a plugin implements. This
     may allow a plugins to be used only in certain contexts. For example, we define
@@ -98 +98 @@
   <h3>JobData</h3>
   <p>
-    The <code>JobData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/JobData.html">API</a>]
+    The <code>JobData</code> [<a href="../../../api/net/sf/basedb/core/data/JobData.html">API</a>]
     class holds information about one execution of a plugin. The job can be in different states:
     <ul>
@@ -112 +112 @@
   <h3>JobAgentData and JobAgentSettingsData</h3>
   <p>
-    A <code>JobAgentData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/JobAgentData.html">API</a>]
+    A <code>JobAgentData</code> [<a href="../../../api/net/sf/basedb/core/data/JobAgentData.html">API</a>]
     holds information about a job agent. A job agent is a program running on the same
     or a different server that is regularly checking for jobs that are waiting
     to be executed. The <code>JobAgentSettingsData</code> 
-    [<a href="../../../api/develop/net/sf/basedb/core/data/JobAgentSettingsData.html">API</a>]
+    [<a href="../../../api/net/sf/basedb/core/data/JobAgentSettingsData.html">API</a>]
     class links to the plugins the job agent is able to execute. The job agent will
     only execute jobs that are owner by users or projects that the job agent has been 

trunk/doc/development/overview/data/reporters.html

@@ -62 +62 @@
   <h3>Reporters</h3>
   <p>
-  The <code>ReporterData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ReporterData.html">API</a>]
+  The <code>ReporterData</code> [<a href="../../../api/net/sf/basedb/core/data/ReporterData.html">API</a>]
   class holds information about reporters. The <code>externalId</code>
   is a unique name for the reporter. In the default setup this 
   table contains nothing more than the external ID, gene name and symbol.
   This class doesn't have an item class in the core, instead
-  it has an utility class <code>Reporter</code> [<a href="../../../api/develop/net/sf/basedb/core/Reporter.html">API</a>]
-  and is saved with <code>ReporterBatcher</code> [<a href="../../../api/develop/net/sf/basedb/core/ReporterBatcher.html">API</a>].
+  it has an utility class <code>Reporter</code> [<a href="../../../api/net/sf/basedb/core/Reporter.html">API</a>]
+  and is saved with <code>ReporterBatcher</code> [<a href="../../../api/net/sf/basedb/core/ReporterBatcher.html">API</a>].
   </p>
   <p>
@@ -75 +75 @@
   into this table. The name and type of the columns must also be
   described in an XML configuration file. The format of this file
-  is described by the <code>ExtendableData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ExtendableData.html">API</a>].
+  is described by the <code>ExtendableData</code> [<a href="../../../api/net/sf/basedb/core/data/ExtendableData.html">API</a>].
   Here is an example:
   </p>
@@ -97 +97 @@
   <h3>ReporterTypes</h3>
   <p>
-  The <code>ReporterTypeData</code> [<a href="../../../api/develop/net/sf/basedb/core/data/ReporterTypeData.html">API</a>]
+  The <code>ReporterTypeData</code> [<a href="../../../api/net/sf/basedb/core/data/ReporterTypeData.html">API</a>]
   class holds reporter type information. A reporter may have, but is 
   not required to have a type. The main reason for a reporter to have a

trunk/doc/development/overview/dynamic/create.html

@@ -55 +55 @@
     <ul>
     <li><a href="../data/experiments.html">Data layer API and database schema</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/datacube.html

@@ -54 +54 @@
     </p>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/extravalues.html

@@ -54 +54 @@
     <ul>
     <li><a href="datacube.html">Understanding the data cube</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/filter.html

@@ -54 +54 @@
     <ul>
     <li><a href="datacube.html">Understanding the data cube</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/index.html

@@ -65 +65 @@
     <ul>
     <li><a href="../data/experiments.html">Data layer API and database schema</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/insert.html

@@ -55 +55 @@
     <ul>
     <li><a href="query.html">Querying the dynamic tables</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/intensities.html

@@ -54 +54 @@
     <ul>
     <li><a href="datacube.html">Understanding the data cube</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/merge.html

@@ -54 +54 @@
     <ul>
     <li><a href="datacube.html">Understanding the data cube</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/query.html

@@ -60 +60 @@
     <ul>
     <li><a href="../query/index.html">Query API overview</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/dynamic/rootbioassayset.html

@@ -60 +60 @@
     <ul>
     <li><a href="datacube.html">Understanding the data cube</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/exceptions/index.html

@@ -49 +49 @@
     </p>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
+    <li><a href="../../../api/net/sf/basedb/core/package-summary.html">Javadoc for the net.sf.basedb.core package</a>
     </ul>
     

trunk/doc/development/overview/query/elements.html

@@ -55 +55 @@
     <ul>
     <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
+    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     </ul>
     

trunk/doc/development/overview/query/index.html

@@ -63 +63 @@
     <ul>
     <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
+    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     </ul>
     

trunk/doc/development/overview/query/overview.html

@@ -63 +63 @@
     <li><a href="../core/batchprocessing.html">Batch processing</code>
     <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
+    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     </ul>
     

trunk/doc/development/overview/query/result.html

@@ -55 +55 @@
     <ul>
     <li><a href="../dynamic/query.html">Dynamic API - Querying the dynamic tables</a>
-    <li><a href="../../../api/develop/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
+    <li><a href="../../../api/net/sf/basedb/core/query/package-summary.html">Javadoc for the net.sf.basedb.core.query package</a>
     </ul>
     

trunk/doc/development/overview/utility/index.html

@@ -49 +49 @@
     </p>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/util/package-summary.html">Javadoc for the net.sf.basedb.util package</a>
+    <li><a href="../../../api/net/sf/basedb/util/package-summary.html">Javadoc for the net.sf.basedb.util package</a>
     </ul>
     

trunk/doc/development/overview/web/index.html

@@ -49 +49 @@
     </p>
     <ul>
-    <li><a href="../../../api/develop/net/sf/basedb/clients/web/package-summary.html">Javadoc for the net.sf.basedb.clients.web package</a>
+    <li><a href="../../../api/net/sf/basedb/clients/web/package-summary.html">Javadoc for the net.sf.basedb.clients.web package</a>
     </ul>
     

trunk/doc/index.html

@@ -27 +27 @@
 <html>
   <head>
-    <title>BASE 2.0 - Development site</title>
+    <title>BASE 2 - Documentation</title>
   <link rel=stylesheet type="text/css" href="styles.css">
-  <meta http-equiv="refresh" content="0;url=http://base.thep.lu.se">
-  </head>
+ </head>
 <body>
 
-<a href="http://base.thep.lu.se">The BASE project site</a>
+<div class="navigation">
+  BASE 2 - Documentation
+</div>
+
+  <h1>BASE 2 - Documentation</h1>
+
+  <div class="abstract">
+    
+    <b>Contents</b><br>
+    <ul>
+    <li><a href="installation.html">Installation instructions</a></li>
+    <li><a href="admin/index.html">Administrator documentation</a></li>
+    <li><a href="development/index.html">Developers documentation</a></li>
+    <li><a href="user/index.html">User documentation</a></li>
+    </ul>
+  </div>
 
 </body>

trunk/doc/specifications/core/defaultdata.html

@@ -111 +111 @@
     <ul>
     <li>One role key for each item type. For permissions
-    see the <a href="../../api/develop/net/sf/basedb/core/doc-files/item_permissions.html">
+    see the <a href="../../api/net/sf/basedb/core/doc-files/item_permissions.html">
     Item permissions</a> document
     </ul>

trunk/src/core/net/sf/basedb/core/BasicItem.java

@@ -384 +384 @@
     @throws BaseException If there is an error
     @see Validatable
-    @see <a href="../../../../../../development/overview/core/datavalidation.html">Core API overview - Data validation</a>
-    @see <a href="../../../../../../development/coding/item/index.html#validation">Coding rules and guidelines for item classes</a>
+    @see <a href="../../../../../development/overview/core/datavalidation.html">Core API overview - Data validation</a>
+    @see <a href="../../../../../development/coding/item/index.html#validation">Coding rules and guidelines for item classes</a>
   */
   void validate()
@@ -400 +400 @@
     @throws BaseException If there is an error
     @see Transactional
-    @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
-    @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
+    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
+    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
   */
   void onBeforeCommit(Transactional.Action action)
@@ -432 +432 @@
     @throws BaseException If there is an error
     @see Transactional
-    @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
-    @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
+    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
+    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
   */
   void onAfterInsert()
@@ -449 +449 @@
 
     @see Transactional
-    @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
-    @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
+    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
+    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
   */
   void onAfterCommit(Transactional.Action action)
@@ -465 +465 @@
 
     @see Transactional
-    @see <a href="../../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
-    @see <a href="../../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
+    @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
+    @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
   */
   void onRollback(Transactional.Action action)

trunk/src/core/net/sf/basedb/core/Batcher.java

@@ -30 +30 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../development/overview/core/batchprocessing.html">Batch processing overview</a>
+  @see <a href="../../../../../development/overview/core/batchprocessing.html">Batch processing overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/ContextKey.java

@@ -28 +28 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/DataCube.java

@@ -68 +68 @@
   @version 2.0
   @base.modified $Date$
-  @see <a href="../../../../../../development/overview/dynamic/index.html">Dynamic API overview</a>
+  @see <a href="../../../../../development/overview/dynamic/index.html">Dynamic API overview</a>
 */
 public class DataCube

trunk/src/core/net/sf/basedb/core/MappingBatcher.java

@@ -40 +40 @@
   implemented).
   <p>
-  Code example: {@link <a href="../../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
+  Code example: {@link <a href="../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
 
   @author Nicklas

trunk/src/core/net/sf/basedb/core/PositionBatcher.java

@@ -40 +40 @@
   Normally this means linking a position to a reporter.
   <p>
-  Code example: {@link <a href="../../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
+  Code example: {@link <a href="../../../../../development/overview/dynamic/rootbioassayset.html">Dynamic API - Creating a root bioassayset</a>}
 
   @author Nicklas

trunk/src/core/net/sf/basedb/core/QueryRuntimeFilter.java

@@ -45 +45 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
+  @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterFactory.java

@@ -44 +44 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../development/overview/query/overview.html#factory">Query API overview - filter factory</a>
+  @see <a href="../../../../../development/overview/query/overview.html#factory">Query API overview - filter factory</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterManager.java

@@ -34 +34 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
+  @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/Validatable.java

@@ -27 +27 @@
   This interface is a tagging interface for items that needs case 2
   validation. See <a 
-  href="../../../../../../development/overview/core/datavalidation,html">Core API overview - 
+  href="../../../../../development/overview/core/datavalidation,html">Core API overview - 
   Data validation</a> and <a 
-  href="../../../../../../development/coding/item/index.html#validation">Coding rules and 
+  href="../../../../../development/coding/item/index.html#validation">Coding rules and 
   guidelines for item classes</a>
   <p>

trunk/src/core/net/sf/basedb/core/data/AnnotatableData.java

@@ -57 +57 @@
   @see AnnotationTypeData
   @see net.sf.basedb.core.Annotatable
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
 */
 public interface AnnotatableData

trunk/src/core/net/sf/basedb/core/data/AnnotatedData.java

@@ -33 +33 @@
   @see AnnotatableData
   @see net.sf.basedb.core.AnnotatedItem
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotation overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotation overview</a>
 */
 public abstract class AnnotatedData

trunk/src/core/net/sf/basedb/core/data/AnnotationData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Annotation
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
   @hibernate.class table="`Annotations`" lazy="false"
  */

trunk/src/core/net/sf/basedb/core/data/AnnotationSetData.java

@@ -35 +35 @@
   @version 2.0
   @see net.sf.basedb.core.AnnotationSet
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
   @hibernate.class table="`AnnotationSets`" lazy="true" batch-size="10"
  */

trunk/src/core/net/sf/basedb/core/data/AnnotationTypeCategoryData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.AnnotationTypeCategory
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
   @base.modified $Date: 2006-04-18 10:48:02 +0100 (Tue, 18 Apr 2006) $
   @hibernate.class table="`AnnotationTypeCategories`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

@@ -35 +35 @@
   @version 2.0
   @see net.sf.basedb.core.AnnotationType
-  @see <a href="../../../../../../../development/overview/data/annotations.html">Annotations overview</a>
+  @see <a href="../../../../../../development/overview/data/annotations.html">Annotations overview</a>
   @base.modified $Date$
   @hibernate.class table="`AnnotationTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/AnyToAnyData.java

@@ -32 +32 @@
   @see net.sf.basedb.core.AnyToAny
   @base.modified $Date$
-  @see <a href="../../../../../../../development/overview/data/misc.html">Misc overview</a>
+  @see <a href="../../../../../../development/overview/data/misc.html">Misc overview</a>
   @hibernate.class table="`AnyToAny`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/ArrayBatchData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ArrayBatch
-  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
   @base.modified $Date$
   @hibernate.class table="`ArrayBatches`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/ArrayDesignBlockData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ArrayDesignBlock
-  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
   @base.modified $Date$
   @hibernate.class table="`ArrayDesignBlocks`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/ArrayDesignData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ArrayDesign
-  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
   @base.modified $Date$
   @hibernate.class table="`ArrayDesigns`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/ArrayDesignPlateData.java

@@ -31 +31 @@
   @see net.sf.basedb.core.ArrayDesign
   @see net.sf.basedb.core.Plate
-  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
   @base.modified $Date$
   @hibernate.class table="`ArrayDesignPlates`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/ArraySlideData.java

@@ -30 +30 @@
  @version 2.0
  @see net.sf.basedb.core.ArraySlide
- @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+ @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
  @base.modified $Date$
  @hibernate.class table="`ArraySlides`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/BasicData.java

@@ -44 +44 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public abstract class BasicData

trunk/src/core/net/sf/basedb/core/data/BatchableData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.BasicBatcher
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
-  @see <a href="../../../../../../../development/overview/core/index.html#batch">Batch processing</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/core/index.html#batch">Batch processing</a>
 */
 public interface BatchableData

trunk/src/core/net/sf/basedb/core/data/BioAssayData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.BioAssay
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`BioAssays`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/BioAssaySetData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.BioAssaySet
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`BioAssaySets`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/BioMaterialData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.BioMaterial
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.class table="`BioMaterials`" lazy="false" discriminator-value="-1"

trunk/src/core/net/sf/basedb/core/data/BioMaterialEventData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.BioMaterialEvent
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.class table="`BioMaterialEvents`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/BioSourceData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.BioSource
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="1"

trunk/src/core/net/sf/basedb/core/data/BooleanParameterValueData.java

@@ -32 +32 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="7"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/ClientData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Client
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`Clients`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/ClientDefaultSettingData.java

@@ -27 +27 @@
   @author enell
   @see net.sf.basedb.core.ClientDefaultSetting
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`ClienDefaultSettings`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/CommonData.java

@@ -32 +32 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public abstract class CommonData

trunk/src/core/net/sf/basedb/core/data/ContextData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.ItemContext
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @base.modified $Date$
   @hibernate.class table="`Contexts`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/ContextIndex.java

@@ -30 +30 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/DataCubeColumnData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.DataCubeColumn
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`DataCubeColumns`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DataCubeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.DataCube
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`DataCubes`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DataCubeExtraValueData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.DataCubeExtraValue
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`DataCubeExtraValues`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DataCubeFilterData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.DataCubeFilter
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`DataCubeFilters`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DataCubeLayerData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.DataCubeLayer
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`DataCubeLayers`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DateParameterValueData.java

@@ -33 +33 @@
   @author Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="8"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/DirectoryData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.Directory
-  @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
+  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
   @base.modified $Date$
   @hibernate.class table="`Directories`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/DiskConsumableData.java

@@ -61 +61 @@
   @see DiskUsageData
   @see net.sf.basedb.core.DiskConsumable
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
 */
 public interface DiskConsumableData

trunk/src/core/net/sf/basedb/core/data/DiskUsageData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.DiskUsage
-  @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
+  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
   @base.modified $Date$
   @hibernate.class table="`DiskUsage`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/DoubleParameterValueData.java

@@ -32 +32 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="4"
   @base.modified $Date: 2005-07-05 15:51:30 +0200 (ti, 05 jul 2005) $

trunk/src/core/net/sf/basedb/core/data/ExperimentData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.Experiment
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`Experiments`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/ExtraValueData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.ExtraValue
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @hibernate.class table="`ExtraValues`" lazy="false"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/ExtraValueTypeData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.ExtraValueType
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @hibernate.class table="`ExtraValueTypes`" lazy="true"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/ExtractData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Extract
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="3" lazy="false"

trunk/src/core/net/sf/basedb/core/data/FeatureData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Feature
-  @see <a href="../../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
+  @see <a href="../../../../../../development/overview/data/slides.html">Array LIMS - slides overview</a>
   @base.modified $Date$
   @hibernate.class table="`Features`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/FileAttachableData.java

@@ -52 +52 @@
   @version 2.0
   @see BasicData
-  @see <a href="../../../../../../../development/overview/data/files.html">File and directory overview</a>
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/files.html">File and directory overview</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface FileAttachableData

trunk/src/core/net/sf/basedb/core/data/FileData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.File
-  @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
+  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
   @base.modified $Date$
   @hibernate.class table="`Files`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/FileTypeData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.File
-  @see <a href="../../../../../../../development/overview/data/file.html">File and directory overview</a>
+  @see <a href="../../../../../../development/overview/data/file.html">File and directory overview</a>
   @base.modified $Date$
   @hibernate.class table="`FileTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/FloatParameterValueData.java

@@ -32 +32 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="3"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/FormulaData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.Formula
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Session and client overview</a>
   @hibernate.class table="`Formulas`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/GlobalDefaultSettingData.java

@@ -27 +27 @@
   @author enell
   @see net.sf.basedb.core.GlobalDefaultSetting
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`GlobalDefaultSettings`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/GroupData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.Group
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.class table="`Groups`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/GuiContextData.java

@@ -34 +34 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins ovreview</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins ovreview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/HardwareData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Hardware
-  @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
+  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
   @base.modified $Date$
   @hibernate.class table="`Hardware`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/HardwareTypeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.HardwareType
-  @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
+  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
   @base.modified $Date$
   @hibernate.class table="`HardwareTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/HelpData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Help
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @base.modified $Date$
   @hibernate.class table="`HelpTexts`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/HybridizationData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Hybridization
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
   @hibernate.class table="`Hybridizations`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/IdentifiableData.java

@@ -46 +46 @@
   @version 2.0
   @see BasicData
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface IdentifiableData

trunk/src/core/net/sf/basedb/core/data/ImageData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.Image
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
   @hibernate.class table="`Images`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/IntegerParameterValueData.java

@@ -32 +32 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="1"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/ItemKeyData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ItemKey
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="1"

trunk/src/core/net/sf/basedb/core/data/ItemParameterValueData.java

@@ -34 +34 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="10"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/JobAgentData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.JobAgent
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
   @base.modified $Date$
   @hibernate.class table="`JobAgents`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/JobAgentSettingsData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.JobAgentSettings
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
   @base.modified $Date$
   @hibernate.class table="`JobAgentSettings`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/JobData.java

@@ -35 +35 @@
   @version 2.0
   @see net.sf.basedb.core.Job
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
   @base.modified $Date$
   @hibernate.class table="`Jobs`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/KeyData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.Key
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.class table="`Keys`" lazy="true" discriminator-value="-1"

trunk/src/core/net/sf/basedb/core/data/LabelData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Label
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @hibernate.class table="`Labels`" lazy="false"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/LabeledExtractData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.LabeledExtract
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="4" lazy="false"

trunk/src/core/net/sf/basedb/core/data/LongParameterValueData.java

@@ -32 +32 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="2"
   @base.modified $Date: 2005-07-14 09:57:11 +0200 (to, 14 jul 2005) $

trunk/src/core/net/sf/basedb/core/data/MappingCoordinate.java

@@ -36 +36 @@
   @version 2.0
   @see PlateMappingData
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.MeasuredBioMaterial
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="-1" lazy="false"

trunk/src/core/net/sf/basedb/core/data/MessageData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Message
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugin/jobs overview</a>
   @hibernate.class table="`Messages`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/MimeTypeData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.MimeType
-  @see <a href="../../../../../../../development/overview/data/files.html">File and directory overview</a>
+  @see <a href="../../../../../../development/overview/data/files.html">File and directory overview</a>
   @base.modified $Date$
   @hibernate.class table="`MimeTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/NameableData.java

@@ -61 +61 @@
   @version 2.0
   @see CommonData
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface NameableData

trunk/src/core/net/sf/basedb/core/data/NewsData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.News
-  @see <a href="../../../../../../../development/overview/data/misc.html">Misc overview</a>
+  @see <a href="../../../../../../development/overview/data/misc.html">Misc overview</a>
   @hibernate.class table="`News`" lazy="false"
  */

trunk/src/core/net/sf/basedb/core/data/OwnableData.java

@@ -53 +53 @@
   @see OwnedData
   @see net.sf.basedb.core.Ownable
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface OwnableData

trunk/src/core/net/sf/basedb/core/data/OwnedData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.OwnedItem
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public abstract class OwnedData

trunk/src/core/net/sf/basedb/core/data/ParameterValueData.java

@@ -31 +31 @@
   @author Nicklas, Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.class table="`ParameterValues`" discriminator-value="-1" lazy="true" batch-size="10"
   @hibernate.discriminator column="`discriminator`" type="int"

trunk/src/core/net/sf/basedb/core/data/PasswordData.java

@@ -32 +32 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @hibernate.class table="`Passwords`" lazy="true"
 */

trunk/src/core/net/sf/basedb/core/data/PlateCoordinate.java

@@ -36 +36 @@
   @version 2.0
   @see PlateData
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/PlateData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.Plate
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`Plates`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/PlateEventData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.PlateEvent
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`PlateEvents`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/PlateEventTypeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.PlateEventType
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`PlateEventTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/PlateGeometryData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.PlateGeometry
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`PlateGeometries`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/PlateMappingData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.PlateMapping
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`PlateMappings`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/PlateTypeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.PlateType
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`PlateTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/PluginConfigurationData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.PluginConfiguration
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
   @hibernate.class table="`PluginConfigurations`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/PluginDefinitionData.java

@@ -37 +37 @@
   @version 2.0
   @see net.sf.basedb.core.PluginDefinition
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
   @hibernate.class table="`PluginDefinitions`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/PluginPermission.java

@@ -28 +28 @@
   @author Martin
   @version 2.1
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
 */
 public class PluginPermission 

trunk/src/core/net/sf/basedb/core/data/PluginTypeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.PluginType
-  @see <a href="../../../../../../../development/overview/data/plugins.html">Plugins</a>
+  @see <a href="../../../../../../development/overview/data/plugins.html">Plugins</a>
   @hibernate.class table="`PluginTypes`" lazy="false"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/ProjectData.java

@@ -34 +34 @@
   @version 2.0
   @see net.sf.basedb.core.Project
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.class table="`Projects`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/ProjectKeyData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ProjectKey
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="2"

trunk/src/core/net/sf/basedb/core/data/PropertyFilterData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.ItemContext
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/ProtocolData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.Protocol
-  @see <a href="../../../../../../../development/overview/data/protocols.html">Protocol overview</a>
+  @see <a href="../../../../../../development/overview/data/protocols.html">Protocol overview</a>
   @hibernate.class table="`Protocols`" lazy="true"
 */

trunk/src/core/net/sf/basedb/core/data/ProtocolTypeData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.ProtocolType
-  @see <a href="../../../../../../../development/overview/data/protocols.html">Protocol overview</a>
+  @see <a href="../../../../../../development/overview/data/protocols.html">Protocol overview</a>
   @hibernate.class table="`ProtocolTypes`" lazy="false"
   

trunk/src/core/net/sf/basedb/core/data/QuotaData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.Quota
-  @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
+  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
   @hibernate.class table="`Quota`" lazy="true"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/QuotaIndex.java

@@ -35 +35 @@
   @author enell
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
+  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/QuotaTypeData.java

@@ -29 +29 @@
   @author enell
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/quota.html">Quota overview</a>
+  @see <a href="../../../../../../development/overview/data/quota.html">Quota overview</a>
   @base.modified $Date$
   @hibernate.class table="`QuotaTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/RawBioAssayData.java

@@ -36 +36 @@
   @version 2.0
   @see net.sf.basedb.core.RawBioAssay
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
   @hibernate.class table="`RawBioAssays`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/RawData.java

@@ -37 +37 @@
   @see net.sf.basedb.core.RawDataBatcher
   @see net.sf.basedb.core.RawDataUtil
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/RemovableData.java

@@ -59 +59 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface RemovableData

trunk/src/core/net/sf/basedb/core/data/ReporterData.java

@@ -47 +47 @@
   @see net.sf.basedb.core.ReporterBatcher
   @see net.sf.basedb.core.ExtendedProperties
-  @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
+  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
   @hibernate.class table="`Reporters`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/ReporterListData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.ReporterList
-  @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
+  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
   @hibernate.class table="`ReporterLists`" lazy="true"
 */

trunk/src/core/net/sf/basedb/core/data/ReporterListScoreData.java

@@ -36 +36 @@
   @version 2.0
   @see net.sf.basedb.core.ReporterList
-  @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
+  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
 */
 @SuppressWarnings({"serial"})

trunk/src/core/net/sf/basedb/core/data/ReporterTypeData.java

@@ -35 +35 @@
   @version 2.0
   @see net.sf.basedb.core.data.ReporterData
-  @see <a href="../../../../../../../development/overview/data/reporters.html">Reporter overview</a>
+  @see <a href="../../../../../../development/overview/data/reporters.html">Reporter overview</a>
   @hibernate.class table="`ReporterTypes`" lazy="true"
 */

trunk/src/core/net/sf/basedb/core/data/RoleData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.Role
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.class table="`Roles`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/RoleKeyData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.RoleKey
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="3"

trunk/src/core/net/sf/basedb/core/data/SampleData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Sample
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
   @hibernate.subclass discriminator-value="2" lazy="false"

trunk/src/core/net/sf/basedb/core/data/ScanData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Scan
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
   @hibernate.class table="`Scans`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/SessionData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.Session
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`Sessions`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/SettingData.java

@@ -28 +28 @@
   @version 2.0
   @see net.sf.basedb.core.Setting
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
 */
 public abstract class SettingData

trunk/src/core/net/sf/basedb/core/data/ShareableData.java

@@ -71 +71 @@
   @see SharedData
   @see net.sf.basedb.core.Shareable
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface ShareableData

trunk/src/core/net/sf/basedb/core/data/SharedData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.SharedItem
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public abstract class SharedData

trunk/src/core/net/sf/basedb/core/data/SoftwareData.java

@@ -29 +29 @@
   @version 2.0
   @see net.sf.basedb.core.Software
-  @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
+  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
   @base.modified $Date$
   @hibernate.class table="`Software`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/SoftwareTypeData.java

@@ -32 +32 @@
   @version 2.0
   @see net.sf.basedb.core.SoftwareType
-  @see <a href="../../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
+  @see <a href="../../../../../../development/overview/data/wares.html">Hardware and software overview</a>
   @base.modified $Date$
   @hibernate.class table="`SoftwareTypes`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/SpotImagesData.java

@@ -31 +31 @@
   @version 2.0
   @see net.sf.basedb.core.SpotImages
-  @see <a href="../../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
+  @see <a href="../../../../../../development/overview/data/hybridizations.html">Hybridzations and raw data overview</a>
   @base.modified $Date$
   @hibernate.class table="`SpotImages`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/StringParameterValueData.java

@@ -32 +32 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="5"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/SystemData.java

@@ -60 +60 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
+  @see <a href="../../../../../../development/overview/data/basic.html">Basic classes and interfaces</a>
 */
 public interface SystemData

trunk/src/core/net/sf/basedb/core/data/TextParameterValueData.java

@@ -32 +32 @@
   @author Samuel
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/parameters.html">Parameters overview</a>
+  @see <a href="../../../../../../development/overview/data/parameters.html">Parameters overview</a>
   @hibernate.subclass discriminator-value="6"
   @base.modified $Date$

trunk/src/core/net/sf/basedb/core/data/TransformationData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.Transformation
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`Transformations`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/UsedQuantity.java

@@ -33 +33 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
+  @see <a href="../../../../../../development/overview/data/biomaterial.html">Biomaterials overview</a>
   @base.modified $Date$
 */

trunk/src/core/net/sf/basedb/core/data/UserClientSettingData.java

@@ -27 +27 @@
   @author enell
   @see net.sf.basedb.core.UserClientSetting
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`UserClientSettings`" lazy="false"
  */

trunk/src/core/net/sf/basedb/core/data/UserData.java

@@ -35 +35 @@
   @version 2.0
   @see net.sf.basedb.core.User
-  @see <a href="../../../../../../../development/overview/data/authentication.html">Authentication overview</a>
+  @see <a href="../../../../../../development/overview/data/authentication.html">Authentication overview</a>
   @base.modified $Date$
   @hibernate.class table="`Users`" lazy="false"

trunk/src/core/net/sf/basedb/core/data/UserDefaultSettingData.java

@@ -27 +27 @@
   @author enell
   @see net.sf.basedb.core.UserDefaultSetting
-  @see <a href="../../../../../../../development/overview/data/clients.html">Session and client overview</a>
+  @see <a href="../../../../../../development/overview/data/clients.html">Session and client overview</a>
   @hibernate.class table="`UserDefaultSettings`" lazy="false"
 */

trunk/src/core/net/sf/basedb/core/data/VirtualDbData.java

@@ -33 +33 @@
   @version 2.0
   @see net.sf.basedb.core.VirtualDb
-  @see <a href="../../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
+  @see <a href="../../../../../../development/overview/data/experiments.html">Experiments and analysis overview</a>
   @base.modified $Date$
   @hibernate.class table="`VirtualDbs`" lazy="true"

trunk/src/core/net/sf/basedb/core/data/WellData.java

@@ -30 +30 @@
   @version 2.0
   @see net.sf.basedb.core.Well
-  @see <a href="../../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
+  @see <a href="../../../../../../development/overview/data/plates.html">Array LIMS - Plates overview</a>
   @base.modified $Date$
   @hibernate.class table="`Wells`" lazy="true"

trunk/src/core/net/sf/basedb/core/query/Query.java

@@ -60 +60 @@
   @author Nicklas
   @version 2.0
-  @see <a href="../../../../../../../development/overview/query/index.html">Query API documentation</a>
+  @see <a href="../../../../../../development/overview/query/index.html">Query API documentation</a>
   @see net.sf.basedb.core.AbstractQuery
   @base.modified $Date$