Changeset 5818


Ignore:
Timestamp:
Oct 21, 2011, 1:15:41 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Some more sections in the developer documentation should now be up-to-date:

  • Web services
  • Parts of "The BASE API"
    • section 1: The public api of BASE.
    • section 2: The data layer api
    • section 3.9: Using files to store data
    • section 3.10: Sending signals to plug-ins


Sections 3.1 -- 3.8 are in the old format and will not be updated now.

"The Query API" and "The Dynamic API" are in the old format and will not be updated now.

"The Extensions API" need a big re-write.

Also fixed a lot of javadoc links leading to the developer documentation.

Location:
trunk
Files:
176 edited

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r5805 r5818  
    12051205        <package name="net.sf.basedb.core.query" />
    12061206        <package name="net.sf.basedb.core.signal" />
     1207        <package name="net.sf.basedb.core.authentication" />
     1208        <package name="net.sf.basedb.core.snapshot" />
     1209        <package name="net.sf.basedb.plugins*" />
    12071210        <package name="net.sf.basedb.util*" />
    12081211        <package name="net.sf.basedb.clients.web.taglib*" />
    1209         <package name="net.sf.basedb.plugins*" />
    1210         <package name="net.sf.basedb.core.authentication" />
     1212        <package name="net.sf.basedb.clients.web.extensions*" />
    12111213        <package name="net.sf.basedb.ws.client" />
    1212         <package name="net.sf.basedb.core.filehandler" />
    1213         <package name="net.sf.basedb.clients.web.extensions*" />
    12141214      </group>
    12151215      <group title="Mixed Public and Internal API">
     
    12171217        <package name="net.sf.basedb.clients.web" />
    12181218        <package name="net.sf.basedb.clients.web.util" />
    1219         <package name="net.sf.basedb.util.overview" />
    12201219      </group>
    12211220      <group title="Extension API">
    12221221        <package name="net.sf.basedb.core.dbengine" />
     1222        <package name="net.sf.basedb.core.log*" />
     1223        <package name="net.sf.basedb.util.overview.*" />
     1224        <package name="net.sf.basedb.util.extensions.manager.*" />
    12231225        <package name="net.sf.basedb.clients.jobagent" />
    12241226        <package name="net.sf.basedb.ws.server*" />
  • trunk/doc/src/docbook/developer/base_api.xml

    r5782 r5818  
    5353   
    5454    <para>
    55       See the <ulink url="../../api/index.html"
     55      See the <ulink url="../../../api/index.html"
    5656        >BASE API javadoc</ulink> for information about
    5757      what parts of the API that contributes to the public API.
     
    851851      <title>Client, session and settings</title>
    852852      <para>
    853          This section gives an overview of hardware and software in BASE.
     853         This section gives an overview of client applications, sessions and settings.
    854854      </para>
    855855     
     
    26192619     
    26202620      <para>
    2621         BASE 2.5 introduced the possibility to use files to store data instead
    2622         of importing it into the database. Files can be attached
    2623         to any item that implements the <interfacename docapi="net.sf.basedb.core">FileStoreEnabled</interfacename>
    2624         interface. Currently this is <classname docapi="net.sf.basedb.core">RawBioAssay</classname>
    2625         and <classname docapi="net.sf.basedb.core">ArrayDesign</classname>. The
    2626         ability to store data in files is not a replacement for storing data in the
     2621        BASE has support for storing data in files instead of importing it into the database.
     2622        Files can be attached to any item that implements the <interfacename
     2623        docapi="net.sf.basedb.core">FileStoreEnabled</interfacename>
     2624        interface. For example, <classname docapi="net.sf.basedb.core">RawBioAssay</classname>,
     2625        and <classname docapi="net.sf.basedb.core">ArrayDesign</classname> and a few other
     2626        classes. The ability to store data in files is not a replacement for storing data in the
    26272627        database. It is possible (for some platforms/raw data types) to have data in
    2628         files and in the database at the same time. We would have liked to enforce
    2629         that (raw) data is always present in files, but this will not be backwards compatible
    2630         with older installations, so there are three cases:
     2628        files and in the database at the same time. There are three cases:
    26312629      </para>
    26322630     
     
    26842682
    26852683      <para>
    2686         One major change from earlier BASE versions is that the registration of raw data types
    2687         has changed. The <filename>raw-data-types.xml</filename> file should
    2688         only be used for raw data types that are stored in the database. The
    2689         <sgmltag>storage</sgmltag> tag has been deprecated and BASE will refuse
    2690         to start if it finds a raw data type definitions with <code>storage="file"</code>.
    2691       </para>
    2692      
     2684        Some <classname docapi="net.sf.basedb.core">FileStoreEnabled</classname> items doesn't
     2685        have a platform (for example, <classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>).
     2686        In this case, the file storage ability is controlled by the subtype of the item.
     2687        See <methodname>getDataFileTypes()</methodname> method in the
     2688        <classname docapi="net.sf.basedb.core">ItemSubtype</classname> class.
     2689      </para>
     2690
    26932691      <para>
    26942692        For backwards compatibility reasons, each <classname docapi="net.sf.basedb.core">Platform</classname>
     
    27062704        <title>See also</title>
    27072705        <listitem><xref linkend="data_api.platforms" /></listitem>
    2708         <listitem><xref linkend="plugin_developer.other.datafiles" /></listitem>
     2706        <listitem><xref linkend="extensions_developer.fileset_validator" /></listitem>
    27092707        <listitem><xref linkend="appendix.rawdatatypes.platforms" /></listitem>
    2710         <listitem>
    2711           <xref linkend="appendix.incompatible.2.5" /> in
    2712           <xref linkend="appendix.incompatible" />
    2713         </listitem>
    27142708      </itemizedlist>
    27152709     
     
    27322726        <para>
    27332727          This is rather large set of classes and methods. The ultimate goal
    2734           is to be able to create links between a <classname docapi="net.sf.basedb.core">RawBioAssay</classname>
    2735           / <classname docapi="net.sf.basedb.core">ArrayDesign</classname> and <classname docapi="net.sf.basedb.core">File</classname>
     2728          is to be able to create links between a <classname docapi="net.sf.basedb.core">FileStoreEnabled</classname>
     2729          item and <classname docapi="net.sf.basedb.core">File</classname>
    27362730          items and to provide some metadata about the files.
    27372731          The <classname docapi="net.sf.basedb.core">FileStoreUtil</classname> class is one of the most
     
    27572751          item we want to find out which <classname docapi="net.sf.basedb.core">DataFileType</classname>
    27582752          items that can be used for that item. The
    2759           <methodname>DataFileType.getQuery(FileStoreEnabled)</methodname>
    2760           can be used for this. Internally, the method uses the result from
    2761           <methodname>FileStoreEnabled.getPlatform()</methodname>
    2762           and <methodname>FileStoreEnabled.getVariant()</methodname>
    2763           methods to restrict the query to only return file types for
    2764           a given platform and/or variant. If the item doesn't have
    2765           a platform or variant the query will return all file types
    2766           that are associated with the given item type. In any case, we get a list
    2767           of <classname>DataFileType</classname> items, each one representing a
     2753          <methodname>Base.getDataFileTypes()</methodname>
     2754          can be used for this. You'll need to supply information about the platform,
     2755          variant and subtype of the item. The method will create a query that returns
     2756          a list of <classname>DataFileType</classname> items, each one representing a
    27682757          specific file type that we should ask the user about. Examples:
    27692758        </para>
     
    27742763          The <constant>Affymetrix</constant> platform defines <constant>CEL</constant>
    27752764          as a raw data file and <constant>CDF</constant> as an array design (reporter map)
    2776           file. If we have a <classname docapi="net.sf.basedb.core">RawBioAssay</classname> the query will only return
     2765          file. If we have a <classname docapi="net.sf.basedb.core">RawBioAssay</classname>
     2766          the query will only return
    27772767          the CEL file type and the client can ask the user for a CEL file.
    27782768          </para>
     
    27862776          </para>
    27872777        </listitem>
     2778        <listitem>
     2779          <para>
     2780          The <constant>Scan</constant> subtype defines <constant>MICROARRAY_IMAGE</constant>
     2781          for derived bioassays.
     2782          </para>
     2783        </listitem>
    27882784        </orderedlist>
    27892785     
    27902786        <para>
    27912787          It might also be interesting to know the currently selected file
    2792           for each file type and if the platform has set the <varname>required</varname>
    2793           flag for a particular file type. Here is a simple code example
     2788          for each file type and if the file is <varname>required</varname>
     2789          and if <varname>multiple</varname> files are allowed.
     2790          Here is a simple code example
    27942791          that may be useful to start from:
    27952792        </para>
     
    28002797Platform platform = item.getPlatform();
    28012798PlatformVariant variant = item.getVariant();
     2799Itemsubtype subtype = item instanceof Subtypable ?
     2800   ((Subtypable)item).getItemSubtype() : null;
    28022801
    28032802// Get list of DataFileTypes used by the platform
    28042803ItemQuery&lt;DataFileType&gt; query =
    2805    DataFileType.getQuery(item);
     2804   Base.getDataFileTypes(item.getType(), item, platform, variant, subtype);
    28062805List&lt;DataFileType&gt; types = query.list(dc);
    28072806
     
    28192818      null : member.getFile();
    28202819   
    2821    // Check if a file is required by the platform
     2820   // Check if a file is required by the platform/subtype
    28222821   PlatformFileType pft = platform == null ?
    2823       null : platform.getFileType(type, variant);
     2822      null : platform.getFileType(type, variant, false);
     2823   ItemSubtypeFileType ift = subtype == null ?
     2824      null : subtype.getAssociatedDataFileType(type, false);
    28242825   boolean isRequired = pft == null ?
    28252826      false : pft.isRequired();
     2827   isRequired |= ift == null ?
     2828      false : ift.isRequired();
    28262829     
    28272830   // Now we can do something with this information to
     
    28492852          When the user has selected the file(s) we must store the links
    28502853          to them in the database. This is done with a <classname docapi="net.sf.basedb.core">FileSet</classname>
    2851           object. A file set can contain any number of files. The only limitation
    2852           is that it can only contain one file for each file type.
    2853           Call <methodname>FileSet.setMember()</methodname> to store
    2854           a file in the file set. If a file already exists for the given file type
    2855           it is replaced, otherwise a new entry is created. The following
     2854          object. A file set can contain any number of files.
     2855          Call <methodname>FileSet.setMember()</methodname> or <methodname>FileSet.addMember()</methodname>
     2856          to store a file in the file set. If a file already exists for the given file type
     2857          it is replaced if the <methodname>setMember</methodname> method is called.
     2858          The following
    28562859          program example assumes that we have a map where <classname docapi="net.sf.basedb.core">File</classname>:s
    28572860          are related to <classname docapi="net.sf.basedb.core">DataFileType</classname>:s. When all files
     
    28752878
    28762879// Validate the files and extract metadata
    2877 fileSet.validate(dc, true);
     2880fileSet.validate(dc);
    28782881</programlisting>
    28792882
     
    28812884          Validation and extraction of metadata is important since we want
    28822885          data in files to be equivalent to data in the database. The validation
    2883           and metadata extraction is done by the core when the
     2886          and metadata extraction is initiated by the core when the
    28842887          <methodname>FileSet.validate()</methodname> is called.
    2885           The process is partly pluggable since each <classname docapi="net.sf.basedb.core">DataFileType</classname>
    2886           can name a class that should do the validation and/or metadata extraction.
     2888          The validation and metadata extraction is handled by extensions
     2889          so the actual outcome depends on what has been installed on the
     2890          BASE server.
    28872891        </para>
    28882892
    28892893        <note>
    28902894          <para>
    2891           The <methodname>FileSet.validate()</methodname> only validates
    2892           the files where the file types have specified plug-ins that can
    2893           do the validation and metadata extraction. The method doesn't
     2895          The <methodname>FileSet.validate()</methodname> method doesn't
    28942896          throw any exceptions. Instead, all validation errors
    28952897          are returned a list of <classname>Throwable</classname>:s. The
     
    29072909        <listitem>
    29082910          <para>
    2909           The core checks the <classname docapi="net.sf.basedb.core">DataFileType</classname> of all
    2910           members in the file set and creates <classname docapi="net.sf.basedb.core.filehandler">DataFileValidator</classname>
    2911           and <classname docapi="net.sf.basedb.core.filehandler">DataFileMetadataReader</classname> objects. Only one instance
    2912           of each class is created. If the file set contains members which has the
    2913           same validator or metadata reader, they will all share the same instance.
    2914           </para>
    2915         </listitem>
    2916        
    2917         <listitem>
    2918           <para>
    2919           Each validator/metadata reader class is initialised with calls to
    2920           <methodname>DataFileHandler.setItem()</methodname> and
    2921           <methodname>DataFileHandler.setFile()</methodname>.
    2922           </para>
    2923         </listitem>
    2924        
    2925         <listitem>
    2926           <para>
    2927           Each validator is called. The result of the validation is saved for each
    2928           file and can be retreieved by <methodname>FileSetMember.isValid()</methodname>
    2929           and <methodname>FileSetMember.getErrorMessage()</methodname>.
    2930           </para>
    2931         </listitem>
    2932        
    2933         <listitem>
    2934           <para>
    2935           Each metadata reader is called, unless the metadata reader is the same class
    2936           as the validator and the validation failed. If the metadata reader is a
    2937           different class, it is called even if the validation failed.
     2911          The core calls the main <classname
     2912          docapi="net.sf.basedb.util.extensions.manager">ExtensionsManager</classname>
     2913          and initiates the action factory for all file set validator extensions.
     2914          </para>
     2915        </listitem>
     2916       
     2917        <listitem>
     2918          <para>
     2919          After inspecting the current item and file set, the factories create
     2920          one or more <interfacename
     2921          docapi="net.sf.basedb.util.fileset">ValidationAction</interfacename>:s.
     2922          </para>
     2923        </listitem>
     2924       
     2925        <listitem>
     2926          <para>
     2927          For each file in the file set, the <methodname>ValidationAction.acceptFile()</methodname>
     2928          method is called on each action, which is supposed to either accept or deny
     2929          validation of the file.
     2930          </para>
     2931        </listitem>
     2932       
     2933        <listitem>
     2934          <para>
     2935          If the file is accepted the <methodname>ValidationAction.validateAndExtractMetadata()</methodname>
     2936          method is called.
    29382937          </para>
    29392938        </listitem>
     
    29432942          <title>Only one instance of each validator class is created</title>
    29442943          <para>
    2945           The validation/metadata extraction is not done until all files have been
    2946           added to the fileset. If the same validator/meta data reader is
    2947           used for more than one file, the same instance is reused. Ie.
    2948           the <methodname>setFile()</methodname> is called one time
    2949           for each file/file type pair. The <methodname>validate()</methodname>
    2950           and <methodname>extractMetadata()</methodname> methods are only
    2951           called once.
     2944          The validation is not done until all files have been
     2945          added to the fileset. If the same validator is
     2946          used for more than one file, the same instance is reused. Eg.
     2947          the <methodname>acceptFile()</methodname> is called one time
     2948          for each file. Depending on the return value, the
     2949          <methodname>validateAndExtractMetadata()</methodname> may be called either
     2950          immediately or not until all files have been processed.
    29522951          </para>
    29532952        </note>
    2954        
    2955         <para>
    2956           All validators and meta data extractors should extend
    2957           the <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> class. The reason
    2958           is that we may want to add more methods to the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileHandler</interfacename>
    2959           interface in the future. The <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> will
    2960           be used to provide default implementations for backwards compatibility.
    2961         </para>
    29622953       
    29632954      </sect3>
     
    31223113          >ThreadSignalHandler</classname> which simply
    31233114          calls <code>Thread.interrupt()</code> to deliver a signal. The target
    3124           object that uses this signal handler it must know that it should check
    3125           <code>Thread.interrupted()</code> at regular intervals from the main
     3115          object that uses this signal handler must know that it should check
     3116          <code>Thread.interrupted()</code> at regular intervals from the worker
    31263117          thread. If that method returns true, it means that the <constant>ABORT</constant>
    31273118          signal has been delivered and the main thread should clean up and exit as
     
    32223213    <title>The Query API</title>
    32233214    <para>
    3224       This documentation is only available in the old format.
     3215      This documentation is only available in the old format which may not be up-to-date with
     3216      the current implementation.
    32253217      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html"
    32263218        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html</ulink>
     
    32333225    <title>The Dynamic API</title>
    32343226    <para>
    3235       This documentation is only available in the old format.
     3227      This documentation is only available in the old format which may not be up-to-date with
     3228      the current implementation.
    32363229      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html"
    32373230        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html</ulink>
  • trunk/doc/src/docbook/developer/webservices.xml

    r5782 r5818  
    105105              find out which raw bioassays that are part of it and
    106106              which bioassay sets have been created as part of the analysis.
     107              Find reporter lists that are part of the experiment and
     108              get information about the experimental factors.
    107109            </para>
    108110          </listitem>
     
    114116          <listitem>
    115117            <para>
    116               Services related to bioassay sets. Get access to the data in a bioassay
    117               set that has been previously exported to a file.
     118              Services related to bioassay sets. Get access data files that are
     119              attached to bioassay sets. Data from the database must first be
     120              exported and saved as a file. Find annotation values on bioassay sets.
    118121            </para>
    119122          </listitem>
     
    126129            <para>
    127130              Services related to raw bioassays. Find out which raw data files that
    128               are present and download them.
     131              are present and download them. Find annotation values on raw bioassays.
    129132            </para>
    130133          </listitem>
     
    137140            <para>
    138141              Services related to array design. Find out which data files that
    139               are present and download them.
     142              are present and download them. Find annotation values on array designs.
    140143            </para>
    141144          </listitem>
     
    149152              Services related to annotation types. Find out which annotation types that
    150153              can be used for different types of items.
     154            </para>
     155          </listitem>
     156        </varlistentry>
     157       
     158        <varlistentry>
     159          <term><classname docapi="net.sf.basedb.ws.server">ReporterService</classname></term>
     160          <term><classname docapi="net.sf.basedb.ws.client">ReporterClient</classname></term>
     161          <listitem>
     162            <para>
     163              Services related to reporters and reporter lists.
     164              Get information about all admin-defined extended properties.
     165              Download reporter information for reporters.
     166            </para>
     167          </listitem>
     168        </varlistentry>
     169
     170        <varlistentry>
     171          <term><classname docapi="net.sf.basedb.ws.server">FileService</classname></term>
     172          <term><classname docapi="net.sf.basedb.ws.client">FileClient</classname></term>
     173          <listitem>
     174            <para>
     175              Services related to files. Download files.
    151176            </para>
    152177          </listitem>
     
    160185    <title>Client development</title>
    161186    <para>
    162       How to develop client applications for the web services in BASE is, of course, depends
     187      How to develop client applications for the web services in BASE depends
    163188      on which program language you are using. BASE comes with a simple client API for java
    164189      for the existing services. If you use this API, you don't have to worry about WSDL
  • trunk/doc/src/javadoc/overview.html

    r4740 r5818  
    7171    the public API.
    7272  </li>
    73  
    74   <li>
    75     In <code>net.sf.basedb.util.overview</code> and sub-packages,
    76     all classes and methods that are from BASE 2.10 (marked with @since 2.10
    77     or @version 2.10) are considered internal. We are expecting things to change
    78     in those classes/methods in BASE 2.11 due to performance improvements that
    79     are needed.
    8073  </ul>
    8174 
  • trunk/lib/docbook/custom-styles/docbook/plain/css/docbook.css

    r5792 r5818  
    221221  background: #E0E0E0;
    222222  border: 1px solid gray;
     223  border-radius: 8px;
     224  -moz-border-radius: 8px;
     225  box-shadow: 3px 3px 5px #cccccc;
     226  -moz-box-shadow: 3px 3px 5px #999999;
     227  margin: 1em;
    223228}
    224229
  • trunk/src/core/net/sf/basedb/core/BasicItem.java

    r5689 r5818  
    398398    @throws BaseException If there is an error
    399399    @see Validatable
    400     @see <a href="../../../../../development/overview/core/datavalidation.html">Core API overview - Data validation</a>
    401     @see <a href="../../../../../development/coding/item/index.html#validation">Coding rules and guidelines for item classes</a>
     400    @see <a href="../../../../../html/developer/api/core_api.datavalidation.html">Developer documentation: Data validation</a>
     401    @see <a href="../../../../../html/developer/core_ref.rules.itemclass.html">Developer documentation: Coding rules and guidelines for item classes</a>
    402402  */
    403403  void validate()
     
    414414    @throws BaseException If there is an error
    415415    @see Transactional
    416     @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    417     @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     416    @see <a href="../../../../../html/developer/api/core_api.transactions.html">Developer documentation: Transactions</a>
     417    @see <a href="../../../../../html/developer/core_ref.rules.itemclass.html">Developer documentation: Coding rules and guidelines for item classes</a>
    418418  */
    419419  void onBeforeCommit(Transactional.Action action)
     
    463463    @throws BaseException If there is an error
    464464    @see Transactional
    465     @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    466     @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     465    @see <a href="../../../../../html/developer/api/core_api.transactions.html">Developer documentation: Transactions</a>
     466    @see <a href="../../../../../html/developer/core_ref.rules.itemclass.html">Developer documentation: Coding rules and guidelines for item classes</a>
    467467  */
    468468  void onAfterInsert()
     
    480480
    481481    @see Transactional
    482     @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    483     @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     482    @see <a href="../../../../../html/developer/api/core_api.transactions.html">Developer documentation: Transactions</a>
     483    @see <a href="../../../../../html/developer/core_ref.rules.itemclass.html">Developer documentation: Coding rules and guidelines for item classes</a>
    484484  */
    485485  void onAfterCommit(Transactional.Action action)
     
    496496
    497497    @see Transactional
    498     @see <a href="../../../../../development/overview/core/transactions.html">Core API overview - Transaction handling</a>
    499     @see <a href="../../../../../development/coding/item/index.html#transactions">Coding rules and guidelines for item classes</a>
     498    @see <a href="../../../../../html/developer/api/core_api.transactions.html">Developer documentation: Transactions</a>
     499    @see <a href="../../../../../html/developer/core_ref.rules.itemclass.html">Developer documentation: Coding rules and guidelines for item classes</a>
    500500  */
    501501  void onRollback(Transactional.Action action)
  • trunk/src/core/net/sf/basedb/core/Batcher.java

    r4889 r5818  
    2929  @author Nicklas
    3030  @version 2.0
    31   @see <a href="../../../../../development/overview/core/batchprocessing.html">Batch processing overview</a>
     31  @see <a href="../../../../../html/developer/api/core_api.batch.html">Developer documentation: Batch operations</a>
    3232  @base.modified $Date$
    3333*/
  • trunk/src/core/net/sf/basedb/core/ContextKey.java

    r4889 r5818  
    2626  @author Nicklas
    2727  @version 2.0
    28   @see <a href="../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     28  @see <a href="../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    2929  @base.modified $Date$
    3030*/
  • trunk/src/core/net/sf/basedb/core/DataCube.java

    r5689 r5818  
    7979  @version 2.0
    8080  @base.modified $Date$
    81   @see <a href="../../../../../development/overview/dynamic/index.html">Dynamic API overview</a>
     81  @see <a href="../../../../../html/developer/api/dynamic_api.html">Developer documentation: The Dynamic API</a>
    8282*/
    8383public class DataCube
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilter.java

    r4889 r5818  
    4444  @author Nicklas
    4545  @version 2.0
    46   @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
     46  @see <a href="../../../../../html/developer/api/query_api.html">Developer documentation: The Query API</a>
    4747  @base.modified $Date$
    4848*/
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterFactory.java

    r4889 r5818  
    4545  @author Nicklas
    4646  @version 2.0
    47   @see <a href="../../../../../development/overview/query/overview.html#factory">Query API overview - filter factory</a>
     47  @see <a href="../../../../../html/developer/api/query_api.html">Developer documentation: The Query API</a>
    4848  @base.modified $Date$
    4949*/
  • trunk/src/core/net/sf/basedb/core/QueryRuntimeFilterManager.java

    r4889 r5818  
    3333  @author Nicklas
    3434  @version 2.0
    35   @see <a href="../../../../../development/overview/query/overview.html#filters">Query API overview - runtime filters</a>
     35  @see <a href="../../../../../html/developer/api/query_api.html">Developer documentation: The Query API</a>
    3636  @base.modified $Date$
    3737*/
  • trunk/src/core/net/sf/basedb/core/Role.java

    r4889 r5818  
    5454  @see Group
    5555  @see Project
    56   @see <a href="../../../../../../specifications/core/defaultpermissions.html">Default permissions</a>
    5756  @base.modified $Date$
    5857*/
  • trunk/src/core/net/sf/basedb/core/data/AnnotatableData.java

    r4889 r5818  
    5656  @see AnnotationTypeData
    5757  @see net.sf.basedb.core.Annotatable
    58   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotations overview</a>
     58  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    5959*/
    6060public interface AnnotatableData
  • trunk/src/core/net/sf/basedb/core/data/AnnotatedData.java

    r5038 r5818  
    3232  @see AnnotatableData
    3333  @see net.sf.basedb.core.AnnotatedItem
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotation overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3535*/
    3636public abstract class AnnotatedData
  • trunk/src/core/net/sf/basedb/core/data/AnnotationData.java

    r5056 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Annotation
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotations overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3535  @hibernate.class table="`Annotations`" lazy="false"
    3636 */
  • trunk/src/core/net/sf/basedb/core/data/AnnotationSetData.java

    r5118 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.AnnotationSet
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotations overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3737  @hibernate.class table="`AnnotationSets`" lazy="true" batch-size="10"
    3838 */
  • trunk/src/core/net/sf/basedb/core/data/AnnotationTypeCategoryData.java

    r4696 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.AnnotationTypeCategory
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotations overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3434  @base.modified $Date: 2006-04-18 10:48:02 +0100 (Tue, 18 Apr 2006) $
    3535  @hibernate.class table="`AnnotationTypeCategories`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

    r5319 r5818  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.AnnotationType
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.annotations.html">Annotations overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`AnnotationTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/AnyToAnyData.java

    r4517 r5818  
    3030  @see net.sf.basedb.core.AnyToAny
    3131  @base.modified $Date$
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.misc.html">Misc overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3333  @hibernate.class table="`AnyToAny`" lazy="false"
    3434*/
  • trunk/src/core/net/sf/basedb/core/data/ArrayBatchData.java

    r4889 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ArrayBatch
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`ArrayBatches`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignBlockData.java

    r5026 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.ArrayDesignBlock
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`ArrayDesignBlocks`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignData.java

    r5590 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ArrayDesign
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`ArrayDesigns`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ArrayDesignPlateData.java

    r4889 r5818  
    3030  @see net.sf.basedb.core.ArrayDesign
    3131  @see net.sf.basedb.core.Plate
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`ArrayDesignPlates`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ArraySlideData.java

    r5642 r5818  
    2828 This class represents a phycsical microarray slide.
    2929
    30  @author enell
    31  @version 2.0
    32  @see net.sf.basedb.core.ArraySlide
    33  @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
    34  @base.modified $Date$
    35  @hibernate.class table="`ArraySlides`" lazy="true"
     30  @author enell
     31  @version 2.0
     32  @see net.sf.basedb.core.ArraySlide
     33  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
     34  @base.modified $Date$
     35  @hibernate.class table="`ArraySlides`" lazy="true"
    3636 */
    3737public class ArraySlideData
  • trunk/src/core/net/sf/basedb/core/data/BasicData.java

    r5384 r5818  
    4242  @author Nicklas
    4343  @version 2.0
    44   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     44  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    4545*/
    4646public abstract class BasicData
  • trunk/src/core/net/sf/basedb/core/data/BatchableData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.BasicBatcher
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
    35   @see <a href="../../../../../../development/overview/core/index.html#batch">Batch processing</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
     35  @see <a href="../../../../../../html/developer/api/core_api.batch.html">Developer documentation: Batch operations</a>
    3636*/
    3737public interface BatchableData
  • trunk/src/core/net/sf/basedb/core/data/BioAssayData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.BioAssay
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`BioAssays`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioAssaySetData.java

    r4910 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.BioAssaySet
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`BioAssaySets`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialData.java

    r5662 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.BioMaterial
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`BioMaterials`" lazy="false" discriminator-value="-1"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialEventData.java

    r5662 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.BioMaterialEvent
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`BioMaterialEvents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialEventSourceData.java

    r5807 r5818  
    3030  @author Nicklas
    3131  @since 3.0
     32  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3233  @base.modified $Date$
    3334  @hibernate.class table="`BioMaterialEventSources2`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialListData.java

    r4889 r5818  
    3232  @version 2.10
    3333  @see net.sf.basedb.core.BioMaterialList
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3535  @hibernate.class table="`BioMaterialLists`" lazy="false"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/BioPlateData.java

    r5566 r5818  
    3232  @version 2.10
    3333  @see net.sf.basedb.core.BioPlate
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3535  @base.modified $Date: 2008-11-27 16:33:55 +0100 (Thu, 27 Nov 2008) $
    3636  @hibernate.class table="`BioPlates`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/BioPlateEventData.java

    r5523 r5818  
    3838  @since 2.17
    3939  @see net.sf.basedb.core.BioPlateEvent
    40   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     40  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    4141  @base.modified $Date$
    4242  @hibernate.class table="`BioPlateEvents`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioPlateEventParticipantData.java

    r5523 r5818  
    3636  @since 2.17
    3737  @see net.sf.basedb.core.BioPlateEventParticipant
    38   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     38  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3939  @base.modified $Date$
    4040  @hibernate.class table="`BioPlateEventParticipants`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BioPlateEventTypeData.java

    r5523 r5818  
    3232  @since 2.17
    3333  @see net.sf.basedb.core.BioPlateEventType
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`BioPlateEventTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/BioPlateTypeData.java

    r5709 r5818  
    3232  @base.modified $Date$
    3333  @hibernate.class table="`BioPlateTypes`" lazy="false"
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3435*/
    3536public class BioPlateTypeData
  • trunk/src/core/net/sf/basedb/core/data/BioSourceData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.BioSource
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3535  @base.modified $Date$
    3636  @hibernate.subclass discriminator-value="1"
  • trunk/src/core/net/sf/basedb/core/data/BioWellData.java

    r5566 r5818  
    2727    @version 2.10
    2828  @see net.sf.basedb.core.BioWell
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3030  @base.modified $Date: 2008-11-27 16:33:55 +0100 (Thu, 27 Nov 2008) $
    3131  @hibernate.class table="`BioWells`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/BooleanParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="7"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ChangeHistoryData.java

    r5071 r5818  
    5151  @base.modified $Date$
    5252  @hibernate.class table="`ChangeHistory`" lazy="false" mutable="false"
     53  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    5354*/
    5455public class ChangeHistoryData
  • trunk/src/core/net/sf/basedb/core/data/ChangeHistoryDetailData.java

    r5071 r5818  
    3232  @base.modified $Date$
    3333  @hibernate.class table="`ChangeHistoryDetails`" lazy="false" mutable="false"
     34  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3435*/
    3536public class ChangeHistoryDetailData
  • trunk/src/core/net/sf/basedb/core/data/ClientData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Client
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3535  @hibernate.class table="`Clients`" lazy="false"
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/ClientDefaultSettingData.java

    r4889 r5818  
    2727  @author nicklas, enell
    2828  @see net.sf.basedb.core.ClientDefaultSetting
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3030  @hibernate.class table="`ClienDefaultSettings`" lazy="false"
    3131  @version 2.0
  • trunk/src/core/net/sf/basedb/core/data/ColoringData.java

    r4620 r5818  
    2929  @version 2.0
    3030  @base.modified $Date$
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.misc.html">Data API - Other classes</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3232*/
    3333public class ColoringData
  • trunk/src/core/net/sf/basedb/core/data/CommonData.java

    r4889 r5818  
    3030  @author Nicklas
    3131  @version 2.0
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    3333*/
    3434public abstract class CommonData
  • trunk/src/core/net/sf/basedb/core/data/ContextData.java

    r5537 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.ItemContext
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Contexts`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ContextIndex.java

    r5384 r5818  
    3232  @author Nicklas
    3333  @version 2.0
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3535  @base.modified $Date$
    3636*/
  • trunk/src/core/net/sf/basedb/core/data/DataCubeColumnData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.DataCubeColumn
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`DataCubeColumns`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.DataCube
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`DataCubes`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeExtraValueData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.DataCubeExtraValue
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`DataCubeExtraValues`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeFilterData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.DataCubeFilter
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`DataCubeFilters`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataCubeLayerData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.DataCubeLayer
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`DataCubeLayers`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DataFileTypeData.java

    r5713 r5818  
    3333  @see net.sf.basedb.core.DataFileType
    3434  @base.modified $Date$
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3636  @hibernate.class table="`DataFileTypes`" lazy="false"
    3737*/
  • trunk/src/core/net/sf/basedb/core/data/DateParameterValueData.java

    r5437 r5818  
    3434  @author Samuel
    3535  @version 2.0
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3737  @hibernate.subclass discriminator-value="8"
    3838  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/DerivedBioAssayData.java

    r5685 r5818  
    11/**
    2   $Id$
     2  $Id: DerivedBioAssayData.java 5685 2011-08-04 10:58:23Z nicklas $
    33
    44  Copyright (C) 2011 Nicklas Nordborg
     
    2929  @author Nicklas
    3030  @since 3.0
    31   @base.modified $Date$
     31  @base.modified $Date: 2011-08-04 12:58:23 +0200 (to, 04 aug 2011) $
    3232  @hibernate.class table="`DerivedBioAssays`" lazy="true"
     33  @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
    3334*/
    3435public class DerivedBioAssayData
  • trunk/src/core/net/sf/basedb/core/data/DirectoryData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Directory
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.files.html">File and directory overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.files.html">Developer documentation: Files and directories</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Directories`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DiskConsumableData.java

    r4889 r5818  
    6060  @see DiskUsageData
    6161  @see net.sf.basedb.core.DiskConsumable
    62   @see <a href="../../../../../../html/developerdoc/api/data_api.quota.html">Quota overview</a>
     62  @see <a href="../../../../../../html/developer/api/data_api.quota.html">Developer documentation: Quota and disk usage</a>
    6363*/
    6464public interface DiskConsumableData
  • trunk/src/core/net/sf/basedb/core/data/DiskUsageData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.DiskUsage
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.quota.html">Quota overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.quota.html">Developer documentation: Quota and disk usage</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`DiskUsage`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/DoubleParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="4"
    3535  @base.modified $Date: 2005-07-05 15:51:30 +0200 (ti, 05 jul 2005) $
  • trunk/src/core/net/sf/basedb/core/data/ExperimentData.java

    r5069 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Experiment
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Experiments`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/ExtendableData.java

    r4889 r5818  
    212212  @author Nicklas, Samuel
    213213  @version 2.0
     214  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    214215*/
    215216public interface ExtendableData
  • trunk/src/core/net/sf/basedb/core/data/ExtraValueData.java

    r4889 r5818  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.ExtraValue
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3333  @hibernate.class table="`ExtraValues`" lazy="false"
    3434  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ExtraValueTypeData.java

    r5319 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.ExtraValueType
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3737  @hibernate.class table="`ExtraValueTypes`" lazy="true"
    3838  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ExtractData.java

    r5752 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Extract
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3434  @base.modified $Date$
    3535  @hibernate.subclass discriminator-value="3" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/FeatureData.java

    r5026 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Feature
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.arrays.html">Developer documentation: Array LIMS (arrays)</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`Features`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/FileAttachableData.java

    r4889 r5818  
    5151  @version 2.0
    5252  @see BasicData
    53   @see <a href="../../../../../../development/overview/data/files.html">File and directory overview</a>
    54   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     53  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    5554*/
    5655public interface FileAttachableData
  • trunk/src/core/net/sf/basedb/core/data/FileData.java

    r5630 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.File
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.files.html">File and directory overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.files.html">Developer documentation: Files and directories</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Files`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/FileServerData.java

    r5618 r5818  
    3333  @base.modified $Date$
    3434  @hibernate.class table="`FileServers`" lazy="true"
     35  @see <a href="../../../../../../html/developer/api/data_api.files.html">Developer documentation: Files and directories</a>
    3536*/
    3637public class FileServerData
  • trunk/src/core/net/sf/basedb/core/data/FileSetData.java

    r5713 r5818  
    3333  @version 2.5
    3434  @see net.sf.basedb.core.FileSet
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`FileSets`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/FileSetMemberData.java

    r5719 r5818  
    3030  @version 2.5
    3131  @see net.sf.basedb.core.FileSetMember
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`FileSetMembers`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/FileStoreEnabledData.java

    r4517 r5818  
    5050  @author Nicklas
    5151  @version 2.5
    52   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     52  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    5353  @base.modified $Date$
    5454*/
  • trunk/src/core/net/sf/basedb/core/data/FileTypeIndex.java

    r5384 r5818  
    3434  @author Nicklas
    3535  @version 2.5
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3737  @base.modified $Date$
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/FloatParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="3"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/FormulaData.java

    r5208 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Formula
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.misc.html">Data API - Other classes</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3737  @hibernate.class table="`Formulas`" lazy="false"
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/GlobalDefaultSettingData.java

    r4889 r5818  
    2727  @author nicklas
    2828  @see net.sf.basedb.core.GlobalDefaultSetting
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3030  @hibernate.class table="`GlobalDefaultSettings`" lazy="false"
    3131  @version 2.0
  • trunk/src/core/net/sf/basedb/core/data/GroupData.java

    r5077 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Group
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Groups`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/GuiContextData.java

    r4889 r5818  
    3333  @author Nicklas
    3434  @version 2.0
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugins ovreview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3636  @base.modified $Date$
    3737*/
  • trunk/src/core/net/sf/basedb/core/data/HardwareData.java

    r5630 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Hardware
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.wares.html">Hardware and software overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.protocols.html">Developer documentation: Protocols, hardware and software</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`Hardware`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/HelpData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Help
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`HelpTexts`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/IdentifiableData.java

    r4889 r5818  
    4444  @version 2.0
    4545  @see BasicData
    46   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     46  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    4747*/
    4848public interface IdentifiableData
  • trunk/src/core/net/sf/basedb/core/data/IntegerParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="1"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ItemKeyData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ItemKey
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3434  @base.modified $Date$
    3535  @hibernate.subclass discriminator-value="1"
  • trunk/src/core/net/sf/basedb/core/data/ItemParameterValueData.java

    r5437 r5818  
    3333  @author Nicklas, Samuel
    3434  @version 2.0
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3636  @hibernate.subclass discriminator-value="10"
    3737  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ItemSubtypeData.java

    r5713 r5818  
    3737  @base.modified $Date$
    3838  @hibernate.class table="`ItemSubtypes`" lazy="false"
     39  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3940*/
    4041public class ItemSubtypeData
  • trunk/src/core/net/sf/basedb/core/data/ItemSubtypeFileTypeData.java

    r5728 r5818  
    2929  @since 3.0
    3030  @see net.sf.basedb.core.ItemSubtypeFileType
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`ItemSubtypeFileTypes`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/JobAgentData.java

    r4517 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.JobAgent
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugin/jobs overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`JobAgents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/JobAgentSettingsData.java

    r5595 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.JobAgentSettings
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugin/jobs overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`JobAgentSettings`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/JobData.java

    r5406 r5818  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.Job
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugin/jobs overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`Jobs`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/KeyData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Key
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`Keys`" lazy="true" discriminator-value="-1"
  • trunk/src/core/net/sf/basedb/core/data/LoggableData.java

    r5038 r5818  
    3030  @version 2.13
    3131  @base.modified $Date$
     32  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    3233*/
    3334public interface LoggableData
  • trunk/src/core/net/sf/basedb/core/data/LongParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas, Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="2"
    3535  @base.modified $Date: 2005-07-14 09:57:11 +0200 (to, 14 jul 2005) $
  • trunk/src/core/net/sf/basedb/core/data/MappingCoordinate.java

    r4889 r5818  
    3535  @version 2.0
    3636  @see PlateMappingData
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3838  @base.modified $Date$
    3939*/
  • trunk/src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java

    r5663 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.MeasuredBioMaterial
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3535  @base.modified $Date$
    3636  @hibernate.subclass discriminator-value="-1" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/MessageData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Message
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.misc.html">Data API - Other classes</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3434  @hibernate.class table="`Messages`" lazy="false"
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/MimeTypeData.java

    r5630 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.MimeType
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.files.html">File and directory overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.files.html">Developer documentation: Files and directories</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`MimeTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/NameableData.java

    r4889 r5818  
    5959  @version 2.0
    6060  @see CommonData
    61   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     61  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    6262*/
    6363public interface NameableData
  • trunk/src/core/net/sf/basedb/core/data/NewsData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.News
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.misc.html">Misc overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.misc.html">Developer documentation: Other classes</a>
    3434  @hibernate.class table="`News`" lazy="false"
    3535 */
  • trunk/src/core/net/sf/basedb/core/data/OwnableData.java

    r4889 r5818  
    5151  @see OwnedData
    5252  @see net.sf.basedb.core.Ownable
    53   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
    54   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     53  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
     54  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    5555*/
    5656public interface OwnableData
  • trunk/src/core/net/sf/basedb/core/data/OwnedData.java

    r4889 r5818  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.OwnedItem
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    3434*/
    3535public abstract class OwnedData
  • trunk/src/core/net/sf/basedb/core/data/ParameterValueData.java

    r5437 r5818  
    3333  @author Nicklas, Samuel
    3434  @version 2.0
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3636  @hibernate.class table="`ParameterValues`" discriminator-value="-1" lazy="true" batch-size="10"
    3737  @hibernate.discriminator column="`discriminator`" type="int"
  • trunk/src/core/net/sf/basedb/core/data/PasswordData.java

    r4889 r5818  
    3030  @author Nicklas
    3131  @version 2.0
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3333  @hibernate.class table="`Passwords`" lazy="true"
    3434*/
  • trunk/src/core/net/sf/basedb/core/data/PermissionTemplateData.java

    r5387 r5818  
    3333  @hibernate.class table="`PermissionTemplates`" lazy="true"
    3434  @base.modified $Date $
     35  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3536*/
    3637public class PermissionTemplateData
  • trunk/src/core/net/sf/basedb/core/data/PhysicalBioAssayData.java

    r5739 r5818  
    3232  @base.modified $Date$
    3333  @hibernate.class table="`PhysicalBioAssays`" lazy="true"
     34  @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
    3435*/
    3536public class PhysicalBioAssayData
  • trunk/src/core/net/sf/basedb/core/data/PlateCoordinate.java

    r4889 r5818  
    3535  @version 2.0
    3636  @see PlateData
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3838  @base.modified $Date$
    3939*/
  • trunk/src/core/net/sf/basedb/core/data/PlateData.java

    r4889 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Plate
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Plates`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateEventData.java

    r5063 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.PlateEvent
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`PlateEvents`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateEventTypeData.java

    r5630 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.PlateEventType
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`PlateEventTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateGeometryData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PlateGeometry
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`PlateGeometries`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlateMappingData.java

    r4889 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.PlateMapping
    35   @see <a href="v">Array LIMS - Plates overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3636  @base.modified $Date$
    3737  @hibernate.class table="`PlateMappings`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/PlateTypeData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PlateType
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`PlateTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlatformData.java

    r4517 r5818  
    3232  @version 2.5
    3333  @see net.sf.basedb.core.Platform
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Platforms`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PlatformFileTypeData.java

    r5713 r5818  
    2929  @version 2.5
    3030  @see net.sf.basedb.core.PlatformFileType
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`PlatformFileTypes`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/PlatformVariantData.java

    r4517 r5818  
    3030  @version 2.5
    3131  @see net.sf.basedb.core.PlatformVariant
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.platforms.html">Data API - Experimental platforms</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`PlatformVariants`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/PluginConfigurationData.java

    r4889 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.PluginConfiguration
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugins</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3737  @hibernate.class table="`PluginConfigurations`" lazy="false"
    3838*/
  • trunk/src/core/net/sf/basedb/core/data/PluginDefinitionData.java

    r5734 r5818  
    3737  @version 2.0
    3838  @see net.sf.basedb.core.PluginDefinition
    39   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugins</a>
     39  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    4040  @hibernate.class table="`PluginDefinitions`" lazy="false"
    4141*/
  • trunk/src/core/net/sf/basedb/core/data/PluginPermission.java

    r4517 r5818  
    2626  @author Martin
    2727  @version 2.1
    28   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     28  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    2930*/
    3031public class PluginPermission
  • trunk/src/core/net/sf/basedb/core/data/PluginTypeData.java

    r5613 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.PluginType
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugins</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3535  @hibernate.class table="`PluginTypes`" lazy="false"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/ProjectData.java

    r5650 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Project
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Projects`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/ProjectKeyData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.ProjectKey
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3434  @base.modified $Date$
    3535  @hibernate.subclass discriminator-value="2"
  • trunk/src/core/net/sf/basedb/core/data/PropertyFilterData.java

    r4889 r5818  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.ItemContext
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3333  @base.modified $Date$
    3434*/
  • trunk/src/core/net/sf/basedb/core/data/ProtocolData.java

    r5630 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Protocol
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.protocols.html">Protocol overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.protocols.html">Developer documentation: Protocols, hardware and software</a>
    3434  @hibernate.class table="`Protocols`" lazy="true"
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/QuantityData.java

    r4541 r5818  
    3232  @base.modified $Date $
    3333  @hibernate.class table="`Quantities`" lazy="true"
     34  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3435*/
    3536public class QuantityData
  • trunk/src/core/net/sf/basedb/core/data/QuotaData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Quota
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.quota.html">Quota overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.quota.html">Developer documentation: Quota and disk usage</a>
    3535  @hibernate.class table="`Quota`" lazy="true"
    3636  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/QuotaIndex.java

    r5384 r5818  
    3737  @author enell
    3838  @version 2.0
    39   @see <a href="../../../../../../html/developerdoc/api/data_api.quota.html">Quota overview</a>
     39  @see <a href="../../../../../../html/developer/api/data_api.quota.html">Developer documentation: Quota and disk usage</a>
    4040  @base.modified $Date$
    4141*/
  • trunk/src/core/net/sf/basedb/core/data/QuotaTypeData.java

    r4889 r5818  
    3030  @author enell
    3131  @version 2.0
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.quota.html">Quota overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.quota.html">Developer documentation: Quota and disk usage</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`QuotaTypes`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/RawBioAssayData.java

    r5657 r5818  
    3636  @version 2.0
    3737  @see net.sf.basedb.core.RawBioAssay
    38   @see <a href="../../../../../../html/developerdoc/api/data_api.rawdata.html">Hybridzations and raw data overview</a>
     38  @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
    3939  @base.modified $Date$
    4040  @hibernate.class table="`RawBioAssays`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/RawData.java

    r4889 r5818  
    3636  @see net.sf.basedb.core.RawDataBatcher
    3737  @see net.sf.basedb.core.RawDataUtil
    38   @see <a href="../../../../../../html/developerdoc/api/data_api.rawdata.html">Hybridzations and raw data overview</a>
     38  @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
    3939  @base.modified $Date$
    4040*/
  • trunk/src/core/net/sf/basedb/core/data/RegisteredData.java

    r4889 r5818  
    3232  @version 2.10
    3333  @see net.sf.basedb.core.BasicBatcher
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    3535*/
    3636public interface RegisteredData
  • trunk/src/core/net/sf/basedb/core/data/RemovableData.java

    r4889 r5818  
    5757  @author Nicklas
    5858  @version 2.0
    59   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     59  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    6060*/
    6161public interface RemovableData
  • trunk/src/core/net/sf/basedb/core/data/ReporterData.java

    r5026 r5818  
    4646  @see net.sf.basedb.core.ReporterBatcher
    4747  @see net.sf.basedb.core.ExtendedProperties
    48   @see <a href="../../../../../../html/developerdoc/api/data_api.reporters.html">Reporter overview</a>
     48  @see <a href="../../../../../../html/developer/api/data_api.reporters.html">Developer documentation: Reporters</a>
    4949  @hibernate.class table="`Reporters`" lazy="true"
    5050*/
  • trunk/src/core/net/sf/basedb/core/data/ReporterListData.java

    r4889 r5818  
    3333  @version 2.0
    3434  @see net.sf.basedb.core.ReporterList
    35   @see <a href="../../../../../../html/developerdoc/api/data_api.reporters.html">Reporter overview</a>
     35  @see <a href="../../../../../../html/developer/api/data_api.reporters.html">Developer documentation: Reporters</a>
    3636  @hibernate.class table="`ReporterLists`" lazy="true"
    3737*/
  • trunk/src/core/net/sf/basedb/core/data/ReporterListScoreData.java

    r5384 r5818  
    3737  @version 2.0
    3838  @see net.sf.basedb.core.ReporterList
    39   @see <a href="../../../../../../html/developerdoc/api/data_api.reporters.html">Reporter overview</a>
     39  @see <a href="../../../../../../html/developer/api/data_api.reporters.html">Developer documentation: Reporters</a>
    4040*/
    4141public class ReporterListScoreData
  • trunk/src/core/net/sf/basedb/core/data/ReporterTypeData.java

    r4889 r5818  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.data.ReporterData
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.reporters.html">Reporter overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.reporters.html">Developer documentation: Reporters</a>
    3838  @hibernate.class table="`ReporterTypes`" lazy="true"
    3939*/
  • trunk/src/core/net/sf/basedb/core/data/RoleData.java

    r4889 r5818  
    3434  @version 2.0
    3535  @see net.sf.basedb.core.Role
    36   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     36  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3737  @base.modified $Date$
    3838  @hibernate.class table="`Roles`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/RoleKeyData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.RoleKey
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3535  @base.modified $Date$
    3636  @hibernate.subclass discriminator-value="3"
  • trunk/src/core/net/sf/basedb/core/data/SampleData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Sample
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.biomaterials.html">Biomaterials overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3232  @base.modified $Date$
    3333  @hibernate.subclass discriminator-value="2" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/SessionData.java

    r4889 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Session
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3434  @hibernate.class table="`Sessions`" lazy="false"
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/SettingData.java

    r4889 r5818  
    2727  @version 2.0
    2828  @see net.sf.basedb.core.Setting
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3030*/
    3131public abstract class SettingData
  • trunk/src/core/net/sf/basedb/core/data/ShareableData.java

    r4889 r5818  
    6969  @see SharedData
    7070  @see net.sf.basedb.core.Shareable
    71   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
    72   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     71  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
     72  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    7373*/
    7474public interface ShareableData
  • trunk/src/core/net/sf/basedb/core/data/SharedData.java

    r4889 r5818  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.SharedItem
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    3434*/
    3535public abstract class SharedData
  • trunk/src/core/net/sf/basedb/core/data/SoftwareData.java

    r5630 r5818  
    3131  @version 2.0
    3232  @see net.sf.basedb.core.Software
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.wares.html">Hardware and software overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.protocols.html">Developer documentation: Protocols, hardware and software</a>
    3434  @base.modified $Date$
    3535  @hibernate.class table="`Software`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/SpotImagesData.java

    r4889 r5818  
    3030  @version 2.0
    3131  @see net.sf.basedb.core.SpotImages
    32   @see <a href="../../../../../../html/developerdoc/api/data_api.rawdata.html">Hybridzations and raw data overview</a>
     32  @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
    3333  @base.modified $Date$
    3434  @hibernate.class table="`SpotImages`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/StringParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="5"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/SubtypableData.java

    r5630 r5818  
    5050  @since 3.0
    5151  @base.modified $Date$
     52  @see <a href="../../../../../../html/developer/api/data_api.platforms.html">Developer documentation: Experimental platforms and item subtypes</a>
    5253*/
    5354public interface SubtypableData
  • trunk/src/core/net/sf/basedb/core/data/SystemData.java

    r4889 r5818  
    5858  @author Nicklas
    5959  @version 2.0
    60   @see <a href="../../../../../../html/developerdoc/api/data_api.basic.html">Basic classes and interfaces</a>
     60  @see <a href="../../../../../../html/developer/api/data_api.basic.html">Developer documentation: Basic classes and interfaces</a>
    6161*/
    6262public interface SystemData
  • trunk/src/core/net/sf/basedb/core/data/TagData.java

    r5632 r5818  
    3232  @hibernate.class table="`Labels`" lazy="false"
    3333  @base.modified $Date$
     34  @see <a href="../../../../../../html/developer/api/data_api.biomaterials.html">Developer documentation: Biomaterials LIMS</a>
    3435*/
    3536public class TagData
  • trunk/src/core/net/sf/basedb/core/data/TextParameterValueData.java

    r5437 r5818  
    3131  @author Samuel
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="6"
    3535  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/data/TimestampParameterValueData.java

    r5437 r5818  
    3131  @author Nicklas
    3232  @since 2.16
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.parameters.html">Parameters overview</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.parameters.html">Developer documentation: Parameters</a>
    3434  @hibernate.subclass discriminator-value="11"
    3535  @base.modified $Date $
  • trunk/src/core/net/sf/basedb/core/data/TransformationData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.Transformation
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`Transformations`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/UnitData.java

    r4888 r5818  
    4545  @base.modified $Date $
    4646  @hibernate.class table="`Units`" lazy="true"
     47  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    4748*/
    4849public class UnitData
  • trunk/src/core/net/sf/basedb/core/data/UnitSymbolData.java

    r4888 r5818  
    3737  @base.modified $Date $
    3838  @hibernate.class table="`UnitSymbols`" lazy="false"
     39  @see <a href="../../../../../../html/developer/api/data_api.annotations.html">Developer documentation: Annotations</a>
    3940*/
    4041public class UnitSymbolData
  • trunk/src/core/net/sf/basedb/core/data/UserClientSettingData.java

    r4889 r5818  
    2727  @author nicklas
    2828  @see net.sf.basedb.core.UserClientSetting
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3030  @hibernate.class table="`UserClientSettings`" lazy="false"
    3131  @version 2.0
  • trunk/src/core/net/sf/basedb/core/data/UserData.java

    r5442 r5818  
    3535  @version 2.0
    3636  @see net.sf.basedb.core.User
    37   @see <a href="../../../../../../html/developerdoc/api/data_api.authentication.html">Authentication overview</a>
     37  @see <a href="../../../../../../html/developer/api/data_api.authentication.html">Developer documentation: User authentication</a>
    3838  @base.modified $Date$
    3939  @hibernate.class table="`Users`" lazy="false"
  • trunk/src/core/net/sf/basedb/core/data/UserDefaultSettingData.java

    r4889 r5818  
    2727  @author nicklas
    2828  @see net.sf.basedb.core.UserDefaultSetting
    29   @see <a href="../../../../../../html/developerdoc/api/data_api.clients.html">Session and client overview</a>
     29  @see <a href="../../../../../../html/developer/api/data_api.clients.html">Developer documentation: Client, session and settings</a>
    3030  @hibernate.class table="`UserDefaultSettings`" lazy="false"
    3131  @version 2.0
  • trunk/src/core/net/sf/basedb/core/data/VersionedParameter.java

    r4517 r5818  
    3131  @author nicklas
    3232  @version 2.0
    33   @see <a href="../../../../../../html/developerdoc/api/data_api.plugins.html">Plugins</a>
     33  @see <a href="../../../../../../html/developer/api/data_api.plugins.html">Developer documentation: Plug-ins, jobs and job agents</a>
    3434  @base.modified $Date$
    3535*/
  • trunk/src/core/net/sf/basedb/core/data/VirtualDbData.java

    r4889 r5818  
    3232  @version 2.0
    3333  @see net.sf.basedb.core.VirtualDb
    34   @see <a href="../../../../../../html/developerdoc/api/data_api.experiments.html">Experiments and analysis overview</a>
     34  @see <a href="../../../../../../html/developer/api/data_api.experiments.html">Developer documentation: Experiments and analysis</a>
    3535  @base.modified $Date$
    3636  @hibernate.class table="`VirtualDbs`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/data/WellData.java

    r4889 r5818  
    2929  @version 2.0
    3030  @see net.sf.basedb.core.Well
    31   @see <a href="../../../../../../html/developerdoc/api/data_api.plates.html">Array LIMS - Plates overview</a>
     31  @see <a href="../../../../../../html/developer/api/data_api.plates.html">Developer documentation: Array LIMS (plates)</a>
    3232  @base.modified $Date$
    3333  @hibernate.class table="`Wells`" lazy="true"
  • trunk/src/core/net/sf/basedb/core/query/Query.java

    r4889 r5818  
    6161  @author Nicklas
    6262  @version 2.0
    63   @see <a href="../../../../../../development/overview/query/index.html">Query API documentation</a>
     63  @see <a href="../../../../../../developer/api/query_api.html">Developer documentation: The Query API</a>
    6464  @see net.sf.basedb.core.AbstractQuery
    6565  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/util/fileset/ValidationAction.java

    r5623 r5818  
    4646   
    4747  <li>For removing metadata when a file in a file set is removed or replaced
    48     with another file. The is done when the {@link FileSet#removeMember(DataFileType)},
    49     {@link FileSet#setMember(File, DataFileType)} and {@link FileSet#removeAllMembers()}
    50     methods are called. The {@link ClientContext} in this case also has the owner of
    51     the file set as the current item, but the action will only be asked to accept
    52     the file(s) that are actually removed/modified.
     48    with another file. For example, when the {@link FileSet#removeMember(FileSetMember)},
     49    {@link FileSet#setMember(File, DataFileType)} or any other method that removs
     50    a file from the fileset is called. The {@link ClientContext} in this case also
     51    has the owner of the file set as the current item, but the action will only be
     52    asked to accept the file(s) that are actually removed/modified.
    5353  </ul>
    5454  <p>
  • trunk/src/core/net/sf/basedb/util/overview/GenericOverview.java

    r5657 r5818  
    7676  @author Nicklas
    7777  @version 2.10
    78   @base.internal This class is still being developed. It may change
    79     without notice in future versions of BASE.
    8078  @base.modified $Date$
    8179*/
  • trunk/src/core/net/sf/basedb/util/overview/OverviewContext.java

    r5185 r5818  
    4242  @author Nicklas
    4343  @version 2.10
    44   @base.internal This class is still being developed. It may change
    45     without notice in future versions of BASE.
    4644  @base.modified $Date$
    4745*/
  • trunk/src/core/net/sf/basedb/util/overview/loader/AbstractNodeLoader.java

    r4768 r5818  
    3737  @author Nicklas
    3838  @version 2.10
    39   @base.internal This class is still being developed. It may change
    40     without notice in future versions of BASE.
    4139  @base.modified $Date$
    4240*/
  • trunk/src/core/net/sf/basedb/util/overview/loader/BasicItemNodeLoader.java

    r4768 r5818  
    3838  @author Nicklas
    3939  @version 2.10
    40   @base.internal This class is still being developed. It may change
    41     without notice in future versions of BASE.
    4240  @base.modified $Date$
    4341*/
  • trunk/src/core/net/sf/basedb/util/overview/loader/NodeLoader.java

    r4768 r5818  
    4141  @author Nicklas
    4242  @version 2.10
    43   @base.internal This class is still being developed. It may change
    44     without notice in future versions of BASE.
    4543  @base.modified $Date$
    4644*/
  • trunk/src/core/net/sf/basedb/util/overview/loader/NodeLoaderFactory.java

    r4768 r5818  
    3131  @author Nicklas
    3232  @version 2.10
    33   @base.internal This class is still being developed. It may change
    34     without notice in future versions of BASE.
    3533  @base.modified $Date$
    3634*/
  • trunk/src/core/net/sf/basedb/util/overview/node/NodeFactory.java

    r4768 r5818  
    4545  @author Nicklas
    4646  @version 2.10
    47   @base.internal This class is still being developed. It may change
    48     without notice in future versions of BASE.
    4947  @base.modified $Date$
    5048*/
  • trunk/src/core/net/sf/basedb/util/overview/node/NodeNameGenerator.java

    r4768 r5818  
    3333  @author Nicklas
    3434  @version 2.10
    35   @base.internal This class is still being developed. It may change
    36     without notice in future versions of BASE.
    3735  @base.modified $Date$
    3836*/
  • trunk/src/core/net/sf/basedb/util/overview/validator/BasicNodeValidator.java

    r5651 r5818  
    3838  @author Nicklas
    3939  @version 2.10
    40   @base.internal This class is still being developed. It may change
    41     without notice in future versions of BASE.
    4240  @base.modified $Date$
    4341*/
  • trunk/src/core/net/sf/basedb/util/overview/validator/NodeValidator.java

    r4768 r5818  
    7979  @author Nicklas
    8080  @version 2.10
    81   @base.internal This class is still being developed. It may change
    82     without notice in future versions of BASE.
    8381  @base.modified $Date$
    8482*/
  • trunk/src/core/net/sf/basedb/util/overview/validator/NodeValidatorFactory.java

    r4864 r5818  
    3131  @author Nicklas
    3232  @version 2.10
    33   @base.internal This class is still being developed. It may change
    34     without notice in future versions of BASE.
    3533  @base.modified $Date$
    3634*/
  • trunk/src/webservices/server/net/sf/basedb/ws/server/BioAssaySetService.java

    r5718 r5818  
    4545  extends AbstractRPCService
    4646{
    47   private static final String SERIAL_BASEFILE = "Serial BASEfile";
    48   private static final String MATRIX_BASEFILE = "Matrix BASEfile";
    49   private static final String MEV = "Mev file";
    50  
    5147  /**
    5248   
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