Changeset 3947


Ignore:
Timestamp:
Nov 12, 2007, 11:33:16 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #819: Last file that needed links to javadoc.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/developerdoc/api_overview.xml

    r3943 r3947  
    222222        <variablelist>
    223223        <varlistentry>
    224           <term><classname>BasicData</classname></term>
     224          <term><classname docapi="net.sf.basedb.core.data">BasicData</classname></term>
    225225          <listitem>
    226226            <para>
     
    235235       
    236236        <varlistentry>
    237           <term><classname>OwnedData</classname></term>
     237          <term><classname docapi="net.sf.basedb.core.data">OwnedData</classname></term>
    238238          <listitem>
    239239            <para>
    240240            Extends the <classname>BasicData</classname> class and adds
    241241            an <varname>owner</varname> property. The owner is a required link to a
    242             <classname>UserData</classname> object, representing the user that
     242            <classname docapi="net.sf.basedb.core.data">UserData</classname> object, representing the user that
    243243            is the owner of the item.
    244244            </para>
     
    247247
    248248        <varlistentry>
    249           <term><classname>SharedData</classname></term>
     249          <term><classname docapi="net.sf.basedb.core.data">SharedData</classname></term>
    250250          <listitem>
    251251            <para>
     
    253253            properties (<varname>itemKey</varname> and <varname>projectKey</varname>)
    254254            that holds access permission information for an item.
    255             Access permissions are held in <classname>ItemKeyData</classname> and/or
    256             <classname>ProjectKeyData</classname> objects. These objects only exists if
     255            Access permissions are held in <classname docapi="net.sf.basedb.core.data">ItemKeyData</classname> and/or
     256            <classname docapi="net.sf.basedb.core.data">ProjectKeyData</classname> objects. These objects only exists if
    257257            the item has been shared.
    258258            </para>
     
    261261
    262262        <varlistentry>
    263           <term><classname>CommonData</classname></term>
     263          <term><classname docapi="net.sf.basedb.core.data">CommonData</classname></term>
    264264          <listitem>
    265265            <para>
    266266            This is a convenience class for items that extends the <classname>SharedData</classname>
    267             class and implements the <interfacename>NameableData</interfacename> and
    268             <interfacename>RemoveableData</interfacename> interfaces. This is one of
     267            class and implements the <interfacename docapi="net.sf.basedb.core.data">NameableData</interfacename> and
     268            <interfacename docapi="net.sf.basedb.core.data">RemoveableData</interfacename> interfaces. This is one of
    269269            the most common situations.
    270270            </para>
     
    273273
    274274        <varlistentry>
    275           <term><classname>AnnotatedData</classname></term>
     275          <term><classname docapi="net.sf.basedb.core.data">AnnotatedData</classname></term>
    276276          <listitem>
    277277            <para>
    278278            This is a convenience class for items that can be annotated.
    279             Annotations are held in <classname>AnnotationSetData</classname> objects.
     279            Annotations are held in <classname docapi="net.sf.basedb.core.data">AnnotationSetData</classname> objects.
    280280            The annotation set only exists if annotations has been created for the item.
    281281            </para>
     
    291291        <variablelist>
    292292        <varlistentry>
    293           <term><classname>IdentifiableData</classname></term>
     293          <term><classname docapi="net.sf.basedb.core.data">IdentifiableData</classname></term>
    294294          <listitem>
    295295            <para>
     
    304304       
    305305        <varlistentry>
    306           <term><classname>OwnableData</classname></term>
     306          <term><classname docapi="net.sf.basedb.core.data">OwnableData</classname></term>
    307307          <listitem>
    308308            <para>
    309309            An ownable item is an item which has an owner. The owner is represented as a
    310             required link to a <classname>UserData</classname> object.
     310            required link to a <classname docapi="net.sf.basedb.core.data">UserData</classname> object.
    311311            </para>
    312312          </listitem>
     
    314314
    315315        <varlistentry>
    316           <term><classname>ShareableData</classname></term>
     316          <term><classname docapi="net.sf.basedb.core.data">ShareableData</classname></term>
    317317          <listitem>
    318318            <para>
    319319            A shareable item is an item which can be shared to other users, groups or projects.
    320             Access permissions are held in <classname>ItemKeyData</classname> and/or
    321             <classname>ProjectKeyData</classname> objects.
     320            Access permissions are held in <classname docapi="net.sf.basedb.core.data">ItemKeyData</classname> and/or
     321            <classname docapi="net.sf.basedb.core.data">ProjectKeyData</classname> objects.
    322322            </para>
    323323          </listitem>
     
    325325             
    326326        <varlistentry>
    327           <term><classname>NameableData</classname></term>
     327          <term><classname docapi="net.sf.basedb.core.data">NameableData</classname></term>
    328328          <listitem>
    329329            <para>
     
    336336       
    337337        <varlistentry>
    338           <term><classname>RemovableData</classname></term>
     338          <term><classname docapi="net.sf.basedb.core.data">RemovableData</classname></term>
    339339          <listitem>
    340340            <para>
     
    349349               
    350350        <varlistentry>
    351           <term><classname>SystemData</classname></term>
     351          <term><classname docapi="net.sf.basedb.core.data">SystemData</classname></term>
    352352          <listitem>
    353353            <para>
     
    363363
    364364        <varlistentry>
    365           <term><classname>DiskConsumableData</classname></term>
     365          <term><classname docapi="net.sf.basedb.core.data">DiskConsumableData</classname></term>
    366366          <listitem>
    367367            <para>
    368368            This interface is used by items which occupies a lot of disk space and
    369369            should be part of the quota system, for example files. The required
    370             <classname>DiskUsageData</classname> contains information about the size,
     370            <classname docapi="net.sf.basedb.core.data">DiskUsageData</classname> contains information about the size,
    371371            location, owner etc. of the item.
    372372            </para>
     
    375375       
    376376        <varlistentry>
    377           <term><classname>AnnotatableData</classname></term>
     377          <term><classname docapi="net.sf.basedb.core.data">AnnotatableData</classname></term>
    378378          <listitem>
    379379            <para>
    380380            This interface is used by items which can be annotated. Annotations are name/value
    381381            pairs that are attached as extra information to an item. All annotations are
    382             contained in an <classname>AnnotationSetData</classname> object.
     382            contained in an <classname docapi="net.sf.basedb.core.data">AnnotationSetData</classname> object.
    383383            </para>
    384384          </listitem>
     
    386386       
    387387        <varlistentry>
    388           <term><classname>ExtendableData</classname></term>
     388          <term><classname docapi="net.sf.basedb.core.data">ExtendableData</classname></term>
    389389          <listitem>
    390390            <para>
     
    399399       
    400400        <varlistentry>
    401           <term><classname>BatchableData</classname></term>
     401          <term><classname docapi="net.sf.basedb.core.data">BatchableData</classname></term>
    402402          <listitem>
    403403            <para>
     
    443443     
    444444        <para>
    445           The <classname>UserData</classname> class holds information about users.
     445          The <classname docapi="net.sf.basedb.core.data">UserData</classname> class holds information about users.
    446446          We keep the passwords in a separate table and use proxies to avoid loading
    447447          password data each time a user is loaded to minimize security risks. It is
    448           only if the password needs to be changed that the <classname>PasswordData</classname>
     448          only if the password needs to be changed that the <classname docapi="net.sf.basedb.core.data">PasswordData</classname>
    449449          object is loaded. The one-to-one mapping between user and password is controlled
    450450          by the password class, but a cascade attribute on the user class makes sure
     
    457457     
    458458        <para>
    459           The <classname>GroupData</classname>, <classname>RoleData</classname> and
    460           <classname>ProjectData</classname> classes holds information about groups, roles
     459          The <classname docapi="net.sf.basedb.core.data">GroupData</classname>, <classname docapi="net.sf.basedb.core.data">RoleData</classname> and
     460          <classname docapi="net.sf.basedb.core.data">ProjectData</classname> classes holds information about groups, roles
    461461          and projects respectively. A user may be a member of any number of groups,
    462462          roles and/or projects. The membership in a project comes with an attached
     
    473473     
    474474        <para>
    475           The <classname>KeyData</classname> class and it's subclasses
    476           <classname>ItemKeyData</classname>, <classname>ProjectKeyData</classname> and
    477           <classname>RoleKeyData</classname>, are used to store information about access
     475          The <classname docapi="net.sf.basedb.core.data">KeyData</classname> class and it's subclasses
     476          <classname docapi="net.sf.basedb.core.data">ItemKeyData</classname>, <classname docapi="net.sf.basedb.core.data">ProjectKeyData</classname> and
     477          <classname docapi="net.sf.basedb.core.data">RoleKeyData</classname>, are used to store information about access
    478478          permissions to items. To get permission to manipulate an item a user must have
    479479          access to a key giving that permission. There are three types of keys:
     
    482482        <variablelist>
    483483        <varlistentry>
    484           <term><classname>ItemKey</classname></term>
     484          <term><classname docapi="net.sf.basedb.core.data">ItemKey</classname></term>
    485485          <listitem>
    486486            <para>
    487487            Is used to give a user or group access to a specific item. The item
    488             must be a <interfacename>ShareableData</interfacename> item.
     488            must be a <interfacename docapi="net.sf.basedb.core.data">ShareableData</interfacename> item.
    489489            The permissions are usually set be the owner of the item. Once created an
    490490            item key cannot be changed. This allows the core to reuse a key if the
     
    496496
    497497        <varlistentry>
    498           <term><classname>ProjectKey</classname></term>
     498          <term><classname docapi="net.sf.basedb.core.data">ProjectKey</classname></term>
    499499          <listitem>
    500500            <para>
    501501            Is used to give members of a project access to a specific item. The item
    502             must be a <interfacename>ShareableData</interfacename> item. Once created a
     502            must be a <interfacename docapi="net.sf.basedb.core.data">ShareableData</interfacename> item. Once created a
    503503            project key cannot be changed. This allows the core to reuse a key if the
    504504            permissions match exactly, ie. for a given set of projects/permissions
     
    509509
    510510        <varlistentry>
    511           <term><classname>RoleKey</classname></term>
     511          <term><classname docapi="net.sf.basedb.core.data">RoleKey</classname></term>
    512512          <listitem>
    513513            <para>
     
    628628          The <constant>RESTRICTED_WRITE</constant> permission is in most cases the same
    629629          as the <constant>WRITE</constant> permission. So far the <constant>RESTRICTED_WRITE</constant>
    630           permission is only given to users to their own <classname>UserData</classname>
     630          permission is only given to users to their own <classname docapi="net.sf.basedb.core.data">UserData</classname>
    631631          object so they can change their address and other contact information,
    632632          but not quota, expiration date and other administrative information.
     
    700700        <title>Reporters</title>
    701701        <para>
    702           The <classname>ReporterData</classname> class holds information about reporters.
     702          The <classname docapi="net.sf.basedb.core.data">ReporterData</classname> class holds information about reporters.
    703703          The <property>externalId</property> is a required property that must be unique
    704704          among all reporters. The external ID is the value BASE uses to match
     
    721721          layer. Client applications and plug-ins should work directly with
    722722          the <classname>ReporterData</classname> class. To help manage the reporters
    723           there is the <classname>Reporter</classname> and <classname>ReporterBatcher</classname>
     723          there is the <classname docapi="net.sf.basedb.core">Reporter</classname> and <classname docapi="net.sf.basedb.core">ReporterBatcher</classname>
    724724          classes. The main reason for this
    725725          is to increase the performance and lower the memory usage by bypassing
     
    780780       
    781781        <para>
    782           The <classname>QuotaData</classname> holds information about a
     782          The <classname docapi="net.sf.basedb.core.data">QuotaData</classname> holds information about a
    783783          single quota registration. The same quota may be used by many different users
    784784          and groups. This object encapsulates allowed
     
    790790        <para>
    791791          The <property>quotaValues</property> property is a map from
    792           <classname>QuotaIndex</classname> to maximum byte values.
     792          <classname docapi="net.sf.basedb.core.data">QuotaIndex</classname> to maximum byte values.
    793793          This map must contain at least one entry for the total
    794794          quota at the primary location.
     
    801801       
    802802        <para>
    803           A <interfacename>DiskConsumableData</interfacename> (for example a file)
    804           item is automatically linked to a <classname>DiskUsageData</classname>
     803          A <interfacename docapi="net.sf.basedb.core.data">DiskConsumableData</interfacename> (for example a file)
     804          item is automatically linked to a <classname docapi="net.sf.basedb.core.data">DiskUsageData</classname>
    805805          item. This holds information about the number of bytes,
    806806          the location and quota type the item uses. It also holds information
     
    840840        <title>Clients</title>
    841841        <para>
    842           The <classname>ClientData</classname> class holds information
     842          The <classname docapi="net.sf.basedb.core.data">ClientData</classname> class holds information
    843843          about a client application. The <property>externalId</property>
    844844          property is a unique identifier for the application. To avoid ID clashes the ID
     
    882882        <para>
    883883          A session represents the time between login and logout for a single
    884           user. The <classname>SessionData</classname> object is entirely
     884          user. The <classname docapi="net.sf.basedb.core.data">SessionData</classname> object is entirely
    885885          managed by the BASE core, and should be considered read-only
    886886          for client applications.
     
    944944        <listitem>
    945945          <para>
    946           Current filtering options (as 1 or more <classname>PropertyFilterData</classname>
     946          Current filtering options (as 1 or more <classname docapi="net.sf.basedb.core.data">PropertyFilterData</classname>
    947947          objects).
    948948          </para>
     
    10131013       
    10141014        <para>
    1015           The <classname>DirectoryData</classname> class holds
     1015          The <classname docapi="net.sf.basedb.core.data">DirectoryData</classname> class holds
    10161016          information about directories. Directories are organised in the
    10171017          ususal way as as tree structure. All directories must have
     
    10201020       
    10211021        <para>
    1022           The <classname>FileData</classname> class holds information about
     1022          The <classname docapi="net.sf.basedb.core.data">FileData</classname> class holds information about
    10231023          a file. The actual file contents is stored on disk in the directory
    10241024          specified by the <varname>userfiles</varname> setting in
     
    11031103       
    11041104        <para>
    1105           The <classname>FileTypeData</classname> class holds information about
     1105          The <classname docapi="net.sf.basedb.core.data">FileTypeData</classname> class holds information about
    11061106          file types. It is used only to make it easier for users to organise
    11071107          their files.
     
    11091109       
    11101110        <para>
    1111           The <classname>MimeTypeData</classname> is used to register mime types and
     1111          The <classname docapi="net.sf.basedb.core.data">MimeTypeData</classname> is used to register mime types and
    11121112          map them to file extensions. The information is only used to lookup values
    11131113          when needed. Given the filename we can set the <varname>File.mimeType</varname>
     
    11601160       
    11611161        <para>
    1162           The <classname>PlatformData</classname> holds information about a
    1163           platform. A platform can have one or more <classname>PlatformVariant</classname>:s.
     1162          The <classname docapi="net.sf.basedb.core.data">PlatformData</classname> holds information about a
     1163          platform. A platform can have one or more <classname docapi="net.sf.basedb.core.data">PlatformVariant</classname>:s.
    11641164          Both the platform and variant are identified by an external ID that
    11651165          is fixed and can't be changed. <emphasis>Affymetrix</emphasis>
     
    11761176        <para>
    11771177          Each platform and it's variant can be connected to one or more
    1178           <classname>DataFileTypeData</classname> items. This item
     1178          <classname docapi="net.sf.basedb.core.data">DataFileTypeData</classname> items. This item
    11791179          describes the kind of files that are used to hold data for
    11801180          the platform and/or variant. The file types are re-usable between
     
    11891189          by a fixed, non-changable external ID. The <varname>itemType</varname>
    11901190          property tells us what type of item the file holds data for (ie.
    1191           array design or raw bioassay). It also links to a <classname>FileType</classname>
     1191          array design or raw bioassay). It also links to a <classname docapi="net.sf.basedb.core.data">FileType</classname>
    11921192          which is the generic type of data in the file. This allows us to query
    11931193          the database for, as an example, files with the generic type
     
    11971197        </para>
    11981198        <para>
    1199           The <varname>required</varname> flag in <classname>PlatformFileTypeData</classname>
     1199          The <varname>required</varname> flag in <classname docapi="net.sf.basedb.core.data">PlatformFileTypeData</classname>
    12001200          is used to signal that the file is a required file. This is not
    12011201          enforeced by the core. It is intended to be used by client applications
     
    12091209       
    12101210        <para>
    1211           An item must implement the <interfacename>FileStoreEnabledData</interfacename>
     1211          An item must implement the <interfacename docapi="net.sf.basedb.core">FileStoreEnabledData</interfacename>
    12121212          interface to be able to store data in files instead of in the database.
    1213           The interface creates a link to a <classname>FileSetData</classname> object,
    1214           which can hold several <classname>FileSetMemberData</classname> items.
    1215           Each member points to specific <classname>FileData</classname> item.
    1216           A file set can only store one file of each <classname>DataFileTypeData</classname>.
     1213          The interface creates a link to a <classname docapi="net.sf.basedb.core.data">FileSetData</classname> object,
     1214          which can hold several <classname docapi="net.sf.basedb.core.data">FileSetMemberData</classname> items.
     1215          Each member points to specific <classname docapi="net.sf.basedb.core.data">FileData</classname> item.
     1216          A file set can only store one file of each <classname docapi="net.sf.basedb.core.data">DataFileTypeData</classname>.
    12171217        </para>
    12181218       
     
    12521252          The parameter system is a generic system that can store almost
    12531253          any kind of simple values (string, numbers, dates, etc.) and
    1254           also links to other items. The <classname>ParameterValueData</classname>
     1254          also links to other items. The <classname docapi="net.sf.basedb.core.data">ParameterValueData</classname>
    12551255          class is an abstract base class that can hold multiple values (all must be of the
    12561256          same type). Unless only a specific type of values should be stored, this is
     
    13301330       
    13311331        <para>
    1332         An item must implement the <interfacename>AnnotatableData</interfacename>
     1332        An item must implement the <interfacename docapi="net.sf.basedb.core.data">AnnotatableData</interfacename>
    13331333        interface to be able to use the annotation system. This interface gives
    1334         a link to a <classname>AnnotationSetData</classname> item. This class
     1334        a link to a <classname docapi="net.sf.basedb.core.data">AnnotationSetData</classname> item. This class
    13351335        encapsulates all annotations for the item. There are two types of
    13361336        annotations:
     
    13451345          annotation are linked with the <property>annotations</property>
    13461346          property. This property is a map with an
    1347           <classname>AnnotationTypeData</classname>  as the key.
     1347          <classname docapi="net.sf.basedb.core.data">AnnotationTypeData</classname>  as the key.
    13481348          </para>
    13491349        </listitem>
     
    13621362       
    13631363        <para>
    1364           The <classname>AnnotationData</classname> class is also
     1364          The <classname docapi="net.sf.basedb.core.data">AnnotationData</classname> class is also
    13651365          just a placeholder. It connects the annotation set and
    1366           annotation type with a <classname>ParameterValueData</classname>
     1366          annotation type with a <classname docapi="net.sf.basedb.core.data">ParameterValueData</classname>
    13671367          object. This is the object that holds the actual annotation
    13681368          values.
     
    13751375       
    13761376        <para>
    1377         Instances of the <classname>AnnotationTypeData</classname> class
     1377        Instances of the <classname docapi="net.sf.basedb.core.data">AnnotationTypeData</classname> class
    13781378        defines the various annotations. It must have a <property>valueType</property>
    13791379        property which cannot be changed. The value of this property controls
    1380         which <classname>ParameterValueData</classname> subclass is used to store
    1381         the annotation values, ie. <classname>IntegerParameterValueData</classname>,
    1382         <classname>StringParameterValueData</classname>, etc.
     1380        which <classname docapi="net.sf.basedb.core.data">ParameterValueData</classname> subclass is used to store
     1381        the annotation values, ie. <classname docapi="net.sf.basedb.core.data">IntegerParameterValueData</classname>,
     1382        <classname docapi="net.sf.basedb.core.data">StringParameterValueData</classname>, etc.
    13831383        The <property>multiplicity</property> property holds the maximum allowed
    13841384        number of values for an annotation, or 0 if an unlimited number is
     
    14301430       
    14311431        <para>
    1432         The <classname>AnnotationTypeCategoryData</classname> class defines
     1432        The <classname docapi="net.sf.basedb.core.data">AnnotationTypeCategoryData</classname> class defines
    14331433        categories that are used to group annotation types that are related to
    14341434        each other. This information is mainly useful for client applications
     
    15331533       
    15341534        <para>
    1535           The <classname>PluginDefinitionData</classname> holds information of the
     1535          The <classname docapi="net.sf.basedb.core.data">PluginDefinitionData</classname> holds information of the
    15361536          installed plugin classes. Much of the information is copied from the
    1537           plug-in itself from the <classname>About</classname> object and by checking
     1537          plug-in itself from the <classname docapi="net.sf.basedb.core.plugin">About</classname> object and by checking
    15381538          which interfaces it implements.
    15391539        </para>
     
    15871587       
    15881588        <para>
    1589           The <classname>PluginTypeData</classname> class is ued to group
     1589          The <classname docapi="net.sf.basedb.core.data">PluginTypeData</classname> class is ued to group
    15901590          plug-ins that share some common functionality, by implementing
    15911591          additional (optional) interfaces. For example, the
    1592           <interfacename>AutoDetectingImporter</interfacename> should be implemented
     1592          <interfacename docapi="net.sf.basedb.core.plugin">AutoDetectingImporter</interfacename> should be implemented
    15931593          by import plug-ins that supports automatic detection of file formats.
    1594           Another example is the <interfacename>AnalysisFilterPlugin</interfacename>
     1594          Another example is the <interfacename docapi="net.sf.basedb.core.plugin">AnalysisFilterPlugin</interfacename>
    15951595          interface which should be implemented by all analysis plug-ins that
    15961596          only filters data.
     
    16041604        <para>
    16051605          A job represents a single invokation of a plug-in to do some work.
    1606           The <classname>JobData</classname> class holds information about this.
     1606          The <classname docapi="net.sf.basedb.core.data">JobData</classname> class holds information about this.
    16071607          A job is usuallu executed by a plug-in, but doesn't have to be. The
    16081608          <property>status</property> property holds the current state of a job.
     
    16491649          A job agent is a program running on the same or a different server that
    16501650          is regularly checking for jobs that are waiting to be executed. The
    1651           <classname>JobAgentData</classname> holds information about a job agent
    1652           and the <classname>JobAgentSettingsData</classname> links the agent
     1651          <classname docapi="net.sf.basedb.core.data">JobAgentData</classname> holds information about a job agent
     1652          and the <classname docapi="net.sf.basedb.core.data">JobAgentSettingsData</classname> links the agent
    16531653          with the plug-ins the agent is able to execute. The job agent will only
    16541654          execute jobs that are owner by users or projects that the job agent has
     
    17111711       
    17121712        <para>
    1713           There are four types of biomaterials: <classname>BioSourceData</classname>,
    1714           <classname>SampleData</classname>, <classname>ExtractData</classname> and
    1715           <classname>LabeledExtractData</classname>.
    1716           All four types of are derived from the base class <classname>BioMaterialData</classname>.
     1713          There are four types of biomaterials: <classname docapi="net.sf.basedb.core.data">BioSourceData</classname>,
     1714          <classname docapi="net.sf.basedb.core.data">SampleData</classname>, <classname docapi="net.sf.basedb.core.data">ExtractData</classname> and
     1715          <classname docapi="net.sf.basedb.core.data">LabeledExtractData</classname>.
     1716          All four types of are derived from the base class <classname docapi="net.sf.basedb.core.data">BioMaterialData</classname>.
    17171717          The reason for this is that they all share common functionality such as pooling
    17181718          and events. By using a common base class we do not have to create duplicate
     
    17211721       
    17221722        <para>
    1723           The <classname>BioSourceData</classname> is the simplest of the biomaterials.
     1723          The <classname docapi="net.sf.basedb.core.data">BioSourceData</classname> is the simplest of the biomaterials.
    17241724          It cannot have parents and can't participate in events. It's only used as a
    17251725          (non-required) parent for samples.
     
    17271727       
    17281728        <para>
    1729           The <classname>MeasuredBioMaterialData</classname> class is used as a base
     1729          The <classname docapi="net.sf.basedb.core.data">MeasuredBioMaterialData</classname> class is used as a base
    17301730          class for the other three biomaterial types. It introduces quantity
    17311731          measurements and can store original and remaining quantities. They are
     
    17491749          <property>pooled</property> property is <constant>false</constant>
    17501750          and the parent is specified in the <property>parent</property> property.
    1751           If the parent is not a <classname>BioSourceData</classname> this information
     1751          If the parent is not a <classname docapi="net.sf.basedb.core.data">BioSourceData</classname> this information
    17521752          is duplicated, with the addition of an optional used quantity value, in the
    1753           <property>sources</property> collection of the <classname>BioMaterialEventData</classname>
     1753          <property>sources</property> collection of the <classname docapi="net.sf.basedb.core.data">BioMaterialEventData</classname>
    17541754          object representing the creation event. It is the responsibility of the
    17551755          core to make sure that everything is properly synchronized and that
     
    17831783        <para>
    17841784          An event represents something that happened to one or more biomaterials, for example
    1785           the creation of another biomaterial. The <classname>BioMaterialEventData</classname>
     1785          the creation of another biomaterial. The <classname docapi="net.sf.basedb.core.data">BioMaterialEventData</classname>
    17861786          holds information about entry and event dates, protocols used, the user who is
    17871787          responsible, etc. There are three types of events represented by the <property>eventType</property>
     
    18481848       
    18491849        <para>
    1850           The <classname>PlateData</classname> is the main class holding information
    1851           about a single plate. The associated <classname>PlateGeometryData</classname>
     1850          The <classname docapi="net.sf.basedb.core.data">PlateData</classname> is the main class holding information
     1851          about a single plate. The associated <classname docapi="net.sf.basedb.core.data">PlateGeometryData</classname>
    18521852          defines how many rows and columns there are on a plate. Since this
    18531853          information is used to create wells, and for various other checks it is
     
    18571857         
    18581858        <para>
    1859           All plates must have a <classname>PlateTypeData</classname> which defines
     1859          All plates must have a <classname docapi="net.sf.basedb.core.data">PlateTypeData</classname> which defines
    18601860          the geometry and a set of event types (see below).
    18611861        </para>
     
    18771877
    18781878        <para>
    1879           The plate type defines a set of <classname>PlateEventTypeData</classname>
     1879          The plate type defines a set of <classname docapi="net.sf.basedb.core.data">PlateEventTypeData</classname>
    18801880          objects, each one represening a particular event a plate of this type
    18811881          usually goes trough. For a plate of a certain type, it is possible to
     
    18991899        <para>
    19001900          A plate can be created either from scratch, with the help of the information
    1901           in a <classname>PlateMappingData</classname>, from a set of parent plates.
     1901          in a <classname docapi="net.sf.basedb.core.data">PlateMappingData</classname>, from a set of parent plates.
    19021902          In the first case it is possible to specify a reporter for each well on the
    19031903          plate. In the second case the mapping code creates all the wells and links
     
    19431943       
    19441944        <para>
    1945           Array designs are stored in <classname>ArrayDesignData</classname> objects
     1945          Array designs are stored in <classname docapi="net.sf.basedb.core.data">ArrayDesignData</classname> objects
    19461946          and can be created either as standalone designs or
    19471947          from plates. In the first case the features on an array design
     
    19511951          Each block can be identified either by a <property>blockNumber</property>
    19521952          or by meta coordinates. This information is stored in
    1953           <classname>ArrayDesignBlockData</classname> items. Each block
    1954           contains several <classname>FeatureData</classname> items, each
     1953          <classname docapi="net.sf.basedb.core.data">ArrayDesignBlockData</classname> items. Each block
     1954          contains several <classname docapi="net.sf.basedb.core.data">FeatureData</classname> items, each
    19551955          one identified by a row and column coordinate. Platforms that doesn't
    19561956          divide the array design into block should create a single super-block
     
    19781978       
    19791979        <para>
    1980           The <classname>ArraySlideData</classname> represents a single
     1980          The <classname docapi="net.sf.basedb.core.data">ArraySlideData</classname> represents a single
    19811981          array. Arrays are usually printed several hundreds in a batch,
    1982           represented by a <classname>ArrayBatchData</classname> item.
     1982          represented by a <classname docapi="net.sf.basedb.core.data">ArrayBatchData</classname> item.
    19831983          The <property>batchIndex</property> is the ordinal number of the
    19841984          array in the batch. The <property>barcode</property> can be used
     
    20372037       
    20382038        <para>
    2039         A <classname>RawBioAssayData</classname> object represents
     2039        A <classname docapi="net.sf.basedb.core.data">RawBioAssayData</classname> object represents
    20402040        the raw data that is produced by analysing the image(s) from a
    20412041        single scan. You may register which software that was used, the
     
    20452045        <para>
    20462046        Files with the analysed data values can be attached to the
    2047         associated <classname>FileSetData</classname> object. The platform
     2047        associated <classname docapi="net.sf.basedb.core.data">FileSetData</classname> object. The platform
    20482048        and, optionally, the variant has information about the file types
    20492049        that can be used for that platform. If the platform file types support
     
    20542054        <para>
    20552055        If the platform support it, raw data can also be imported into the database.
    2056         This is handled by batchers and <classname>RawData</classname> objects.
    2057         Which table to store the data in depends on the <classname>rawDataType</classname>
     2056        This is handled by batchers and <classname docapi="net.sf.basedb.core.data">RawData</classname> objects.
     2057        Which table to store the data in depends on the <property>rawDataType</property>
    20582058        property. The properties shown for the <classname>RawData</classname> class
    20592059        in the diagram are the mandatory properties. Each raw data type defines additional
     
    23522352        BASE 2.5 introduced the possibility to use files to store data instead
    23532353        of importing it into the database. Files can be attached
    2354         to any item that implements the <interfacename>FileStoreEnabled</interfacename>
    2355         interface. Currently this is <classname>RawBioAssay</classname>
    2356         and <classname>ArrayDesign</classname>. The
     2354        to any item that implements the <interfacename docapi="net.sf.basedb.core">FileStoreEnabled</interfacename>
     2355        interface. Currently this is <classname docapi="net.sf.basedb.core">RawBioAssay</classname>
     2356        and <classname docapi="net.sf.basedb.core">ArrayDesign</classname>. The
    23572357        ability to store data in files is not a replacement for storing data in the
    23582358        database. It is possible (for some platforms/raw data types) to have data in
     
    23822382      <para>
    23832383        Not all three cases are supported for all types of data. This is controlled
    2384         by the <classname>Platform</classname> class, which may disallow
     2384        by the <classname docapi="net.sf.basedb.core">Platform</classname> class, which may disallow
    23852385        that data is stored in the database. To check this call
    23862386        <methodname>Platform.isFileOnly()</methodname> and/or
     
    24012401      <listitem>
    24022402        <para>
    2403         A <classname>RawDataType</classname> that has <code>isStoredInDb() == true</code>:
     2403        A <classname docapi="net.sf.basedb.core">RawDataType</classname> that has <code>isStoredInDb() == true</code>:
    24042404        The platform can store data in the database but only data with the specified raw
    24052405        data type.
     
    24082408      <listitem>
    24092409        <para>
    2410         A <classname>RawDataType</classname> that has <code>isStoredInDb() == false</code>:
     2410        A <classname docapi="net.sf.basedb.core">RawDataType</classname> that has <code>isStoredInDb() == false</code>:
    24112411        The platform can't store data in the database.
    24122412        </para>
     
    24232423     
    24242424      <para>
    2425         For backwards compatibility reasons, each <classname>Platform</classname>
     2425        For backwards compatibility reasons, each <classname docapi="net.sf.basedb.core">Platform</classname>
    24262426        that can only store data in files will create "virtual" raw data type
    24272427        objects internally. These raw data types all return <constant>false</constant>
     
    24632463        <para>
    24642464          This is rather large set of classes and methods. The ultimate goal
    2465           is to be able to create links between a <classname>RawBioAssay</classname>
    2466           / <classname>ArrayDesign</classname> and <classname>File</classname>
     2465          is to be able to create links between a <classname docapi="net.sf.basedb.core">RawBioAssay</classname>
     2466          / <classname docapi="net.sf.basedb.core">ArrayDesign</classname> and <classname docapi="net.sf.basedb.core">File</classname>
    24672467          items and to provide some metadata about the files.
    2468           The <classname>FileStoreUtil</classname> class is one of the most
     2468          The <classname docapi="net.sf.basedb.core">FileStoreUtil</classname> class is one of the most
    24692469          important ones. It is intended to make it easy for plug-in (and other)
    24702470          developers to access the files without having to mess with platform
     
    24852485       
    24862486        <para>
    2487           Given that we have a <interfacename>FileStoreEnabled</interfacename>
    2488           item we want to find out which <classname>DataFileType</classname>
     2487          Given that we have a <interfacename docapi="net.sf.basedb.core">FileStoreEnabled</interfacename>
     2488          item we want to find out which <classname docapi="net.sf.basedb.core">DataFileType</classname>
    24892489          items that can be used for that item. The
    24902490          <methodname>DataFileType.getQuery(FileStoreEnabled)</methodname>
     
    25052505          The <constant>Affymetrix</constant> platform defines <constant>CEL</constant>
    25062506          as a raw data file and <constant>CDF</constant> as an array design (reporter map)
    2507           file. If we have a <classname>RawBioAssay</classname> the query will only return
     2507          file. If we have a <classname docapi="net.sf.basedb.core">RawBioAssay</classname> the query will only return
    25082508          the CEL file type and the client can ask the user for a CEL file.
    25092509          </para>
     
    25132513          The <constant>Generic</constant> platform defines <constant>PRINT_MAP</constant>
    25142514          and <constant>REPORTER_MAP</constant> for array designs. If we have
    2515           an <classname>ArrayDesign</classname> the query will return those two
     2515          an <classname docapi="net.sf.basedb.core">ArrayDesign</classname> the query will return those two
    25162516          items.
    25172517          </para>
     
    25792579        <para>
    25802580          When the user has selected the file(s) we must store the links
    2581           to them in the database. This is done with a <classname>FileSet</classname>
     2581          to them in the database. This is done with a <classname docapi="net.sf.basedb.core">FileSet</classname>
    25822582          object. A file set can contain any number of files. The only limitation
    25832583          is that it can only contain one file for each file type.
     
    25852585          a file in the file set. If a file already exists for the given file type
    25862586          it is replaced, otherwise a new entry is created. The following
    2587           program example assumes that we have a map where <classname>File</classname>:s
    2588           are related to <classname>DataFileType</classname>:s. When all files
     2587          program example assumes that we have a map where <classname docapi="net.sf.basedb.core">File</classname>:s
     2588          are related to <classname docapi="net.sf.basedb.core">DataFileType</classname>:s. When all files
    25892589          have been added we call <methodname>FileSet.validate()</methodname>
    25902590          to validate the files and extract metadata.
     
    26142614          and metadata extraction is done by the core when the
    26152615          <methodname>FileSet.validate()</methodname> is called.
    2616           The process is partly pluggable since each <classname>DataFileType</classname>
     2616          The process is partly pluggable since each <classname docapi="net.sf.basedb.core">DataFileType</classname>
    26172617          can name a class that should do the validation and/or metadata extraction.
    26182618        </para>
     
    26382638        <listitem>
    26392639          <para>
    2640           The core checks the <classname>DataFileType</classname> of all
    2641           members in the file set and creates <classname>DataFileValidator</classname>
    2642           and <classname>DataFileMetadataReader</classname> objects. Only one instance
     2640          The core checks the <classname docapi="net.sf.basedb.core">DataFileType</classname> of all
     2641          members in the file set and creates <classname docapi="net.sf.basedb.core.filehandler">DataFileValidator</classname>
     2642          and <classname docapi="net.sf.basedb.core.filehandler">DataFileMetadataReader</classname> objects. Only one instance
    26432643          of each class is created. If the file set contains members which has the
    26442644          same validator or metadata reader, they will all share the same instance.
     
    26862686        <para>
    26872687          All validators and meta data extractors should extend
    2688           the <classname>AbstractDataFileHandler</classname> class. The reason
    2689           is that we may want to add more methods to the <interfacename>DataFileHandler</interfacename>
    2690           interface in the future. The <classname>AbstractDataFileHandler</classname> will
     2688          the <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> class. The reason
     2689          is that we may want to add more methods to the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileHandler</interfacename>
     2690          interface in the future. The <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> will
    26912691          be used to provide default implementations for backwards compatibility.
    26922692        </para>
     
    27002700          This should be done by existing plug-ins in the same way as before.
    27012701          A slight modification is needed since it is good if the importers
    2702           are made aware of already selected files in the <classname>FileSet</classname>
    2703           to provide good default values. The <classname>FileStoreUtil</classname>
     2702          are made aware of already selected files in the <classname docapi="net.sf.basedb.core">FileSet</classname>
     2703          to provide good default values. The <classname docapi="net.sf.basedb.core">FileStoreUtil</classname>
    27042704          class is very useful in cases like this:
    27052705        </para>
     
    27472747        <para>
    27482748          Just as before, an experiment is still locked to a single
    2749           <classname>RawDataType</classname>. This is a design issue that
     2749          <classname docapi="net.sf.basedb.core">RawDataType</classname>. This is a design issue that
    27502750          would break too many things if changed. If data is stored in files
    2751           the experiment is also locked to a single <classname>Platform</classname>.
     2751          the experiment is also locked to a single <classname docapi="net.sf.basedb.core">Platform</classname>.
    27522752          This has been designed to have as little impact on existing
    27532753          plug-ins as possible. In most cases, the plug-ins will continue
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