Changeset 3944

Timestamp:

Nov 9, 2007, 4:31:00 PM (16 years ago)

Author:

Martin Svensson

Message:

References #819 The class-tag and interface-tag are now linking to the javadoc for the tagged class or interface.
Updated the source files of the documentation.

Location:

trunk

Files:

• doc/src/docbook/admindoc/plugin_installation.xml (modified) (1 diff)
• doc/src/docbook/admindoc/user_administration.xml (modified) (1 diff)
• doc/src/docbook/appendix/base.config.xml (modified) (3 diffs)
• doc/src/docbook/appendix/incompatible.xml (modified) (2 diffs)
• doc/src/docbook/appendix/jobagent.properties.xml (modified) (7 diffs)
• doc/src/docbook/appendix/raw_data_types.xml (modified) (1 diff)
• doc/src/docbook/developerdoc/core_ref.xml (modified) (7 diffs)
• doc/src/docbook/developerdoc/plugin_developer.xml (modified) (80 diffs)
• doc/src/docbook/developerdoc/webservices.xml (modified) (2 diffs)
• doc/src/docbook/userdoc/platforms.xml (modified) (2 diffs)
• lib/docbook/custom-styles/docbook/plain/admonitions/docapi.gif (added)
• lib/docbook/custom-styles/docbook/plain/xsl/customized.chunked.xsl (modified) (1 diff)
• lib/docbook/preprocess/dweiss-docbook-extensions.dtd (modified) (1 diff)

trunk/doc/src/docbook/admindoc/plugin_installation.xml

@@ -343 +343 @@
           each row is an icon that displays summarized information about the plug-in when
           the mouse pointer is held over it. Most of this information is from the plug-in's
-          <classname>About</classname>
+          <classname docapi="net.sf.basedb.core.plugins">About</classname>
           property but some, like 'Works with', 'Class' and 'Jar' is from the installation
           file included in the JAR file. A plug-in can also be distributed with one or many

trunk/doc/src/docbook/admindoc/user_administration.xml

@@ -352 +352 @@
                 <guilabel>Additional info</guilabel>
                 tab is only visible if there is one or more property defined for
-                <classname>UserData</classname>
+                <classname docapi="net.sf.basedb.core.data">UserData</classname>
                 in the configuration file for extended properties.
               </para>

trunk/doc/src/docbook/appendix/base.config.xml

@@ -288 +288 @@
         BASE ships with a simple plugin that checks if a user has a valid email 
         account on a POP3 server. It is not enabled by default. The class name 
-        of that plugin is <classname>net.sf.basedb.core.authentication.POP3Authenticator</classname>. 
+        of that plugin is <classname docapi="net.sf.basedb.core.authentication">net.sf.basedb.core.authentication.POP3Authenticator</classname>. 
         If no class is specified internal authentication is used.
           </para>
@@ -300 +300 @@
         Initialisation parameters sent to the plug-in when calling the 
         <methodname>init()</methodname> method. The syntax and meaning of this 
-        string depends on the plugin. For the <classname>POP3Authenticator</classname> 
+        string depends on the plugin. For the <classname docapi="net.sf.basedb.core.authentication">POP3Authenticator</classname> 
         this is simply the name or IP-address of the mail server.
           </para>
@@ -477 +477 @@
         BASE ships with a simple plug-in that just moves files to another directory, 
         but it is not enabled by default. The class name of that plug-in is 
-        <classname>net.sf.basedb.core.InternalStorageController</classname>. 
+        <classname docapi="net.sf.basedb.core">net.sf.basedb.core.InternalStorageController</classname>. 
         If no class is specified the secondary storage feature is disabled.
           </para>

trunk/doc/src/docbook/appendix/incompatible.xml

@@ -55 +55 @@
       for the <filename>raw-data-types.xml</filename> file. BASE will refuse
       to start if it finds this attribute. Raw data types which doesn't use
-      the database for storing data should be registered as <classname>Platform</classname>:s
+      the database for storing data should be registered as <classname docapi="net.sf.basedb.core">Platform</classname>:s
       instead.
     </para>
@@ -61 +61 @@
     <para>
       Applications or plug-ins that filters on the <property>rawDataType</property>
-      property for <classname>RawBioAssay</classname> or <classname>Experiment</classname>
+      property for <classname docapi="net.sf.basedb.core">RawBioAssay</classname> or <classname docapi="net.sf.basedb.core">Experiment</classname>
       may need to change. The ID given to raw data types that doesn't use the
       database for storing data are prefixed with "<constant>platform.</constant>".

trunk/doc/src/docbook/appendix/jobagent.properties.xml

@@ -211 +211 @@
           <listitem>            
             <para>
-            <classname>net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor</classname>:
+            <classname docapi="net.sf.basedb.clients.jobagent.executors">
+              net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
+            </classname>:
             Executes the job in an 
             external process. This is the recommended executor and is the default
@@ -223 +225 @@
           <listitem>
             <para>
-            <classname>net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor</classname>:      
+            <classname docapi="net.sf.basedb.clients.jobagent.executors">
+              net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
+            </classname>:     
             Executes the job in a separate thread. This is only recommended 
             for plugins that are  trusted and safe. A misbehaving plugin can affect the job agent 
@@ -233 +237 @@
           <listitem>
             <para>
-            <classname>net.sf.basedb.clients.jobagent.executors.DummyJobExecutor</classname>:     
+            <classname docapi="net.sf.basedb.clients.jobagent.executors">net.sf.basedb.clients.jobagent.executors.DummyJobExecutor</classname>:     
             Does not execute the job. It only marks the job as being executed, 
             and after waiting some time, as finished successfully. 
@@ -243 +247 @@
           It is possible to create your own implementation of a job executor. 
           Create a class that implements the 
-          <interfacename>net.sf.basedb.clients.jobagent.JobExecutor</interfacename>
+          <interfacename docapi="net.sf.basedb.clients.jobagent">net.sf.basedb.clients.jobagent.JobExecutor</interfacename>
           interface.          
         </para>
@@ -254 +258 @@
         <para>
           Optional. The path to the Java executable used by the 
-          <classname>ProcessJobExecutor</classname>. If not specified the 
+          <classname docapi="net.sf.basedb.clients.jobagent.executors">
+            ProcessJobExecutor
+          </classname>. If not specified the 
           <envar>JAVA_HOME</envar> environment variable will be checked. 
           As a last resort <command>java</command> is used without path 
@@ -271 +277 @@
           <option>-Ms</option>), it will be added automatically by the 
           executor. This setting is used by the 
-          <classname>ProcessJobExecutor</classname> only.
+          <classname docapi="net.sf.basedb.clients.jobagent.executors">ProcessJobExecutor</classname> only.
         </para>
       </listitem>
@@ -280 +286 @@
       <listitem>
         <para>
-          Optional. Number of seconds the <classname>DummyJobExecutor</classname> should 
+          Optional. Number of seconds the <classname docapi="net.sf.basedb.clients.jobagent.executors">DummyJobExecutor</classname> should 
           wait before returning from the "job execution". The executor first sets 
           the progress to 50% then waits the specified number of seconds before 

trunk/doc/src/docbook/appendix/raw_data_types.xml

@@ -32 +32 @@
   <para>
     Raw data can be stored either as files attached to items or in
-    the database. The <classname>Platform</classname> item has information
+    the database. 
+    The <classname docapi="net.sf.basedb.core">Platform</classname> item has information
     about this. Configuration information for the database tables
     and columns used to store raw data in the database is found in the

trunk/doc/src/docbook/developerdoc/core_ref.xml

@@ -201 +201 @@
       <listitem>
         <para>
-        Add code to the <classname>net.sf.basedb.core.Update</classname> class
+        Add code to the <classname docapi="net.sf.basedb.core">net.sf.basedb.core.Update</classname> class
         to increase the schema version and modify data in existing installations.
         </para>
@@ -567 +567 @@
           The second-level cache is suitable for objects that are rarely modified but 
           are often needed. For example, we do not expect the user information represented 
-          by the <classname>UserData</classname> object to change very often, but it is 
+          by the <classname docapi="net.sf.basedb.core.data">UserData</classname> object to change very often, but it is 
           displayed all the time as the owner of various items.
         </para>
@@ -597 +597 @@
           The first question is the most important. Good candidates are classes with few 
           objects that change rarely, but are read often. Also, objects which are linked 
-          to by many other objects are good candidates. The <classname>UserData</classname>
-          class is an example which matches all three requirements. The <classname>LabelData</classname>
-          class is an example which fulfils the first two. The <classname>BioMaterialEventData</classname>
+          to by many other objects are good candidates. The <classname docapi="net.sf.basedb.core.data">UserData</classname>
+          class is an example which matches all three requirements. The <classname docapi="net.sf.basedb.core.data">LabelData</classname>
+          class is an example which fulfils the first two. The <classname docapi="net.sf.basedb.core.data">BioMaterialEventData</classname>
           class is on the other hand a bad cache candidate, since it is not linked to any 
-          other object than a <classname>BioMaterialData</classname> object.
+          other object than a <classname docapi="net.sf.basedb.core.data">BioMaterialData</classname> object.
         </para>
         
@@ -716 +716 @@
             since they are many and we want to use as little memory as possible. Here it 
             is required that proxies are enabled for all items that are linked from any of 
-            the batchable items, ie. <classname>RawBioAssay</classname>, 
-            <classname>ReporterType</classname>, <classname>ArrayDesignBlock</classname>, etc.
+            the batchable items, ie. <classname docapi="net.sf.basedb.core">RawBioAssay</classname>, 
+            <classname docapi="net.sf.basedb.core">ReporterType</classname>, <classname docapi="net.sf.basedb.core">ArrayDesignBlock</classname>, etc.
           </para>
           
@@ -872 +872 @@
             where Hibernate can find the name of the table where items of this type are stored. 
             The table name should generally be the same as the class name, without the ending 
-            <code>Data</code> and in a plural form. For example <classname>UserData</classname>
+            <code>Data</code> and in a plural form. For example <classname docapi="net.sf.basedb.core.data">UserData</classname>
             --&gt; <code>Users</code>. The back-ticks (`) around the table name tells Hibernate
             to enclose the name in whatever the actual database manager uses for such things 
@@ -1274 +1274 @@
             are package private. This is required because Hibernate will get confused if 
             we modify both ends. Thus, we are forced to always add/remove users to/from 
-            the set in the <classname>GroupData</classname> object. The methods in the
-            <classname>RoleData</classname> class are never used by us.
+            the set in the <classname docapi="net.sf.basedb.core.data">GroupData</classname> object. The methods in the
+            <classname docapi="net.sf.basedb.core.data">RoleData</classname> class are never used by us.
             Note that we do not have to check for null and create a new set since Hibernate 
             will handle null values as an empty set.
@@ -1584 +1584 @@
           <para>
             In this case, we use the <code>@hibernate.one-to-one</code> mapping
-            in both classes. The <code>constrained="true"</code> tag in <classname>UserData</classname>
+            in both classes. The <code>constrained="true"</code> tag in <classname docapi="net.sf.basedb.core.data">UserData</classname>
             tells Hibernate to always insert the password first, and then the user. The makes it
             possible to use the (auto-generated) id for the password as the id 

trunk/doc/src/docbook/developerdoc/plugin_developer.xml

@@ -296 +296 @@
           <listitem>
             <simpara>
-              <interfacename>net.sf.basedb.core.plugin.Plugin</interfacename>
+              <interfacename docapi="net.sf.basedb.core.plugin">net.sf.basedb.core.plugin.Plugin</interfacename>
             </simpara>
           </listitem>
           <listitem>
             <simpara>
-              <interfacename>net.sf.basedb.core.plugin.InteractivePlugin</interfacename>
+              <interfacename docapi="net.sf.basedb.core.plugin">net.sf.basedb.core.plugin.InteractivePlugin</interfacename>
             </simpara>
           </listitem>
           <listitem>
             <simpara>
-              <classname>net.sf.basedb.core.plugin.AbstractPlugin</classname>
+              <classname docapi="net.sf.basedb.core.plugin">net.sf.basedb.core.plugin.AbstractPlugin</classname>
             </simpara>
           </listitem>
@@ -312 +312 @@
         
         A plug-in must always implement the 
-        <interfacename>Plugin</interfacename> interface. 
-        The <interfacename>InteractivePlugin</interfacename>
+        <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename> interface. 
+        The <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
         interface is optional, and is only needed if you want user interaction.
-        The <classname>AbstractPlugin</classname> is a useful base class
+        The <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname> is a useful base class
         that your plug-in can use as a superclass. It provides default implementations
         for some of the interface methods and also has utility methods for
@@ -321 +321 @@
         reason to use this class as a superclass is that it will shield your 
         plug-in from future changes to the Plug-in API. For example, if
-        we decide that a new method is needed in the <interfacename>Plugin</interfacename> 
+        we decide that a new method is needed in the <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename> 
         interface we will also try to add a default implementation in 
-        the <classname>AbstractPlugin</classname> class.
+        the <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname> class.
       </para>
   
@@ -353 +353 @@
                 Return information about the plug-in, i.e. the name, version, and a short
                 description about what the plug-in does. The
-                <classname>About</classname>
+                <classname docapi="net.sf.basedb.core.plugin">About</classname>
                 object also has fields for naming the author and various other contact
                 information. The returned information is copied by the core at
@@ -393 +393 @@
               <para>
                 Return information about the main type of plug-in. The
-                <classname>MainType</classname>
+                <classname docapi="net.sf.basedb.core.plugin">Plugin.MainType</classname>
                 is an enumeration with five possible values:
                 <itemizedlist>
@@ -457 +457 @@
                 If this method returns true, the plug-in can have different
                 configurations, (i.e.
-                <classname>PluginConfiguration</classname>).
+                <classname docapi="net.sf.basedb.core">PluginConfiguration</classname>).
                 Note that this method may return true even if the
-                <interfacename>InteractivePlugin</interfacename>
+                <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
                 interface is not implemented. The
-                <classname>AbstractPlugin</classname>
+                <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname>
                 returns true for this method, which is the old way before the
                 introduction of this method.
@@ -483 +483 @@
                 any data. 
                 The
-                <classname>AbstractPlugin</classname>
+                <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname>
                 returns false for this method, which is the old way before the
                 introduction of this method.
@@ -553 +553 @@
                 The parameters passed to this method has vital information that is
                 needed to execute the plug-in. The
-                <classname>SessionControl</classname>
+                <classname docapi="net.sf.basedb.core">SessionControl</classname>
                 is a central core object holding information about the logged in
                 user and is used to create
-                <classname>DbControl</classname>
+                <classname docapi="net.sf.basedb.core">DbControl</classname>
                 objects which allows a plug-in to connect to the database to read, add or
                 update information. The two
-                <classname>ParameterValues</classname>
+                <classname docapi="net.sf.basedb.core.plugin">ParameterValues</classname>
                 objects contain information about the configuration and job 
                 parameters to the plug-in. 
                 The <varname>configuration</varname> object holds all parameters stored
-                together with a <classname>PluginConfiguration</classname>
+                together with a <classname docapi="net.sf.basedb.core">PluginConfiguration</classname>
                 object in the database. If the plug-in is started without
                 a configuration this object is null.
                 The <varname>job</varname> object holds all parameters that are
-                stored together with a <classname>Job</classname> object in the 
+                stored together with a <classname docapi="net.sf.basedb.core">Job</classname> object in the 
                 database. This object is null if the plug-in is started without a job.
               </para>
@@ -580 +580 @@
               <para>
                 The
-                <classname>AbstractPlugin</classname>
+                <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname>
                 contains an implementation of this method that saves the passed objects
                 in protected instance variables. If you override this method 
@@ -586 +586 @@
               </para>
               <example id="net.sf.basedb.core.plugin.Plugin.init">
-                <title>The <classname>AbstractPlugin</classname> implementation of Plugin.init()</title>
+                <title>The <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname> implementation of Plugin.init()</title>
 <programlisting language="java">
 protected SessionControl sc = null;
@@ -722 +722 @@
                 <title>
                   The
-                  <classname>AbstractPlugin</classname>
+                  <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname>
                   contains an implementation of the <methodname>done()</methodname>
                   method simply sets the
@@ -752 +752 @@
           this interface. This is probably the case for most plug-ins. Among the core plug-ins
           shipped with BASE the
-          <classname>SpotImageCreator</classname>
+          <classname docapi="net.sf.basedb.plugins">SpotImageCreator</classname>
           is one plug-in that does not interact with the user. Instead, the web client has
           special JSP pages that handles all the interaction, creates a job for it and sets
@@ -761 +761 @@
         <para>
           The
-          <interfacename>InteractivePlugin</interfacename>
+          <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
           has three main tasks:
           
@@ -802 +802 @@
                 Return information about where the plug-in should be plugged in. Each
                 place is identified by a
-                <classname>GuiContext</classname>
+                <classname docapi="net.sf.basedb.core.plugin">GuiContext</classname>
                 object, which is an
-                <classname>Item</classname>
+                <classname docapi="net.sf.basedb.core">Item</classname>
                 and a
-                <classname>Type</classname>.
+                <classname docapi="net.sf.basedb.core">Type</classname>.
                 The item is one of the objects defined by the
-                <classname>net.sf.basedb.core.Item</classname>
+                <classname docapi="net.sf.basedb.core">Item</classname>
                 enumeration and the type is either
                 <constant>Type.LIST</constant>
@@ -834 +834 @@
                 The returned information is copied by the core at installation time to
                 make it easy to ask for all plug-ins for a certain
-                <classname>GuiContext</classname>.
+                <classname docapi="net.sf.basedb.core.plugin">GuiContext</classname>.
               </para>
               <para>
@@ -923 +923 @@
               <para>
                 Here is a real example from the
-                <classname>RawDataFlatFileImporter</classname>
+                <classname docapi="net.sf.basedb.plugins">RawDataFlatFileImporter</classname>
                 plug-in which imports raw data to a
-                <classname>RawBioAssay</classname>. 
+                <classname docapi="net.sf.basedb.core">RawBioAssay</classname>. 
                 
                 Thus,
@@ -1011 +1011 @@
               <para>
                 Ask the plug-in for parameters that need to be entered by the user. The
-                <classname>GuiContext</classname>
+                <classname docapi="net.sf.basedb.core.plugin">GuiContext</classname>
                 parameter is one of the contexts returned by the
                 <methodname>getGuiContexts</methodname>
@@ -1018 +1018 @@
                 plug-in may define its own commands. The two predefined commands are
                 defined in the
-                <classname>net.sf.basedb.core.plugin.Request</classname>
+                <classname docapi="net.sf.basedb.core.plugin">net.sf.basedb.core.plugin.Request</classname>
                 class.
                 <variablelist>
@@ -1045 +1045 @@
                 </variablelist>
                 Given this information the plug-in must return a
-                <classname>RequestInformation</classname>
+                <classname docapi="net.sf.basedb.core">RequestInformation</classname>
                 object. This is simply a title, a description, and a list of parameters.
                 Usually the title will end up as the input form title and the
@@ -1125 +1125 @@
               <para>
                 As you can see it takes a lot of code to put together a
-                <classname>RequestInformation</classname>
+                <classname docapi="net.sf.basedb.core">RequestInformation</classname>
                 object. For each parameter you need one
-                <classname>PluginParameter</classname>
+                <classname docapi="net.sf.basedb.core">PluginParameter</classname>
                 object and one
-                <classname>ParameterType</classname>
+                <classname docapi="net.sf.basedb.core">ParameterType</classname>
                 object. To make life a little easier, a
-                <classname>ParameterType</classname>
+                <classname docapi="net.sf.basedb.core">ParameterType</classname>
                 can be reused for more than one
-                <classname>PluginParameter</classname>.
+                <classname docapi="net.sf.basedb.core">PluginParameter</classname>.
               </para>
               
@@ -1144 +1144 @@
               <para>
                 The
-                <classname>ParameterType</classname>
+                <classname docapi="net.sf.basedb.core">ParameterType</classname>
                 is an abstract base class for several subclasses each implementing a
                 specific type of parameter. The list of subclasses may grow in the
@@ -1160 +1160 @@
                 <varlistentry>
                   <term>
-                    <classname>StringParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">StringParameterType</classname>
                   </term>
                   <listitem>
@@ -1171 +1171 @@
                 <varlistentry>
                   <term>
-                    <classname>FloatParameterType</classname>, 
-                    <classname>DoubleParameterType</classname>, 
-                    <classname>IntegerParameterType</classname>, 
-                    <classname>LongParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">FloatParameterType</classname>, 
+                    <classname docapi="net.sf.basedb.core">DoubleParameterType</classname>, 
+                    <classname docapi="net.sf.basedb.core">IntegerParameterType</classname>, 
+                    <classname docapi="net.sf.basedb.core">LongParameterType</classname>
                   </term>
                   <listitem>
@@ -1185 +1185 @@
                 <varlistentry>
                   <term>
-                    <classname>BooleanParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">BooleanParameterType</classname>
                   </term>
                   <listitem>
@@ -1194 +1194 @@
                 <varlistentry>
                   <term>
-                    <classname>DateParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">DateParameterType</classname>
                   </term>
                   <listitem>
@@ -1203 +1203 @@
                 <varlistentry>
                   <term>
-                    <classname>FileParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">FileParameterType</classname>
                   </term>
                   <listitem>
@@ -1212 +1212 @@
                 <varlistentry>
                   <term>
-                    <classname>ItemParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">ItemParameterType</classname>
                   </term>
                   <listitem>
@@ -1218 +1218 @@
                       Asks for any other item. This parameter type requires
                       that a list of options is supplied, except when the item
-                      type asked for matches the current <classname>GuiContext</classname>, in which
+                      type asked for matches the current <classname docapi="net.sf.basedb.core.plugin">GuiContext</classname>, in which
                       case the currently selected item is used as the
                       parameter value.
@@ -1226 +1226 @@
                 <varlistentry>
                   <term>
-                    <classname>PathParameterType</classname>
+                    <classname docapi="net.sf.basedb.core">PathParameterType</classname>
                   </term>
                   <listitem>
@@ -1240 +1240 @@
               <para>
                 You can also create a
-                <classname>PluginParameter</classname>
+                <classname docapi="net.sf.basedb.core">PluginParameter</classname>
                 with a null name and
-                <classname>ParameterType</classname>.
+                <classname docapi="net.sf.basedb.core">ParameterType</classname>.
                 In this case, the web client will not ask for input from the user, instead
                 it is used as a section header, allowing you to group parameters into
@@ -1297 +1297 @@
                 the input string is parsed and converted to a 
                 <classname>Float</classname>. If you have extended the
-                <classname>AbstractPlugin</classname>
+                <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname>
                 class it is very easy to validate the parameters with the
                 <methodname>AbstractPlugin.validateRequestParameters()</methodname>
                 method. This method takes the same list of
-                <classname>PluginParameter</classname>:s
+                <classname docapi="net.sf.basedb.core">PluginParameter</classname>:s
                 as used in the
-                <classname>RequestInformation</classname>
+                <classname docapi="net.sf.basedb.core">RequestInformation</classname>
                 object and uses that information for validation. It returns null or a
                 list of
@@ -1321 +1321 @@
               <para>
                 The configure method works much like the <methodname>Plugin.run()</methodname> 
-                method. It must return the result in the <classname>Response</classname> object, 
+                method. It must return the result in the <classname docapi="net.sf.basedb.core.plugin">Response</classname> object, 
                 and should not throw any exceptions.
               </para>
@@ -1380 +1380 @@
               </para>
               <para>
-                The <classname>Response</classname> class also has a
+                The <classname docapi="net.sf.basedb.core.plugin">Response</classname> class also has a
                 <methodname>setContinue()</methodname>
                 method which tells the core that the plug-in needs more parameters,
@@ -1478 +1478 @@
         <listitem>
           <para>
-          If the plug-in implements the <interfacename>InteractivePlugin</interfacename>
+          If the plug-in implements the <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
           interface the <methodname>InteractivePlugin.getGuiContexts()</methodname>
           method is called. This is the only time this method is called and the information it
@@ -1500 +1500 @@
         
         <para>
-          The plug-in must implement the <interfacename>InteractivePlugin</interfacename>
+          The plug-in must implement the <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
           interface and the <methodname>Plugin.supportsConfigurations()</methodname> method
           must return <constant>TRUE</constant>. The configuration is done with
@@ -1553 +1553 @@
           The plug-in must validate the values and decide whether they should be
           stored in the database or not. We recommend that you use the
-          methods in the <classname>AbstractPlugin</classname> class for this.
+          methods in the <classname docapi="net.sf.basedb.core.plugin">AbstractPlugin</classname> class for this.
           </para>
         </listitem>
@@ -1601 +1601 @@
         
         <para>
-          If the plug-in is an <interfacename>InteractivePlugin</interfacename>
+          If the plug-in is an <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
           it has specified in which contexts it can be used by the 
           information returned from <methodname>InteractivePlugin.getGuiContexts()</methodname>
@@ -1797 +1797 @@
           <listitem>
             <simpara>
-            Generate the list of <classname>PluginParameter</classname> 
+            Generate the list of <classname docapi="net.sf.basedb.core">PluginParameter</classname> 
             objects as usual.
             </simpara>
@@ -1859 +1859 @@
             <para>
               In your JSP page you will probably need to access some information like the
-              <classname>SessionControl</classname>, <classname>Job</classname>
-              and possible even the <classname>RequestInformation</classname>
+              <classname docapi="net.sf.basedb.core">SessionControl</classname>, <classname docapi="net.sf.basedb.core">Job</classname>
+              and possible even the <classname docapi="net.sf.basedb.core">RequestInformation</classname>
               object created by your plug-in.
             </para>
@@ -1898 +1898 @@
         Your plug-in can be part of that feature if it reads it data
         from a single file. It must also implement the 
-        <interfacename>AutoDetectingImporter</interfacename>
+        <interfacename docapi="net.sf.basedb.core.plugin">AutoDetectingImporter</interfacename>
         interface. 
       </para>
@@ -1926 +1926 @@
             </para>
             <para>
-              The <classname>AbstractFlatFileImporter</classname> implements this method 
+              The <classname docapi="net.sf.basedb.plugins">AbstractFlatFileImporter</classname> implements this method 
               by reading the headers from the input stream and checking if 
               it stopped at an unknown type of line or not:
@@ -2072 +2072 @@
       <title>The AbstractFlatFileImporter superclass</title>
       <para>
-        The <classname>AbstractFlatFileImporter</classname> is a very useful abstract 
+        The <classname docapi="net.sf.basedb.plugins">AbstractFlatFileImporter</classname> is a very useful abstract 
         class to use as a superclass for your own import plug-ins. It can be used
         if your plug-in uses regular text files that can be parsed by an instance of the 
-        <classname>net.sf.basedb.util.FlatFileParser</classname> class. This class parses a file
+        <classname docapi="net.sf.basedb.util">net.sf.basedb.util.FlatFileParser</classname> class. This class parses a file
         by checking each line against a few regular expressions. Depending on which regular
         expression matches the line, it is classified as a header line, a section line, 
@@ -2084 +2084 @@
       
       <para>
-        The <classname>AbstractFlatFileImporter</classname> defines 
-        <classname>PluginParameter</classname> objects
+        The <classname docapi="net.sf.basedb.plugins">AbstractFlatFileImporter</classname> defines 
+        <classname docapi="net.sf.basedb.core">PluginParameter</classname> objects
         for each of the regular expressions and other parameters used by the parser. It also
         implements the <methodname>Plugin.run()</methodname> method and does most of 
         the ground work for instantiating a <methodname>FlatFileParser</methodname> and 
         parsing the file. What you have to do in your plugin is to put together the 
-        <classname>RequestInformation</classname> objects
+        <classname docapi="net.sf.basedb.core">RequestInformation</classname> objects
         for configuring the plugin and creating a job and implement the 
         <methodname>InteractivePlugin.configure()</methodname> method for validating and 
@@ -2111 +2111 @@
       <listitem>
         <para>
-        Implement the <interfacename>InteractivePlugin</interfacename> methods.
+        Implement the <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename> methods.
         See <xref linkend="plugin_developer.api.interfaces.interactive" /> for more information. Note that the 
-        <classname>AbstractFlatFileImporter</classname>
+        <classname docapi="net.sf.basedb.plugins">AbstractFlatFileImporter</classname>
         has defined many parameters for regular expressions used by the parser
-        already. You should just pick them and put in your <classname>RequestInformation</classname>
+        already. You should just pick them and put in your <classname docapi="net.sf.basedb.core">RequestInformation</classname>
         object.
         </para>
@@ -2199 +2199 @@
         <listitem>
           <para>
-          The method is called to create a <classname>FlatFileParser</classname>
+          The method is called to create a <classname docapi="net.sf.basedb.util.parser">FlatFileParser</classname>
           and set the regular expressions that should be used for parsing the file.
           The default implementation assumes that your plug-in has used the built-in
-          <classname>PluginParameter</classname> objects and has stored the values
+          <classname docapi="net.sf.basedb.core">PluginParameter</classname> objects and has stored the values
           at the configuration level. You should override this method if you need to
           initialise the parser in a different way. See for example the
-          code for the <classname>PrintMapFlatFileImporter</classname> plug-in which
+          code for the <classname docapi="net.sf.basedb.plugins">PrintMapFlatFileImporter</classname> plug-in which
           has a fixed format and doesn't use configurations.
           </para>
@@ -2248 +2248 @@
           if it wants to do more checks, for example, make that a certain header is present
           with a certain value. It may also continue parsing the file. Here is a code example from
-          the <classname>PrintMapFlatFileImporter</classname> which checks if a 
+          the <classname docapi="net.sf.basedb.plugins">PrintMapFlatFileImporter</classname> which checks if a 
           <constant>FormatName</constant> header is present and contains either 
           <constant>TAM</constant> or <constant>MwBr</constant>.
@@ -2288 +2288 @@
           begins. Override this method if you need to initialise some
           internal state. This is, for example, a good place to open 
-          a <classname>DbControl</classname> object, read parameters from the 
+          a <classname docapi="net.sf.basedb.core">DbControl</classname> object, read parameters from the 
           job and configuration and put them into more useful variables. The default 
           implementation does nothing, but we recommend that 
@@ -2491 +2491 @@
             Called when the parsing has ended, either because the end of
             file was reached or because an error has occurred. The subclass
-            should close any open resources, ie. the <classname>DbControl</classname>
+            should close any open resources, ie. the <classname docapi="net.sf.basedb.core">DbControl</classname>
             object. The <varname>success</varname> parameter is <constant>true</constant>
             if the parsing was successful, <constant>false</constant> otherwise.
@@ -2557 +2557 @@
 
       <para>
-        The <classname>AbstractFlatFileImporter</classname> has a lot of
+        The <classname docapi="net.sf.basedb.plugins">AbstractFlatFileImporter</classname> has a lot of
         other methods that you may use and/or override in your own plug-in.
         Check the javadoc for more information. 
@@ -2584 +2584 @@
         or to download it immediately to the client computer. With the basic 
         plug-in API the second option is not possible. The 
-        <interfacename>ImmediateDownloadExporter</interfacename> is an
-        interface that extends the <interfacename>Plugin</interfacename>
+        <interfacename docapi="net.sf.basedb.core.plugin">ImmediateDownloadExporter</interfacename> is an
+        interface that extends the <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename>
         interface to provide this functionality. If your export
         plug-in wants to provide immediate download functionality it must
-        implement the <interfacename>ImmediateDownloadExporter</interfacename>
+        implement the <interfacename docapi="net.sf.basedb.core.plugin">ImmediateDownloadExporter</interfacename>
         interface.
       </para>
@@ -2630 +2630 @@
       
       <para>
-        The <classname>ExportOutputStream</classname> is extends
+        The <classname docapi="net.sf.basedb.core.plugin">ExportOutputStream</classname> is extends
         <classname>java.io.OutputStream</classname>. Use the regular 
         <methodname>write()</methodname> methods to write data to it.
@@ -2762 +2762 @@
         This is an abstract superclass that will make it easier
         to implement export plug-ins that support immediate 
-        download. It defines <classname>PluginParameter</classname>
+        download. It defines <classname docapi="net.sf.basedb.core">PluginParameter</classname>
         objects for asking a user about a path where the exported
         data should be saved and if existing files should be overwritten or not.
@@ -2770 +2770 @@
         <methodname>ImmediateDownloadExporter.doExport()</methodname> method.
         Here is what you need to do in your own plug-in code (code examples are
-        taken from the <classname>HelpExporter</classname>):
+        taken from the <classname docapi="net.sf.basedb.plugins">HelpExporter</classname>):
       </para>
       
@@ -2776 +2776 @@
       <listitem>
         <para>
-          Your plug-in should extend the <classname>AbstractExporterPlugin</classname>
+          Your plug-in should extend the <classname docapi="net.sf.basedb.core.plugin">AbstractExporterPlugin</classname>
           class:
           <programlisting language="java">
@@ -2874 +2874 @@
         <para>
         Implement the <methodname>performExport()</methodname> method.
-        This is defined as abstract in the <classname>AbstractExporterPlugin</classname>
+        This is defined as abstract in the <classname docapi="net.sf.basedb.core.plugin">AbstractExporterPlugin</classname>
         class. It has the same parameters as the <methodname>ImmediateDownloadExporter.doExport()</methodname>
         method and they have the same meaning. The only difference is that the 
@@ -2892 +2892 @@
       
       <para>
-        The call sequence for plug-ins extending <classname>AbstractExporterPlugin</classname>
+        The call sequence for plug-ins extending <classname docapi="net.sf.basedb.core.plugin">AbstractExporterPlugin</classname>
         is:
       </para>
@@ -3153 +3153 @@
         This class is an abstract base class. It is a useful
         class for most analysis plug-ins to inherit from. Its main 
-        purpose is to define <classname>PluginParameter</classname>
+        purpose is to define <classname docapi="net.sf.basedb.core">PluginParameter</classname>
         objects that are commonly used in analysis plug-ins. This includes:
       </para>
@@ -3200 +3200 @@
       
       <para>
-        The <interfacename>net.sf.basedb.core.plugin.AnalysisFilterPlugin</interfacename> 
+        The <interfacename docapi="net.sf.basedb.core.plugin">net.sf.basedb.core.plugin.AnalysisFilterPlugin</interfacename> 
         is a tagging interface, with no methods, that all analysis plug-ins that only filters
         data should implement. The benefit is that they will be linked from the
@@ -3233 +3233 @@
         This plug-in mechanism is not the same as the regular plug-in API.
         That is, you do not have worry about user interaction or implementing the 
-        <interfacename>Plugin</interfacename> interface.
+        <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename> interface.
       </para>
       
@@ -3347 +3347 @@
           To be able to use external authentication you must create a class 
           that implements the 
-          <interfacename>net.sf.based.core.authentication.Authenticator</interfacename> 
+          <interfacename docapi="net.sf.basedb.core.authentication">net.sf.based.core.authentication.Authenticator</interfacename> 
           interface. Specify the name of the class in the <property>auth.driver</property> 
           setting in <filename>base.config</filename> and 
@@ -3426 +3426 @@
             <para>
             Try to authenticate a login/password combination. The plug-in should return 
-            an <classname>AuthenticationInformation</classname> object if the 
+            an <classname docapi="net.sf.basedb.core.authentication">AuthenticationInformation</classname> object if the 
             authentication is successful or throw an exception if not. 
             
@@ -3595 +3595 @@
           All you have to do to create a secondary storage controller is to 
           create a class that implements the 
-          <interfacename>net.sf.basedb.core.SecondaryStorageController</interfacename>
+          <interfacename docapi="net.sf.basedb.core">net.sf.basedb.core.SecondaryStorageController</interfacename>
           interface. In your <filename>base.config</filename> file you then specify the
           class name in the <varname>secondary.storage.driver</varname> setting and its 
@@ -3763 +3763 @@
         Behind the scenes, this support is provided by plug-ins. The standard 
         BASE distribution comes with support for ZIP files 
-        (<classname>net.sf.basedb.plugins.ZipFileUnpacker</classname>)
-        and TAR files (<classname>net.sf.basedb.plugins.TarFileUnpacker</classname>).
+        (<classname docapi="net.sf.basedb.plugins">net.sf.basedb.plugins.ZipFileUnpacker</classname>)
+        and TAR files (<classname docapi="net.sf.basedb.plugins">net.sf.basedb.plugins.TarFileUnpacker</classname>).
       </para>
       <para>
         To add support for additional compressed formats you have to create a plug-in that
-        implements the <interfacename>net.sf.basedb.util.zip.FileUnpacker</interfacename>
+        implements the <interfacename docapi="net.sf.basedb.util.zip">net.sf.basedb.util.zip.FileUnpacker</interfacename>
         interface. The best way to do this is to extend the 
-        <classname>net.sf.basedb.util.zip.AbstractFileUnpacker</classname> which 
-        implements all methods in the <interfacename>Plugin</interfacename>
-        and <interfacename>InteractivePlugin</interfacename>
+        <classname docapi="net.sf.basedb.util.zip">net.sf.basedb.util.zip.AbstractFileUnpacker</classname> which 
+        implements all methods in the <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename>
+        and <interfacename docapi="net.sf.basedb.core.plugin">InteractivePlugin</interfacename>
         interfaces except <methodname>Plugin.getAbout()</methodname>. This leaves
         you with the actual unpacking of the files as the only thing to implement.
@@ -3784 +3784 @@
       
       <variablelist>
-        <title>Methods in the <interfacename>FileUnpacker</interfacename> interface</title>
+        <title>Methods in the <interfacename docapi="net.sf.basedb.util.zip">FileUnpacker</interfacename> interface</title>
         <varlistentry>
           <term>
@@ -3882 +3882 @@
               Do not <methodname>close()</methodname> or 
               <methodname>commit()</methodname> the 
-              <classname>DbControl</classname> passed to this method.
+              <classname docapi="net.sf.basedb.core">DbControl</classname> passed to this method.
               This is done automatically by the 
-              <classname>AbstractFileUnpacker</classname> or by the web client.
+              <classname docapi="net.sf.basedb.util.zip">AbstractFileUnpacker</classname> or by the web client.
               </para>
             </listitem>
@@ -3921 +3921 @@
               the number of bytes read from the <varname>in</varname>
               stream. If it is not possible by other means the stream can
-              be wrapped by a <classname>net.sf.basedb.util.InputStreamTracker</classname>
+              be wrapped by a <classname docapi="net.sf.basedb.util">net.sf.basedb.util.InputStreamTracker</classname>
               object which has a <methodname>getNumRead()</methodname> method.
               </para>
@@ -3967 +3967 @@
         BASE has support for compressing and downloading a set of selected files and/or
         directories. This functionality is provided by a plug-in, the 
-        <classname>PackedFileExporter</classname>. This plug-in doesn't do the actual
+        <classname docapi="net.sf.basedb.plugins">PackedFileExporter</classname>. This plug-in doesn't do the actual
         packing itself. This is delegated to classes implementing the 
-        <interfacename>net.sf.basedb.util.zip.FilePacker</interfacename> interface.
+        <interfacename docapi="net.sf.basedb.util.zip">net.sf.basedb.util.zip.FilePacker</interfacename> interface.
       </para>
       
@@ -3975 +3975 @@
         BASE ships with a number of packing methods, including ZIP and TAR. To
         add support for other methods you have to provide an implementation
-        of the <interfacename>FilePacker</interfacename>
-        interface. Then, create a new configuration for the <classname>PackerFileExporter</classname>
+        of the <interfacename docapi="net.sf.basedb.util.zip">FilePacker</interfacename>
+        interface. Then, create a new configuration for the <classname docapi="net.sf.basedb.plugins">PackedFileExporter</classname>
         and enter the name of your class in the configuration wizard.
       </para>
       
       <para>
-        The <interfacename>FilePacker</interfacename> interface is not a regular
+        The <interfacename docapi="net.sf.basedb.util.zip">FilePacker</interfacename> interface is not a regular
         plug-in interface (ie. it is not a subinterface to 
-        <interfacename>Plugin</interfacename>). This means that you don't have to
+        <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename>). This means that you don't have to
         mess with configuration or job parameters. Another difference is that your
         class must be installed in Tomcat's classpath (ie. in one of the 
@@ -3991 +3991 @@
       
       <variablelist>
-        <title>Methods in the <interfacename>FilePacker</interfacename> interface</title>
+        <title>Methods in the <interfacename docapi="net.sf.basedb.util.zip">FilePacker</interfacename> interface</title>
         <varlistentry>
           <term>
@@ -4135 +4135 @@
         check that the supplied files are valid and also to extract
         metadata from the files. For example, the 
-        <classname>net.sf.basedb.core.filehandler.CelFileHandler</classname>
+        <classname docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.CelFileHandler</classname>
         is used to check if a file is a valid Affymetrix CEL file and
         to extract data headers and the number of spots from it.
@@ -4142 +4142 @@
       <para>
         The validator and metadata reader plug-ins are not regular plug-ins
-        (ie. they don't have to implement the <interfacename>Plugin</interfacename>
+        (ie. they don't have to implement the <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename>
         interface). This means that you don't have to mess with configuration or 
         job parameters. Another difference is that the plug-ins must be installed in
@@ -4152 +4152 @@
       <para>
         Validator plug-ins must implement the 
-        <interfacename>net.sf.basedb.core.filehandler.DataFileHandler</interfacename>
-        and <interfacename>net.sf.basedb.core.filehandler.DataValidator</interfacename>
+        <interfacename docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.DataFileHandler</interfacename>
+        and <interfacename docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.DataValidator</interfacename>
         interfaces. Metadata reader plug-ins should implement the 
-        <interfacename>net.sf.basedb.core.filehandler.DataFileHandler</interfacename>
-        and <interfacename>net.sf.basedb.core.filehandler.DataFileMetadataReader</interfacename>
+        <interfacename docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.DataFileHandler</interfacename>
+        and <interfacename docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.DataFileMetadataReader</interfacename>
         interfaces.
       </para>
@@ -4172 +4172 @@
         <title>
           Always extend the 
-          <classname>net.sf.basedb.core.filehandler.AbstractDataFileHandler</classname>
+          <classname docapi="net.sf.basedb.core.filehandler">net.sf.basedb.core.filehandler.AbstractDataFileHandler</classname>
           class
         </title>
@@ -4179 +4179 @@
           from the caller side, not from the implementor side. Thus, we may
           add methods to those interfaces in the future without prior notice.
-          The <classname>AbstractDataFileHandler</classname> will provide default
+          The <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> will provide default
           implementations of the new methods in order to not break existing
           plug-ins.
@@ -4186 +4186 @@
       
       <variablelist>
-        <title>Methods in the <interfacename>DataFileHandler</interfacename> interface</title>
+        <title>Methods in the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileHandler</interfacename> interface</title>
         <varlistentry>
           <term>
@@ -4231 +4231 @@
       
       <variablelist>
-        <title>Methods in the <interfacename>DataFileValidator</interfacename> interface</title>
+        <title>Methods in the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileValidator</interfacename> interface</title>
         <varlistentry>
           <term>
@@ -4270 +4270 @@
 
       <variablelist>
-        <title>Methods in the <interfacename>DataFileMetadataReader</interfacename> interface</title>
+        <title>Methods in the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileMetadataReader</interfacename> interface</title>
         <varlistentry>
           <term>
@@ -4287 +4287 @@
               Extract metadata from the file. It is up to the plug-in
               to decide what to extract and how to store it.
-              The <classname>CelFileHandler</classname> will, for
+              The <classname docapi="net.sf.basedb.core.filehandler">CelFileHandler</classname> will, for
               example, extract headers and the number of spots from the file
               and store it with the raw bioassay. 
@@ -4318 +4318 @@
 
       <variablelist>
-        <title>Methods in the <classname>AbstractDataFileHandler</classname> class</title>
+        <title>Methods in the <classname docapi="net.sf.basedb.core.filehandler">AbstractDataFileHandler</classname> class</title>
         <varlistentry>
           <term>
@@ -4351 +4351 @@
               <methodname>setFile()</methodname>. The 
               <parameter>dataFileTypeId</parameter> is
-              the external ID of the <classname>DataFileType</classname>.
+              the external ID of the <classname docapi="net.sf.basedb.core">DataFileType</classname>.
             </para>
           </listitem>

trunk/doc/src/docbook/developerdoc/webservices.xml

@@ -56 +56 @@
           includes and restrictions on a query before it is executed. For those who intend
           to develop services it is recommended to have a look in javadoc for
-          <classname>net.sf.basedb.ws.info.QueryOptions</classname>
+          <classname docapi="net.sf.basedb.ws.info">QueryOptions</classname>
           . This is on the first hand for the service developers but it can be useful for
           client developers to also know that this may be available in some services.
@@ -487 +487 @@
           <para>
             Create a new class that extends
-            <classname>net.sf.basedb.ws.server.AbstractRPCService</classname>
+            <classname api="net.sf.basedb.ws.server">AbstractRPCService</classname>
           </para>
         </listitem>

trunk/doc/src/docbook/userdoc/platforms.xml

@@ -377 +377 @@
             The name of the Java class that can be used to 
             validate if a given file is a valid file of this type.
-            The class must implement the <interfacename>DataFileValidator</interfacename>
+            The class must implement the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileValidator</interfacename>
             interface. <nohelp>See <xref linkend="plugin_developer.other.datafiles" />.</nohelp>
           </para>
@@ -388 +388 @@
             The name of the Java class that can be used to 
             extract metadata from a file of this type.
-            The class must implement the <interfacename>DataFileMetadataReader</interfacename>
+            The class must implement the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileMetadataReader</interfacename>
             interface. <nohelp>See <xref linkend="plugin_developer.other.datafiles" />.</nohelp>
           </para>

trunk/lib/docbook/custom-styles/docbook/plain/xsl/customized.chunked.xsl

@@ -272 +272 @@
     <xsl:value-of select="$admon.graphics.extension" />
   </xsl:template>
+  
+  <xsl:template match="classname">                  
+    <xsl:call-template name="inline.monoseq"/>    
+    <xsl:if test = "@docapi != ''">
+      <xsl:variable name="packagePath">
+        <xsl:call-template name="replaceCharsInString">
+          <xsl:with-param name="stringIn" select="string(@docapi)"/>
+          <xsl:with-param name="charsIn" select="'.'" />
+          <xsl:with-param name="charsOut" select="'/'" />
+        </xsl:call-template>
+        </xsl:variable>
+        
+        <xsl:variable name="cleanClassName">
+          <xsl:choose>
+            <xsl:when test="starts-with(., @docapi)">
+              <xsl:value-of select="substring-after(., concat(@docapi, '.'))" />
+            </xsl:when>
+            <xsl:otherwise>
+              <xsl:value-of select="." />
+            </xsl:otherwise>
+          </xsl:choose>                     
+        </xsl:variable>
+        
+        <xsl:variable name="pathtorootdir">
+          <xsl:call-template name="pathtorootdir" />
+        </xsl:variable>
+        
+        <xsl:text> </xsl:text>
+      <a>
+        <xsl:attribute name="href">
+          <xsl:value-of select="concat('../../../api/',$packagePath,'/',$cleanClassName,'.html')" />
+        </xsl:attribute>
+        <xsl:attribute name="title">Javadoc for this class.</xsl:attribute>
+        <image>
+          <xsl:attribute name="src">
+          <xsl:value-of select="concat($pathtorootdir, $admon.graphics.path, 'docapi.gif')"/>
+          </xsl:attribute> 
+          <xsl:attribute name="border">0</xsl:attribute>
+        </image>
+      </a>
+    </xsl:if>   
+  </xsl:template>
+  
+  <xsl:template match="interfacename">
+    <xsl:call-template name="inline.monoseq"/>    
+    <xsl:if test = "@docapi != ''">
+      <xsl:variable name="packagePath">
+        <xsl:call-template name="replaceCharsInString">
+          <xsl:with-param name="stringIn" select="string(@docapi)"/>
+          <xsl:with-param name="charsIn" select="'.'" />
+          <xsl:with-param name="charsOut" select="'/'" />
+        </xsl:call-template>
+        </xsl:variable>
+        
+        <xsl:variable name="cleanClassName">
+          <xsl:choose>
+            <xsl:when test="starts-with(., @docapi)">
+              <xsl:value-of select="substring-after(., concat(@docapi, '.'))" />
+            </xsl:when>
+            <xsl:otherwise>
+              <xsl:value-of select="." />
+            </xsl:otherwise>
+          </xsl:choose>                     
+        </xsl:variable>
+            
+        <xsl:variable name="pathtorootdir">
+          <xsl:call-template name="pathtorootdir" />
+        </xsl:variable>
+        <xsl:text> </xsl:text>
+      <a>
+        <xsl:attribute name="href">
+          <xsl:value-of select="concat('../../../api/',$packagePath,'/', $cleanClassName,'.html')" />
+        </xsl:attribute>
+        <xsl:attribute name="title">Javadoc for this interface.</xsl:attribute>
+        
+        <image>
+          <xsl:attribute name="src">
+          <xsl:value-of select="concat($pathtorootdir, $admon.graphics.path, 'docapi.gif')"/>
+          </xsl:attribute> 
+          <xsl:attribute name="border">0</xsl:attribute>
+        </image>
+      </a>
+    </xsl:if>   
+  </xsl:template>
+  
+  <xsl:template name="replaceCharsInString">
+      <xsl:param name="stringIn"/>
+      <xsl:param name="charsIn"/>
+      <xsl:param name="charsOut"/>
+      <xsl:choose>
+      <xsl:when test="contains($stringIn,$charsIn)">
+          <xsl:value-of select="concat(substring-before($stringIn,$charsIn),$charsOut)"/>
+          <xsl:call-template name="replaceCharsInString">
+            <xsl:with-param name="stringIn" select="substring-after($stringIn,$charsIn)"/>
+            <xsl:with-param name="charsIn" select="$charsIn"/>
+            <xsl:with-param name="charsOut" select="$charsOut"/>
+          </xsl:call-template>
+      </xsl:when>
+      <xsl:otherwise>
+          <xsl:value-of select="$stringIn"/>
+        </xsl:otherwise>
+      </xsl:choose>
+  </xsl:template>
 
 </xsl:stylesheet>

trunk/lib/docbook/preprocess/dweiss-docbook-extensions.dtd

@@ -28 +28 @@
 <!ATTLIST include file CDATA #REQUIRED>
 
+<!ATTLIST classname docapi CDATA #IMPLIED>
+
+<!ATTLIST interfacename docapi CDATA #IMPLIED>
 
 <!-- help text element -->