Changeset 2981


Ignore:
Timestamp:
Nov 30, 2006, 10:50:05 AM (17 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #447: Fix javadoc warnings

Location:
trunk
Files:
59 edited

Legend:

Unmodified
Added
Removed

  • trunk/build.xml

    r2979 r2981  
    964964      <tag name="hibernate.many-to-any" description="Hibernate: many-to-any" scope="methods" />
    965965      <tag name="hibernate.many-to-any-column" description="Hibernate: many-to-any-column" scope="methods" />
     966      <tag name="hibernate.component" description="Hibernate: component" scope="methods" />
    966967    </javadoc>
    967968  </target>

  • trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/Agent.java

    r2865 r2981  
    145145  </tr>
    146146  <tr>
    147     <td>agent.executor.init</td>
    148     <td>-</td>
    149     <td>
    150       Initialisation parameters for the executor class. They are sent to the
    151       {@link JobExecutor#init(String)} method. For a meaning and syntax description
    152       of this string see the excutor implementation you are using.
    153     </td>
    154   </tr>
    155   <tr>
    156147    <td>agent.checkinterval</td>
    157148    <td>30</td>
    … …  
    419410    Get the thread priority to use for the specified execution time slot.
    420411    @param slot
    421     @return
    422412  */
    423413  public int getThreadPriority(Job.ExecutionTime slot)
    … …  
    669659    job agent if it's name or ip-address is listed in the
    670660    <code>agent.remotecontrol</code> property. This method is called from
    671     the {@link DefaultRequestHandler#handleCmd(Socket, String)} method
     661    the {@link DefaultRequestHandler#handleCmd(java.net.Socket, String)} method
    672662    to determine if a service request should be accepted or not.
    673663    <p>
    … …  
    804794    used when they are not.
    805795   
    806     @param requested The slot the job requested
     796    @param job The job that wants a slot
    807797    @return The assigned slot or null if no slot is available
    808798  */

  • trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobExecutor.java

    r2648 r2981  
    3737  that a job executor must be thread-safe and able to execute more than
    3838  one job at a time. It is not a good solution to put the <code>synchonrized</code>
    39   keyword on the {@link #executeJob(Agent, Job, Job.ExecutionTime)} method
    40   since it would limit the execution to one job at a time.
     39  keyword on the {@link #executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime)}
     40  method since it would limit the execution to one job at a time.
    4141  <p>
    4242  A job executor must provide a public no-argument constructor.
    … …  
    6363    to kill the job or let it continue as if nothing happened.
    6464    <p>
    65     The job sent to this method has it's status set to {@link Job.Status#PREPARED}.
     65    The job sent to this method has it's status set to {@link
     66    net.sf.basedb.core.Job.Status#PREPARED}.
    6667    The implementation of this method must change the status to either
    67     {@link Job.Status#DONE} or {@link Job.Status#ERROR}. If the status hasn't changed
     68    {@link net.sf.basedb.core.Job.Status#DONE} or {@link
     69    net.sf.basedb.core.Job.Status#ERROR}. If the status hasn't changed
    6870    the job agent will set the status to signal an unknown error.
    6971   

  • trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobQueueChecker.java

    r2648 r2981  
    2727import java.util.TimerTask;
    2828
     29import net.sf.basedb.core.Application;
    2930import net.sf.basedb.core.DbControl;
    3031import net.sf.basedb.core.ItemQuery;

  • trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobRunner.java

    r2648 r2981  
    7878  */
    7979  /**
    80     Find a free slot to use and then pass control to the
    81     {@link JobExecutor#executeJob(Agent, Job, Job.ExecutionTime)} method.
     80    Find a free slot to use and then pass control to the {@link
     81    JobExecutor#executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime)}
     82    method.
    8283  */
    8384  public void run()

  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java

    r2614 r2981  
    128128  @param dc {@link DbControl} used to create a new ArrayDesignBlock
    129129  @param arrayDesign <code>ArrayDesign</code>
    130   @param arrayDesignId Base 1 ArrayDesign Id
     130  @param base1ArrayDesignId Base 1 ArrayDesign Id
    131131   */
    132132  private void addArrayDesignBlock(DbControl dc, ArrayDesign arrayDesign,

  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/HybridizationTransfer.java

    r2690 r2981  
    131131  @param dc <code>DbControl</code>
    132132  @param hybridization The hybridization
    133   @param base1Id The corresponding base 1 id for this hybridization
     133  @param base1HybridizationId The corresponding base 1 id for this hybridization
    134134   */
    135135  private void connectToLabeledExtracts(DbControl dc, Hybridization hybridization,

  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java

    r2690 r2981  
    564564    Get the number of mapped ID:s. This should equal the number of
    565565    migrated items.
    566     @return
    567566  */
    568567  public int getCount()
    … …  
    576575Integer base2Id = map.get(base1Id);
    577576</pre>
    578     @return
    579577  */
    580578  public Map<Integer, Integer> getIdMap()

  • trunk/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java

    r2942 r2981  
    666666    {@link net.sf.basedb.core.DataQuery}. This means that we don't get
    667667    {@link ReporterData} objects as a result and that we must specify the
    668     properties to select (see {@link ItemContext#configureQuery(DynamicQuery, List)}).
     668    properties to select (see {@link ItemContext#configureQuery(DbControl, DynamicQuery, List)}).
    669669    <p>
    670670    The reporter id is always included as the first selected property so it
    … …  
    674674    @param selectionList The properties that the query should select
    675675    @return A query
    676     @see ItemContext#configureQuery(DynamicQuery, List)
     676    @see ItemContext#configureQuery(DbControl, DynamicQuery, List)
    677677  */
    678678  public DynamicSpotQuery getReporterQuery(DbControl dc, List<String> selectionList)
    … …  
    701701   
    702702    <p>
    703     See {@link ItemContext#getDynamicExpression(String, DynamicJoins)} for more information
     703    See {@link ItemContext#getDynamicExpression(DbControl, String)} for more information
    704704    about how to specify additional selection properties.
    705705   

  • trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java

    r2942 r2981  
    243243   
    244244    @param sc The logged in user's session control
    245     @param ep The extended property
    246     @return A formatter for the extended property
     245    @param coloring The coloring object that keeps information about how
     246      to generate colors
     247    @param valueFormatter A formatter for the actual values
     248    @return A formatter that adds color to the values
    247249    @see ColorFormatter
    248250  */

  • trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterSettings.java

    r2942 r2981  
    136136   
    137137    @param sc The logged in user's session control
    138     @param dateFormat The format string
     138    @param dateTimeFormat The format string
    139139    @see #DEFAULT_DATETIME_FORMAT
    140140    @see FormatterFactory#getDateTimeFormatter(SessionControl)

  • trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ExportTemplate.java

    r2868 r2981  
    3939  /**
    4040    Get the MIME type to assign to files generated by this template.
    41     @return
    4241  */
    4342  public String getMimeType();

  • trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ReporterScoreQueryWrapper.java

    r2868 r2981  
    2828import net.sf.basedb.core.ReporterScore;
    2929import net.sf.basedb.core.ReporterScoreQuery;
     30import net.sf.basedb.core.data.ReporterData;
    3031import net.sf.basedb.core.data.ReporterListScoreData;
    3132import net.sf.basedb.core.query.ResultIterator;

  • trunk/src/clients/web/net/sf/basedb/clients/web/util/ServletExportOutputStream.java

    r2854 r2981  
    7878  }
    7979  /**
    80     Calls {@link HttpServletResponse#setHeader(java.lang.String, java.lang.String)
     80    Calls {@link HttpServletResponse#setHeader(java.lang.String, java.lang.String)}
    8181    with the following values:
    8282    <code>response.setHeader("Content-Disposition", "attachment;filename=&lt;filename&gt;");</code>

  • trunk/src/core/net/sf/basedb/core/BioAssaySet.java

    r2892 r2981  
    719719   
    720720    @return An <code>ItemQuery</code> object
    721     @see #getSpotExtraValueBatcher(Class, ExtraValueType)
    722     @see #getPositionExtraValueBatcher(Class, ExtraValueType)
     721    @see #getSpotExtraValueBatcher(Class, ExtraValueType, Job)
     722    @see #getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    723723  */
    724724  public ItemQuery<ExtraValue> getExtraValues()
    … …  
    733733    @return An <code>ExtraValue</code> item, or null if no extra value
    734734      of the specified type has been created  for this bioassayset
    735     @see #getSpotExtraValueBatcher(Class, ExtraValueType)
    736     @see #getPositionExtraValueBatcher(Class, ExtraValueType)
     735    @see #getSpotExtraValueBatcher(Class, ExtraValueType, Job)
     736    @see #getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    737737  */
    738738  public ExtraValue getExtraValue(ExtraValueType extraValueType)
    … …  
    749749    to reporters. To insert extra values (which can be done at any time)
    750750    based on the position use the {@link
    751     #getPositionExtraValueBatcher(Class, ExtraValueType)} method to get a batcher for
     751    #getPositionExtraValueBatcher(Class, ExtraValueType, Job)} method to get a batcher for
    752752    that.
    753753   
    … …  
    756756      have write permission or if the data cube has already been committed
    757757      to the database
    758     @see #getPositionExtraValueBatcher(Class, ExtraValueType)
     758    @see #getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    759759  */
    760760  public PositionBatcher getPositionBatcher()
    … …  
    802802    committed to the database no more intensities can be inserted.
    803803    To insert extra values (which can be done at any time) based on the
    804     position use the {@link #getSpotExtraValueBatcher(Class, ExtraValueType)}
     804    position use the {@link #getSpotExtraValueBatcher(Class, ExtraValueType, Job)}
    805805    method to get a batcher for that.
    806806
    … …  
    809809      have write permission or if the data cube layer has already been committed
    810810      to the database
    811     @see #getSpotExtraValueBatcher(Class, ExtraValueType)
     811    @see #getSpotExtraValueBatcher(Class, ExtraValueType, Job)
    812812  */
    813813  public SpotBatcher getSpotBatcher()
    … …  
    862862  /**
    863863    Cache of already created spot extra value batchers.
    864     @see #getSpotExtraValueBatcher(Class, ExtraValueType)
     864    @see #getSpotExtraValueBatcher(Class, ExtraValueType, Job)
    865865  */
    866866  private Map<ExtraValueType, SpotExtraValueBatcher> spotExtraValueBatchers;
    … …  
    920920  /**
    921921    Cache of already created position extra value batchers.
    922     @see #getPositionExtraValueBatcher(Class, ExtraValueType)
     922    @see #getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    923923  */
    924924  private Map<ExtraValueType, PositionExtraValueBatcher> positionExtraValueBatchers;

  • trunk/src/core/net/sf/basedb/core/Coloring.java

    r2733 r2981  
    3131  This class keeps coloring information for items which can be colored when values
    3232  are displayed in a client application. Color values are calculated by a
    33   {@link ColorGenerator} based on this coloring information and the colors
     33  {@link net.sf.basedb.util.ColorGenerator} based on this coloring information and the colors
    3434  specified by user settings.
    3535
    … …  
    164164    Set the value that represents the minimum value. All values below this will get
    165165    the same color.
    166     @return The min value
    167166  */
    168167  public void setMinValue(Float minValue)
    … …  
    204203    Set the value that represents the maximum value. All values above this will get
    205204    the same color.
    206     @return The max value
    207205  */
    208206  public void setMaxValue(Float maxValue)

  • trunk/src/core/net/sf/basedb/core/DiskUsageStatistics.java

    r2927 r2981  
    267267    /**
    268268      Check if this summary object is old by comparing it's
    269       age to the {@link DiskUsageStatics#getMaxAge()}.
     269      age to the {@link #getMaxAge()}.
    270270      @return TRUE if the summary is old, FALSE otherwise
    271271    */

  • trunk/src/core/net/sf/basedb/core/DynamicRawDataQuery.java

    r2726 r2981  
    5252
    5353  /**
    54     Create a new dynamic query for raw data.
    55    
    56     @param rawDataType The type of raw data
     54    Create a new dynamic query for raw data.   
     55    @param rawBioAssay The raw bioassay to query on
    5756  */
    5857  DynamicRawDataQuery(RawBioAssay rawBioAssay)

  • trunk/src/core/net/sf/basedb/core/ExtraValueType.java

    r2898 r2981  
    4141  @version 2.0
    4242  @see ExtraValue
    43   @see BioAssaySet#getSpotExtraValueBatcher(Class, ExtraValueType)
    44   @see BioAssaySet#getPositionExtraValueBatcher(Class, ExtraValueType)
     43  @see BioAssaySet#getSpotExtraValueBatcher(Class, ExtraValueType, Job)
     44  @see BioAssaySet#getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    4545  @base.modified $Date$
    4646*/

  • trunk/src/core/net/sf/basedb/core/ItemContext.java

    r2942 r2981  
    11201120
    11211121    <li>$: The rest of the string is a raw data property name. We use
    1122       the {@link Dynamic#rawData(String)} to create the expression. The
    1123       {@link DynamicJoins#joinRawData} flag is set to true.
     1122      the {@link Dynamic#rawData(String)} to create the expression.
    11241123     
    11251124    <li>@: The rest of the string is a reporter property name. We use
    11261125      the {@link Dynamic#reporter(String)} to create the expression.
    1127       The {@link DynamicJoins#joinReporters} flag is set to true.
    11281126     
    11291127    <li>#: The rest of the string is the id of an extra value.
    … …  
    11461144    @param dc A DbControl to use if the database needs to be accessed
    11471145    @param propertyDef The string to use for creating the expression.
    1148     @param joins Holds flags so we know what must be joined when this
    1149       method returns
    11501146    @return An expression object
    11511147  */
    … …  
    12031199 
    12041200  /**
    1205     Same as {@link #getDynamicExpression(String, DynamicJoins)} but generates
     1201    Same as {@link #getDynamicExpression(DbControl, String)} but generates
    12061202    a select object instead.
    12071203  */

  • trunk/src/core/net/sf/basedb/core/Job.java

    r2898 r2981  
    630630    Register the job as completed with an error.
    631631   
    632     @param statusMessage A message
    633     @param t The exception that caused the job to fail
     632    @param statusMessage A short message describing the error
     633    @param errors A list of one or more errors that caused the job to fail, the
     634      complete stack trace for those errors are stored in the {@link #getStackTrace()}
     635      property
    634636    @throws PermissionDeniedException If the logged in user doesn't have
    635637      write permission

  • trunk/src/core/net/sf/basedb/core/JobAgentSettings.java

    r2648 r2981  
    121121    @param plugin The plugin to retreive settings for, null is not allowed
    122122    @return An {@link ItemQuery} object
    123     @see PluginDefintion#getJobAgentSettings()
    124123  */
    125124  static ItemQuery<JobAgentSettings> getQuery(PluginDefinition plugin)
    … …  
    294293    the max memory returned by the plugin definition should be used.
    295294    @return The maximum amount of memory or null
    296     @see PluginDefinition#getMaxMemory()()
    297     @see #getEffectiveMaxMemory()()
     295    @see PluginDefinition#getMaxMemory()
     296    @see #getEffectiveMaxMemory()
    298297  */
    299298  public Long getMaxMemory()
    … …  
    307306    plugin definition is returned.
    308307    @return The maximum memory or null if no maximum has been specified
    309     @see PluginDefinition#getMaxMemory()()
    310     @see #getMaxMemory()()
     308    @see PluginDefinition#getMaxMemory()
     309    @see #getMaxMemory()
    311310  */
    312311  public Long getEffectiveMaxMemory()

  • trunk/src/core/net/sf/basedb/core/Keyring.java

    r2722 r2981  
    613613 
    614614  /**
    615       Load all {@link PluginDefinitionKeys}:s for the active plugin.
     615      Load all {@link PluginKeys}:s for the active plugin.
    616616      @param session The session to get the query through.
    617617      @throws BaseException If there is an error.

  • trunk/src/core/net/sf/basedb/core/LabeledExtract.java

    r2898 r2981  
    163163    Get all:
    164164    <ul>
    165     <li>{@link Hybridzation}:s created from this labeled extract
     165    <li>{@link Hybridization}:s created from this labeled extract
    166166    <ul>
    167167    @since 2.2

  • trunk/src/core/net/sf/basedb/core/Path.java

    r2854 r2981  
    8181    {@link #INVALID_CHARACTERS} charactes with the specified string.
    8282   
    83     @param orginalName The original name
     83    @param originalName The original name
    8484    @param replaceWith The string to replace all unsafe characters with
    85     @return
    8685    @since 2.2
    8786  */

  • trunk/src/core/net/sf/basedb/core/PluginDefinition.java

    r2898 r2981  
    450450    @base.internal
    451451    This value is initialised upon installation to: plugin.about().getName()
    452     See: {@link #loadPluginInformation(String, String)}
     452    See: {@link #loadPluginInformation(String, String, boolean)}
    453453    @throws InvalidDataException If the name is null or too long
    454454  */
    … …  
    482482    @base.internal
    483483    This value is initialised upon installation to: plugin.about().getDescription()
    484     See: {@link #loadPluginInformation(String, String)}
     484    See: {@link #loadPluginInformation(String, String, boolean)}
    485485    @throws InvalidDataException If the description is too long
    486486  */
    … …  
    504504    @base.internal
    505505    This value is initialised upon installation to: plugin.about().getVersion()
    506     See: {@link #loadPluginInformation(String, String)}
     506    See: {@link #loadPluginInformation(String, String, boolean)}
    507507    @throws InvalidDataException If the version is too long
    508508  */
    … …  
    526526    @base.internal
    527527    This value is initialised upon installation to: plugin.about().getCopyright()
    528     See: {@link #loadPluginInformation(String, String)}
     528    See: {@link #loadPluginInformation(String, String, boolean)}
    529529    @throws InvalidDataException If the copyright is too long
    530530  */
    … …  
    548548    @base.internal
    549549    This value is initialised upon installation to: plugin.about().getContact()
    550     See: {@link #loadPluginInformation(String, String)}
     550    See: {@link #loadPluginInformation(String, String, boolean)}
    551551    @throws InvalidDataException If the contact is too long
    552552  */
    … …  
    570570    @base.internal
    571571    This value is initialised upon installation to: plugin.about().getEmail()
    572     See: {@link #loadPluginInformation(String, String)}
     572    See: {@link #loadPluginInformation(String, String, boolean)}
    573573    @throws InvalidDataException If the email is too long
    574574  */
    … …  
    592592    @base.internal
    593593    This value is initialised upon installation to: plugin.about().getUrl()
    594     See: {@link #loadPluginInformation(String, String)}
     594    See: {@link #loadPluginInformation(String, String, boolean)}
    595595    @throws InvalidDataException If the url is too long
    596596  */
    … …  
    664664    @base.internal
    665665    This value is initialised upon installation to: plugin.getMainType()
    666     See: {@link #loadPluginInformation(String, String)}
     666    See: {@link #loadPluginInformation(String, String, boolean)}
    667667 
    668668    @throws InvalidDataException If the type is null
    … …  
    728728      To be sure that the plugin will execute under certain permissions
    729729      this should be set to TRUE.
    730       @see #setPermissions(RoleKey, Set, boolean)
     730      @see #setPermissions(RoleKey, Set, Set)
    731731  */
    732732  public boolean getUsePermissions()
    … …  
    989989      permissions which differs from the defaults are stored in the database.
    990990     
    991       @param rolekey The rolekey for this plugin
     991      @param roleKey The rolekey for this plugin
    992992      @param granted The permission to grant to the plugin
    993993      @param denied The permissions to deny the plugin

  • trunk/src/core/net/sf/basedb/core/PluginRequest.java

    r2854 r2981  
    255255  /**
    256256    Get the job for the request or null if we are not configuring/executing a job.
    257     @return
    258257    @since 2.2
    259258  */

  • trunk/src/core/net/sf/basedb/core/PositionExtraValueBatcher.java

    r2669 r2981  
    8383  @author Nicklas
    8484  @version 2.0
    85   @see BioAssaySet#getPositionExtraValueBatcher(Class, ExtraValueType)
     85  @see BioAssaySet#getPositionExtraValueBatcher(Class, ExtraValueType, Job)
    8686  @base.modified $Date$
    8787*/

  • trunk/src/core/net/sf/basedb/core/SpotExtraValueBatcher.java

    r2669 r2981  
    7575  @author Nicklas
    7676  @version 2.0
    77   @see BioAssaySet#getSpotExtraValueBatcher(Class, ExtraValueType)
     77  @see BioAssaySet#getSpotExtraValueBatcher(Class, ExtraValueType, Job)
    7878  @base.modified $Date$
    7979*/

  • trunk/src/core/net/sf/basedb/core/Update.java

    r2941 r2981  
    163163    <td>
    164164      <ul>
    165       <li>Fixed incorrect {@link PlateMappings}:s. The 96-to-384 and 384-to-1536 were
     165      <li>Fixed incorrect {@link PlateMapping}:s. The 96-to-384 and 384-to-1536 were
    166166        wrong. The fix renames and flags the old ones as removed.
    167167      </ul>
    … …  
    185185      <ul>
    186186      <li>Added {@link net.sf.basedb.core.data.PluginPermission} and related classes.
    187         The update sets the {@link net.sf.basedb.core.data.PluginDefinitionData#usePermissions}
     187        The update sets the {@link net.sf.basedb.core.data.PluginDefinitionData#getUsePermissions()}
    188188        property to true for all existing plugins.
    189189      </ul>
    … …  
    272272    <td>
    273273      <ul>
    274       <li>Added {@link net.sf.basedb.core.data.ProtocolData#getParameters()()}
     274      <li>Added {@link net.sf.basedb.core.data.ProtocolData#getParameters()}
    275275      <li>Added {@link net.sf.basedb.core.data.AnnotationTypeData#isProtocolParameter()}
    276276      </ul>
    … …  
    715715 
    716716  /**
    717     Load all plugins and call {@link PluginDefinition#loadPluginInformation(String, String)}
     717    Load all plugins and call {@link PluginDefinition#loadPluginInformation(String, String, boolean)}
    718718    for each one so that the {@link PluginDefinition#supportsConfigurations()} and
    719719    {@link PluginDefinition#requiresConfiguration()} return correct values.

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

    r2962 r2981  
    100100    The plugins that can be executed by this job agent. This is the
    101101    inverse end.
    102     @see JobAgentPluginDate#getJobAgent()
     102    @see JobAgentSettingsData#getJobAgent()
    103103    @hibernate.map lazy="true" cascade="delete" inverse="true"
    104104    @hibernate.collection-key column="`jobagent_id`"

  • trunk/src/core/net/sf/basedb/core/plugin/AbstractExporterPlugin.java

    r2868 r2981  
    5555  This class doesn't override any methods of the {@link InteractivePlugin}
    5656  interface. It is your responsibility to ask for the correct parameters
    57   and save them to the job. See the {@link HelpExporter} implementation for
    58   example code.
     57  and save them to the job. See the {@link net.sf.basedb.plugins.HelpExporter}
     58  implementation forexample code.
    5959
    6060  @author nicklas
    … …  
    198198    Called just before the export starts. A subclass may override
    199199    this method if it needs to initialise some resources.
    200     @param DbControl The DbControl that is used to write to the database.
     200    @param dc The DbControl that is used to write to the database.
    201201      A subclass may use this read from the database as well
    202202    @see #end(boolean)
    … …  
    237237 
    238238  /**
    239     Parameter name for the {@link #getSaveAsParameter(String, String, String)}
     239    Parameter name for the {@link #getSaveAsParameter(String, String, String, boolean)}
    240240    parameter.
    241241  */

  • trunk/src/core/net/sf/basedb/core/plugin/ExportOutputStream.java

    r2854 r2981  
    3636  suitable for the type of download. For example the {@link
    3737  net.sf.basedb.clients.web.util.ServletExportOutputStream} implements direct download
    38   from web clients and the {@link net.sf.based.util.FileExportOutputStream} implements
     38  from web clients and the {@link net.sf.basedb.util.FileExportOutputStream} implements
    3939  direct download to the BASE file system.
    4040

  • trunk/src/core/net/sf/basedb/core/plugin/ImmediateDownloadExporter.java

    r2854 r2981  
    2525
    2626import java.io.IOException;
    27 import java.io.OutputStream;
    2827
     28import net.sf.basedb.core.Job;
    2929import net.sf.basedb.core.ProgressReporter;
    3030
    … …  
    3737  {@link InteractivePlugin#configure(GuiContext, Request, Response)}.
    3838  When the configuration is complete the plugin may respond with
    39   a {@link Response#setExportImmediately()} instead of a {@link
    40   Response#setDone(String, Job.ExecutionTime)}. This will prevent the
     39  a {@link Response#setDownloadImmediately(String, Job.ExecutionTime, boolean)}
     40  instead of a {@link Response#setDone(String, Job.ExecutionTime)}. This will prevent the
    4141  core from saving a job in the job queue. Instead it will call the
    42   {@link #doExport(OutputStream, ExportInfo)} method to let the plugin
     42  {@link #doExport(ExportOutputStream, ProgressReporter)} method to let the plugin
    4343  generate it's output. The {@link Plugin#run(Request, Response, ProgressReporter)}
    4444  method is never called.

  • trunk/src/core/net/sf/basedb/core/plugin/Request.java

    r2854 r2981  
    2626import java.util.List;
    2727
     28import net.sf.basedb.core.Job;
    2829import net.sf.basedb.core.ParameterException;
    2930import net.sf.basedb.core.ProgressReporter;

  • trunk/src/core/net/sf/basedb/core/plugin/Response.java

    r2854 r2981  
    2626import net.sf.basedb.core.PermissionDeniedException;
    2727import net.sf.basedb.core.Job;
     28import net.sf.basedb.core.ProgressReporter;
    2829
    2930import java.util.List;

  • trunk/src/core/net/sf/basedb/core/query/AutoJoiner.java

    r2669 r2981  
    2727  An <code>AutoJoiner</code> is an object that automatically joins
    2828  other tables in query depending on other query elements. For example,
    29   if we use the {@link Dynamic#select(ExtraValue, String)} to select
    30   an extra value, the {@link net.sf.basedb.core.SpotQueryExtraValueJoiner}
     29  if we use the {@link Dynamic#select(net.sf.basedb.core.ExtraValue, String)} to select
     30  an extra value, the {@link net.sf.basedb.core.DynamicSpotQueryJoiners}
    3131  makes sure that the table containing the extra values is joined to the
    3232  query by calling the
    33   {@link net.sf.basedb.core.DynamicSpotQuery#joinExtraValue(ExtraValue, JoinType)}
     33  {@link net.sf.basedb.core.DynamicSpotQuery#joinExtraValue(net.sf.basedb.core.ExtraValue, JoinType)}
    3434  method.
    3535  <p>

  • trunk/src/core/net/sf/basedb/core/query/ReporterListExpression.java

    r2669 r2981  
    5454 
    5555  /**
    56     Create a new expression for the specified extra value. It is assumed
    57     that the extra value has been joined before it is used in an expression.
    58     @param extraValue The extra value
    59     @see net.sf.basedb.core.ExtraValueJoin
    60     @see net.sf.basedb.core.query.Dynamic#extraValue(ExtraValue)
     56    Create a new expression for the specified reporter list.
     57   
     58    @param reporterList The reporter list
     59    @param tableColumn The name of the column we should select
     60    @param autoJoinType If an automatic join is done use this type, the join
     61      type depends on if we are checking if a reporter is part of or not part
     62      of a reporter list
     63    @see net.sf.basedb.core.query.Dynamic#isPartOf(ReporterList)
     64    @see net.sf.basedb.core.query.Dynamic#isNotPartOf(ReporterList)
     65    @see net.sf.basedb.core.query.Dynamic#score(ReporterList)
    6166  */
    6267  ReporterListExpression(ReporterList reporterList, String tableColumn, JoinType autoJoinType)

  • trunk/src/core/net/sf/basedb/util/BioAssaySetFilterUtil.java

    r2778 r2981  
    6262    Create a filtered bioassay set from a parent bioassay set using
    6363    a simple restriction. The filtering is done by the
    64     {@link FilterBatcher#insert(AbstractSqlQuery)} which is very fast since
    65     most of the work is done by the database.
     64    {@link FilterBatcher#insert(net.sf.basedb.core.AbstractSqlQuery)} which is
     65    very fast since most of the work is done by the database.
    6666    <p>
    6767    The calling code mustn't forget to commit the transaction.

  • trunk/src/core/net/sf/basedb/util/BioAssaySetUtil.java

    r2942 r2981  
    9999    Find the values of parent properties for a given bioassay. This method
    100100    starts by loading all raw bioassays that are parents to the bioassay.
    101     For each raw bioassay it uses the {@link Metadata#getPropertyValue(DbControl, C, String)}
     101    For each raw bioassay it uses the {@link Metadata#getPropertyValue(DbControl, Object, String)}
    102102    method to find the value of the given property for that raw bioassay.
    103103    <p>
    … …  
    137137    Parse a JEP expression and create a restrictions that is suitable to
    138138    be used in a dynamic query. In addition to the standard functions defined
    139     by JEP (see {@link Jep#getFunctions()) this method defines the following functions:
     139    by JEP (see {@link Jep#getFunctions()}) this method defines the following functions:
    140140    <ul>
    141     <li>all functions defined by the {@link #createJepExpression(DbControl, String)} method
     141    <li>all functions defined by the {@link #createJepExpression(DbControl, BioAssaySet, String)}
     142      method
    142143    <li>inList(list): Checks if the reporter is included in the specified list
    143144    <li>notInList(list): Checks if the reporter isn't included in the specified list
    … …  
    163164    Parse a JEP expression and create a restrictions that is suitable to
    164165    be used in a dynamic query. In addition to the standard functions defined
    165     by JEP (see {@link Jep#getFunctions()) this method defines the following functions:
     166    by JEP (see {@link Jep#getFunctions()}) this method defines the following functions:
    166167    <ul>
    167168    <li>raw(property): The value of the specified raw data property
    168169    <li>rep(property): The value of the specified reporter property
    169170    <li>ch(n): The intensity in channel n
    170     <li>score(list): The score of the {@link Reporter} in the specified {@link ReporterList}
    171       (numeric or external ID)
    172     <li>xtra(extraValue): The value of the specified {@link ExtraValue} (numeric ID or the external
    173       ID of the {@link ExtraValueType})
     171    <li>score(list): The score of the {@link net.sf.basedb.core.data.ReporterData} in the
     172      specified {@link net.sf.basedb.core.ReporterList} (numeric or external ID)
     173    <li>xtra(extraValue): The value of the specified {@link net.sf.basedb.core.ExtraValue}
     174      (numeric ID or the external ID of the {@link net.sf.basedb.core.ExtraValueType})
    174175    </ul>
    175176    @see net.sf.basedb.util.jep.Jep

  • trunk/src/core/net/sf/basedb/util/DynamicFilter.java

    r2601 r2981  
    3232
    3333import java.sql.SQLException;
     34import java.util.List;
    3435
    3536/**
    … …  
    3738  class to help a plugin filter the data of a bioassay set. A plugin
    3839  must supply an implementation of this interface to be able to use the
    39   {@link BioAssaySetFilterUtil#createFilteredBioAssaySet(DbControl, BioAssaySet, Job, DynamicFilter, ProgressReporter)}
     40  {@link BioAssaySetFilterUtil#createFilteredBioAssaySet(DbControl, BioAssaySet,
     41  List, Job, DynamicFilter, ProgressReporter)}
    4042  method.
    4143 

  • trunk/src/core/net/sf/basedb/util/Values.java

    r2942 r2981  
    680680  /**
    681681    Parses a string containing the number of bytes formatted as
    682     the {@link #formatBytes(long)} method.
     682    the {@link #formatBytes(Long)} method.
    683683    @param fBytes The string containing the value to parse
    684684    @param defaultValue This value is returned if the string cannot be parsed

  • trunk/src/core/net/sf/basedb/util/jep/ChannelFunction.java

    r2669 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
     28import net.sf.basedb.core.DbControl;
    2729import net.sf.basedb.core.VirtualColumn;
    2830import net.sf.basedb.core.query.Dynamic;
    2931import net.sf.basedb.core.query.Expression;
    3032import net.sf.basedb.core.query.SqlResult;
     33import net.sf.basedb.util.BioAssaySetUtil;
    3134
    3235import java.sql.SQLException;

  • trunk/src/core/net/sf/basedb/util/jep/ExtraValueFunction.java

    r2669 r2981  
    3232import net.sf.basedb.core.query.Expression;
    3333import net.sf.basedb.core.query.SqlResult;
     34import net.sf.basedb.util.BioAssaySetUtil;
    3435import net.sf.basedb.util.Values;
    3536

  • trunk/src/core/net/sf/basedb/util/jep/InReporterListFunction.java

    r2876 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.DbControl;
    2829import net.sf.basedb.core.ReporterList;
    … …  
    3031import net.sf.basedb.core.query.Restriction;
    3132import net.sf.basedb.core.query.SqlResult;
     33import net.sf.basedb.util.BioAssaySetUtil;
    3234
    3335import java.util.Stack;

  • trunk/src/core/net/sf/basedb/util/jep/MeanFunction.java

    r2726 r2981  
    119119  */
    120120  /**
    121     Use the {@link Expression#aFloat(mean)} method to create an
     121    Use the {@link Dynamic#meanRawData(String)} method to create an
    122122    expression for the mean of the given raw data property.
    123123  */

  • trunk/src/core/net/sf/basedb/util/jep/NotInReporterListFunction.java

    r2876 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.DbControl;
    2829import net.sf.basedb.core.ReporterList;
    … …  
    3031import net.sf.basedb.core.query.Restriction;
    3132import net.sf.basedb.core.query.SqlResult;
     33import net.sf.basedb.util.BioAssaySetUtil;
    3234
    3335import java.util.Stack;

  • trunk/src/core/net/sf/basedb/util/jep/RawFunction.java

    r2669 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.RawDataType;
    2829import net.sf.basedb.core.DbControl;
    … …  
    3132import net.sf.basedb.core.query.Dynamic;
    3233import net.sf.basedb.core.query.Expression;
     34import net.sf.basedb.util.BioAssaySetUtil;
    3335
    3436import java.util.Stack;

  • trunk/src/core/net/sf/basedb/util/jep/ReporterFunction.java

    r2669 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.RawDataType;
    2829import net.sf.basedb.core.DbControl;
    … …  
    3132import net.sf.basedb.core.query.Dynamic;
    3233import net.sf.basedb.core.query.Expression;
     34import net.sf.basedb.util.BioAssaySetUtil;
    3335
    3436import java.util.Stack;

  • trunk/src/core/net/sf/basedb/util/jep/ScoreFunction.java

    r2669 r2981  
    2525
    2626import net.sf.basedb.core.BaseException;
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.DbControl;
    2829import net.sf.basedb.core.ReporterList;
    … …  
    3031import net.sf.basedb.core.query.Expression;
    3132import net.sf.basedb.core.query.SqlResult;
     33import net.sf.basedb.util.BioAssaySetUtil;
    3234
    3335import java.sql.SQLException;

  • trunk/src/core/net/sf/basedb/util/jobagent/JobAgentInfo.java

    r2634 r2981  
    4040  @author nicklas
    4141  @version 2.0
    42   @see JobAgentConnection#getInfo()
     42  @see JobAgentConnection#getInfo(boolean)
    4343  @base.modified $Date$
    4444*/

  • trunk/src/core/net/sf/basedb/util/jobagent/JobAgentServerConnection.java

    r2641 r2981  
    7171    Start listening for incoming connections. This method starts a new listener
    7272    thread that answers incoming requests. For each request a new thread
    73     is created and control is passed on to the {@?ink RequestHandler}. If a listener
     73    is created and control is passed on to the {@link RequestHandler}. If a listener
    7474    has already been create thi method does nothing.
    7575    @throws IOException If there is an error

  • trunk/src/core/net/sf/basedb/util/jobagent/RequestHandler.java

    r2634 r2981  
    2626import java.net.Socket;
    2727
     28import org.apache.log4j.Logger;
     29
     30
    2831/**
    2932  A request handler object takes care of an incoming request from a
    … …  
    3336  @author nicklas
    3437  @version 2.0
    35   @see JobAgentServerConnection(int, RequestHandler)
     38  @see JobAgentServerConnection#JobAgentServerConnection(int, RequestHandler, Logger)
    3639  @base.modified $Date$
    3740*/

  • trunk/src/core/net/sf/basedb/util/zip/AbstractFileUnpacker.java

    r2722 r2981  
    288288    The name of the parameter that asks for the directory where the
    289289    unpacked files are stored.
    290     @see #getZipFileParameter(String, String, String)
     290    @see #getZipFileParameter(String, String)
    291291  */
    292292  protected static final String UNPACK_DIRECTORY = "unpackDirectory";
    … …  
    330330    The name of the parameter that asks if existing files should be
    331331    overwritten or not.
    332     @see #getOverwriteParameter(String, String, String)
     332    @see #getOverwriteParameter(String, String)
    333333  */
    334334  protected static final String OVERWRITE = "overwrite";

  • trunk/src/core/net/sf/basedb/util/zip/FileUnpacker.java

    r2691 r2981  
    5757    Get the name of the compressed file format this unpacker supports.
    5858    For example: ZIP files
    59     @return
    6059  */
    6160  public String getFormatName();

  • trunk/src/core/net/sf/basedb/util/zip/ZipUnpacker.java

    r2691 r2981  
    7676    @param overwrite If existing files should be overwritten or ignored
    7777    @param progress An optional progress reporter for displaying progress
    78     @param zipSize The total size of the zip file, or 0 if not known
    7978    @return The number of files unpacked
    8079    @throws IOException If there is an error when unpacking the zip file

  • trunk/src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java

    r2803 r2981  
    711711    a mapper, if the map expression isn't null. If a max string length has been
    712712    specified the created mapper is wrapped by a {@link CropStringMapper}
    713     that crops strings returned by the {@link Mapper#getValue(Data)} method
     713    that crops strings returned by the {@link Mapper#getValue(FlatFileParser.Data)} method
    714714    to the specified length.
    715715   

  • trunk/src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java

    r2872 r2981  
    3737import net.sf.basedb.core.Permission;
    3838import net.sf.basedb.core.PluginParameter;
    39 import net.sf.basedb.core.RawDataType;
    4039import net.sf.basedb.core.RequestInformation;
    4140import net.sf.basedb.core.StringParameterType;

  • trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

    r2938 r2981  
    6666  by the root user.
    6767  <ol>
    68   <li>Create a project {@link #createProject(DbControl)} and activate it
    69   <li>Create several protocols: {@link #createProject(DbControl)}
     68  <li>Create a project {@link #createProject(DbControl, String)} and activate it
     69  <li>Create several protocols: {@link #createProtocol(DbControl, String, String)}
    7070  <li>Create hardware: {@link #createHardware(DbControl, String, String)}
    7171  <li>Create software: {@link #createSoftware(DbControl, String, String)}
    72   <li>Create annotation types: {@link #createAnnotationType(DbControl, String, Type, Object[], Item[])
     72  <li>Create annotation types: {@link #createAnnotationType(DbControl, String, Type, Object[], Item[])}
    7373  <li>Create plate type: {@link #createPlateType(DbControl, String, int, int)}
    7474  <li>Create file formats for import:
Note: See TracChangeset for help on using the changeset viewer.