Changeset 2981


Ignore:
Timestamp:
Nov 30, 2006, 10:50:05 AM (15 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:
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