Changeset 4011


Ignore:
Timestamp:
Nov 28, 2007, 12:11:45 PM (14 years ago)
Author:
Martin Svensson
Message:

References #847 Updated some javadocs. Removed an exception, that is never thrown, in ArrayBatch?.setProtocol(..)

Location:
trunk/src
Files:
24 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTypeTransfer.java

    r3683 r4011  
    163163  @param dbc DbControl used to get the annotationType
    164164  @param base1AnnotationTypeId Base1 annotationtype id
     165  @throws BaseException If accessing the data fails.
    165166   */
    166167  public AnnotationType getAnnotationTypeById(DbControl dbc,
  • trunk/src/core/net/sf/basedb/core/AccessControlled.java

    r3679 r4011  
    4747    Check if the logged in user has the desired permission on
    4848    the item.
    49    
     49      @param permission The permission to check if the user has.   
    5050    @return TRUE if the user has the permission, FALSE otherwise
    5151  */
     
    5555    Check if the logged in user has the desired permission on
    5656    the item, otherwise throw an exception.
    57    
     57      @param permission Permission the user should have.   
    5858    @throws PermissionDeniedException If the user doesn't have the
    5959      requested permission
  • trunk/src/core/net/sf/basedb/core/AccountExpiredException.java

    r3679 r4011  
    4040  /**
    4141    Creates a new <code>AccountExpiredException</code>.
     42      @param login Login name for the expired account
     43    @param expirationDate Date when the account expired.
    4244  */
    4345  public AccountExpiredException(String login, Date expirationDate)
  • trunk/src/core/net/sf/basedb/core/AlreadyLoggedInException.java

    r3679 r4011  
    3838  /**
    3939    Creates a new <code>AlreadyLoggedInException</code>.
     40      @param login Login name of the already logged in account.
    4041  */
    4142  public AlreadyLoggedInException(String login)
  • trunk/src/core/net/sf/basedb/core/AnnotatedItem.java

    r3974 r4011  
    3636  @author Nicklas
    3737  @version 2.0
     38    @param <D> Kind of annotated data the item is annotated with.
    3839  @see Annotatable
    3940  @base.modified $Date$
  • trunk/src/core/net/sf/basedb/core/Annotation.java

    r3679 r4011  
    173173    @throws PermissionDeniedException If the logged in user doesn't have
    174174      read permission for the annotation set (should never happen)
     175    @throws BaseException If anything else goes wrong when getting the annotation set.
    175176  */
    176177  public AnnotationSet getAnnotationSet()
     
    192193    @throws PermissionDeniedException If the logged in user doesn't have
    193194      read permission for the annotation type
     195   * @throws BaseException If anything else goes wrong when getting the annotation type.
    194196  */
    195197  public AnnotationType getAnnotationType()
     
    203205    Get the value type for this annotation type. It can't be change once
    204206    the object has been created.
     207      @return Type value type as an enum.
    205208    @since 2.2
    206209  */
     
    230233    they were read from the database. Unlike other items the version number of the
    231234    annotation item doesn't change when the values are modified.
     235      @return The version number as an int.
    232236  */
    233237  public int getValuesVersion()
  • trunk/src/core/net/sf/basedb/core/AnnotationInRestriction.java

    r3679 r4011  
    5959  /**
    6060    Create a new annotation restriction.
    61    
     61   
     62    @param alias The alias to use in the restriction.   
    6263    @param annotationType The annotation type to use in the query
    6364    @param includeInheriting If items inherting the annotation should be returned
  • trunk/src/core/net/sf/basedb/core/AnnotationSet.java

    r4007 r4011  
    349349      annotation so far
    350350    @return A list <code>Annotation</code> objects (may be empty)
     351    @throws PermissionDeniedException If the logged in user don't have the
     352      proper permissions to access the database.
    351353    @since 2.5
    352354  */
     
    491493    Check if an annotation is inherited or not by this annotation set.
    492494    @param annotation The annotation to check
     495      @return TRUE if inherited, FALSE otherwise.
    493496    @throws InvalidDataException If the annotation is null
    494497  */
     
    506509    @see #inheritAnnotation(Annotation)
    507510    @return An <code>ItemQuery</code> object
     511    @throws BaseException If getting the query fails.
    508512  */
    509513  public ItemQuery<Annotation> getInheritedAnnotations()
     
    582586    Check if an annotation set is inherited or not by this annotation set.
    583587    @param annotationSet The annotation set to check
     588    @return TRUE if inherited, FALSE otherwise.
    584589    @throws InvalidDataException If the annotation set is null
    585590  */
  • trunk/src/core/net/sf/basedb/core/AnnotationType.java

    r3977 r4011  
    393393    Get the value type for this annotation type. It can't be change once
    394394    the object has been created.
     395    @return A {@link Type} constant
    395396  */
    396397  public Type getValueType()
     
    400401 
    401402  /**
    402     Get the multiplicity. The multiplicity tells the core how many valus an annotation
     403    Get the multiplicity. The multiplicity tells the core how many values an annotation
    403404    of this annotation type may contain. The default is one. Zero denotes unlimited
    404405    values.
     406    @return the multiplicity as an int.
    405407  */
    406408  public int getMultiplicity()
     
    409411  }
    410412  /**
    411     Set the multiplicity. The multiplicity tells the core how many valus an annotation
     413    Set the multiplicity. The multiplicity tells the core how many values an annotation
    412414    of this annotation type may contain. The default is one. Zero denotes unlimited
    413415    values.
    414     @throws PermissionDeniedException If the logged in user doesn't
    415       have write permission
    416     @throws InvalidDataException If the multiplicit is lower than zero
     416      @param multiplicity Multiplicity to set.
     417    @throws PermissionDeniedException If the logged in user doesn't
     418      have write permission
     419    @throws InvalidDataException If the multiplicity is lower than zero
    417420  */
    418421  public void setMultiplicity(int multiplicity)
     
    426429    Check an annotation of this annotation type required for an item to
    427430    be compliant with the MIAME recommendation.
     431    @return TRUE if required, FALSE otherwise.
    428432    @see <a href="http://www.mged.org/Workgroups/MIAME/miame.html">MIAME</a>
    429433  */
     
    435439    Set if an annotation of this annotation type is required for an item to
    436440    be compliant with the MIAME recommendation.
     441      @param required Should be TRUE if required or FALSE if it is not.
    437442    @throws PermissionDeniedException If the logged in user doesn't
    438443      have write permission
     
    448453  /**
    449454    Check if this annotation type provides a list of predefined allowed values.
     455    @return TRUE if it is provided, FALSE otherwise.
    450456  */
    451457  public boolean isEnumeration()
     
    455461  /**
    456462    Set if this annotation type should provide a list of predefined allowed values.
     463    @param isEnumeration TRUE if this should be provided, FALSE otherwise
    457464    @throws PermissionDeniedException If the logged in user doesn't
    458465      have write permission
     
    475482    or as radio buttons/checkboxes by the client application. The client application
    476483    may decide to use some other display format that better suits the situation.
     484    @return TRUE if it should be displayed as a selection list,
     485      FALSE if radio buttons/check-boxes.
    477486  */
    478487  public boolean getDisplayAsList()
     
    485494    or as radio buttons/checkboxes by the client application. The client application
    486495    may decide to use some other display format that better suits the situation.
     496    @param displayAsList Set to TRUE to display as a selection list or
     497      set to FALSE to display as radio buttons/check-boxes.
    487498    @throws PermissionDeniedException If the logged in user doesn't
    488499      have write permission
     
    501512    application is not required to use this value if it is not appropriate for
    502513    the situation.
     514    @return Characters height as an int.
    503515  */
    504516  public int getHeight()
     
    528540    application is not required to use this value if it is not appropriate for
    529541    the situation.
     542    @return The width as an int.
    530543  */
    531544  public int getWidth()
     
    558571    It is not certain that the string represents a value that can be converted
    559572    to the correct value type as specified by the {@link #getValueType()} setting.
     573    @return Default value as a String.
    560574  */
    561575  public String getDefaultValue()
     
    567581    It is not checked that the string can be converted to the correct value type
    568582    as specified by the {@link #getValueType()} setting.
     583    @param defaultValue The default value for new annotation.
    569584    @throws PermissionDeniedException If the logged in user doesn't
    570585      have write permission
     
    10181033      is an enumeration
    10191034    </ul>
     1035    @param value The object to be validated
     1036    @throws InvalidDataException If the value object can not be used.
    10201037  */
    10211038  public void validateAnnotationValue(Object value)
  • trunk/src/core/net/sf/basedb/core/AnyToAny.java

    r3675 r4011  
    232232 
    233233  /**
    234     @throws PermissionDeniedException If the logged in user doesn't have
     234    @param dc DbControl to use when accessing the database
     235    @param from BasicItem to unlink from.
     236      @param name Name of the link.
     237      @throws PermissionDeniedException If the logged in user doesn't have
    235238      WRITE permission for the item
    236239    @throws InvalidDataException If the from or name parameter is null
     
    559562    If this link counts as using the destination item. This affects the
    560563    possibility to delete items.
     564    @return TRUE when it is not possible to delete, FALSE otherwise.
    561565  */
    562566  public boolean isUsingTo()
     
    568572    If this link counts as using the destination item. This affects the
    569573    possibility to delete items.
     574    @param usesTo TRUE if this counts as using the item, FALSE otherwise.
    570575    @throws PermissionDeniedException If the logged in user doesn't
    571576      have write permission
  • trunk/src/core/net/sf/basedb/core/ArrayBatch.java

    r3679 r4011  
    233233  */
    234234  public void setProtocol(Protocol protocol)
    235     throws PermissionDeniedException, InvalidDataException
     235    throws PermissionDeniedException
    236236  {
    237237    checkPermission(Permission.WRITE);
  • trunk/src/core/net/sf/basedb/core/ArrayDesign.java

    r3974 r4011  
    424424    Get a query that returns the plates that are used by this arraydesign.
    425425    @return An {@link ItemQuery} object
     426    @throws BaseException If something fails when getting the query.
    426427  */
    427428  public ItemQuery<Plate> getPlates()
     
    643644    file-only platform. The must store feature information in files
    644645    instead. See {@link Platform} and {@link DataFileType}.
    645 
     646    @return The feature batcher of the array design.
    646647    @throws PermissionDeniedException If raw data has already been added
    647648      or the logged in user doesn't have write permission
     
    686687    Get a feature when you know the id.
    687688    @param id The id of the feature
     689    @throws ItemNotFoundException If the feature could not be found.
     690    @throws BaseException If something else fails when getting the feature.
    688691  */
    689692  public FeatureData getFeatureById(int id)
  • trunk/src/core/net/sf/basedb/core/BasicItem.java

    r3974 r4011  
    216216    that the item is used by some other means.
    217217    @return TRUE if this item is used, FALSE otherwise
     218    @throws BaseException If not able to tell if item is used or not.
    218219    @see #getUsingItems()
    219220  */
  • trunk/src/core/net/sf/basedb/core/BioAssay.java

    r3679 r4011  
    113113      is not allowed
    114114    @return An {@link ItemQuery} object
     115    @throws InvalidDataException If the parameter is null.
    115116  */
    116117  public static ItemQuery<BioAssay> getQuery(BioAssaySet bioAssaySet)
  • trunk/src/core/net/sf/basedb/core/BioAssaySet.java

    r3974 r4011  
    139139      is not allowed
    140140    @return An {@link ItemQuery} object
     141    @throws InvalidDataException If the parameter is null.
    141142  */
    142143  public static ItemQuery<BioAssaySet> getQuery(Experiment experiment)
     
    160161      is not allowed
    161162    @return An {@link ItemQuery} object
     163    @throws InvalidDataException If the transformation parameter is null.
    162164  */
    163165  public static ItemQuery<BioAssaySet> getQuery(Transformation transformation)
     
    569571      of a root transformation or if any of the raw bioassay parents
    570572      isn't a member of the transformation
     573    @throws BaseException If something else goes wrong.
    571574    @see #newBioAssay(BioAssay)
    572575    @see #newBioAssay(Collection)
     
    760763    Get the extra value of the specified type in this bioassayset. To add
    761764    extra values use one of the methods that returns a batcher.
    762    
     765    @param extraValueType For which extra value should be returned.
    763766    @return An <code>ExtraValue</code> item, or null if no extra value
    764767      of the specified type has been created  for this bioassayset
     768    @throws BaseException If something fails when getting the extra value.
    765769    @see #getSpotExtraValueBatcher(Class, ExtraValueType, Job)
    766770    @see #getPositionExtraValueBatcher(Class, ExtraValueType, Job)
  • trunk/src/core/net/sf/basedb/core/authentication/Authenticator.java

    r3679 r4011  
    5454    Should return TRUE or FALSE depending on if the authentication
    5555    server returns additional information about the user.
     56      @return TRUE if additional information is returned, FALSE otherwise.
    5657    @see AuthenticationInformation
    5758    @see #authenticate(String,String)
  • trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

    r3675 r4011  
    152152    Check that the item is a bioassayset and that the logged in user has
    153153    permission to use the current experiment.
     154      @param context Current guicontext
     155      @param item The item to check.
    154156    @return null if the item is a bioassayset, an error message otherwise
    155157    @throws PermissionDeniedException If the logged in user dosen't have
  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/AnnotationTypeClient.java

    r3977 r4011  
    5454    @param itemId The ID of the annotation type
    5555    @return An AnnotationTypeInfo object
     56      @throws AxisFault If communication with web service fails.
    5657  */
    5758  public AnnotationTypeInfo getById(int itemId)
  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ArrayDesignClient.java

    r3983 r4011  
    6363    @param itemId The ID of the array design
    6464    @return An ArrayDesignInfo object
     65    @throws AxisFault If communication with web service fails.
    6566  */
    6667  public ArrayDesignInfo getById(int itemId)
  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java

    r3983 r4011  
    5858    @param itemId The ID of the experiment
    5959    @return An ExperimentInfo object
     60    @throws AxisFault If communication with web service fails.
    6061  */
    6162  public ExperimentInfo getById(int itemId)
  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ProjectClient.java

    r3983 r4011  
    5454    @param itemId The ID of the project
    5555    @return An ExperimentInfo object
     56    @throws AxisFault If communication with web service fails.
    5657  */
    5758  public ProjectInfo getById(int itemId)
  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/RawBioAssayClient.java

    r3983 r4011  
    6666    @param itemId The ID of the raw bioassay
    6767    @return An RawBioAssayInfo object
     68    @throws AxisFault If communication with web service fails.
    6869  */
    6970  public RawBioAssayInfo getById(int itemId)
  • trunk/src/webservices/server/net/sf/basedb/ws/server/BioAssaySetService.java

    r3973 r4011  
    9494      @return An OMElement containing the exported file or
    9595        NULL if there an exception is thrown.
     96   * @throws Exception If the data could not be exported to the file.
    9697   */
    9798  @SuppressWarnings("unchecked")
  • trunk/src/webservices/server/net/sf/basedb/ws/server/ServicesUtil.java

    r4008 r4011  
    9797   
    9898    See for example: {@link net.sf.basedb.core.Experiment#toTransferable(net.sf.basedb.info.ExperimentInfo)}
    99    
     99      @param <T> The kind of info object the items can be transfered into.
    100100    @param list A list of {@link ToTransferable} objects
    101101    @param clazz The {@link Transferable} class that the objects in the list
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