Changeset 4034


Ignore:
Timestamp:
Dec 5, 2007, 8:21:26 AM (16 years ago)
Author:
Martin Svensson
Message:

References #847 Updated some javadocs. Added some missing tags.

Location:
trunk/src
Files:
44 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/FileUpload.java

    r4020 r4034  
    433433    by one thread and the progress display in another. This method is also called
    434434    if an exception occures internally in this object.
     435    @param t The throwable object to set.
    435436  */
    436437  public void setException(Throwable t)

  • trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/TableColumn.java

    r3679 r4034  
    165165
    166166  /**
     167    @return This table column's
     168      {@link net.sf.basedb.core.Formula.AverageMethod} enum.
    167169    @since 2.4
    168170  */
    … …  
    173175 
    174176  /**
    175      @since 2.0.2
     177    @return This column's {@link net.sf.basedb.util.formatter.Formatter} object 
     178    @since 2.0.2
    176179  */
    177180  public Formatter<?> getFormatter()
    … …  
    181184
    182185  /**
    183      @since 2.0.2
     186    @param formatter Formatter to be set.
     187    @since 2.0.2
    184188  */
    185189  public void setFormatter(Formatter<?> formatter)

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

    r3679 r4034  
    350350    Escape a string to make it safe for use in a JavaScript statement.
    351351    Replaces \ with \\, newline with \n, ' with \' and " with \".
     352    @param in String to escape.
     353    @return a String object, ready to be used in javaScripts.
    352354  */
    353355  public static String javaScriptEncode(String in)

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

    r4026 r4034  
     1
    12/**
    23  $Id$

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

    r3679 r4034  
    4949    @param dc The <code>DbControl</code> which will be used for
    5050      permission checking and database access.
     51    @param feature Feature to get array design block from.
    5152    @return An {@link ArrayDesignBlock} object.
    5253    @throws PermissionDeniedException If the logged in user doesn't
    … …  
    6768    @param dc The <code>DbControl</code> which will be used for
    6869      permission checking and database access.
     70    @param feature The feature to get well from.
    6971    @return A {@link Well} object or null if no well is connected
    7072    @throws PermissionDeniedException If the logged in user doesn't

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

    r3820 r4034  
    212212  /**
    213213    Get the array design this batcher is used for.
     214    @return An {@link net.sf.basedb.core.ArrayDesign}
    214215  */
    215216  public ArrayDesign getArrayDesign()
    … …  
    220221  /**
    221222    Create a new feature.
     223    @param adb  The array design of the feature.
     224    @param well The well of the feature. Null is not allowed. The plate of the well must
     225      have a position on the ArrayDesign of the current FeatureBatcher.
    222226    @return A feature data object
    223227    @throws BaseException If there is an error
    … …  
    236240  /**
    237241    Create a new feature.
     242    @param adb
     243    @param reporter
    238244    @return A feature data object
    239245    @throws BaseException If there is an error

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

    r3679 r4034  
    5454  /**
    5555    Create new object with the specified row and column.
     56    @param block Block number the feature belongs to.
     57    @param metaRow Meta row number
     58    @param metaColumn Meta column number
     59    @param row Row number of the feature
     60    @param column Column number of the feature.
    5661  */
    5762  public FeatureCoordinate(Integer block, Integer metaRow, Integer metaColumn, Integer row, Integer column)

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

    r3679 r4034  
    4848  /**
    4949    Create a new file parameter type.
     50    @param defaultValue Default value of the parameter. Null is allowed
    5051    @param notNull FALSE if nulls values are allowed, TRUE otherwise
     52    @param multiplicity How many values that can be tied to this
     53      parameter. 0 is unlimited values and 1 is default.
    5154  */
    5255  public FileParameterType(File defaultValue, boolean notNull, int multiplicity)

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

    r3820 r4034  
    4949    {@link FileStoreEnabled} item's file set. Optionally, check if the
    5050    file has been validated as a valid file.
    51    
     51   
     52    @param dc DbControl to use when accessing the database.   
    5253    @param item The {@link FileStoreEnabled} item to check
    5354    @param dataFileType The external ID of the {@link DataFileType} to check for
    … …  
    8889    Get the file of the given data file type in the
    8990    {@link FileStoreEnabled} item's file set.
    90    
     91   
     92    @param dc DbControl used to access the database.
    9193    @param item The {@link FileStoreEnabled} item to check
    9294    @param dataFileType The external ID of the {@link DataFileType} to check for

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

    r3679 r4034  
    6565    @param lowerLimit The lowest allowed value, or null to have no limit
    6666    @param upperLimit The highest allowed value, or null to have no limit
     67    @param defaultValue A value to use by default with the parameter.
    6768    @param notNull FALSE if nulls values are allowed, TRUE otherwise
    6869  */

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

    r3905 r4034  
    16231623  /**
    16241624    Check if theta joins or ANSI joins are used by the database.
     1625    @param queryType  Query type to be checked.
     1626    @return TRUE if theta joins are used, FALSE if ANSI joins are used.
    16251627  */
    16261628  public static boolean useThetaJoin(QueryType queryType)

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

    r3979 r4034  
    157157    required for BASE to work properly. Items that already exists
    158158    will not be modified.
    159  
     159   
     160    @param update TRUE if the run is an update, FALSE otherwise.
    160161    @param progress An object implementing the {@link ProgressReporter}
    161162      interface
     163    @param rootLogin The root user's login name.
     164    @param rootPassword The root user's password.
    162165    @throws BaseException This exception is thrown if there is an error
    163166  */

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

    r3679 r4034  
    5151    couldn't be parsed default value is returned.
    5252    @param value The <code>Integer</code>
     53    @param defaultValue Default value to return if the parsing fails.
    5354    @return The value of the <code>Integer</code> or defaultValue if it is not parseable
    5455  */

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

    r3679 r4034  
    5454    Create a new <code>InvalidAnnotationException</code> object when
    5555    the annotation type cannot be used for the specified item type.
     56    @param annotationType The annotation type used to annotate.
     57    @param itemType Kind of item that couldn't be annotated.
    5658  */
    5759  public InvalidAnnotationException(AnnotationType annotationType, Item itemType)

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

    r3679 r4034  
    4444  /**
    4545    Create a new <code>InvalidDataException</code> object.
     46    @param cause Throwable object that caused this exception.
    4647  */
    4748  public InvalidDataException(Throwable cause)
    … …  
    6667 
    6768    @param message The message to throw with the exception
     69    @param cause Throwable object that caused this exception.
    6870  */
    6971  public InvalidDataException(String message, Throwable cause)

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

    r3820 r4034  
    4747  /**
    4848    Create a new <code>InvalidRelationException</code> object.
     49    @param cause Throwable object that caused this exception to be thrown.
    4950  */
    5051  public InvalidRelationException(Throwable cause)
    … …  
    6970 
    7071    @param message The message to throw with the exception
     72    @param cause Throwable object that caused this exception to be thrown.
    7173  */
    7274  public InvalidRelationException(String message, Throwable cause)

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

    r3820 r4034  
    733733  /**
    734734    Get the <code>Item</code> object when you know the integer code.
     735    @param value Integer code 
     736    @return an Item enumeration.
    735737  */
    736738  public static Item fromValue(int value)
    … …  
    743745  /**
    744746    Get the <code>Item</code> object when you know the item class.
     747    @param itemClass Item class for which <code>Item</code> object should be returned
     748    @return an Item enumeration.
    745749  */
    746750  public static Item fromItemClass(Class<? extends BasicItem> itemClass)
    … …  
    753757  /**
    754758    Get the <code>Item</code> object when you know the data class.
     759    @param dataClass Data class for which the Item should be returned.
     760    @return an Item enumeration.
    755761  */
    756762  public static Item fromDataClass(Class<? extends BasicData> dataClass)
    … …  
    764770    Get the <code>Item</code> object when you know either the item or
    765771    data class.
     772    @param anyClass The class to get corresponding <code>Item</code> for.
    766773    @return The Item object, or null if no matching item is found
    767774  */
    … …  
    784791    Get the <code>Item</code> object when you have a data layer object.
    785792    This method takes Hibernate proxies into account.
     793    @param data The data layer object for which corresponding
     794      <code>Item</code> should be returned.
     795    @return The Item object, or null if no matching item is found.
    786796  */
    787797  @SuppressWarnings({"unchecked"})

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

    r4020 r4034  
    13041304    Same as {@link #getDynamicExpression(DbControl, String)} but generates
    13051305    a select object instead.
     1306    @param dc DbControl used to access the database
     1307    @param propertyDef The string to use for creating the expression.
     1308    @return An Expression object.
    13061309  */
    13071310  public static Select getDynamicSelect(DbControl dc, String propertyDef)

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

    r3679 r4034  
    4545    Create a new item parameter type, allowing null values.
    4646    @param clazz The class object of the type of items that are accepted
     47    @param items List of items to choose from.
    4748  */
    4849  public ItemParameterType(Class<T> clazz, List<T> items)

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

    r4020 r4034  
    9191    @param dc The <code>DbControl</code> which will be used for
    9292      permission checking and database access.
     93    @param plugin The plugin this job should use.
    9394    @param config The plugin configuration this job should use
    9495      or null if the job is executed by an external program
    … …  
    432433  /**
    433434    Set if a message should be sent to owner when the job finishes.
     435    @param sendMessage TRUE if a message should be sent, FALSE otherwise.
    434436    @throws PermissionDeniedException If the logged in user doesn't have
    435437      write permission
    … …  
    443445 
    444446  /**
    445     If the job should be deleted after it's done successfully
     447    If the job should flagged for deletion after it's done successfully.
     448    @return TRUE if job is flagged to be removed, FALSE otherwise
    446449  */
    447450  public boolean getRemoveJobWhenFinished()
    … …  
    452455  /**
    453456    Set if the job should be deleted after it has finished successfully.
     457    @param removeJobWhenFinished TRUE if the job should be
     458      flagged for deletion when finished, FALSE otherwise.
    454459    @throws PermissionDeniedException If the logged in user doesn't have
    455460      write permission
    … …  
    526531    Set the priority of the job. The priority is a value between 1 and 10,
    527532    with 1 as the highest priority.
     533    @param priority The priority to set.
    528534    @throws PermissionDeniedException If the logged in user doesn't have
    529535      write permission or the job's status isn't <code>WAITING</code>
    … …  
    789795    is done. See {@link net.sf.basedb.core.PluginRequest} for more  information. This method changes
    790796    the status of the job to {@link Status#WAITING}.
    791 
     797   
     798    @param context GUI context from where the configuration is called.
    792799    @return A <code>PluginRequest</code> object
    793800    @throws PermissionDeniedException If the logged in user doesn't have

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

    r3675 r4034  
    188188  /**
    189189    Set the external id for the job agent.
     190    @param externalId External id to be set.
    190191    @throws PermissionDeniedException If the logged in user doesn't have
    191192      write permission
    … …  
    331332    @param plugin The plugin to the settings for, or null if none exists
    332333      and the <code>create</code> parameter is false
     334    @param create TRUE if new settings should be created if no one was found, FALSE otherwise.
    333335    @return A <code>JobAgentSettings</code> object for the specified plugin
    334336  */

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

    r3679 r4034  
    235235    of this labeled extract.
    236236    @param extract The new <code>Extract</code> item
     237    @param usedQuantity Used quantity of the extract.
    237238    @throws PermissionDeniedException If the logged in user doesn't have
    238239      write permission for this labeled extract or use permission for the extract

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

    r3679 r4034  
    6565    @param lowerLimit The lowest allowed value, or null to have no limit
    6666    @param upperLimit The highest allowed value, or null to have no limit
     67    @param defaultValue Default value for the parameter.
    6768    @param notNull FALSE if nulls values are allowed, TRUE otherwise
    6869  */

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

    r4020 r4034  
    244244  /**
    245245    Check if this biomaterial was created by pooling or not.
     246    @return TRUE if pooled, FALSE otherwise.
    246247  */
    247248  public boolean isPooled()
    … …  
    253254    Specify if this biomaterial was created by pooling or not. Changing this property
    254255    also clears the parent biomaterial and the sources collection for the creation event.
     256    @param pooled set to TRUE if pooled, FALSE otherwise.
    255257    @throws PermissionDeniedException If the logged in user doesn't have
    256258      write permission
    … …  
    273275  /**
    274276    Create a new event for this biomaterial.
     277    @return a {@link net.sf.basedb.core.BioMaterialEvent} object.
    275278    @throws PermissionDeniedException If the logged in user doesn't have
    276279      use permission for this biomaterial

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

    r3679 r4034  
    7979    Get the title of the request. A client application can use this text as
    8080    a page header.
     81    @return A String object or null if not specified.
    8182  */
    8283  public String getTitle()
    … …  
    8889    Get a description of the request. A client application can use this information
    8990    as a help text describing the current configuration page.
     91    @return A String object or null if not specified.
    9092  */
    9193  public String getDescription()
    … …  
    9799    Get a list containing the information about the parameters
    98100    needed for the current request.
     101    @return A {@link java.util.List} with {@link net.sf.basedb.core.PluginParameter}:s
    99102  */
    100103  public List<PluginParameter<?>> getParameters()
    … …  
    105108  /**
    106109    Get the plugin parameter with the specified name.
     110    @param name Name of the plugin parameter.
    107111    @return The PluginParameter objec or null if no parameter with that name
    108112      exists

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

    r3998 r4034  
    197197    Get the time this object last was accessed. Used by the cleanup timer
    198198    in {@link Application#cleanSessionControlCache(boolean)}
     199    @return A long object. 
    199200    @since 2.4.5
    200201  */
    … …  
    250251    Get the id of the <code>Client</code> application in use. Use
    251252    {@link Client#getById(DbControl, int)} to get the {@link Client} object.
     253    @return Client id as an int.
    252254  */
    253255  public int getClientId()
    … …  
    259261  /**
    260262    Get the external id of the <code>Client</code> application in use.
     263    @return A java.lang.String object.
    261264    @see #getClientId()
    262265  */
    … …  
    589592  /**
    590593    Log in as the owner of the specified item.
     594    @param item Login as the owner of this Item. Null is not allowed
     595    @param comment A comment that will be placed in the {@link Session} information
     596    @return A {@link net.sf.basedb.core.SessionControl} for the created session.
    591597    @see #impersonateLogin(int, String)
    592598  */
    … …  
    728734    Get the id of the logged in user, or 0 if no user is logged in.
    729735    Use {@link User#getById(DbControl, int)} to get the {@link User} object.
     736    @return User id as an int.
    730737    @see #login(String, String, String, boolean)
    731738    @see #logout()
    … …  
    808815    Get the id of the active project, or 0 if no project is active.
    809816    Use {@link Project#getById(DbControl, int)} to get the {@link Project} object.
     817    @return An int.
    810818    @see #setActiveProject(Project)
    811819  */
    … …  
    10881096    Get the id of all item keys where the logged in user has the
    10891097    requested permission.
     1098    @param permission Requested permissions.
    10901099    @return A <code>Set</code> containing item key id:s
    10911100  */
    … …  
    11071116    Get the id of all project keys where the logged in user has the
    11081117    requested permission.
     1118    @param permission The requested permissions
    11091119    @return A <code>Set</code> containing project key id:s
    11101120  */
    … …  
    11341144  /**
    11351145    Same as: <code>getCurrentContext(item, "", defaultContext)</code>.
     1146    @param item Type of item for which current context should be returned. 
     1147    @param defaultContext A default context to copy values from if a new context
     1148      must be created
     1149    @return A {@link net.sf.basedb.core.ItemContext} object.
    11361150    @see #getCurrentContext(Item, String, ItemContext)
    11371151  */
    … …  
    11501164   
    11511165    @param item The type of item to get the context for
     1166    @param subContext Current sub context.
    11521167    @param defaultContext A default context to copy values from if a new context
    1153       must be created
     1168      must be created.
     1169    @return A {@link net.sf.basedb.core.ItemContext} object.
    11541170    @throws InvalidDataException If the item is null
    11551171    @throws BaseException If there is another error
    … …  
    12551271    @param name The name of the context
    12561272    @param overwrite If TRUE, an existing context with the same name is
    1257       overwritted, otherwise an exception is thrown
     1273      overwritten, otherwise an exception is thrown
    12581274    @param isPublic If the saved context should be visible to everyone
    12591275      or not (requires {@link Permission#SHARE_TO_EVERYONE} permission)
     1276    @return Saved context's id as an int.
    12601277    @throws PermissionDeniedException If no user is logged in,
    12611278      or if the logged in user is a multi-user account or if the <code>isPublic</code>
    … …  
    14001417    Get a list with the names of all named contexts for a given item and
    14011418    subcontext.
     1419    @param item Item for which named contexts should be returned
     1420    @param subContext Certain sub context to return contexts for.
    14021421    @return A enumeration containing the id and names, the list will be empty if no user
    14031422      is logged in or if no names contexts exists for the specified item type/subcontext

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

    r3679 r4034  
    111111  /**
    112112    Get the name of this setting.
     113    @return A String object.
    113114  */
    114115  public String getName()
    … …  
    118119  /**
    119120    Set the name for this setting.
     121    @param name Name to be set.
    120122    @throws PermissionDeniedException If the logged in user doesn't have
    121123      write permission
    … …  
    132134  /**
    133135    Get the value of this setting.
     136    @return A String object.
    134137  */
    135138  public String getValue()
    … …  
    139142  /**
    140143    Set the value for this setting.
     144    @param value The string value to be set. Can not be longer then {@value #MAX_VALUE_LENGTH}
    141145    @throws PermissionDeniedException If the logged in user doesn't have
    142146      write permission

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

    r3679 r4034  
    4141  /**
    4242    Set the item key of a {@link ShareableData} object.
     43    @param shareableData The data object to set the item key on. Null is not allowed.
     44    @param itemKey Item key to be set.
    4345  */
    4446  public static void setItemKey(ShareableData shareableData, ItemKey itemKey)
    … …  
    4951  /**
    5052    Set the project key of a {@link ShareableData} object.
     53    @param shareableData The data object to set project key to. Null is not allowed.
     54    @param projectKey Project key to be set.
    5155  */
    5256  public static void setProjectKey(ShareableData shareableData, ProjectKey projectKey)

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

    r3900 r4034  
    4646  /**
    4747    Create a new <code>UnsavedItemException</code> object.
     48    @param cause Throwable object that caused this exception.
    4849  */
    4950  public UnsavedItemException(Throwable cause)
    … …  
    6869 
    6970    @param message The message to throw with the exception
     71    @param cause A throwable exception that caused the exception.
    7072  */
    7173  public UnsavedItemException(String message, Throwable cause)

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

    r4023 r4034  
    124124    Load the ID:s of all users that are direct members of
    125125    the specified groups.
     126    @param dc DbControl used to access database.
    126127    @param groupIds The ID:s of the groups
    127128    @return The ID:s of all members
    … …  
    209210  /**
    210211    Check if a login name already exists in the database
     212    @param dc An open DbControl used to access the database. 
    211213      @param login The login name to look for
    212214    @return TRUE if an user has the login. FALSE if the login is not in use.
    … …  
    229231  /**
    230232      Check if an external ID already exists in the database
     233      @param dc An open DbControl used to access the database.
    231234      @param externalId The externalID to look for
    232235      @return TRUE if an user has the external ID. FALSE if the externalID is not in use.
    … …  
    396399
    397400  /**
    398     Set the password. A null password is not allowed.
     401    Set the password.
     402    @param password Password to set. A null password is not allowed.
    399403    @throws PermissionDeniedException If the logged in user doesn't have
    400404      restricted_write permission
    … …  
    433437    the user can't login. A null value indicates that the account will
    434438    never expire.
     439    @return A {@link java.util.Date} object or null.
    435440  */
    436441  public Date getExpirationDate()
    … …  
    441446    Sets the expiration date of the account. A null value indicates that
    442447    the account will never expire.
    443 
     448   
     449    @param expirationDate Date when the account should expire.
    444450    @throws PermissionDeniedException If the logged in user doesn't have
    445451      write permission
    … …  
    487493  /**
    488494    Sets if the user account is multiuser account.
     495    @param multiuserAccount Set to TRUE if it is, FALSE otherwise.
    489496    @throws PermissionDeniedException If the logged in user doesn't have
    490497      write permission
    … …  
    506513    be used by external applications which need to synchronize data between
    507514    the BASE database and some external database. It is not used by the core.
     515    @return A String object or null if not set.
    508516  */
    509517  public String getExternalId()
    … …  
    513521  /**
    514522    Set the external id for the user account.
     523    @param externalId External id to be set, null is allowed.
    515524    @throws PermissionDeniedException If the logged in user doesn't have
    516525      write permission
    … …  
    533542  /**
    534543    Get the login for the user account.
     544    @return A String object.
    535545  */
    536546  public String getLogin()
    … …  
    540550  /**
    541551    Set the login for the user account.
     552    @param login Login name to set. Null is not allowed.
    542553    @throws PermissionDeniedException If the logged in user doesn't have
    543554      write permission
    … …  
    559570  /**
    560571    Get the organisation this user works for, or null if unknown.
     572    @return A String object or null if not set.
    561573  */
    562574  public String getOrganisation()
    … …  
    566578  /**
    567579    Set the organisation this user works for, or null if unknown.
     580    @param organisation Some kind of name or description of
     581      the organisation to associate with the user. Not longer then {@value #MAX_ORGANISATION_LENGTH}
    568582    @throws PermissionDeniedException If the logged in user doesn't have
    569583      restricted write permission
    … …  
    585599  /**
    586600    Get the address for the user, or null if unknown.
     601    @return A String object, or null if not set.
    587602  */
    588603  public String getAddress()
    … …  
    592607  /**
    593608    Set the address for the user, or null if unknown.
     609    @param address Address to be set.
    594610    @throws PermissionDeniedException If the logged in user doesn't have
    595611      write permission
    … …  
    611627  /**
    612628    Get the phone number to the user, or null if unknown.
     629    @return A String object or null if not set.
    613630  */
    614631  public String getPhone()
    … …  
    618635  /**
    619636    Set the phone number to the user, or null if unknown.
     637    @param phone Phone number to set.
    620638    @throws PermissionDeniedException If the logged in user doesn't have
    621639      write permission
    … …  
    637655  /**
    638656    Get the fax number to the user, or null if unknown.
     657    @return A String object or null if not set.
    639658  */
    640659  public String getFax()
    … …  
    644663  /**
    645664    Set the fax number to the user, or null if unknown.
     665    @param fax Fax number to be set.
    646666    @throws PermissionDeniedException If the logged in user doesn't have
    647667      write permission
    … …  
    662682  public static final int MAX_EMAIL_LENGTH = UserData.MAX_EMAIL_LENGTH;
    663683  /**
    664     Get the email address to the user, or null if unknown.
     684    Get the email address to the user.
     685    @return A java.lang.String object, or null if unknown.
    665686  */
    666687  public String getEmail()
    … …  
    670691  /**
    671692    Set the email address to the user, or null if unknown.
     693    @param email Email to be set, null is allowed.
    672694    @throws PermissionDeniedException If the logged in user doesn't have
    673695      write permission
    … …  
    688710  public static final int MAX_URL_LENGTH = UserData.MAX_URL_LENGTH;
    689711  /**
    690     Get the URL to the user's homepage, or null if unknown.
     712    Get the URL to the user's homepage.
     713    @return A String object, or null if unknown.
    691714  */
    692715  public String getUrl()
    … …  
    696719  /**
    697720    Set the URL to the user's homepage, or null if unknown.
     721    @param url URL to set. The String can be at maximum {@value #MAX_URL_LENGTH}.
    698722    @throws PermissionDeniedException If the logged in user doesn't have
    699723      write permission
    … …  
    912936    member. The query excludes roles that the logged in user doesn't have
    913937    permission to read.
    914    
     938    @return a restricted {@link net.sf.basedb.core.ItemQuery}.
    915939    @see Role#getQuery()
    916940  */
    … …  
    932956    member. The query excludes groups that the logged in user doesn't have
    933957    permission to read.
    934 
     958    @return A restricted {@link net.sf.basedb.core.ItemQuery}.
    935959    @see Group#getQuery()
    936960  */
    … …  
    953977    permission to read. The query doesn't include projects where this user is
    954978    the owner.
     979    @return A restricted {@link net.sf.basedb.core.ItemQuery}
    955980    @see Project#getQuery()
    956981  */

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

    r3679 r4034  
    4444 
    4545  /**
     46    @param item Item the context holds.
     47    @param type Type of context,
     48      shows if it is a list or single view.
    4649   
    4750  */

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

    r3900 r4034  
    7171
    7272    @param entity The entity
     73    @return an object implementing {@link net.sf.basedb.core.query.Expression}
    7374    @throws InvalidDataException If the entity is null or isn't saved to the database
    7475    @see #entity(BasicData)
    … …  
    436437 
    437438  /**
     439    @param restrictionString A restriction as a string.
     440      Null or empty string is not allowed.
     441    @param prefix Prefix used in the restriction string.
     442      The prefix will be replaced in the returned object by the query's root-alias.
     443      Null is allowed.
     444    @return a Restriction to use in a query.
    438445    @since 2.5
    439446   */
    … …  
    446453 
    447454  /**
     455    @param exprString An expression as a string.
     456      Null or empty string is not allowed.
     457    @param prefix Prefix used in the expression string.
     458      The prefix will be replaced in the returned object by the query's root-alias.
     459      Null is allowed.
     460    @return an Object implementing {@link net.sf.basedb.core.query.Expression}.
    448461    @since 2.5
    449462   */

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

    r2290 r4034  
    8888  /**
    8989    If the current database supports column aliases in that part of the query.
     90    @param engine 
     91    @return TRUE if column alias is supported, FALSE otherwise.
    9092   */
    9193  public abstract boolean supportsColumnAlias(DbEngine engine);

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

    r3832 r4034  
    200200 
    201201  /**
    202     Get the complete tree of subdirectories from a given directory.
     202    Get the complete tree of sub-directories from a given directory.
     203    @param dc DbControl used to access the database.
    203204    @param directory The directory to start with
    204205    @return A <code>Map</code> which maps a directory to a
    205       list of it's subdirectories. Directories without subdirectories
     206      list of it's sub-directories. Directories without sub-directories
    206207      are not included in the map.
    207208    @throws InvalidDataException If the directory is null

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

    r3675 r4034  
    8181    Create a new input stream splitter. Skipped bytes are not copied
    8282    and the remainder of the stream is not copied if closed.
    83     @param in The input stream to read from
    84     @param copyTo The output streams to copy data to
     83    @param in The input stream to read from. Null is not allowed
     84    @param copySkipped  TRUE if skipped bytes should be copied, FALSE otherwise
     85    @param readToEnd If the remainder of the input stream should be copied
     86      if it is closed before the end
     87    @param copyTo The output streams to copy data to. Null is not allowed
    8588    @since 2.4
    8689  */

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

    r3679 r4034  
    7979    Gets a list with the projects, groups and users(in that order) that
    8080    an item is shared to.
    81       @param item The item that is shared
     81    @param dc DbControl to use when accessing the database.
     82      @param item The item that is shared
    8283      @return A <code>List</code> with items implementing {@link net.sf.basedb.core.Nameable}
    8384      @since 2.4

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

    r3973 r4034  
    441441    is specified, the {@link Formatter#format(Object)} method is used, otherwise
    442442    {@link Object#toString()}.
     443    @param values Collection to be converted.
     444    @param formatter
     445    @return A String array
    443446  */
    444447  public static final <T> String[] toStrings(Collection<T> values, Formatter<T> formatter)
    … …  
    470473    @param value The string to trim
    471474    @param maxLength
     475    @return A string or null if value is null.
    472476  */
    473477  public static final String trimString(String value, int maxLength)
    … …  
    712716    @param fBytes The string containing the value to parse
    713717    @param defaultValue This value is returned if the string cannot be parsed
     718    @return Bytes as a Long object.
    714719  */
    715720  public static final Long parseBytes(String fBytes, Long defaultValue)
    … …  
    845850    Trim a string to a maximum length. If the input string is longer than
    846851    maxLength the string is cut of at the end and ... is added to it.
     852    @param s String to be trimmed.
     853    @param maxLength The maximum length the string is allowed to be.
     854    @return A string or null if s is null.
    847855  */
    848856  public static String trim(String s, int maxLength)

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

    r4017 r4034  
    7070    to dynamically evaluate expressions. It should only be used for converting
    7171    JEP formulas to {@link Expression}:s.
     72    @param dc DbControl to use when accessing the database
     73    @param bas Bioassay set for this extra value function.
    7274    @see Jep#formulaToExpression(String, JepFunction[])
    7375  */
    … …  
    8183    Create a new instance of this function which can be used
    8284    to dynamically evaluate expressions.
     85    @param dc DbControl to use when accessing the database
    8386    @param extraToIndex An map from extra value ID to column indexes in
    8487      the SqlResult

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

    r3675 r4034  
    6464    to dynamically evaluate expressions. It should only be used for converting
    6565    JEP formulas to {@link Restriction}:s.
     66    @param dc DbControl used to access database.
    6667    @see Jep#formulaToRestriction(String, JepFunction[]) 
    6768  */

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

    r4023 r4034  
    6767    to dynamically evaluate expressions. It should only be used for converting
    6868    JEP formulas to {@link Expression}:s.
     69    @param dc DbControl to use when this ScoreFunction accessing the database.
    6970    @see Jep#formulaToExpression(String, JepFunction[])
    7071  */
    … …  
    7778    Create a new instance of this function which can be used
    7879    to dynamically evaluate expressions.
     80    @param dc DbControl to use when this ScoreFunction accessing the database.
    7981    @param scoreIndex The column index in the SqlResult that holds the score value
    8082    @see #setSqlResult(SqlResult)

  • trunk/src/core/net/sf/basedb/util/overview/Failure.java

    r3675 r4034  
    136136  /**
    137137    Add a suggested fix to this failure.
     138    @param fix The fix to add.
    138139  */
    139140  public void addFix(Fix fix)

  • trunk/src/info/net/sf/basedb/info/ToTransferable.java

    r3974 r4034  
    22  $Id$
    33
    4   Copyright (C) Authors contributing to this file.
     4  Copyright (C) 2007 Nicklas Nordborg
    55
    66  This file is part of BASE - BioArray Software Environment.
    … …  
    3131  @author nicklas
    3232  @version 2.5
     33  @param <T> A kind of object that implements {@link net.sf.basedb.info.ToTransferable}
    3334  @base.modified $Date$
    3435*/
    … …  
    3940    The method should return the same object that is
    4041    passed in as an argument.
     42    @param to The transferable object to use
     43    @return The transferable object with values set.
    4144  */
    4245  public T toTransferable(T to);

  • trunk/src/install/net/sf/basedb/install/Webclient.java

    r3900 r4034  
    6363    The user must have enough permissions to create a new client
    6464    application and share it to everyone.
     65    @param args a String array with user account and password.
    6566  */
    6667  public static void main(String[] args)

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

    r3887 r4034  
    310310    @param iterations
    311311    @param blockGroupSize
     312    @param progress Progress reporter used by the caller to keep track of the progress. Null is allowed   
    312313    @return The normalized bioassayset
    313314    @since 2.5
Note: See TracChangeset for help on using the changeset viewer.