Changeset 4034


Ignore:
Timestamp:
Dec 5, 2007, 8:21:26 AM (14 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
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