Help-Site Computer Manuals
  Algorithms & Data Structures   Programming Languages   Revision Control
  Cameras   Computers   Displays   Keyboards & Mice   Motherboards   Networking   Printers & Scanners   Storage
  Windows   Linux & Unix   Mac

Methods for processing data from the GeneX DB linking table: UserCanonicalLink

Bio::Genex::UserCanonicalLink - Methods for processing data from the GeneX DB linking table: UserCanonicalLink


Bio::Genex::UserCanonicalLink - Methods for processing data from the GeneX DB linking table: UserCanonicalLink


  use Bio::Genex::UserCanonicalLink;

  # instantiating a linking table instance

  my $UserCanonicalLink = Bio::Genex::UserCanonicalLink->new(id=>47,pkey_link=>'usf_fk');

  # or 

  my $UserCanonicalLink = Bio::Genex::UserCanonicalLink->new(id=>47,pkey_link=>'csf_fk');

  # retrieve data from the DB for all columns


  # creating an instance, without pre-fetching all columns

  my $UserCanonicalLink = new Bio::Genex::UserCanonicalLink(id=>47,


  # creating an instance with pre-fetched data

  my $UserCanonicalLink = new Bio::Genex::UserCanonicalLink(id=>47, 



  # retrieving multiple instances via primary keys

  my @objects = Bio::Genex::UserCanonicalLink->get_objects('pkey_link'=>'usf_fk',


  # retrieving all instances from a table

  my @objects = Bio::Genex::UserCanonicalLink->get_objects('ALL');

  # retrieving the primary key for an object, generically

  my $primary_key = $UserCanonicalLink->id();

  # retrieving other DB column attributes

  my $usf_fk_val = $UserCanonicalLink->usf_fk();


  my $csf_fk_val = $UserCanonicalLink->csf_fk();



Each Genex class has a one to one correspondence with a GeneX DB table of the same name (i.e. the corresponding table for Bio::Genex::UserCanonicalLink is UserCanonicalLink).

NOTE: Class Bio::Genex::UserCanonicalLink is linking table class. This means that it represents a table in the Genex DB which has no primary key. Instead, there are two foreign keys that can be used to lookup a value from the database. In Bio::Genex::UserCanonicalLink, those two columns are 'usf_fk' and 'usf_fk'. When an instance of Bio::Genex::UserCanonicalLink is instantiated, either via new() or get_objects(@id_list), the 'pkey_link' parameter must be specified as one of these two values, otherwise, an error will result.

Most applications will first create an instance of Bio::Genex::UserCanonicalLink and then fetch the data for the object from the DB by invoking fetch(). However, in cases where you may only be accessing a single value from an object the built-in delayed fetch mechanism can be used. All objects are created without pre-fetching any data from the DB. Whenever an attribute of the object is accessed via a getter method, the data for that attribute will be fetched from the DB if it has not already been. Delayed fetching happens transparently without the user needing to enable or disable any features.

Since data is not be fetched from the DB until it is accessed by the calling application, it could presumably save a lot of access time for large complicated objects when only a few attribute values are needed.


There are three different types of attributes which instances of Bio::Genex::UserCanonicalLink can access: raw foreign key attributes, Obect-Oriented foreign key attributes, and simple column attributes.

Raw Foreign Keys Attributes
Object Oriented Foreign Key Attributes
This mode presents foreign key attributes in a special way, with all non-foreign key attributes presented normally. Foreign keys are first retrieved from the DB, and then objects of the appropriate classes are created and stored in slots. This mode is useful for applications that want to process information from the DB because it automates looking up information.

Specifying the 'recursive_fetch' parameter when calling new(), modifies the behavior of this mode. The value given specifies the number of levels deep that fetch will be invoked on sub-objects created.

Simple Column Attributes


Class Bio::Genex::UserCanonicalLink defines the following utility variables for assisting programmers to access the UserCanonicalLink table.

If defined, $LIMIT will set a limit on any select statements that can return multiple instances of this class (for example get_objects() or any call to a ONE_TO_MANY or LOOKUP_TABLE foreign key accessor method).

This variable controls whether the class will cache any objects created in calls to new(). Objects are cached by primary key. The caching is very simple, and no effort is made to track whether different invocations of new() are being made for an object with the same primary key value, but with different options set. If you desire to reinstantiate an object with a different set of parameters, you would need to undefine $USE_CACHE first.

WARNING: variables other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.


It is possible to retrieve only the subset of attributes one chooses by simply creating an object instance and then calling the appropriate getter function. The object will automatically fetch the value from the DB when requested. This can potentially save time for large complicated objects. This triggers a separate DB query for each attribute that is accessed, whereas calling fetch() will retrieve all fields of the object with a single query.

For example:

  my $UserCanonicalLink = Bio::Genex::UserCanonicalLink->new(id=>47);

  my $val = $UserCanonicalLink->usf_fk();

The attribute's value is then cached in the object so any further calls to that attribute's getter method do not trigger a DB query.

NOTE: Methods may still return undef if their value in the DB is NULL.


The following methods can all be called without first having an instance of the class via the Bio::Genex::UserCanonicalLink->methodname() syntax.

new() accepts the following arguments:
Numeric or string value. The value of the primary key for looking up the object in the DB.

For linking tables this specifies which of the two possible values should be used as the primary key to fetch an instance from the DB. For class Bio::Genex::UserCanonicalLink, 'pkey_link' can be either 'usf_fk' or 'csf_fk'.

For linking table classes, this method returns a hash table (not a hashref) that defines the fkey access map. Linking tables have no class-wide primary key, instead the column which is used to fetch rows from the DB is determined on a per-instance basis depending on which of the two linked-to tables is accessing the data. For example, in Bio::Genex::UserCanonicalLink if a method in class UserSequenceFeature invokes its foreign key accessor function, the column 'csf_fk' will be used to fetch values from the DB.

Used by generic functions to determine if a specified class is a linking table class. For Bio::Genex::UserCanonicalLink it returns 1, since it is a linking table class.

Returns the name of the DB table represented by this class. For Bio::Genex::UserCanonicalLink it returns 'UserCanonicalLink';

This method returns a hashref that translates DB column names into human readable format.

This method returns a hashref that is a reverse lookup table to translate the human readable version of a DB column name back into the column_name. This is useful for preparing table output in CGI scripts:

    %column2name = %{$class->column2name()};

    if (exists $column2name{$_}) {




    # now that we've translated the names, we sort them

    @column_copy = sort @column_copy;


    # make a header element. 


This method returns a hashref that holds all the foreign key entries for the UserCanonicalLink table.

This method returns an array ref which holds the names of all the columns in table UserCanonicalLink.

    # first retrieve the data from the DB

    $object = $full_module_name->new(id=>$id);


    # now extract the data from the object

    foreach (@{$class->column_names}) {

    # we use this to temporarily relax the strict pragma

    # to use symbolic references

      no strict 'refs';

      $tmp_values{$_} = $object->$_;

    # back to our regularily scheduled strictness


get_objects({pkey_link=>'usf_fk'}, @id_list)
This method is used to retrieve multiple instances of class Bio::Genex::UserCanonicalLink simultaneously. For linking tables, there are three different ways to invoke this method.

By passing in an @id_list, get_objects() uses each element of the list as a primary key for the UserCanonicalLink table and returns a single instance for each entry. This form of the method requires a hash reference as the first argument. The hash must have the 'pkey_link' key defined.

WARNING: Passing incorrect id values to get_objects() will cause a warning from Bio::Genex::UserCanonicalLink::initialize(). Objects will be created for other correct id values in the list.

ERROR: When using the @id_list form of this method with a linking table, the 'pkey_list' attribute must be specified, otherwise an error will result. This is because linking tables have two possible columns to lookup from.

By passing the 'ALL' parameter, get_objects() returns an instance for every entry in the table, and therefore, 'pkey_list' doesn't need to be specified.

By passing a hash reference that contains the 'column' and 'name' keys, the method will return all objects from the DB whose that have the specified value in the specified column.

NOTE: When passing a hash reference with the 'column' and 'value' keys specified, it is not necessary to specify the 'pkey_link' attribute.

NOTE: All objects must have the 'id' parameter set before attempting to use fetch() or any of the objects getter functions.


The following methods can only be called by first having valid instance of class Bio::Genex::UserCanonicalLink.

This method triggers a DB query to retrieve ALL columns from the DB associated with this object.

WARNING: methods other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.


There are two major categories of foreign key accessor methods: Object Oriented foreign key methods, and raw foreign key methods.

Each foreign key column in the table is represented by two methods, one OO method and one raw method. The raw method enables fethcing the exact numeric or string values stored in the DB. The OO method creates objects of the class the fkey column refers to. The idea is that if only the numeric fkey value is desired, the raw fkey method can be used. If it is necessary to get attributes from the table referred to by the fkey column, then the OO method should be invoked, and the necessary methods on that object can be queried.

The names of the raw fkey methods is the same as the fkey columns in the DB table they represent (all fkey columns end in the suffix '_fk'). The OO methods have the same names as the column they represent, with the difference that they have the suffix '_obj' instead of '_fk'.

So for example, in class Bio::Genex::ArrayMeasurement the 'primary_es_fk' column is represented by two methods, the raw method primary_es_fk(), and the OO method primary_es_obj.

The following foreign key accessors are defined for class Bio::Genex::UserCanonicalLink:

Every foreign key in a DB table belongs to a certain class of foreign keys. Each type of foreign key confers a different behavior on the class that contains it. The classifications used in are:


    If a class contains a foreign key of this type it will not be visible to the API of that class, but instead it confers a special method to the class that it references.

    For example, the Chromosome table has a MANY_TO_ONE foreign key, spc_fk, that refers to the species table. Class the Bio::Genex::Chromosome manpage, has it\'s normal spc_fk() attribute method, but no special foreign key accessor method. However, class the Bio::Genex::Species manpage is given a special foreign key accessor method, chromosome_fk() of type ONE_TO_MANY. When invoked, this method returns a list of objects of class the Bio::Genex::Species manpage.


    The inverse of type MANY_TO_ONE. It is not an attribute inherent to a given foreign key in any DB table, but instead is created by the existence of a MANY_TO_ONE foreign key in another table. See the above discussion about MANY_TO_ONE foreign keys.


    This type of key is similar to type ONE_TO_MANY. However, However the API will never retrieve an object of this type. Instead it retrieves a matrix of values, that represent the list of objects. It is used in only two places in the API: the Bio::Genex::ArrayMeasurement manpage and the Bio::Genex::ArrayLayout manpage classes with the am_spots() and al_spots() accessor functions.


    Foreign keys of this type appear in tables without primary keys. The foreign keys are each of type LINKING_TABLE, and when invoked return an object of the class referred to by the foreign key.

  • FKEY

    A generic foreign key with no special properties. When invoked it returns an object of the class referred to by the foreign key.


These are the setter and getter methods for attributes in class Bio::Genex::UserCanonicalLink.

NOTE: To use the getter methods, you may either invoke the fetch() method to retrieve all the values for an object, or else rely on delayed fetching to retrieve the attributes as needed.

id() is a special attribute method that is common to all the Genex classes. This method returns the primary key of the given instance. Class Bio::Genex::UserCanonicalLink is a linking table and therefore it can two possible columns that represent the 'id' ('usf_fk' and 'csf_fk'). When an instance of class Bio::Genex::UserCanonicalLink is created using either new() or get_objects(@id_list) the 'pkey_link' attribute must specified as one of the two possible values.

The id() method can be useful in writing generic methods because it avoids having to know the name of the primary key column.

Methods for the usf_fk attribute. This attribute is the first possible value for the 'pkey_link' attribute at object creation time.

Methods for the csf_fk attribute. This attribute is the second possible value for the 'pkey_link' attribute at object creation time.

WARNING: methods other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.


These classes are automatically generated by the script. Each class is a subclass of the ObjectTemplate class (written by Sriram Srinivasan, described in Advanced Perl Programming, and heavily modified by Jason Stewart). ObjectTemplate implements automatic class creation in perl (there exist other options such as Class::Struct and Class::MethodMaker by Damian Conway) via an attributes() method call at class creation time.


Please send bug reports to


on Thu Dec 7 18:35:48 2000 by /home/jasons/Genex/scripts/ --target=UserCanonicalLink


Jason E. Stewart (