MOSES::MOBY::Base - Hash-based abstract super-class for all MOBY objects


  use base qw( MOSES::MOBY::Base );

  $self->throw ("This is an error");

  $LOG->info ('This is an info message.');
  $LOG->error ('This is an error to be logged.');


This is a hash-based implementation of a general Moby super-class. Most BioMoby objects should inherit from this.


Re-factored by Martin Senger <> from a similar module in Bioperl (Bio::Root::Roo) created by Steve Chervitz <> and others.


Most of the Moby objects (and especially objects representing various Moby data types) are just containers of other objects (attributes, members). Therefore, in order to crete a new Moby data type object it is often enough to inherit from this Moby::Base and to list allowed attributes. The object lists only new, additional, attributes (those defined in its parent classes are already available).

This is done by creating a closure with a list of allowed attribute names. These names correspond with the allowed get and set methods. For example:

    my %_allowed =
         id         => undef,
         namespace  => undef,

The closure above allows to call:

    $obj->id;                    # a get method
    $obj->id ('my id');          # a set method

    $obj->namespace;             # a get method
    $obj->namespace ('my ns');   # a set method

Well, not yet. The closure also needs two methods that access these (and only these - that is why it is a closure, after all) attributes. You can copy them from the MobyObject. Here they are:

    my %_allowed =
         id         => undef,
         namespace  => undef,
    sub _accessible {
        my ($self, $attr) = @_;
        exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
    sub _attr_prop {
        my ($self, $attr_name, $prop_name) = @_;
        my $attr = $_allowed {$attr_name};
        return ref ($attr) ? $attr->{$prop_name} : $attr if $attr;
        return $self->SUPER::_attr_prop ($attr_name, $prop_name);

More about these methods in a moment.

Each attribute has also associated some properties (that is why we need the second method in the closure, the _attr_prop). For example (these are all attributes for MobyObject):

    my %_allowed =
         id         => undef,
         namespace  => undef,
         provision  => {type => 'MOSES::MOBY::Data::ProvisionInformation'},
         xrefs      => {type => 'MOSES::MOBY::Data::Xref', is_array => 1},
         primitive  => {type => MOSES::MOBY::Base->BOOLEAN},

The recognized property names are:


It defines a type of its attribute. It can be a primitive type - one of those defined as constants in MOSES::MOBY::Base (e.g. "MOSES::MOBY::Base->INTEGER") - or a name of a real object (e.g. MOSES::MOBY::Data::MobyProvisionInfo).

When an attribute new value is being set it is checked against this type, and an exception is thrown if the value does not comply with the type.

Default type (used also when the whole properties are undef) is "MOSES::MOBY::Base->STRING".


A boolean property. If set to true it allows to set more values to this attribute. It also allows to call a method prefixed with add_ to add a new value (or values) to this attribute. For example (using the list of attributes shown above):

   use MOSES::MOBY::Data::Object;
   my $moby = new MOSES::MOBY::Data::Object;

   use MOSES::MOBY::Data::Xref;
   my $xref = new MOSES::MOBY::Data::Xref;
   $xref->description ('he is looking at you, kid');

   # set the first cross reference
   $moby->xrefs ($xref);

   # later add anothet cross reference
   my $xref2 = new MOSES::MOBY::Data::Xref;
   $xref2->description ('she is looking at you, kid');
   $moby->add_xrefs ($xref);

Default value is false.

Recognized values for true are: 1, yes, true, + and ano. Anything else is considered false.


A boolean property. If set to true the atribute can only be read.


A property containing a reference to a subroutine. This subroutine is called after a new value was set. It allows to do some post-processing. For example:

    my %_allowed =
         value  => {post => sub { shift->{isValueCDATA} = 0; } },

Now we know what attribute properties are - so we can define what these methods in closure do (even though you do not need to know - unless The Law of Leaky Abstractions starts showing).

_accessible ($attr_name)

Return 1 if the parameter $attr_name is an allowed name to be set/get in this class; otherwise, pass it to the parent class.

_attr_prop ($attr_name, $prop_name)

Return a value of a property given by name $prop_name for given attribute $attr_name; if such attribute does not exist here, pass it to the parent class.


One of the functionalities that MOSES::MOBY::Base provides is the ability to throw() exceptions with pretty stack traces.


Throw an exception. An argument is an error message.


Return a nicely formatted stack trace. The resul includes also an error message given as a scalar argument. Usually, this method is not called directly but via throw (unless enable_throw_with_stack was set to true).

    print $self->format_stack ("Something terrible happen.");




Create an empty hash-based object. Then call init() in order to do any initializing steps. This class provides only an empty init() but sub-classes may have it richer. Finally, fill the new object with the given arguments (name/value pairs). The filling is done via set methods - which means that only attributes allowed for this particular object can be used.

Arguments are name/value pairs. A special case is allowed: when a single element argument occurs, it is treated as a "value". For example, it is allowed to write:

    $mobyint = new MOSES::MOBY::Data::Integer (42);

instead of a long way (doing the same):

    $mobyint = new MOSES::MOBY::Data::Integer (value => 42);


Called after an object has been created (in new()) and before the values given in the constructor have been set. No arguments.

If your sub-class implements this method, make sure that it calls also the same method of its super class:

   sub init {
       my ($self) = shift;
       # ... here do what you wish to do
       # ...


Return an (almost) human-readable description of any object.

Without any parameter, it stringifies the caller object (self). Otherwise it stringifies the object given as parameter.

    print $self->toString;

    my $good_stuff = { yes => [1,2,3],
                       no  => { net => 'R', nikoliv => 'C' },
    print $self->toString ($good_stuff);


Find and read given configuration files (and perhaps some others). Import all their properties into MOBYCFG namespace. More about how to use configuration properties is in MOSES::MOBY::Config module.

But making a long story short, this is all what you need in your service implementation to use a property (excluding the fact that you need to know the property name):

    $self->init_config ('my.conf');
        or $self->throw ('Mabuhay resource file not found.');

Arguments are optional and contain the file names of the configuration files to be read, and/or hash references with the direct configuration arguments. The files are looking for at the paths defined in the @INC, and - if set - by the environment variable BIOMOBY_CFG_DIR.