biodesign(3)

NAME
Biodesign 1.3 - Bioperl Design Documentation

SYNOPSIS
Not appropriate. Read on...

DESCRIPTION
Bioperl is a coordinated project which has a number of design features which allow it to be well used and extensible as well as collaborate with other packages. biodesign focuses on a number of areas.

  Bioperl etiquette and learning about it
  Bioperl root object - exception throwing, exceptions etc.
  Bioperl interface design
  Bioperl sequence object design notes

AUTHOR
This was written by Ewan Birney in a variety of airports across the US.

Additions added by: Brian Osborne Jason Stajich

Reusing code and working in collaborative projects
The biggest problem often in reusing a code base like Bioperl is that it requires both the people using it and the people contributing to it to change their attitude towards code. Generally people in bioinformatics are more likely to be self-taught programmers who put together most of their scripts/programs working alone. Bioperl is a truly collaborative project (the core code is the product of about 15 individuals) and anyone will be only contributing some part of it in the future.

Here are some notes about how my coding style has changed to work in collaborative projects.

  Learn to read documentation
Reading documentation is sometimes as tough as writing the documentation. Try to read documentation before you ask a question - not only might it answer your question, but more importantly it will give you idea why the person who wrote the module wrote it - and this will be the frame work in which you can understand his or her answer.

You might also want to examine the models, or class diagrams, in the models directory. These diagrams are not guaranteed to include every single class but may help you understand the overall layout of Bioperl's modules.

Documentation on Bio::Root can also be found in the form of scripts - check the scripts/root_object directory for a start, as well as Bio::Root. We have also created a "howto" directory that addresses specific design questions, not necessarily related to Bio::Root. See doc/howto.

  Respect people's code (in particular if it works)
If the code does what you want, the fact that it is not written the way you would write should not be a big issue. Of course, if there is some glaring error then that is worth pointing out to someone. Dismissing a module on the basis of its coding style is a tremendously wrong thing to do.

  Learn how to provide good feedback
This ranges from giving very accurate bug reports (this script --> makes this error, giving all data), through to pointing out design issues in a constructive manner (not - this *sucks*). If you find a problem, then providing a patch using diff or a work around is a great thing to do - the author/maintainer of the module will love you for it.

Providing "I used XXX and it did just what I wanted it to do" feedback is also really great. Developers generally only hear about their mistakes. To hear about successes gives everyone a warm glow.

One trick we have learnt is that when we download a new project/code or use a new module we open up a fresh buffer in emacs and keep a mini diary of everything that we did or thought when we started to use the package. After we used it we could go back, edit the buffer and then send it to the author either with "it was great - it did just what I wanted, but I found that the documentation here was misleading" to "to get it to install I had to incant the following things..."

  Taking on a project
When you want to get involved, hopefully it will be because you want to extend something or provide better facilities to something. The important thing here is not to work in a vacuum. Providing the main list with a good proposal before you start about what you are going to do (and listen to the responses) is a must. We have been pulled up so many times by other people looking at our designs that we can't imagine coding stuff now without feedback.

  Designing good tests
Sadly, you might think that you have written good code, but you don't know that until you manage to test it! The CPAN style perl modules have a wonderful test suite system (delve around into the t/ directories) and we have extended the makefile system so that the test script which you write to test the module can be part of the t/ system from the start. Once a test is in the t/ system it will be run millions of times worldwide when Bioperl is downloaded, providing incredible and continual regression testing of your module (for free!).

  Having fun
The coding process should be enjoyable, and we get very proud of people who tell us that they picked up Bioperl and it worked for them, even if they don't use a single module that we wrote. There is a brilliant sense of community in Bioperl about providing useful, stable code and it should be a pleasure to contribute to it.

So - we are always looking forward to people posting on the guts list with their feedback/questions/proposals. As well as the long standing fun we have making new releases.

Bioperl Bio::Root::Root Object
All objects in Bioperl (but for interfaces) inherit from the Bio::Root::Root. The Bioperl root object allows a number of very useful concepts to be provided. In particular.

exceptions, warning, and debugging
    The Bioperl Root object allows exceptions to be throw on the object with very nice debugging output. These are throw by calling the method throw() and passing in the message string. This will cause the execution of the script to die with a stack trace.

    Similarly the warn() method can be called which will produce a warning message - use this instead of print for warning messages to the user because if the verbose flag is set to -1 warnings will be skipped. Additionally setting the verbose flag to 1 will print a stack trace for every warning in addition to the message and setting verbose to 2 will convert warnings into thrown exceptions.

    Finally, the the debug() method prints messages to STDERR when the verbose flag is set to 1.

rearrange
    Bioperl root object have some helper methods, in particular rearrange() to help functions which take hash inputs. This allows one to specify named arguments as a hash and map them to the expected input parameters specified by an array.

You can go to Bio::Root::Root for more information. There are also a number of useful example scripts in the scripts/root_object directory.

  Using the root object
To use the root object, the object has to inherit from it. This means the @ISA array should have (Bio::Root::Root) in it and that the module has a "use Bio::Root::Root". (If you are an emacs user, consider using the boilerplate methods in the bioperl.lisp to lay out your module initially for you). The root object provides a top level ->new function. You should inherit from this new method by calling the new method of the superclass which is accessible by using SUPER. This is called chaining the constructors and allows a child class to utilize the initialization procedure of the superclass in addition to executing its own. This is a very powerful technique and allows Bioperl to behave in an Object Oriented manner.

The full code is given below for a basic skeleton object that uses bioperl.

  # convention is that if you are using the Bio::Root object you
  # should put it inside the Bio namespace

  package Bio::MyNewObject;
  use vars qw(@ISA);
  use strict;

  use Bio::Root::Root;
  @ISA = qw(Bio::Root::Root);

  sub new {
     my($class,@args) = @_;
     # call superclasses initialize
     my $self = $class->SUPER::new(@args);

     # do your own argument processing here

     my ($arg1) = $self->_rearrange([qw(NAMEDARGUMENT1)], @args);

     # set default attributes etc...

     return $self;
  }

  Throwing Exceptions
Exceptions are die functions, in which the $@ variable (a scalar) is used to indicate how it died. The exceptions can be caught using the eval {} system. The Bioperl root object has a method called "->throw" which calls die but also provides a full stack trace of where this throw happened on. So an exception like

  $obj->throw("I am throwing an exception");

Provides the following output on STDERR if is not caught.

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: I am throwing an exception STACK: Error::throw STACK: Bio::Root::Root::throw /home/jason/bioperl/core/Bio/Root/Root.pm:313 -----------------------------------------------------------

indicating that this exception was thrown at line 7 of subroutine my_subroutine, in myscript.pl

Exceptions can be caught using an eval block, such as

 my $obj = Bio::SomeObject->new();
 my $obj2
 eval {
   $obj2 = $obj->method1();
   $obj2->method2(10);
 }

 if( $@ ) {
   # exception was thrown
   &tell_user("Exception was thrown, preventing whatever I wanted to do.
              Actual exception $@");
   exit(0);
 }

 # else - use $obj2

Notice that the eval block can have multiple statements in it, and also that if you want to use variables outside of the eval block, they must be declared with my outside of the eval block (you are planning to "use strict" in your scripts, aren't you!).

This context is particularly useful when objects are produced from a database. This is because some exceptions are really due to problems with the data in an object rather than the code. These sort of exceptions are better tracked down when you know where the object came from, not where in the code the exception is thrown.

One of the drawbacks to this scheme is that the attribute ->name is "special" from Bioperl's perspective. We believe it is best to stay away from using $obj->name() to mean anything from the object's perspective (for example ->id() ), leaving it free to be used as a context for debugging purposes. You might prefer to overload the name attribute to be "useful" for the object.

See scripts/root_object/error.pl for demonstration code.

Bioperl Interface design
Bioperl has been moving to a split between interface and implementation definitions. An interface is solely the definition of what methods one can call on an object, without any knowledge of how it is implemented. An implementation is an actual, working implementation of an object. In languages like Java, interface definition is part of the language. In Perl, like many aspects of Perl you have to roll your own.

In Bioperl, the interface names are called Bio::MyObjectI, with the trailing I indicating it is an interface definition of an object. The interface files (sometimes nicknamed the 'I files') provide mainly documentation on what the interface is, and how to use and implement it. All the functions which the implementation is expected to provide are defined as subroutines, and then die with an informative warning. The exception to this rule are the implementation independent functions (see "Implementation functions in Interface files").

Objects which want to implement this interface should inherit the Bio::MyObjectI file in their @ISA array. This means that if the implementation does not provide a method which the interface defines, rather than the user getting a "method not found error" it gets a "mymethod() was not defined in MyObjectI, but should have been" which makes it clearer that whoever provided the implementation was to blame, and not the caller/script writer.

When people want to check they have valid objects being passed to their functions they should test the presence of the interface, not the implementation. for example

  sub my_sequence_routine {
    my($seq,$other_argument) = @_;

    $seq->isa('Bio::SeqI') || die "[$seq] is not a sequence. Cannot process";

    # do stuff
  }

This is in contrast to

  sub my_incorrect_sequence_routine {
    my($seq,$other_argument) = @_;

    # this line is INCORRECT
    $seq->isa('Bio::Seq') || die "[$seq] is not a sequence. Cannot process";

    # do stuff
  }

  Rationale of interface design
Some people might justifiably argue "why do this?". The main reason is to support external objects from Bioperl, and allow them to masquerade as real Bioperl objects. For example you might have your own quite intricate sequence object which you want to use in Bioperl functions, but don't want to lose your own neat coding. One option would be to have a function which built a Bioperl sequence object from your object, but then you would be endlessly building temporary objects and destroying them, in particular if the script yo-yoed between your code and Bioperl code.

A better solution would be to implement the Bio::SeqI interface. You would read Bio::SeqI, and then provide the methods which it required, and put Bio::SeqI in your @ISA array. Then you could pass in your object into Bioperl routines and eh voila - you are a Bioperl sequence object.

(A problem might arise if your object has the same methods as the Bio::SeqI methods but use them differently - your $obj->id() might mean provide the raw memory location of the object, whereas the documentation for Bio::SeqI $obj->id() says it should return the human-readable name. If so you need to look into providing an 'Adaptor' class, as suggested in the Gang-of-four).

Interface classes really come into their own when we start leaving Perl and enter extensions wrapped over C or over databases, or through systems like CORBA to other languages, like Java/Python etc. Here the "object" is often a very thin wrapper over the a DBI interface, or an XS interface, and how it stores the object is really different. By providing a very clear, implementation free interface with good documentation there is a very clear target to hit.

Some people might complain that we are doing something very "un-perl-like" by providing these separate interface files. They are 90% documentation, and could be provided anywhere, in many ways they could be merged with the actual implementation classes and just made clear that if someone wants to mimic a class they should override the following methods. However, we (and in particular myself - Ewan) prefers a clear separation of the interface. It gives us a much clearer way of defining what is going on. It is in many ways just "design sugar" (as opposed to syntactic sugar) to help us, but it really helps, so that's good enough justification to me.

  Implementation functions in Interface files
One of the issues we discovered early on in using Interface files was that there were methods that we would like to provide for classes which were independent of their implementation. A good example is a "Range" interface, which might define the following methods

  $obj->start()
  $obj->end()

Now a client to the object might want to use a $obj->length() method. because it is much easier than retrieving the two attributes and substracting them. However, the ->length() method is just a pain for someone providing the implementation to provide - once start() and end() is defined, length is. There seems to be a catch-22 here: to make an object definition good for a client one needs to have additional, helper methods "on top of" the interface, however to make life easier for the object implementation one wants to have the bare minimum of functions defined which the implementer has to provide.

In the Range interface this became more than annoyance, as a lot of the "smarts" of the Range system was that we wanted to have the ability to say

  if( $range->intersection($someother_range) )

We wanted a generic RangeI interface that we could apply to many objects, with definitions required only for ->start, ->end and ->strand. However we wanted the ->intersection, and ->union methods to be on all ranges, without us having to reimplement this every time.

Our (Matt Pocock and Ewan Birney's) solution was to allow implementation into the RangeI interface file, but only when these implementations sat "on top" of the interface definition and therefore provided helper client operations. In a language like Java, we would clearly have two classes, with a composition/delegation method:

   MyPublicSomethingClass has-a MyInternalSomethingInterface, with

   ADifferentImplemtation implements MyInternalSomethingInterface

However this is really heavy handed in Perl (and people were complaining about having different implementation/interface classes). We were quite happy about merging the implementation independent functions with the interface definition, and we have used this in other interfaces since then. The documentation has to be clear about what is going on, but we think in general it is.

A Note on performance
Since Object Oriented programming in perl is not as elegant as intentionally object oriented programming languages we incur some overhead when calling the chained new constructors. For most cases this is perfectly okay as the object creation is not a significant portion of many of the procedures. However in certain cases - reading in a large number of sequences with features requires the creation of many objects and can perform poorly. One can work around this by creating the hashes directly and NOT chaining the new calls. An example of this is implemented in the Bio::SeqIO::FTHelper objects in the treatment of Location objects for features. Please see Bio::SeqIO::FTHelper for details.

Getting Started
The Bioperl effort has managed to strike that balance between creating reliable and powerful software and providing outlets for individual creativity and imagination. In this spirit of open-mindedness we invite you to share your ideas with us at bioperl-l at bioperl.org.