Perl Coding style

Coding rules

• All code that doesn't belong to D-Integrator itself goes into Dint::Utils.
• Common initialization code for the program interface goes into Dint::Init and related modules.
• Exceptions are handled via the Error module.
• EnsEMBL exceptions are trapped via Dint::EnsEMBL::Utils::ens_except().
• All exceptions derive from Dint::Error (which is an Error itself).
• In general, exceptions are reserved for non-recoverable errors (that is: re-running the code again will always fail with the same input).
• Error::EAgain exceptions are special and can be handled via Dint::EnsEMBL::auto_retry(). Internally all Dint classes should automatically retry EnsEMBL exceptions unless explicitly mentioned.
• Transient errors return undef instead.
• All functionality is broken up into classes.
• All classes use the Class::InsideOut module.
• All logging is performed via Log::Log4perl.
• Read-only variables and globals are declared using the Readonly module.
• All code is strict (warnings recommended).
• One-class per module.
• Real EnsEMBL modules should be included using Dint::EnsEMBL::use_ens(), which performs delayed inclusion for runtime version switching.
• Real EnsEMBL functions and variables cannot be used in the module body and/or before a Dint::EnsEMBL::Connector instance has been created.

Formatting conventions

A couple of Perl formatting conventions are followed:

• Indentation is 2 spaces (expanded tabs).
• Built-in Perl functions don't use parentheses, unless required for precedence rules.
• No propotypes for functions.
• Methods/functions use lower_case_with_underscores.
• Class cames use CamelCase.
• The constructor, if any, is always new().
• All modules use Exporter.
• Conditionals use the right-side evaluation, without negation, for a single branch/statement:

# simple statement
function() if(condition);
 
# do not use negation
function() unless(condition);

• Multi-branch conditionals use the right-hanging brace only for single-statement blocks, left-on-newline otherwise:

# fully packed
if(condition) {
  iftrue();
} else {
  iffalse();
}
 
# conditional branch with multiple statement
if(condition)
{
  statement;
  statement;
}
 
# right-handing brace to conserve space
if(condition) {
  statement;
}
else
{
  statement;
  statement;
}
 
# no single-line statement
if(condition)
{
  statement;
  statement;
  statement;
}
else
{
  statement;
  statement;
}

• The same brace rules apply for blocks and subs.
• As a recommendation, for conditional branches, the likely-branch should be the first. For cases without any likelihood, the shortest branch is first.