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.\" ========================================================================
.\"
.IX Title "Class::AutoClass::Root 3"
.TH Class::AutoClass::Root 3 "2006-04-06" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
Class::AutoClass::Root
.SH "SYNOPSIS # Here's how to throw and catch an exception using the eval-based syntax."
.IX Header "SYNOPSIS # Here's how to throw and catch an exception using the eval-based syntax."
.Vb 1
\&  $obj->throw("This is an exception");
.Ve
.PP
.Vb 3
\&  eval {
\&      $obj->throw("This is catching an exception");
\&  };
.Ve
.PP
.Vb 5
\&  if( $@ ) {
\&      print "Caught exception";
\&  } else {
\&      print "no exception";
\&  }
.Ve
.SH "DESCRIPTION This class provides some basic functionality for Class::* classes."
.IX Header "DESCRIPTION This class provides some basic functionality for Class::* classes."
This package is borrowed from bioperl project (http://bioperl.org/). Because of the 
formidable size of the bioperl library, Root.pm is included here with modifications.
These modifications were to pare its functioanlity down for its simple job here
(removing routines that are out of context and removing references to bioperl to avoid confusion).
.PP
Functions originally from Steve Chervitz of bioperl. Refactored by Ewan
Birney of bioperl. Re-refactored by Lincoln Stein of bioperl.
.Sh "Throwing Exceptions"
.IX Subsection "Throwing Exceptions"
One of the functionalities that Class::AutoClass::Root provides is the
ability to \fIthrow()\fR exceptions with pretty stack traces.
.SH "CONTACT"
.IX Header "CONTACT"
contact: Chris Cavnor \-> ccavnor@systemsbiology.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.Sh "new"
.IX Subsection "new"
.Vb 2
\& Purpose   : generic instantiation function can be overridden if 
\&             special needs of a module cannot be done in _initialize
.Ve
.Sh "verbose"
.IX Subsection "verbose"
.Vb 9
\& Title   : verbose
\& Usage   : $self->verbose(1)
\& Function: Sets verbose level for how ->warn behaves
\&           -1 = no warning
\&            0 = standard, small warning
\&            1 = warning with stack trace
\&            2 = warning becomes throw
\& Returns : The current verbosity setting (integer between -1 to 2)
\& Args    : -1,0,1 or 2
.Ve
.Sh "throw"
.IX Subsection "throw"
.Vb 6
\& Title   : throw
\& Usage   : $obj->throw("throwing exception message")
\& Function: Throws an exception, which, if not caught with an eval brace
\&           will provide a nice stack trace to STDERR with the message
\& Returns : nothing
\& Args    : A string giving a descriptive error message
.Ve
.Sh "stack_trace"
.IX Subsection "stack_trace"
.Vb 6
\& Title   : stack_trace
\& Usage   : @stack_array_ref= $self->stack_trace
\& Function: gives an array to a reference of arrays with stack trace info
\&           each coming from the caller(stack_number) call
\& Returns : array containing a reference of arrays
\& Args    : none
.Ve
.Sh "_stack_trace_dump"
.IX Subsection "_stack_trace_dump"
.Vb 6
\& Title   : _stack_trace_dump
\& Usage   :
\& Function:
\& Example :
\& Returns : 
\& Args    :
.Ve
.Sh "deprecated"
.IX Subsection "deprecated"
.Vb 6
\& Title   : deprecated
\& Usage   : $obj->deprecated("Method X is deprecated");
\& Function: Prints a message about deprecation 
\&           unless verbose is < 0 (which means be quiet)
\& Returns : none
\& Args    : Message string to print to STDERR
.Ve
.Sh "warn"
.IX Subsection "warn"
.Vb 11
\& Title   : warn
\& Usage   : $object->warn("Warning message");
\& Function: Places a warning. What happens now is down to the
\&           verbosity of the object  (value of $obj->verbose) 
\&            verbosity 0 or not set => small warning
\&            verbosity -1 => no warning
\&            verbosity 1 => warning with stack trace
\&            verbosity 2 => converts warnings into throw
\& Example :
\& Returns : 
\& Args    :
.Ve
.Sh "debug"
.IX Subsection "debug"
.Vb 5
\& Title   : debug
\& Usage   : $obj->debug("This is debugging output");
\& Function: Prints a debugging message when verbose is > 0
\& Returns : none
\& Args    : message string(s) to print to STDERR
.Ve