use Bio::EnsEMBL::Utils::Exception
    qw(throw warning deprecate verbose try catch);

  or to get all methods just

  use Bio::EnsEMBL::Utils::Exception;

  eval { throw("this is an exception with a stack trace") };
  if ($@) {
    print "Caught exception:\n$@";
  }

  # Or you can us the try/catch confortable syntax instead to deal with
  # throw or die.  Don't forget the ";" after the catch block.  With
  # this syntax, the original $@ is in $_ in the catch subroutine.

  try {
    throw("this is an exception with a stack trace");
  }
  catch { print "Caught exception:\n$_" };

  # silence warnings
  verbose('OFF');

  warning('this is a silent warning');

  #show deprecated and warning messages but not info
  verbose('DEPRECATE');

  warning('this is a warning');

  # show all messages
  verbose('ALL');

  info('this is an informational message');

  sub my_sub { deprecate('use other_sub() instead') }

  verbose('EXCEPTION');
  info( 'This is a high priority info message.', 1000 );

(&) {  shift;
}

1;

  my $mesg = shift;
  $mesg = shift if($mesg eq "Bio::EnsEMBL::Utils::Exception"); #skip object if one provided

  my $level = shift;

  $level = $DEFAULT_DEPRECATE if(!defined($level));

  return if($VERBOSITY < $level);
                                 
  my @caller = caller(1);
  my $subname = $caller[3] ;
  my $line = $caller[2];

  #use only 2 subdirs for brevity when reporting the filename
  my $file;
  my @path = $caller[1];
  $file = pop(@path);
  my $i = 0;
  while(@path && $i < 2) {
    $i++;
    $file .= pop(@path);
  }

  #keep track of who called this method so that the warning is only displayed
  #once per deprecated call
  return if $DEPRECATED{"$line:$file:$subname"};

  if($VERBOSITY > -1) {
    print STDERR "\n------------------ DEPRECATED ---------------------\n" .
                   "Deprecated method call in file $file line $line.\n" .
                   "Method $subname is deprecated.\n" .
                   "$mesg\n" .
                   "---------------------------------------------------\n";
  }

  $DEPRECATED{"$line:$file:$subname"} = 1;

  my $string = shift;
  $string = shift if($string eq "Bio::EnsEMBL::Utils::Exception");
  my $level  = shift;

  $level = $DEFAULT_INFO if(!defined($level));

  return if($VERBOSITY < $level);

  print STDERR "INFO: $string\n";

  my $i = 0;
  my @out;
  my $prev;
  while ( my @call = caller($i++)) {

    # major annoyance that caller puts caller context as
    # function name. Hence some monkeying around...
    $prev->[3] = $call[3];
    push(@out,$prev);
    $prev =\@ call;
  }
  $prev->[3] = 'toplevel';
  push(@out,$prev);
  return @out;

  my @stack = stack_trace();

  my $levels = 2; #default is 2 levels so stack_trace_dump call is not present
  $levels = shift if(@_);
  $levels = shift if($levels eq "Bio::EnsEMBL::Utils::Exception");
  $levels = 1 if($levels < 1);
  
  while($levels) {
    $levels--;
    shift @stack;
  }

  my $out;
  my ($module,$function,$file,$position);


  foreach my $stack ( @stack) {
    ($module,$file,$position,$function) = @{$stack};
    $out .= "STACK $function $file:$position\n";
  }

  return $out;

  my $string = shift;

  #for backwards compatibility with Bio::EnsEMBL::Root::throw
  #allow to be called as an object method as well as class method
  #Root function now deprecated so call will have the string instead.

  $string = shift if(ref($string)); #skip object if one provided
  $string = shift if($string eq "Bio::EnsEMBL::Utils::Exception");

  my $level  = shift;

  $level = $DEFAULT_EXCEPTION if(!defined($level));

  if($VERBOSITY < $level) {
    die("\n"); #still die, but silently
  }

  my $std = stack_trace_dump(3);

  my $out = "\n-------------------- EXCEPTION --------------------\n" .
              "MSG: $string\n" .
              "$std" .
              "---------------------------------------------------\n";
  die $out;

(&$) {  my ($try, $catch) = @_;
  eval { &$try };
  if ($@) {
    chop $@;
    local $_ = $@;
    &$catch;
  }

  if(@_) {
    my $verbosity = shift;
    $verbosity = shift if($verbosity eq "Bio::EnsEMBL::Utils::Exception");
    if($verbosity =~ /\d+/) { #check if verbosity is an integer
      $VERBOSITY = $verbosity;
    } else {
      $verbosity = uc($verbosity);
      if($verbosity eq 'OFF' || $verbosity eq 'NOTHING' || 
         $verbosity eq 'NONE') {
        $VERBOSITY = 0;
      } elsif($verbosity eq 'EXCEPTION' || $verbosity eq 'THROW') {
        $VERBOSITY = $DEFAULT_EXCEPTION;
      } elsif($verbosity eq 'WARNING' || $verbosity eq 'WARN') {
        $VERBOSITY = $DEFAULT_WARNING;
      } elsif($verbosity eq 'DEPRECATE' || $verbosity eq 'DEPRECATED') {
        $VERBOSITY = $DEFAULT_DEPRECATE;
      } elsif($verbosity eq 'INFO') {
        $VERBOSITY = $DEFAULT_INFO;
      } elsif($verbosity eq 'ON' || $verbosity eq 'ALL') {
        $VERBOSITY = 1e6;
      } else {
        $VERBOSITY = $DEFAULT_WARNING;
        warning("Unknown level of verbosity: $verbosity");
      }
    }
  }

  return $VERBOSITY;

  my $string = shift;
  $string = shift if($string eq "Bio::EnsEMBL::Utils::Exception"); #skip object if one provided
  my $level  = shift;

   $level = $DEFAULT_WARNING if(!defined($level));

  return if ($VERBOSITY < $level);

  my @caller = caller;
  my $line = $caller[2] || '';

  #use only 2 subdirs for brevity when reporting the filename
  my $file;
  my @path = split(/\//, $caller[1]);
  $file = pop(@path);
  my $i = 0;
  while(@path && $i < 2) {
    $i++;
    $file = pop(@path) ."/$file";
  }

  @caller = caller(1);
  my $caller_line;
  my $caller_file;
  $i=0;
  if(@caller) {
     @path = split(/\//, $caller[1]);
     $caller_line = $caller[2];
     $caller_file = pop(@path);
     while(@path && $i < 2) {
       $i++;
       $caller_file = pop(@path) ."/$caller_file";
     }
  }

  
  my $out = "\n-------------------- WARNING ----------------------\n".
              "MSG: $string\n".
              "FILE: $file LINE: $line\n";
  $out .=     "CALLED BY: $caller_file  LINE: $caller_line\n" if($caller_file);
  $out .=     "---------------------------------------------------\n";
  print STDERR $out;

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.