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package Class::AutoClass::Root; |
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use strict; |
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723
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=head1 NAME |
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Class::AutoClass::Root |
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=head1 SYNOPSIS |
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# Here's how to throw and catch an exception using the eval-based syntax. |
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$obj->throw("This is an exception"); |
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eval { |
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$obj->throw("This is catching an exception"); |
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}; |
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if( $@ ) { |
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print "Caught exception"; |
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} else { |
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print "no exception"; |
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} |
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=head1 DESCRIPTION |
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This class provides some basic functionality for Class::* classes. |
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This package is borrowed from bioperl project (http://bioperl.org/). Because of the |
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formidable size of the bioperl library, Root.pm is included here with modifications. |
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These modifications were to pare its functioanlity down for its simple job here |
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(removing routines that are out of context and removing references to bioperl to avoid confusion). |
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Functions originally from Steve Chervitz of bioperl. Refactored by Ewan |
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Birney of bioperl. Re-refactored by Lincoln Stein of bioperl. |
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=head2 Throwing Exceptions |
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One of the functionalities that Class::AutoClass::Root provides is the |
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ability to throw() exceptions with pretty stack traces. |
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=head1 CONTACT |
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41
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contact: Chris Cavnor -> ccavnor@systemsbiology.org |
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=head1 APPENDIX |
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45
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The rest of the documentation details each of the object |
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methods. Internal methods are usually preceded with a _ |
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48
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=cut |
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50
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#' |
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51
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52
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74
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use vars qw(@ISA $DEBUG $ID $Revision $VERSION $VERBOSITY $ERRORLOADED @EXPORT); |
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1518
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53
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13
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68
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use strict; |
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22
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852
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54
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55
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BEGIN { |
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57
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$ID = 'Class::AutoClass::Root'; |
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58
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$VERSION = 1.0; |
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$Revision = ''; |
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135
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$DEBUG = 0; |
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61
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$VERBOSITY = 0; |
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62
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19195
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$ERRORLOADED = 0; |
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63
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} |
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64
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65
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66
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67
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=head2 new |
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68
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69
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Purpose : generic instantiation function can be overridden if |
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70
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special needs of a module cannot be done in _initialize |
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71
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72
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=cut |
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73
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74
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sub new { |
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75
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1
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1
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1
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13
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my $class = shift; |
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76
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1
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3
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my $self = {}; |
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77
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1
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33
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8
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bless $self, ref($class) || $class; |
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78
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79
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1
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50
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5
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if(@_ > 1) { |
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80
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# if the number of arguments is odd but at least 3, we'll give |
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81
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# it a try to find -verbose |
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82
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0
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0
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0
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shift if @_ % 2; |
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83
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0
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0
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my %param = @_; |
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84
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0
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0
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0
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$self->verbose($param{'-VERBOSE'} || $param{'-verbose'}); |
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85
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} |
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86
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1
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4
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return $self; |
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87
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} |
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88
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89
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=head2 verbose |
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90
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91
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Title : verbose |
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92
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Usage : $self->verbose(1) |
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93
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Function: Sets verbose level for how ->warn behaves |
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94
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-1 = no warning |
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95
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0 = standard, small warning |
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96
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1 = warning with stack trace |
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97
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2 = warning becomes throw |
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98
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Returns : The current verbosity setting (integer between -1 to 2) |
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99
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Args : -1,0,1 or 2 |
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100
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101
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102
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=cut |
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103
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104
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sub verbose { |
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105
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3
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3
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1
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6
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my ($self,$value) = @_; |
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106
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# allow one to set global verbosity flag |
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107
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3
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50
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12
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return $DEBUG if $DEBUG; |
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108
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3
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50
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8
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return $VERBOSITY unless ref $self; |
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109
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110
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3
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100
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66
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22
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if (defined $value || ! defined $self->{'_root_verbose'}) { |
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111
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1
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50
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7
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$self->{'_root_verbose'} = $value || 0; |
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112
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} |
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113
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3
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11
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return $self->{'_root_verbose'}; |
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114
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} |
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115
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116
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sub _register_for_cleanup { |
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117
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0
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0
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0
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my ($self,$method) = @_; |
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118
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0
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0
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0
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if($method) { |
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119
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0
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0
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0
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if(! exists($self->{'_root_cleanup_methods'})) { |
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120
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0
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0
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$self->{'_root_cleanup_methods'} = []; |
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121
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} |
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122
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0
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0
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push(@{$self->{'_root_cleanup_methods'}},$method); |
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0
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0
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123
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} |
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124
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} |
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125
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126
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sub _unregister_for_cleanup { |
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127
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0
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0
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0
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my ($self,$method) = @_; |
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128
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0
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0
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my @methods = grep {$_ ne $method} $self->_cleanup_methods; |
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0
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0
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129
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0
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0
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$self->{'_root_cleanup_methods'} = \@methods; |
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130
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} |
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131
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132
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133
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sub _cleanup_methods { |
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134
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69
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69
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98
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my $self = shift; |
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135
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69
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50
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33
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656
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return unless ref $self && $self->isa('HASH'); |
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136
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69
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50
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7334
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my $methods = $self->{'_root_cleanup_methods'} or return; |
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137
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0
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0
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@$methods; |
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138
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139
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} |
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140
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141
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=head2 throw |
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142
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143
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Title : throw |
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144
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Usage : $obj->throw("throwing exception message") |
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145
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Function: Throws an exception, which, if not caught with an eval brace |
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146
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will provide a nice stack trace to STDERR with the message |
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147
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Returns : nothing |
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148
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Args : A string giving a descriptive error message |
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149
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150
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151
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=cut |
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152
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153
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sub throw{ |
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154
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1
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1
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1
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466
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my ($self,$string) = @_; |
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155
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156
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1
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4
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my $std = $self->_stack_trace_dump(); |
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157
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158
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1
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10
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my $out = "\n-------------------- EXCEPTION --------------------\n". |
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159
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"MSG: ".$string."\n".$std."-------------------------------------------\n"; |
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160
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1
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8
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die $out; |
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161
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162
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} |
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163
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164
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=head2 stack_trace |
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165
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166
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Title : stack_trace |
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167
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Usage : @stack_array_ref= $self->stack_trace |
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168
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Function: gives an array to a reference of arrays with stack trace info |
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169
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each coming from the caller(stack_number) call |
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170
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Returns : array containing a reference of arrays |
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171
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Args : none |
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172
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173
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174
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=cut |
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175
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176
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sub stack_trace{ |
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177
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3
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3
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1
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506
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my ($self) = @_; |
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178
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179
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3
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10
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my $i = 0; |
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180
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3
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4
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my @out; |
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181
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my $prev; |
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182
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3
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25
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while( my @call = caller($i++)) { |
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183
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# major annoyance that caller puts caller context as |
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184
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# function name. Hence some monkeying around... |
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185
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9
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17
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$prev->[3] = $call[3]; |
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186
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9
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11
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push(@out,$prev); |
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187
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9
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62
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$prev = \@call; |
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188
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} |
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189
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3
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6
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$prev->[3] = 'toplevel'; |
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190
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3
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5
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push(@out,$prev); |
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191
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3
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9
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return @out; |
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192
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} |
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193
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194
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=head2 _stack_trace_dump |
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195
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196
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Title : _stack_trace_dump |
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197
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Usage : |
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198
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Function: |
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199
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Example : |
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200
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Returns : |
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201
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Args : |
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202
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203
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204
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=cut |
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205
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206
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sub _stack_trace_dump{ |
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207
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2
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2
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3
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my ($self) = @_; |
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208
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209
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2
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14
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my @stack = $self->stack_trace(); |
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210
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211
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2
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5
|
shift @stack; |
|
212
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2
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|
15
|
shift @stack; |
|
213
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2
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5
|
shift @stack; |
|
214
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|
215
|
2
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|
7
|
my $out; |
|
216
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2
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4
|
my ($module,$function,$file,$position); |
|
217
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218
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219
|
2
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4
|
foreach my $stack ( @stack) { |
|
220
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4
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6
|
($module,$file,$position,$function) = @{$stack}; |
|
|
4
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13
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221
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4
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18
|
$out .= "STACK $function $file:$position\n"; |
|
222
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|
|
} |
|
223
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|
224
|
2
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|
14
|
return $out; |
|
225
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|
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} |
|
226
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|
227
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|
228
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|
|
=head2 deprecated |
|
229
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|
230
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|
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|
|
Title : deprecated |
|
231
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|
|
Usage : $obj->deprecated("Method X is deprecated"); |
|
232
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|
|
Function: Prints a message about deprecation |
|
233
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|
|
unless verbose is < 0 (which means be quiet) |
|
234
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|
|
Returns : none |
|
235
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|
|
Args : Message string to print to STDERR |
|
236
|
|
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|
237
|
|
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|
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|
|
=cut |
|
238
|
|
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|
|
239
|
|
|
|
|
|
|
sub deprecated{ |
|
240
|
1
|
|
|
1
|
1
|
1128
|
my ($self,$msg) = @_; |
|
241
|
1
|
50
|
|
|
|
4
|
if( $self->verbose >= 0 ) { |
|
242
|
1
|
|
|
|
|
5
|
print STDERR $msg, "\n", $self->_stack_trace_dump; |
|
243
|
|
|
|
|
|
|
} |
|
244
|
|
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|
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|
|
} |
|
245
|
|
|
|
|
|
|
|
|
246
|
|
|
|
|
|
|
=head2 warn |
|
247
|
|
|
|
|
|
|
|
|
248
|
|
|
|
|
|
|
Title : warn |
|
249
|
|
|
|
|
|
|
Usage : $object->warn("Warning message"); |
|
250
|
|
|
|
|
|
|
Function: Places a warning. What happens now is down to the |
|
251
|
|
|
|
|
|
|
verbosity of the object (value of $obj->verbose) |
|
252
|
|
|
|
|
|
|
verbosity 0 or not set => small warning |
|
253
|
|
|
|
|
|
|
verbosity -1 => no warning |
|
254
|
|
|
|
|
|
|
verbosity 1 => warning with stack trace |
|
255
|
|
|
|
|
|
|
verbosity 2 => converts warnings into throw |
|
256
|
|
|
|
|
|
|
Example : |
|
257
|
|
|
|
|
|
|
Returns : |
|
258
|
|
|
|
|
|
|
Args : |
|
259
|
|
|
|
|
|
|
|
|
260
|
|
|
|
|
|
|
=cut |
|
261
|
|
|
|
|
|
|
|
|
262
|
|
|
|
|
|
|
sub warn{ |
|
263
|
2
|
|
|
2
|
1
|
1035
|
my ($self,$string) = @_; |
|
264
|
|
|
|
|
|
|
|
|
265
|
2
|
|
|
|
|
4
|
my $verbose; |
|
266
|
2
|
50
|
|
|
|
50
|
if( $self->can('verbose') ) { |
|
267
|
2
|
|
|
|
|
6
|
$verbose = $self->verbose; |
|
268
|
|
|
|
|
|
|
} else { |
|
269
|
0
|
|
|
|
|
0
|
$verbose = 0; |
|
270
|
|
|
|
|
|
|
} |
|
271
|
|
|
|
|
|
|
|
|
272
|
2
|
50
|
|
|
|
11
|
if( $verbose == 2 ) { |
|
|
|
50
|
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
|
273
|
0
|
|
|
|
|
0
|
$self->throw($string); |
|
274
|
|
|
|
|
|
|
} elsif( $verbose == -1 ) { |
|
275
|
0
|
|
|
|
|
0
|
return; |
|
276
|
|
|
|
|
|
|
} elsif( $verbose == 1 ) { |
|
277
|
0
|
|
|
|
|
0
|
my $out = "\n-------------------- WARNING ---------------------\n". |
|
278
|
|
|
|
|
|
|
"MSG: ".$string."\n"; |
|
279
|
0
|
|
|
|
|
0
|
$out .= $self->_stack_trace_dump; |
|
280
|
|
|
|
|
|
|
|
|
281
|
0
|
|
|
|
|
0
|
print STDERR $out; |
|
282
|
0
|
|
|
|
|
0
|
return; |
|
283
|
|
|
|
|
|
|
} |
|
284
|
|
|
|
|
|
|
|
|
285
|
2
|
|
|
|
|
7
|
my $out = "\n-------------------- WARNING ---------------------\n". |
|
286
|
|
|
|
|
|
|
"MSG: ".$string."\n". |
|
287
|
|
|
|
|
|
|
"---------------------------------------------------\n"; |
|
288
|
2
|
|
|
|
|
6
|
print STDERR $out; |
|
289
|
|
|
|
|
|
|
} |
|
290
|
|
|
|
|
|
|
|
|
291
|
|
|
|
|
|
|
=head2 debug |
|
292
|
|
|
|
|
|
|
|
|
293
|
|
|
|
|
|
|
Title : debug |
|
294
|
|
|
|
|
|
|
Usage : $obj->debug("This is debugging output"); |
|
295
|
|
|
|
|
|
|
Function: Prints a debugging message when verbose is > 0 |
|
296
|
|
|
|
|
|
|
Returns : none |
|
297
|
|
|
|
|
|
|
Args : message string(s) to print to STDERR |
|
298
|
|
|
|
|
|
|
|
|
299
|
|
|
|
|
|
|
=cut |
|
300
|
|
|
|
|
|
|
|
|
301
|
|
|
|
|
|
|
sub debug{ |
|
302
|
0
|
|
|
0
|
1
|
0
|
my ($self,@msgs) = @_; |
|
303
|
|
|
|
|
|
|
|
|
304
|
0
|
0
|
|
|
|
0
|
if( $self->verbose > 0 ) { |
|
305
|
0
|
|
|
|
|
0
|
print STDERR join("", @msgs); |
|
306
|
|
|
|
|
|
|
} |
|
307
|
|
|
|
|
|
|
} |
|
308
|
|
|
|
|
|
|
|
|
309
|
|
|
|
|
|
|
sub DESTROY { |
|
310
|
69
|
|
|
69
|
|
20803
|
my $self = shift; |
|
311
|
69
|
50
|
|
|
|
342
|
my @cleanup_methods = $self->_cleanup_methods or return; |
|
312
|
0
|
|
|
|
|
|
for my $method (@cleanup_methods) { |
|
313
|
0
|
|
|
|
|
|
$method->($self); |
|
314
|
|
|
|
|
|
|
} |
|
315
|
|
|
|
|
|
|
} |
|
316
|
|
|
|
|
|
|
|
|
317
|
|
|
|
|
|
|
|
|
318
|
|
|
|
|
|
|
|
|
319
|
|
|
|
|
|
|
1; |
|
320
|
|
|
|
|
|
|
|