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| 1 |  |  |  |  |  |  | package Class::AutoClass::Root; | 
| 2 | 13 |  |  | 13 |  | 22152 | use strict; | 
|  | 13 |  |  |  |  | 25 |  | 
|  | 13 |  |  |  |  | 723 |  | 
| 3 |  |  |  |  |  |  |  | 
| 4 |  |  |  |  |  |  | =head1 NAME | 
| 5 |  |  |  |  |  |  |  | 
| 6 |  |  |  |  |  |  | Class::AutoClass::Root | 
| 7 |  |  |  |  |  |  |  | 
| 8 |  |  |  |  |  |  | =head1 SYNOPSIS | 
| 9 |  |  |  |  |  |  | # Here's how to throw and catch an exception using the eval-based syntax. | 
| 10 |  |  |  |  |  |  |  | 
| 11 |  |  |  |  |  |  | $obj->throw("This is an exception"); | 
| 12 |  |  |  |  |  |  |  | 
| 13 |  |  |  |  |  |  | eval { | 
| 14 |  |  |  |  |  |  | $obj->throw("This is catching an exception"); | 
| 15 |  |  |  |  |  |  | }; | 
| 16 |  |  |  |  |  |  |  | 
| 17 |  |  |  |  |  |  | if( $@ ) { | 
| 18 |  |  |  |  |  |  | print "Caught exception"; | 
| 19 |  |  |  |  |  |  | } else { | 
| 20 |  |  |  |  |  |  | print "no exception"; | 
| 21 |  |  |  |  |  |  | } | 
| 22 |  |  |  |  |  |  |  | 
| 23 |  |  |  |  |  |  | =head1 DESCRIPTION | 
| 24 |  |  |  |  |  |  | This class provides some basic functionality for Class::* classes. | 
| 25 |  |  |  |  |  |  |  | 
| 26 |  |  |  |  |  |  | This package is borrowed from bioperl project (http://bioperl.org/). Because of the | 
| 27 |  |  |  |  |  |  | formidable size of the bioperl library, Root.pm is included here with modifications. | 
| 28 |  |  |  |  |  |  | These modifications were to pare its functioanlity down for its simple job here | 
| 29 |  |  |  |  |  |  | (removing routines that are out of context and removing references to bioperl to avoid confusion). | 
| 30 |  |  |  |  |  |  |  | 
| 31 |  |  |  |  |  |  | Functions originally from Steve Chervitz of bioperl. Refactored by Ewan | 
| 32 |  |  |  |  |  |  | Birney of bioperl. Re-refactored by Lincoln Stein of bioperl. | 
| 33 |  |  |  |  |  |  |  | 
| 34 |  |  |  |  |  |  | =head2 Throwing Exceptions | 
| 35 |  |  |  |  |  |  |  | 
| 36 |  |  |  |  |  |  | One of the functionalities that Class::AutoClass::Root provides is the | 
| 37 |  |  |  |  |  |  | ability to throw() exceptions with pretty stack traces. | 
| 38 |  |  |  |  |  |  |  | 
| 39 |  |  |  |  |  |  | =head1 CONTACT | 
| 40 |  |  |  |  |  |  |  | 
| 41 |  |  |  |  |  |  | contact: Chris Cavnor -> ccavnor@systemsbiology.org | 
| 42 |  |  |  |  |  |  |  | 
| 43 |  |  |  |  |  |  | =head1 APPENDIX | 
| 44 |  |  |  |  |  |  |  | 
| 45 |  |  |  |  |  |  | The rest of the documentation details each of the object | 
| 46 |  |  |  |  |  |  | methods. Internal methods are usually preceded with a _ | 
| 47 |  |  |  |  |  |  |  | 
| 48 |  |  |  |  |  |  | =cut | 
| 49 |  |  |  |  |  |  |  | 
| 50 |  |  |  |  |  |  | #' | 
| 51 |  |  |  |  |  |  |  | 
| 52 | 13 |  |  | 13 |  | 74 | use vars qw(@ISA $DEBUG $ID $Revision $VERSION $VERBOSITY $ERRORLOADED @EXPORT); | 
|  | 13 |  |  |  |  | 26 |  | 
|  | 13 |  |  |  |  | 1518 |  | 
| 53 | 13 |  |  | 13 |  | 68 | use strict; | 
|  | 13 |  |  |  |  | 22 |  | 
|  | 13 |  |  |  |  | 852 |  | 
| 54 |  |  |  |  |  |  |  | 
| 55 |  |  |  |  |  |  | BEGIN { | 
| 56 |  |  |  |  |  |  |  | 
| 57 | 13 |  |  | 13 |  | 30 | $ID        = 'Class::AutoClass::Root'; | 
| 58 | 13 |  |  |  |  | 41 | $VERSION   = 1.0; | 
| 59 | 13 |  |  |  |  | 28 | $Revision  = ''; | 
| 60 | 13 |  |  |  |  | 135 | $DEBUG     = 0; | 
| 61 | 13 |  |  |  |  | 22 | $VERBOSITY = 0; | 
| 62 | 13 |  |  |  |  | 19195 | $ERRORLOADED = 0; | 
| 63 |  |  |  |  |  |  | } | 
| 64 |  |  |  |  |  |  |  | 
| 65 |  |  |  |  |  |  |  | 
| 66 |  |  |  |  |  |  |  | 
| 67 |  |  |  |  |  |  | =head2 new | 
| 68 |  |  |  |  |  |  |  | 
| 69 |  |  |  |  |  |  | Purpose   : generic instantiation function can be overridden if | 
| 70 |  |  |  |  |  |  | special needs of a module cannot be done in _initialize | 
| 71 |  |  |  |  |  |  |  | 
| 72 |  |  |  |  |  |  | =cut | 
| 73 |  |  |  |  |  |  |  | 
| 74 |  |  |  |  |  |  | sub new { | 
| 75 | 1 |  |  | 1 | 1 | 13 | my $class = shift; | 
| 76 | 1 |  |  |  |  | 3 | my $self = {}; | 
| 77 | 1 |  | 33 |  |  | 8 | bless $self, ref($class) || $class; | 
| 78 |  |  |  |  |  |  |  | 
| 79 | 1 | 50 |  |  |  | 5 | if(@_ > 1) { | 
| 80 |  |  |  |  |  |  | # if the number of arguments is odd but at least 3, we'll give | 
| 81 |  |  |  |  |  |  | # it a try to find -verbose | 
| 82 | 0 | 0 |  |  |  | 0 | shift if @_ % 2; | 
| 83 | 0 |  |  |  |  | 0 | my %param = @_; | 
| 84 | 0 |  | 0 |  |  | 0 | $self->verbose($param{'-VERBOSE'} || $param{'-verbose'}); | 
| 85 |  |  |  |  |  |  | } | 
| 86 | 1 |  |  |  |  | 4 | return $self; | 
| 87 |  |  |  |  |  |  | } | 
| 88 |  |  |  |  |  |  |  | 
| 89 |  |  |  |  |  |  | =head2 verbose | 
| 90 |  |  |  |  |  |  |  | 
| 91 |  |  |  |  |  |  | Title   : verbose | 
| 92 |  |  |  |  |  |  | Usage   : $self->verbose(1) | 
| 93 |  |  |  |  |  |  | Function: Sets verbose level for how ->warn behaves | 
| 94 |  |  |  |  |  |  | -1 = no warning | 
| 95 |  |  |  |  |  |  | 0 = standard, small warning | 
| 96 |  |  |  |  |  |  | 1 = warning with stack trace | 
| 97 |  |  |  |  |  |  | 2 = warning becomes throw | 
| 98 |  |  |  |  |  |  | Returns : The current verbosity setting (integer between -1 to 2) | 
| 99 |  |  |  |  |  |  | Args    : -1,0,1 or 2 | 
| 100 |  |  |  |  |  |  |  | 
| 101 |  |  |  |  |  |  |  | 
| 102 |  |  |  |  |  |  | =cut | 
| 103 |  |  |  |  |  |  |  | 
| 104 |  |  |  |  |  |  | sub verbose { | 
| 105 | 3 |  |  | 3 | 1 | 6 | my ($self,$value) = @_; | 
| 106 |  |  |  |  |  |  | # allow one to set global verbosity flag | 
| 107 | 3 | 50 |  |  |  | 12 | return $DEBUG  if $DEBUG; | 
| 108 | 3 | 50 |  |  |  | 8 | return $VERBOSITY unless ref $self; | 
| 109 |  |  |  |  |  |  |  | 
| 110 | 3 | 100 | 66 |  |  | 22 | if (defined $value || ! defined $self->{'_root_verbose'}) { | 
| 111 | 1 |  | 50 |  |  | 7 | $self->{'_root_verbose'} = $value || 0; | 
| 112 |  |  |  |  |  |  | } | 
| 113 | 3 |  |  |  |  | 11 | return $self->{'_root_verbose'}; | 
| 114 |  |  |  |  |  |  | } | 
| 115 |  |  |  |  |  |  |  | 
| 116 |  |  |  |  |  |  | sub _register_for_cleanup { | 
| 117 | 0 |  |  | 0 |  | 0 | my ($self,$method) = @_; | 
| 118 | 0 | 0 |  |  |  | 0 | if($method) { | 
| 119 | 0 | 0 |  |  |  | 0 | if(! exists($self->{'_root_cleanup_methods'})) { | 
| 120 | 0 |  |  |  |  | 0 | $self->{'_root_cleanup_methods'} = []; | 
| 121 |  |  |  |  |  |  | } | 
| 122 | 0 |  |  |  |  | 0 | push(@{$self->{'_root_cleanup_methods'}},$method); | 
|  | 0 |  |  |  |  | 0 |  | 
| 123 |  |  |  |  |  |  | } | 
| 124 |  |  |  |  |  |  | } | 
| 125 |  |  |  |  |  |  |  | 
| 126 |  |  |  |  |  |  | sub _unregister_for_cleanup { | 
| 127 | 0 |  |  | 0 |  | 0 | my ($self,$method) = @_; | 
| 128 | 0 |  |  |  |  | 0 | my @methods = grep {$_ ne $method} $self->_cleanup_methods; | 
|  | 0 |  |  |  |  | 0 |  | 
| 129 | 0 |  |  |  |  | 0 | $self->{'_root_cleanup_methods'} = \@methods; | 
| 130 |  |  |  |  |  |  | } | 
| 131 |  |  |  |  |  |  |  | 
| 132 |  |  |  |  |  |  |  | 
| 133 |  |  |  |  |  |  | sub _cleanup_methods { | 
| 134 | 69 |  |  | 69 |  | 98 | my $self = shift; | 
| 135 | 69 | 50 | 33 |  |  | 656 | return unless ref $self && $self->isa('HASH'); | 
| 136 | 69 | 50 |  |  |  | 7334 | my $methods = $self->{'_root_cleanup_methods'} or return; | 
| 137 | 0 |  |  |  |  | 0 | @$methods; | 
| 138 |  |  |  |  |  |  |  | 
| 139 |  |  |  |  |  |  | } | 
| 140 |  |  |  |  |  |  |  | 
| 141 |  |  |  |  |  |  | =head2 throw | 
| 142 |  |  |  |  |  |  |  | 
| 143 |  |  |  |  |  |  | Title   : throw | 
| 144 |  |  |  |  |  |  | Usage   : $obj->throw("throwing exception message") | 
| 145 |  |  |  |  |  |  | Function: Throws an exception, which, if not caught with an eval brace | 
| 146 |  |  |  |  |  |  | will provide a nice stack trace to STDERR with the message | 
| 147 |  |  |  |  |  |  | Returns : nothing | 
| 148 |  |  |  |  |  |  | Args    : A string giving a descriptive error message | 
| 149 |  |  |  |  |  |  |  | 
| 150 |  |  |  |  |  |  |  | 
| 151 |  |  |  |  |  |  | =cut | 
| 152 |  |  |  |  |  |  |  | 
| 153 |  |  |  |  |  |  | sub throw{ | 
| 154 | 1 |  |  | 1 | 1 | 466 | my ($self,$string) = @_; | 
| 155 |  |  |  |  |  |  |  | 
| 156 | 1 |  |  |  |  | 4 | my $std = $self->_stack_trace_dump(); | 
| 157 |  |  |  |  |  |  |  | 
| 158 | 1 |  |  |  |  | 10 | my $out = "\n-------------------- EXCEPTION --------------------\n". | 
| 159 |  |  |  |  |  |  | "MSG: ".$string."\n".$std."-------------------------------------------\n"; | 
| 160 | 1 |  |  |  |  | 8 | die $out; | 
| 161 |  |  |  |  |  |  |  | 
| 162 |  |  |  |  |  |  | } | 
| 163 |  |  |  |  |  |  |  | 
| 164 |  |  |  |  |  |  | =head2 stack_trace | 
| 165 |  |  |  |  |  |  |  | 
| 166 |  |  |  |  |  |  | Title   : stack_trace | 
| 167 |  |  |  |  |  |  | Usage   : @stack_array_ref= $self->stack_trace | 
| 168 |  |  |  |  |  |  | Function: gives an array to a reference of arrays with stack trace info | 
| 169 |  |  |  |  |  |  | each coming from the caller(stack_number) call | 
| 170 |  |  |  |  |  |  | Returns : array containing a reference of arrays | 
| 171 |  |  |  |  |  |  | Args    : none | 
| 172 |  |  |  |  |  |  |  | 
| 173 |  |  |  |  |  |  |  | 
| 174 |  |  |  |  |  |  | =cut | 
| 175 |  |  |  |  |  |  |  | 
| 176 |  |  |  |  |  |  | sub stack_trace{ | 
| 177 | 3 |  |  | 3 | 1 | 506 | my ($self) = @_; | 
| 178 |  |  |  |  |  |  |  | 
| 179 | 3 |  |  |  |  | 10 | my $i = 0; | 
| 180 | 3 |  |  |  |  | 4 | my @out; | 
| 181 |  |  |  |  |  |  | my $prev; | 
| 182 | 3 |  |  |  |  | 25 | while( my @call = caller($i++)) { | 
| 183 |  |  |  |  |  |  | # major annoyance that caller puts caller context as | 
| 184 |  |  |  |  |  |  | # function name. Hence some monkeying around... | 
| 185 | 9 |  |  |  |  | 17 | $prev->[3] = $call[3]; | 
| 186 | 9 |  |  |  |  | 11 | push(@out,$prev); | 
| 187 | 9 |  |  |  |  | 62 | $prev = \@call; | 
| 188 |  |  |  |  |  |  | } | 
| 189 | 3 |  |  |  |  | 6 | $prev->[3] = 'toplevel'; | 
| 190 | 3 |  |  |  |  | 5 | push(@out,$prev); | 
| 191 | 3 |  |  |  |  | 9 | return @out; | 
| 192 |  |  |  |  |  |  | } | 
| 193 |  |  |  |  |  |  |  | 
| 194 |  |  |  |  |  |  | =head2 _stack_trace_dump | 
| 195 |  |  |  |  |  |  |  | 
| 196 |  |  |  |  |  |  | Title   : _stack_trace_dump | 
| 197 |  |  |  |  |  |  | Usage   : | 
| 198 |  |  |  |  |  |  | Function: | 
| 199 |  |  |  |  |  |  | Example : | 
| 200 |  |  |  |  |  |  | Returns : | 
| 201 |  |  |  |  |  |  | Args    : | 
| 202 |  |  |  |  |  |  |  | 
| 203 |  |  |  |  |  |  |  | 
| 204 |  |  |  |  |  |  | =cut | 
| 205 |  |  |  |  |  |  |  | 
| 206 |  |  |  |  |  |  | sub _stack_trace_dump{ | 
| 207 | 2 |  |  | 2 |  | 3 | my ($self) = @_; | 
| 208 |  |  |  |  |  |  |  | 
| 209 | 2 |  |  |  |  | 14 | my @stack = $self->stack_trace(); | 
| 210 |  |  |  |  |  |  |  | 
| 211 | 2 |  |  |  |  | 5 | shift @stack; | 
| 212 | 2 |  |  |  |  | 15 | shift @stack; | 
| 213 | 2 |  |  |  |  | 5 | shift @stack; | 
| 214 |  |  |  |  |  |  |  | 
| 215 | 2 |  |  |  |  | 7 | my $out; | 
| 216 | 2 |  |  |  |  | 4 | my ($module,$function,$file,$position); | 
| 217 |  |  |  |  |  |  |  | 
| 218 |  |  |  |  |  |  |  | 
| 219 | 2 |  |  |  |  | 4 | foreach my $stack ( @stack) { | 
| 220 | 4 |  |  |  |  | 6 | ($module,$file,$position,$function) = @{$stack}; | 
|  | 4 |  |  |  |  | 13 |  | 
| 221 | 4 |  |  |  |  | 18 | $out .= "STACK $function $file:$position\n"; | 
| 222 |  |  |  |  |  |  | } | 
| 223 |  |  |  |  |  |  |  | 
| 224 | 2 |  |  |  |  | 14 | return $out; | 
| 225 |  |  |  |  |  |  | } | 
| 226 |  |  |  |  |  |  |  | 
| 227 |  |  |  |  |  |  |  | 
| 228 |  |  |  |  |  |  | =head2 deprecated | 
| 229 |  |  |  |  |  |  |  | 
| 230 |  |  |  |  |  |  | Title   : deprecated | 
| 231 |  |  |  |  |  |  | Usage   : $obj->deprecated("Method X is deprecated"); | 
| 232 |  |  |  |  |  |  | Function: Prints a message about deprecation | 
| 233 |  |  |  |  |  |  | unless verbose is < 0 (which means be quiet) | 
| 234 |  |  |  |  |  |  | Returns : none | 
| 235 |  |  |  |  |  |  | Args    : Message string to print to STDERR | 
| 236 |  |  |  |  |  |  |  | 
| 237 |  |  |  |  |  |  | =cut | 
| 238 |  |  |  |  |  |  |  | 
| 239 |  |  |  |  |  |  | sub deprecated{ | 
| 240 | 1 |  |  | 1 | 1 | 1128 | my ($self,$msg) = @_; | 
| 241 | 1 | 50 |  |  |  | 4 | if( $self->verbose >= 0 ) { | 
| 242 | 1 |  |  |  |  | 5 | print STDERR $msg, "\n", $self->_stack_trace_dump; | 
| 243 |  |  |  |  |  |  | } | 
| 244 |  |  |  |  |  |  | } | 
| 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 |  |  |  |  |  |  |  |