File: MAGE.pm

package info (click to toggle)
libbio-mage-perl 20030502.3-5
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 10,744 kB
  • sloc: perl: 47,077; makefile: 2
file content (1373 lines) | stat: -rw-r--r-- 39,693 bytes parent folder | download | duplicates (5)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
##############################
#
# Bio::MAGE
#
##############################
# C O P Y R I G H T   N O T I C E
#  Copyright (c) 2001-2006 by:
#    * The MicroArray Gene Expression Database Society (MGED)
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.



package Bio::MAGE;

use strict;

use base qw(Bio::MAGE::Base);

use Carp;
use Tie::IxHash;

use Bio::MAGE::NameValueType;
use Bio::MAGE::Extendable;
use Bio::MAGE::Identifiable;
use Bio::MAGE::Describable;

use base qw(Exporter);
use vars qw(%EXPORT_TAGS $__XML_PACKAGES $__CLASS2FULLCLASS $__XML_LISTS $VERSION);

$VERSION = 20030502.3;

 %EXPORT_TAGS = (ALL => ['']);

sub import {
  my ($pkg,@tags) = @_;
  foreach (@tags) {
    if ($_ =~ /ALL/) {
      import_all();
    }
  }
}

sub import_all {
  eval qq[
          require Bio::MAGE::HigherLevelAnalysis;
          require Bio::MAGE::BioEvent;
          require Bio::MAGE::BioMaterial;
          require Bio::MAGE::BioSequence;
          require Bio::MAGE::AuditAndSecurity;
          require Bio::MAGE::BioAssayData;
          require Bio::MAGE::BQS;
          require Bio::MAGE::Array;
          require Bio::MAGE::QuantitationType;
          require Bio::MAGE::Experiment;
          require Bio::MAGE::BioAssay;
          require Bio::MAGE::DesignElement;
          require Bio::MAGE::Protocol;
          require Bio::MAGE::Description;
          require Bio::MAGE::ArrayDesign;
          require Bio::MAGE::Measurement;
	 ];
  if ($@) {
    die __PACKAGE__ . "::import_all: load error: $@\n";
  }
}

sub initialize {
  my ($self) = shift;
  $self->identifiers({});
  $self->packages({});		# create packages on a per-need basis
  $self->registered_objects({});
  $self->tagname('MAGE-ML')
    unless defined $self->tagname();
  $self->add_objects($self->objects())
    if defined $self->objects();
  return 1;
}



=head1 NAME

Bio::MAGE - Container module for classes in the MAGE package: MAGE

=head1 SYNOPSIS

  use Bio::MAGE;

=head1 DESCRIPTION

This is a I<package> module that encapsulates a number of classes in
the Bio::MAGE hierarchy. These classes belong to the
MAGE package of the MAGE-OM object model.

=head1 CLASSES

The Bio::MAGE module contains the following
Bio::MAGE classes:

=over


=item * NameValueType


=item * Extendable


=item * Identifiable


=item * Describable


=back



=head1 CLASS METHODS

=over

=item @class_list = Bio::MAGE::classes();

This method returns a list of non-fully qualified class names
(i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.

=cut

sub classes {
  return ('NameValueType','Extendable','Identifiable','Describable');
}

BEGIN {
  $__XML_PACKAGES = [
          'AuditAndSecurity',
          'Description',
          'Measurement',
          'BQS',
          'BioEvent',
          'Protocol',
          'BioMaterial',
          'BioSequence',
          'DesignElement',
          'ArrayDesign',
          'Array',
          'BioAssay',
          'QuantitationType',
          'BioAssayData',
          'Experiment',
          'HigherLevelAnalysis'
        ]
;
  $__CLASS2FULLCLASS = {
          'ReporterGroup' => 'Bio::MAGE::ArrayDesign::ReporterGroup',
          'SeqFeatureLocation' => 'Bio::MAGE::BioSequence::SeqFeatureLocation',
          'BibliographicReference' => 'Bio::MAGE::BQS::BibliographicReference',
          'BioDataTuples' => 'Bio::MAGE::BioAssayData::BioDataTuples',
          'ArrayGroup' => 'Bio::MAGE::Array::ArrayGroup',
          'DistanceUnit' => 'Bio::MAGE::Measurement::DistanceUnit',
          'ProtocolApplication' => 'Bio::MAGE::Protocol::ProtocolApplication',
          'ManufactureLIMS' => 'Bio::MAGE::Array::ManufactureLIMS',
          'FeatureReporterMap' => 'Bio::MAGE::DesignElement::FeatureReporterMap',
          'Hybridization' => 'Bio::MAGE::BioAssay::Hybridization',
          'Security' => 'Bio::MAGE::AuditAndSecurity::Security',
          'PositionDelta' => 'Bio::MAGE::Array::PositionDelta',
          'DerivedBioAssayData' => 'Bio::MAGE::BioAssayData::DerivedBioAssayData',
          'CompositePosition' => 'Bio::MAGE::DesignElement::CompositePosition',
          'Hardware' => 'Bio::MAGE::Protocol::Hardware',
          'ParameterValue' => 'Bio::MAGE::Protocol::ParameterValue',
          'CompositeCompositeMap' => 'Bio::MAGE::DesignElement::CompositeCompositeMap',
          'Audit' => 'Bio::MAGE::AuditAndSecurity::Audit',
          'BioAssay' => 'Bio::MAGE::BioAssay::BioAssay',
          'HardwareApplication' => 'Bio::MAGE::Protocol::HardwareApplication',
          'Unit' => 'Bio::MAGE::Measurement::Unit',
          'BioSource' => 'Bio::MAGE::BioMaterial::BioSource',
          'CompositeSequence' => 'Bio::MAGE::DesignElement::CompositeSequence',
          'PValue' => 'Bio::MAGE::QuantitationType::PValue',
          'BioAssayDimension' => 'Bio::MAGE::BioAssayData::BioAssayDimension',
          'StandardQuantitationType' => 'Bio::MAGE::QuantitationType::StandardQuantitationType',
          'MismatchInformation' => 'Bio::MAGE::DesignElement::MismatchInformation',
          'DesignElementDimension' => 'Bio::MAGE::BioAssayData::DesignElementDimension',
          'Parameter' => 'Bio::MAGE::Protocol::Parameter',
          'Feature' => 'Bio::MAGE::DesignElement::Feature',
          'FeatureGroup' => 'Bio::MAGE::ArrayDesign::FeatureGroup',
          'QuantitationType' => 'Bio::MAGE::QuantitationType::QuantitationType',
          'ExternalReference' => 'Bio::MAGE::Description::ExternalReference',
          'SequencePosition' => 'Bio::MAGE::BioSequence::SequencePosition',
          'BioEvent' => 'Bio::MAGE::BioEvent::BioEvent',
          'MeasuredBioAssay' => 'Bio::MAGE::BioAssay::MeasuredBioAssay',
          'CompositeGroup' => 'Bio::MAGE::ArrayDesign::CompositeGroup',
          'BioAssayDatum' => 'Bio::MAGE::BioAssayData::BioAssayDatum',
          'BioAssayTreatment' => 'Bio::MAGE::BioAssay::BioAssayTreatment',
          'Extendable' => 'Bio::MAGE::Extendable',
          'SoftwareApplication' => 'Bio::MAGE::Protocol::SoftwareApplication',
          'Node' => 'Bio::MAGE::HigherLevelAnalysis::Node',
          'NodeValue' => 'Bio::MAGE::HigherLevelAnalysis::NodeValue',
          'DerivedBioAssay' => 'Bio::MAGE::BioAssay::DerivedBioAssay',
          'DatabaseEntry' => 'Bio::MAGE::Description::DatabaseEntry',
          'Compound' => 'Bio::MAGE::BioMaterial::Compound',
          'ArrayDesign' => 'Bio::MAGE::ArrayDesign::ArrayDesign',
          'BioMaterialMeasurement' => 'Bio::MAGE::BioMaterial::BioMaterialMeasurement',
          'ConcentrationUnit' => 'Bio::MAGE::Measurement::ConcentrationUnit',
          'Transformation' => 'Bio::MAGE::BioAssayData::Transformation',
          'BioMaterial' => 'Bio::MAGE::BioMaterial::BioMaterial',
          'Treatment' => 'Bio::MAGE::BioMaterial::Treatment',
          'BioAssayData' => 'Bio::MAGE::BioAssayData::BioAssayData',
          'BioAssayCreation' => 'Bio::MAGE::BioAssay::BioAssayCreation',
          'ReporterDimension' => 'Bio::MAGE::BioAssayData::ReporterDimension',
          'ConfidenceIndicator' => 'Bio::MAGE::QuantitationType::ConfidenceIndicator',
          'Failed' => 'Bio::MAGE::QuantitationType::Failed',
          'ArrayManufactureDeviation' => 'Bio::MAGE::Array::ArrayManufactureDeviation',
          'SpecializedQuantitationType' => 'Bio::MAGE::QuantitationType::SpecializedQuantitationType',
          'FeatureInformation' => 'Bio::MAGE::DesignElement::FeatureInformation',
          'ExperimentDesign' => 'Bio::MAGE::Experiment::ExperimentDesign',
          'PhysicalArrayDesign' => 'Bio::MAGE::ArrayDesign::PhysicalArrayDesign',
          'PhysicalBioAssay' => 'Bio::MAGE::BioAssay::PhysicalBioAssay',
          'Ratio' => 'Bio::MAGE::QuantitationType::Ratio',
          'FeatureLocation' => 'Bio::MAGE::DesignElement::FeatureLocation',
          'DesignElement' => 'Bio::MAGE::DesignElement::DesignElement',
          'QuantitationTypeDimension' => 'Bio::MAGE::BioAssayData::QuantitationTypeDimension',
          'DerivedSignal' => 'Bio::MAGE::QuantitationType::DerivedSignal',
          'Fiducial' => 'Bio::MAGE::Array::Fiducial',
          'BioSequence' => 'Bio::MAGE::BioSequence::BioSequence',
          'ReporterPosition' => 'Bio::MAGE::DesignElement::ReporterPosition',
          'QuantitationTypeMapping' => 'Bio::MAGE::BioAssayData::QuantitationTypeMapping',
          'MeasuredBioAssayData' => 'Bio::MAGE::BioAssayData::MeasuredBioAssayData',
          'Identifiable' => 'Bio::MAGE::Identifiable',
          'Position' => 'Bio::MAGE::DesignElement::Position',
          'Array' => 'Bio::MAGE::Array::Array',
          'ExperimentalFactor' => 'Bio::MAGE::Experiment::ExperimentalFactor',
          'BioAssayMap' => 'Bio::MAGE::BioAssayData::BioAssayMap',
          'SeqFeature' => 'Bio::MAGE::BioSequence::SeqFeature',
          'OntologyEntry' => 'Bio::MAGE::Description::OntologyEntry',
          'ImageAcquisition' => 'Bio::MAGE::BioAssay::ImageAcquisition',
          'FeatureExtraction' => 'Bio::MAGE::BioAssay::FeatureExtraction',
          'Error' => 'Bio::MAGE::QuantitationType::Error',
          'ArrayManufacture' => 'Bio::MAGE::Array::ArrayManufacture',
          'Map' => 'Bio::MAGE::BioEvent::Map',
          'Organization' => 'Bio::MAGE::AuditAndSecurity::Organization',
          'Database' => 'Bio::MAGE::Description::Database',
          'SecurityGroup' => 'Bio::MAGE::AuditAndSecurity::SecurityGroup',
          'CompositeSequenceDimension' => 'Bio::MAGE::BioAssayData::CompositeSequenceDimension',
          'Image' => 'Bio::MAGE::BioAssay::Image',
          'Zone' => 'Bio::MAGE::ArrayDesign::Zone',
          'NodeContents' => 'Bio::MAGE::HigherLevelAnalysis::NodeContents',
          'Reporter' => 'Bio::MAGE::DesignElement::Reporter',
          'FeatureDimension' => 'Bio::MAGE::BioAssayData::FeatureDimension',
          'Protocol' => 'Bio::MAGE::Protocol::Protocol',
          'Describable' => 'Bio::MAGE::Describable',
          'ExpectedValue' => 'Bio::MAGE::QuantitationType::ExpectedValue',
          'Contact' => 'Bio::MAGE::AuditAndSecurity::Contact',
          'CompoundMeasurement' => 'Bio::MAGE::BioMaterial::CompoundMeasurement',
          'MassUnit' => 'Bio::MAGE::Measurement::MassUnit',
          'FactorValue' => 'Bio::MAGE::Experiment::FactorValue',
          'ZoneDefect' => 'Bio::MAGE::Array::ZoneDefect',
          'VolumeUnit' => 'Bio::MAGE::Measurement::VolumeUnit',
          'DesignElementGroup' => 'Bio::MAGE::ArrayDesign::DesignElementGroup',
          'ReporterCompositeMap' => 'Bio::MAGE::DesignElement::ReporterCompositeMap',
          'LabeledExtract' => 'Bio::MAGE::BioMaterial::LabeledExtract',
          'TimeUnit' => 'Bio::MAGE::Measurement::TimeUnit',
          'FeatureDefect' => 'Bio::MAGE::Array::FeatureDefect',
          'QuantityUnit' => 'Bio::MAGE::Measurement::QuantityUnit',
          'BioAssayMapping' => 'Bio::MAGE::BioAssayData::BioAssayMapping',
          'ZoneGroup' => 'Bio::MAGE::ArrayDesign::ZoneGroup',
          'BioAssayDataCluster' => 'Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster',
          'DesignElementMapping' => 'Bio::MAGE::BioAssayData::DesignElementMapping',
          'Parameterizable' => 'Bio::MAGE::Protocol::Parameterizable',
          'BioDataValues' => 'Bio::MAGE::BioAssayData::BioDataValues',
          'DesignElementMap' => 'Bio::MAGE::BioAssayData::DesignElementMap',
          'QuantitationTypeMap' => 'Bio::MAGE::BioAssayData::QuantitationTypeMap',
          'Person' => 'Bio::MAGE::AuditAndSecurity::Person',
          'ZoneLayout' => 'Bio::MAGE::ArrayDesign::ZoneLayout',
          'ParameterizableApplication' => 'Bio::MAGE::Protocol::ParameterizableApplication',
          'Channel' => 'Bio::MAGE::BioAssay::Channel',
          'BioDataCube' => 'Bio::MAGE::BioAssayData::BioDataCube',
          'MeasuredSignal' => 'Bio::MAGE::QuantitationType::MeasuredSignal',
          'ManufactureLIMSBiomaterial' => 'Bio::MAGE::Array::ManufactureLIMSBiomaterial',
          'BioSample' => 'Bio::MAGE::BioMaterial::BioSample',
          'NameValueType' => 'Bio::MAGE::NameValueType',
          'TemperatureUnit' => 'Bio::MAGE::Measurement::TemperatureUnit',
          'Experiment' => 'Bio::MAGE::Experiment::Experiment',
          'Software' => 'Bio::MAGE::Protocol::Software',
          'PresentAbsent' => 'Bio::MAGE::QuantitationType::PresentAbsent',
          'Measurement' => 'Bio::MAGE::Measurement::Measurement',
          'Description' => 'Bio::MAGE::Description::Description'
        }
;
}

=item @list_names = Bio::MAGE::xml_packages();

This method returns an ordered list of the MAGE-ML packages that exist
in the top level MAGE-ML element.

=cut

sub xml_packages {
  return @{$__XML_PACKAGES};
}

=item $hash_ref = Bio::MAGE::class2fullclass();

This method returns a hash table that maps the fully qualified class
name of a class given the abbreviated name for the complete
Bio::MAGE class hierarchy.

=cut

sub class2fullclass {
  return %{$__CLASS2FULLCLASS};
}




=item $obj = class->new(%parameters)

The C<new()> method is the class constructor.

B<Parameters>: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their
initial values set by the constructor.

B<Return value>: It returns a reference to an object of the class.

B<Side effects>: It invokes the C<initialize()> method if it is defined
by the class.

=cut

#
# code for new() inherited from Base.pm
#

=item @names = class->get_slot_names()

The C<get_slot_names()> method is used to retrieve the name of all
slots defined in a given class.

B<NOTE>: the list of names does not include attribute or association
names.

B<Return value>: A list of the names of all slots defined for this class.

B<Side effects>: none

=cut

#
# code for get_slot_names() inherited from Base.pm
#

=item @name_list = get_attribute_names()

returns the list of attribute data members for this class.

=cut

#
# code for get_attribute_names() inherited from Base.pm
#

=item @name_list = get_association_names()

returns the list of association data members for this class.

=cut

#
# code for get_association_names() inherited from Base.pm
#

=item @class_list = get_superclasses()

returns the list of superclasses for this class.

=cut

#
# code for get_superclasses() inherited from Base.pm
#

=item @class_list = get_subclasses()

returns the list of subclasses for this class.

=cut

#
# code for get_subclasses() inherited from Base.pm
#

=item $name = class_name()

Returns the full class name for this class.

=cut

#
# code for class_name() inherited from Base.pm
#

=item $package_name = package_name()

Returns the base package name (i.e. no 'namespace::') of the package
that contains this class.

=cut

#
# code for package_name() inherited from Base.pm
#

=item %assns = associations()

returns the association meta-information in a hash where the keys are
the association names and the values are C<Association> objects that
provide the meta-information for the association.

=cut

#
# code for associations() inherited from Base.pm
#



=back

=head1 INSTANCE METHODS

=over

=cut

=item $obj_copy = $obj->new()

When invoked with an existing object reference and not a class name,
the C<new()> method acts as a copy constructor - with the new object's
initial values set to be those of the existing object.

B<Parameters>: No input parameters  are used in the copy  constructor,
the initial values are taken directly from the object to be copied.

B<Return value>: It returns a reference to an object of the class.

B<Side effects>: It invokes the C<initialize()> method if it is defined
by the class.

=cut

#
# code for new() inherited from Base.pm
#

=item $obj->set_slots(%parameters)

=item $obj->set_slots(\@name_list, \@value_list)

The C<set_slots()> method is used to set a number of slots at the same
time. It has two different invocation methods. The first takes a named
parameter list, and the second takes two array references.

B<Return value>: none

B<Side effects>: will call C<croak()> if a slot_name is used that the class
does not define.

=cut

#
# code for set_slots() inherited from Base.pm
#

=item @obj_list = $obj->get_slots(@name_list)

The C<get_slots()> method is used to get the values of a number of
slots at the same time.

B<Return value>: a list of instance objects

B<Side effects>: none

=cut

#
# code for get_slots() inherited from Base.pm
#

=item $val = $obj->set_slot($name,$val)

The C<set_slot()> method sets the slot C<$name> to the value C<$val>

B<Return value>: the new value of the slot, i.e. C<$val>

B<Side effects>: none

=cut

#
# code for set_slot() inherited from Base.pm
#

=item $val = $obj->get_slot($name)

The C<get_slot()> method is used to get the values of a number of
slots at the same time.

B<Return value>: a single slot value, or undef if the slot has not been
initialized.

B<Side effects>: none

=cut

#
# code for get_slot() inherited from Base.pm
#



=item $val = $mage->objects()

=item $inval = $mage->objects($inval)

This is the unified setter/getter method for the objects slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the objects
slot

Side effects: none

Exceptions: none

=cut


sub objects {
  my $self = shift;
  if (@_) {
    $self->{__OBJECTS} = shift;
  }
  return $self->{__OBJECTS};
}





=item $val = $mage->tagname()

=item $inval = $mage->tagname($inval)

This is the unified setter/getter method for the tagname slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the tagname
slot

Side effects: none

Exceptions: none

=cut


sub tagname {
  my $self = shift;
  if (@_) {
    $self->{__TAGNAME} = shift;
  }
  return $self->{__TAGNAME};
}





=item $val = $mage->identifier()

=item $inval = $mage->identifier($inval)

This is the unified setter/getter method for the identifier slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the identifier
slot

Side effects: none

Exceptions: none

=cut


sub identifier {
  my $self = shift;
  if (@_) {
    $self->{__IDENTIFIER} = shift;
  }
  return $self->{__IDENTIFIER};
}





=item $val = $mage->registered_objects()

=item $inval = $mage->registered_objects($inval)

This is the unified setter/getter method for the registered_objects slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the registered_objects
slot

Side effects: none

Exceptions: none

=cut


sub registered_objects {
  my $self = shift;
  if (@_) {
    $self->{__REGISTERED_OBJECTS} = shift;
  }
  return $self->{__REGISTERED_OBJECTS};
}





=item $val = $mage->identifiers()

=item $inval = $mage->identifiers($inval)

This is the unified setter/getter method for the identifiers slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the identifiers
slot

Side effects: none

Exceptions: none

=cut


sub identifiers {
  my $self = shift;
  if (@_) {
    $self->{__IDENTIFIERS} = shift;
  }
  return $self->{__IDENTIFIERS};
}





=item $val = $mage->packages()

=item $inval = $mage->packages($inval)

This is the unified setter/getter method for the packages slot.

If C<$inval> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.

Input parameters: the optional C<$inval> will invoke the setter method.

Return value: for both setter and getter the current value of the packages
slot

Side effects: none

Exceptions: none

=cut


sub packages {
  my $self = shift;
  if (@_) {
    $self->{__PACKAGES} = shift;
  }
  return $self->{__PACKAGES};
}






=item $mage->add_objects(@list)

The objects in C<@list> are added to the MAGE
object. This method will recursively descend that association hierarcy
of each object and place all Identifiable objects in their appropriate
lists for writing as MAGE-ML.

=cut

sub add_objects {
  my ($self,$list_ref) = @_;
  croak __PACKAGE__ . "::add_objects: Expected array reference but got $list_ref"
    unless UNIVERSAL::isa($list_ref,'ARRAY');
  foreach my $object (@{$list_ref}) {
    # we've been asked to register the objects, so we do it
    $self->register($object,1);
  }
}


=item $pkg_obj = $mage->getHigherLevelAnalysis_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::HigherLevelAnalysis> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getHigherLevelAnalysis_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'HigherLevelAnalysis'}) {
    eval "require Bio::MAGE::HigherLevelAnalysis";
    die "Couldn't require Bio::MAGE::HigherLevelAnalysis"
      if $@;
    $self->{__PACKAGES}{'HigherLevelAnalysis'} = Bio::MAGE::HigherLevelAnalysis->new();
  }
  return $self->{__PACKAGES}{'HigherLevelAnalysis'};
}


=item $pkg_obj = $mage->getBioEvent_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BioEvent> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBioEvent_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioEvent'}) {
    eval "require Bio::MAGE::BioEvent";
    die "Couldn't require Bio::MAGE::BioEvent"
      if $@;
    $self->{__PACKAGES}{'BioEvent'} = Bio::MAGE::BioEvent->new();
  }
  return $self->{__PACKAGES}{'BioEvent'};
}


=item $pkg_obj = $mage->getBioMaterial_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BioMaterial> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBioMaterial_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioMaterial'}) {
    eval "require Bio::MAGE::BioMaterial";
    die "Couldn't require Bio::MAGE::BioMaterial"
      if $@;
    $self->{__PACKAGES}{'BioMaterial'} = Bio::MAGE::BioMaterial->new();
  }
  return $self->{__PACKAGES}{'BioMaterial'};
}


=item $pkg_obj = $mage->getBioSequence_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BioSequence> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBioSequence_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioSequence'}) {
    eval "require Bio::MAGE::BioSequence";
    die "Couldn't require Bio::MAGE::BioSequence"
      if $@;
    $self->{__PACKAGES}{'BioSequence'} = Bio::MAGE::BioSequence->new();
  }
  return $self->{__PACKAGES}{'BioSequence'};
}


=item $pkg_obj = $mage->getAuditAndSecurity_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::AuditAndSecurity> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getAuditAndSecurity_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'AuditAndSecurity'}) {
    eval "require Bio::MAGE::AuditAndSecurity";
    die "Couldn't require Bio::MAGE::AuditAndSecurity"
      if $@;
    $self->{__PACKAGES}{'AuditAndSecurity'} = Bio::MAGE::AuditAndSecurity->new();
  }
  return $self->{__PACKAGES}{'AuditAndSecurity'};
}


=item $pkg_obj = $mage->getBioAssayData_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BioAssayData> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBioAssayData_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioAssayData'}) {
    eval "require Bio::MAGE::BioAssayData";
    die "Couldn't require Bio::MAGE::BioAssayData"
      if $@;
    $self->{__PACKAGES}{'BioAssayData'} = Bio::MAGE::BioAssayData->new();
  }
  return $self->{__PACKAGES}{'BioAssayData'};
}


=item $pkg_obj = $mage->getBQS_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BQS> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBQS_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BQS'}) {
    eval "require Bio::MAGE::BQS";
    die "Couldn't require Bio::MAGE::BQS"
      if $@;
    $self->{__PACKAGES}{'BQS'} = Bio::MAGE::BQS->new();
  }
  return $self->{__PACKAGES}{'BQS'};
}


=item $pkg_obj = $mage->getArray_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::Array> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getArray_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Array'}) {
    eval "require Bio::MAGE::Array";
    die "Couldn't require Bio::MAGE::Array"
      if $@;
    $self->{__PACKAGES}{'Array'} = Bio::MAGE::Array->new();
  }
  return $self->{__PACKAGES}{'Array'};
}


=item $pkg_obj = $mage->getQuantitationType_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::QuantitationType> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getQuantitationType_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'QuantitationType'}) {
    eval "require Bio::MAGE::QuantitationType";
    die "Couldn't require Bio::MAGE::QuantitationType"
      if $@;
    $self->{__PACKAGES}{'QuantitationType'} = Bio::MAGE::QuantitationType->new();
  }
  return $self->{__PACKAGES}{'QuantitationType'};
}


=item $pkg_obj = $mage->getExperiment_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::Experiment> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getExperiment_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Experiment'}) {
    eval "require Bio::MAGE::Experiment";
    die "Couldn't require Bio::MAGE::Experiment"
      if $@;
    $self->{__PACKAGES}{'Experiment'} = Bio::MAGE::Experiment->new();
  }
  return $self->{__PACKAGES}{'Experiment'};
}


=item $pkg_obj = $mage->getBioAssay_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::BioAssay> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getBioAssay_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'BioAssay'}) {
    eval "require Bio::MAGE::BioAssay";
    die "Couldn't require Bio::MAGE::BioAssay"
      if $@;
    $self->{__PACKAGES}{'BioAssay'} = Bio::MAGE::BioAssay->new();
  }
  return $self->{__PACKAGES}{'BioAssay'};
}


=item $pkg_obj = $mage->getDesignElement_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::DesignElement> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getDesignElement_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'DesignElement'}) {
    eval "require Bio::MAGE::DesignElement";
    die "Couldn't require Bio::MAGE::DesignElement"
      if $@;
    $self->{__PACKAGES}{'DesignElement'} = Bio::MAGE::DesignElement->new();
  }
  return $self->{__PACKAGES}{'DesignElement'};
}


=item $pkg_obj = $mage->getProtocol_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::Protocol> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getProtocol_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Protocol'}) {
    eval "require Bio::MAGE::Protocol";
    die "Couldn't require Bio::MAGE::Protocol"
      if $@;
    $self->{__PACKAGES}{'Protocol'} = Bio::MAGE::Protocol->new();
  }
  return $self->{__PACKAGES}{'Protocol'};
}


=item $pkg_obj = $mage->getDescription_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::Description> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getDescription_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Description'}) {
    eval "require Bio::MAGE::Description";
    die "Couldn't require Bio::MAGE::Description"
      if $@;
    $self->{__PACKAGES}{'Description'} = Bio::MAGE::Description->new();
  }
  return $self->{__PACKAGES}{'Description'};
}


=item $pkg_obj = $mage->getArrayDesign_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::ArrayDesign> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getArrayDesign_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'ArrayDesign'}) {
    eval "require Bio::MAGE::ArrayDesign";
    die "Couldn't require Bio::MAGE::ArrayDesign"
      if $@;
    $self->{__PACKAGES}{'ArrayDesign'} = Bio::MAGE::ArrayDesign->new();
  }
  return $self->{__PACKAGES}{'ArrayDesign'};
}


=item $pkg_obj = $mage->getMeasurement_package()

This method manages the handling of the singleton class object for the
C<Bio::MAGE::Measurement> class. When called it will return
the object, creating one if it has not already been created.

This is useful when retrieving data from parsed MAGE-ML file.

=cut

sub getMeasurement_package {
  my $self = shift;
  if (not exists $self->{__PACKAGES}{'Measurement'}) {
    eval "require Bio::MAGE::Measurement";
    die "Couldn't require Bio::MAGE::Measurement"
      if $@;
    $self->{__PACKAGES}{'Measurement'} = Bio::MAGE::Measurement->new();
  }
  return $self->{__PACKAGES}{'Measurement'};
}


=item $mage->obj2xml($writer)

Write out this object, and all sub-objects, as XML using the supplied
$writer to actually do the XML formatting.

Input parameters: $writer must be an XML writer, e.g. an instance of
Bio::MAGE::XML::Writer. It must have methods: write_start_tag() and
write_end_tag().

Return value: none

Side effects: all writing is delegated to the $writer - it's
write_start_tag() and write_end_tag() methods are invoked with the
appropriate data, and all package sub-objects of the C<Bio::MAGE> instance will have their obj2xml() methods
invoked in turn. By allowing the $writer to do the actual formatting
of the output XML, it enables the user to precisely control the
format.

Exceptions: will call C<croak()> if no identifier has been set for the
C<Bio::MAGE> instance.

=cut

sub obj2xml {
  my ($self,$writer) = @_;

  # require and identifier for the top-level XML element
  my $identifier = $self->identifier();
  croak __PACKAGE__ . '::obj2xml: Identifier not specified for topmost level object'
    unless defined $identifier;
  my @attrs = (identifier=>$identifier);

  my $empty = 0;
  my $tag = $self->tagname();
  $writer->write_start_tag($tag,$empty,@attrs);

  my %packages = %{$self->packages()};
  foreach my $package ($self->xml_packages()) {
    next unless exists $packages{$package};
    my $pkg_obj = $packages{$package};
    $pkg_obj->obj2xml($writer);
  }

  # and we're done
  $writer->write_end_tag($tag);
}

=item $mage->register($obj)

Store an object for later writing as XML.

Input parameters: object to be added to the list of registered objects.

Return value: none

Side effects: if $obj needs to be stored by this class, a reference
will be stored in the correct XML list for this class.

Exceptions: die() will be called if the object does not have it's
identifier set, or if the object has incorrectly set an association of
list cardinality to a single object.

=cut

sub register {
  my ($self,$obj,$register) = @_;

  # to avoid circular references keep track of objects that
  # we have already or are in the process of registering
  #

  my $registered = $self->registered_objects();
  return if exists $registered->{$obj};
  $registered->{$obj}++;

  # objects only register themselves if they are Identifiable
  # and we have been told to register them
  my $known_identifiers = $self->identifiers();
  if ($register and $obj->isa('Bio::MAGE::Identifiable')) {
    my $id = $obj->getIdentifier();
    die __PACKAGE__ . "::register: object must have identifier: $obj"
      unless $id;
    unless (exists $known_identifiers->{$id}) {
      my $packages = $self->packages();
      my $package_name = $obj->package_name();
      my $pkg_obj = $packages->{$package_name};
      unless (defined $pkg_obj) {
	# we only create the package objects if we need them.
	# register is the first time they will be needed
	my $class = "Bio::MAGE::$package_name";
	$pkg_obj = $class->new();
	$packages->{$package_name} = $pkg_obj;
      }
      $pkg_obj->register($obj);
      $known_identifiers->{$id}++;
    }
  }

  # regardless, they must enable their sub objects to register themselves
  my %assns_hash = $obj->associations();
  foreach my $association ($obj->get_association_names()) {
    my $association_obj;
    {
      no strict 'refs';
      my $assoc_name = 'get' . ucfirst($association);
      $association_obj = $obj->$assoc_name();
    }
    next unless defined $association_obj;

    # we need to know what kind of an association this is if it is an
    # aggregate association we don't want to register it whether it is
    # Identifiable or not, but we still want to register it's
    # sub-objects so we need to alert register()
    #
    # to decide if the association is aggregate, we look at
    # the 'self' end of the association
    my $register = $assns_hash{$association}->self->is_ref();

    # register a list of sub objects or a single one
    if ($assns_hash{$association}->other->cardinality() eq "0..N" or
	$assns_hash{$association}->other->cardinality() eq "1..N") {
      if (UNIVERSAL::isa($association_obj, 'ARRAY')) {
	foreach my $element (@$association_obj) {
	  $self->register($element,$register)
	    if defined $element;
	}
      } else {
	die __PACKAGE__ . "::register: expected array ref: $obj, association: $association, got $association_obj\n";
      }
    } else {
      $self->register($association_obj,$register);
    }
  }
}




=back

=head1 SLOTS, ATTRIBUTES, AND ASSOCIATIONS

In the Perl implementation of MAGE-OM classes, there are
three types of class data members: C<slots>, C<attributes>, and
C<associations>.

=head2 SLOTS

This API uses the term C<slot> to indicate a data member of the class
that was not present in the UML model and is used for mainly internal
purposes - use only if you understand the inner workings of the
API. Most often slots are used by generic methods such as those in the
XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

=over

=item $var = $obj->slot_name();

Retrieves the current value of the slot.

=item $new_var = $obj->slot_name($new_var);

Store $new_var in the slot - the return value is also $new_var.

=item @names = $obj->get_slot_names()

Returns the list of all slots in the class.

=back

B<DATA CHECKING>: No data type checking is made for these methods.

=head2 ATTRIBUTES AND ASSOCIATIONS

The terms C<attribute> and C<association> indicate data members of the
class that were specified directly from the UML model.

In the Perl implementation of MAGE-OM classes,
association and attribute accessors are implemented using three
separate methods:

=over

=item get*

Retrieves the current value.

B<NOTE>: For associations, if the association has list cardinality, an
array reference is returned.

B<DATA CHECKING>: Ensure that no argument is provided.

=item set*

Sets the current value, B<replacing> any existing value.

B<NOTE>: For associations, if the association has list cardinality,
the argument must be an array reference. Because of this, you probably
should be using the add* methods.

B<DATA CHECKING>: For attributes, ensure that a single value is
provided as the argument. For associations, if the association has
list cardinality, ensure that the argument is a reference to an array
of instances of the correct MAGE-OM class, otherwise
ensure that there is a single argument of the correct MAGE-OM class.

=item add*

B<NOTE>: Only present in associations with list cardinality. 

Appends a list of objects to any values that may already be stored
in the association.

B<DATA CHECKING>: Ensure that all arguments are of the correct MAGE-OM class.

=back

=head2 GENERIC METHODS

The unified base class of all MAGE-OM classes, C<Bio::MAGE::Base>, provides a set of generic methods that
will operate on slots, attributes, and associations:

=over

=item $val = $obj->get_slot($name)

=item \@list_ref = $obj->get_slots(@name_list);

=item $val = $obj->set_slot($name,$val)

=item $obj->set_slots(%parameters)

=item $obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these
methods.

=back

=cut


=head1 BUGS

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

=head1 AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org)

=head1 SEE ALSO

perl(1).

=cut

# all perl modules must be true...
1;