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SSL is default for redmine connection

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commit 3394bb6c660a42b7626861dbfdd84076bce8e47d 1 parent 99c7dec
Jason Stajich hyphaltip authored

Showing 800 changed files with 301 additions and 301 deletions. Show diff stats Hide diff stats

  1. +2 2 BUGS
  2. +1 1  Bio/Align/AlignI.pm
  3. +1 1  Bio/Align/DNAStatistics.pm
  4. +1 1  Bio/Align/PairwiseStatistics.pm
  5. +1 1  Bio/Align/ProteinStatistics.pm
  6. +1 1  Bio/Align/StatisticsI.pm
  7. +1 1  Bio/Align/Utilities.pm
  8. +1 1  Bio/AlignIO.pm
  9. +1 1  Bio/AlignIO/Handler/GenericAlignHandler.pm
  10. +1 1  Bio/AlignIO/arp.pm
  11. +1 1  Bio/AlignIO/bl2seq.pm
  12. +1 1  Bio/AlignIO/clustalw.pm
  13. +1 1  Bio/AlignIO/emboss.pm
  14. +1 1  Bio/AlignIO/fasta.pm
  15. +1 1  Bio/AlignIO/largemultifasta.pm
  16. +1 1  Bio/AlignIO/maf.pm
  17. +1 1  Bio/AlignIO/mase.pm
  18. +1 1  Bio/AlignIO/mega.pm
  19. +1 1  Bio/AlignIO/meme.pm
  20. +1 1  Bio/AlignIO/metafasta.pm
  21. +1 1  Bio/AlignIO/msf.pm
  22. +1 1  Bio/AlignIO/nexml.pm
  23. +1 1  Bio/AlignIO/nexus.pm
  24. +1 1  Bio/AlignIO/pfam.pm
  25. +1 1  Bio/AlignIO/phylip.pm
  26. +1 1  Bio/AlignIO/po.pm
  27. +1 1  Bio/AlignIO/proda.pm
  28. +1 1  Bio/AlignIO/prodom.pm
  29. +1 1  Bio/AlignIO/psi.pm
  30. +1 1  Bio/AlignIO/selex.pm
  31. +1 1  Bio/AlignIO/stockholm.pm
  32. +1 1  Bio/AlignIO/xmfa.pm
  33. +1 1  Bio/AnalysisI.pm
  34. +1 1  Bio/AnalysisParserI.pm
  35. +1 1  Bio/AnalysisResultI.pm
  36. +1 1  Bio/AnnotatableI.pm
  37. +1 1  Bio/Annotation/AnnotationFactory.pm
  38. +1 1  Bio/Annotation/Collection.pm
  39. +1 1  Bio/Annotation/OntologyTerm.pm
  40. +1 1  Bio/Annotation/Relation.pm
  41. +1 1  Bio/Annotation/SimpleValue.pm
  42. +1 1  Bio/Annotation/StructuredValue.pm
  43. +1 1  Bio/Annotation/TagTree.pm
  44. +1 1  Bio/Annotation/TypeManager.pm
  45. +1 1  Bio/AnnotationCollectionI.pm
  46. +1 1  Bio/AnnotationI.pm
  47. +1 1  Bio/Assembly/Contig.pm
  48. +1 1  Bio/Assembly/ContigAnalysis.pm
  49. +1 1  Bio/Assembly/IO.pm
  50. +1 1  Bio/Assembly/IO/ace.pm
  51. +1 1  Bio/Assembly/IO/bowtie.pm
  52. +1 1  Bio/Assembly/IO/maq.pm
  53. +1 1  Bio/Assembly/IO/phrap.pm
  54. +1 1  Bio/Assembly/IO/sam.pm
  55. +1 1  Bio/Assembly/IO/tigr.pm
  56. +1 1  Bio/Assembly/Scaffold.pm
  57. +1 1  Bio/Assembly/ScaffoldI.pm
  58. +1 1  Bio/Assembly/Singlet.pm
  59. +1 1  Bio/Assembly/Tools/ContigSpectrum.pm
  60. +1 1  Bio/Biblio.pm
  61. +1 1  Bio/Biblio/Article.pm
  62. +1 1  Bio/Biblio/BiblioBase.pm
  63. +1 1  Bio/Biblio/Book.pm
  64. +1 1  Bio/Biblio/BookArticle.pm
  65. +1 1  Bio/Biblio/IO.pm
  66. +1 1  Bio/Biblio/IO/medline2ref.pm
  67. +1 1  Bio/Biblio/IO/medlinexml.pm
  68. +1 1  Bio/Biblio/IO/pubmed2ref.pm
  69. +1 1  Bio/Biblio/IO/pubmedxml.pm
  70. +1 1  Bio/Biblio/Journal.pm
  71. +1 1  Bio/Biblio/JournalArticle.pm
  72. +1 1  Bio/Biblio/MedlineArticle.pm
  73. +1 1  Bio/Biblio/MedlineBook.pm
  74. +1 1  Bio/Biblio/MedlineBookArticle.pm
  75. +1 1  Bio/Biblio/MedlineJournal.pm
  76. +1 1  Bio/Biblio/MedlineJournalArticle.pm
  77. +1 1  Bio/Biblio/Organisation.pm
  78. +1 1  Bio/Biblio/Patent.pm
  79. +1 1  Bio/Biblio/Person.pm
  80. +1 1  Bio/Biblio/Proceeding.pm
  81. +1 1  Bio/Biblio/Provider.pm
  82. +1 1  Bio/Biblio/PubmedArticle.pm
  83. +1 1  Bio/Biblio/PubmedBookArticle.pm
  84. +1 1  Bio/Biblio/PubmedJournalArticle.pm
  85. +1 1  Bio/Biblio/Ref.pm
  86. +1 1  Bio/Biblio/Service.pm
  87. +1 1  Bio/Biblio/TechReport.pm
  88. +1 1  Bio/Biblio/Thesis.pm
  89. +1 1  Bio/Biblio/WebResource.pm
  90. +1 1  Bio/Cluster/ClusterFactory.pm
  91. +1 1  Bio/Cluster/FamilyI.pm
  92. +1 1  Bio/Cluster/SequenceFamily.pm
  93. +1 1  Bio/Cluster/UniGene.pm
  94. +1 1  Bio/Cluster/UniGeneI.pm
  95. +1 1  Bio/ClusterI.pm
  96. +1 1  Bio/ClusterIO.pm
  97. +1 1  Bio/ClusterIO/dbsnp.pm
  98. +1 1  Bio/ClusterIO/unigene.pm
  99. +1 1  Bio/CodonUsage/IO.pm
  100. +1 1  Bio/CodonUsage/Table.pm
  101. +1 1  Bio/Coordinate/Chain.pm
  102. +1 1  Bio/Coordinate/Collection.pm
  103. +1 1  Bio/Coordinate/ExtrapolatingPair.pm
  104. +1 1  Bio/Coordinate/GeneMapper.pm
  105. +1 1  Bio/Coordinate/Graph.pm
  106. +1 1  Bio/Coordinate/MapperI.pm
  107. +1 1  Bio/Coordinate/Pair.pm
  108. +1 1  Bio/Coordinate/Result.pm
  109. +1 1  Bio/Coordinate/Result/Gap.pm
  110. +1 1  Bio/Coordinate/Result/Match.pm
  111. +1 1  Bio/Coordinate/ResultI.pm
  112. +1 1  Bio/Coordinate/Utils.pm
  113. +1 1  Bio/DB/Ace.pm
  114. +1 1  Bio/DB/Biblio/biofetch.pm
  115. +1 1  Bio/DB/Biblio/eutils.pm
  116. +1 1  Bio/DB/Biblio/soap.pm
  117. +1 1  Bio/DB/BiblioI.pm
  118. +1 1  Bio/DB/BioFetch.pm
  119. +1 1  Bio/DB/CUTG.pm
  120. +1 1  Bio/DB/DBFetch.pm
  121. +1 1  Bio/DB/EMBL.pm
  122. +1 1  Bio/DB/EUtilities.pm
  123. +1 1  Bio/DB/EntrezGene.pm
  124. +1 1  Bio/DB/Expression.pm
  125. +1 1  Bio/DB/Expression/geo.pm
  126. +1 1  Bio/DB/Failover.pm
  127. +1 1  Bio/DB/FileCache.pm
  128. +1 1  Bio/DB/Flat.pm
  129. +1 1  Bio/DB/Flat/BDB.pm
  130. +1 1  Bio/DB/Flat/BDB/embl.pm
  131. +1 1  Bio/DB/Flat/BDB/fasta.pm
  132. +1 1  Bio/DB/Flat/BDB/genbank.pm
  133. +1 1  Bio/DB/Flat/BDB/swiss.pm
  134. +1 1  Bio/DB/Flat/BinarySearch.pm
  135. +1 1  Bio/DB/GenBank.pm
  136. +1 1  Bio/DB/GenPept.pm
  137. +1 1  Bio/DB/GenericWebAgent.pm
  138. +1 1  Bio/DB/HIV.pm
  139. +1 1  Bio/DB/HIV/HIVAnnotProcessor.pm
  140. +1 1  Bio/DB/HIV/HIVQueryHelper.pm
  141. +1 1  Bio/DB/InMemoryCache.pm
  142. +1 1  Bio/DB/LocationI.pm
  143. +1 1  Bio/DB/MeSH.pm
  144. +1 1  Bio/DB/NCBIHelper.pm
  145. +1 1  Bio/DB/Query/GenBank.pm
  146. +1 1  Bio/DB/Query/HIVQuery.pm
  147. +1 1  Bio/DB/Query/WebQuery.pm
  148. +1 1  Bio/DB/QueryI.pm
  149. +1 1  Bio/DB/RandomAccessI.pm
  150. +1 1  Bio/DB/RefSeq.pm
  151. +1 1  Bio/DB/ReferenceI.pm
  152. +1 1  Bio/DB/Registry.pm
  153. +1 1  Bio/DB/SeqI.pm
  154. +1 1  Bio/DB/SeqVersion.pm
  155. +1 1  Bio/DB/SeqVersion/gi.pm
  156. +1 1  Bio/DB/SwissProt.pm
  157. +1 1  Bio/DB/TFBS.pm
  158. +1 1  Bio/DB/TFBS/transfac_pro.pm
  159. +1 1  Bio/DB/Taxonomy.pm
  160. +1 1  Bio/DB/Taxonomy/entrez.pm
  161. +1 1  Bio/DB/Taxonomy/flatfile.pm
  162. +1 1  Bio/DB/Taxonomy/list.pm
  163. +1 1  Bio/DB/Universal.pm
  164. +1 1  Bio/DB/UpdateableSeqI.pm
  165. +1 1  Bio/DB/WebDBSeqI.pm
  166. +1 1  Bio/DBLinkContainerI.pm
  167. +1 1  Bio/Das/FeatureTypeI.pm
  168. +1 1  Bio/Das/SegmentI.pm
  169. +1 1  Bio/DasI.pm
  170. +1 1  Bio/DescribableI.pm
  171. +1 1  Bio/Draw/Pictogram.pm
  172. +1 1  Bio/Event/EventGeneratorI.pm
  173. +1 1  Bio/Event/EventHandlerI.pm
  174. +1 1  Bio/Factory/AnalysisI.pm
  175. +1 1  Bio/Factory/ApplicationFactoryI.pm
  176. +1 1  Bio/Factory/DriverFactory.pm
  177. +1 1  Bio/Factory/FTLocationFactory.pm
  178. +1 1  Bio/Factory/LocationFactoryI.pm
  179. +1 1  Bio/Factory/MapFactoryI.pm
  180. +1 1  Bio/Factory/ObjectBuilderI.pm
  181. +1 1  Bio/Factory/ObjectFactory.pm
  182. +1 1  Bio/Factory/ObjectFactoryI.pm
  183. +1 1  Bio/Factory/SeqAnalysisParserFactory.pm
  184. +1 1  Bio/Factory/SeqAnalysisParserFactoryI.pm
  185. +1 1  Bio/Factory/SequenceFactoryI.pm
  186. +1 1  Bio/Factory/SequenceProcessorI.pm
  187. +1 1  Bio/Factory/SequenceStreamI.pm
  188. +1 1  Bio/Factory/TreeFactoryI.pm
  189. +1 1  Bio/FeatureHolderI.pm
  190. +1 1  Bio/FeatureIO.pm
  191. +1 1  Bio/FeatureIO/bed.pm
  192. +1 1  Bio/FeatureIO/gff.pm
  193. +1 1  Bio/FeatureIO/gtf.pm
  194. +1 1  Bio/FeatureIO/interpro.pm
  195. +1 1  Bio/FeatureIO/ptt.pm
  196. +1 1  Bio/FeatureIO/vecscreen_simple.pm
  197. +1 1  Bio/HandlerBaseI.pm
  198. +1 1  Bio/IdCollectionI.pm
  199. +1 1  Bio/IdentifiableI.pm
  200. +1 1  Bio/Index/Abstract.pm
  201. +1 1  Bio/Index/AbstractSeq.pm
  202. +1 1  Bio/Index/Blast.pm
  203. +1 1  Bio/Index/BlastTable.pm
  204. +1 1  Bio/Index/EMBL.pm
  205. +1 1  Bio/Index/Fasta.pm
  206. +1 1  Bio/Index/Fastq.pm
  207. +1 1  Bio/Index/GenBank.pm
  208. +1 1  Bio/Index/Hmmer.pm
  209. +1 1  Bio/Index/Qual.pm
  210. +1 1  Bio/Index/Stockholm.pm
  211. +1 1  Bio/Index/SwissPfam.pm
  212. +1 1  Bio/Index/Swissprot.pm
  213. +1 1  Bio/LiveSeq/ChainI.pm
  214. +1 1  Bio/LiveSeq/Mutation.pm
  215. +1 1  Bio/LiveSeq/Mutator.pm
  216. +1 1  Bio/LiveSeq/SeqI.pm
  217. +1 1  Bio/LocatableSeq.pm
  218. +1 1  Bio/Location/Atomic.pm
  219. +1 1  Bio/Location/AvWithinCoordPolicy.pm
  220. +1 1  Bio/Location/CoordinatePolicyI.pm
  221. +1 1  Bio/Location/Fuzzy.pm
  222. +1 1  Bio/Location/FuzzyLocationI.pm
  223. +1 1  Bio/Location/NarrowestCoordPolicy.pm
  224. +1 1  Bio/Location/Simple.pm
  225. +1 1  Bio/Location/Split.pm
  226. +1 1  Bio/Location/SplitLocationI.pm
  227. +1 1  Bio/Location/WidestCoordPolicy.pm
  228. +1 1  Bio/LocationI.pm
  229. +1 1  Bio/Map/Clone.pm
  230. +1 1  Bio/Map/Contig.pm
  231. +1 1  Bio/Map/CytoMap.pm
  232. +1 1  Bio/Map/CytoMarker.pm
  233. +1 1  Bio/Map/CytoPosition.pm
  234. +1 1  Bio/Map/EntityI.pm
  235. +1 1  Bio/Map/FPCMarker.pm
  236. +1 1  Bio/Map/Gene.pm
  237. +1 1  Bio/Map/GeneMap.pm
  238. +1 1  Bio/Map/GenePosition.pm
  239. +1 1  Bio/Map/GeneRelative.pm
  240. +1 1  Bio/Map/LinkageMap.pm
  241. +1 1  Bio/Map/LinkagePosition.pm
  242. +1 1  Bio/Map/MapI.pm
  243. +1 1  Bio/Map/Mappable.pm
  244. +1 1  Bio/Map/MappableI.pm
  245. +1 1  Bio/Map/Marker.pm
  246. +1 1  Bio/Map/MarkerI.pm
  247. +1 1  Bio/Map/Microsatellite.pm
  248. +1 1  Bio/Map/OrderedPosition.pm
  249. +1 1  Bio/Map/OrderedPositionWithDistance.pm
  250. +1 1  Bio/Map/Physical.pm
  251. +1 1  Bio/Map/Position.pm
  252. +1 1  Bio/Map/PositionHandler.pm
  253. +1 1  Bio/Map/PositionHandlerI.pm
  254. +1 1  Bio/Map/PositionI.pm
  255. +1 1  Bio/Map/PositionWithSequence.pm
  256. +1 1  Bio/Map/Prediction.pm
  257. +1 1  Bio/Map/Relative.pm
  258. +1 1  Bio/Map/RelativeI.pm
  259. +1 1  Bio/Map/SimpleMap.pm
  260. +1 1  Bio/Map/TranscriptionFactor.pm
  261. +1 1  Bio/MapIO.pm
  262. +1 1  Bio/MapIO/fpc.pm
  263. +1 1  Bio/MapIO/mapmaker.pm
  264. +1 1  Bio/Matrix/Generic.pm
  265. +1 1  Bio/Matrix/IO.pm
  266. +1 1  Bio/Matrix/IO/mlagan.pm
  267. +1 1  Bio/Matrix/IO/phylip.pm
  268. +1 1  Bio/Matrix/IO/scoring.pm
  269. +1 1  Bio/Matrix/MatrixI.pm
  270. +1 1  Bio/Matrix/Mlagan.pm
  271. +1 1  Bio/Matrix/PSM/IO.pm
  272. +1 1  Bio/Matrix/PSM/IO/mast.pm
  273. +1 1  Bio/Matrix/PSM/IO/masta.pm
  274. +1 1  Bio/Matrix/PSM/IO/meme.pm
  275. +1 1  Bio/Matrix/PSM/IO/psiblast.pm
  276. +1 1  Bio/Matrix/PSM/IO/transfac.pm
  277. +1 1  Bio/Matrix/PSM/InstanceSite.pm
  278. +1 1  Bio/Matrix/PSM/InstanceSiteI.pm
  279. +1 1  Bio/Matrix/PSM/ProtMatrix.pm
  280. +1 1  Bio/Matrix/PSM/ProtPsm.pm
  281. +1 1  Bio/Matrix/PSM/Psm.pm
  282. +1 1  Bio/Matrix/PSM/PsmHeader.pm
  283. +1 1  Bio/Matrix/PSM/PsmHeaderI.pm
  284. +1 1  Bio/Matrix/PSM/PsmI.pm
  285. +1 1  Bio/Matrix/PSM/SiteMatrix.pm
  286. +1 1  Bio/Matrix/PSM/SiteMatrixI.pm
  287. +1 1  Bio/Matrix/PhylipDist.pm
  288. +1 1  Bio/Matrix/Scoring.pm
  289. +1 1  Bio/MolEvol/CodonModel.pm
  290. +1 1  Bio/Nexml/Factory.pm
  291. +1 1  Bio/NexmlIO.pm
  292. +1 1  Bio/Ontology/DocumentRegistry.pm
  293. +1 1  Bio/Ontology/GOterm.pm
  294. +1 1  Bio/Ontology/InterProTerm.pm
  295. +1 1  Bio/Ontology/OBOEngine.pm
  296. +1 1  Bio/Ontology/OBOterm.pm
  297. +1 1  Bio/Ontology/Ontology.pm
  298. +1 1  Bio/Ontology/OntologyEngineI.pm
  299. +1 1  Bio/Ontology/OntologyI.pm
  300. +1 1  Bio/Ontology/OntologyStore.pm
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4 BUGS
@@ -3,7 +3,7 @@
3 3 Known Bugs
4 4
5 5 Bugs are tracked at this URL:
6   -http://redmine.open-bio.org/projects/bioperl/
  6 +https://redmine.open-bio.org/projects/bioperl/
7 7
8 8 Bioperl 1.6 series
9 9 =============
@@ -11,7 +11,7 @@ Bioperl 1.6 series
11 11 Though a stable release, some bugs and enhancements remain for this series
12 12 that will be addressed in future point releases. For a full list please see:
13 13
14   -http://redmine.open-bio.org/projects/bioperl/
  14 +https://redmine.open-bio.org/projects/bioperl/
15 15
16 16 Bug Summary (additional info)
17 17
2  Bio/Align/AlignI.pm
@@ -70,7 +70,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
70 70 of the bugs and their resolution. Bug reports can be submitted via the
71 71 web:
72 72
73   - http://redmine.open-bio.org/projects/bioperl/
  73 + https://redmine.open-bio.org/projects/bioperl/
74 74
75 75 =head1 AUTHOR - Jason Stajich
76 76
2  Bio/Align/DNAStatistics.pm
@@ -313,7 +313,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
313 313 of the bugs and their resolution. Bug reports can be submitted via the
314 314 web:
315 315
316   - http://redmine.open-bio.org/projects/bioperl/
  316 + https://redmine.open-bio.org/projects/bioperl/
317 317
318 318 =head1 AUTHOR - Jason Stajich
319 319
2  Bio/Align/PairwiseStatistics.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
58 58 of the bugs and their resolution. Bug reports can be submitted via the
59 59 web:
60 60
61   - http://redmine.open-bio.org/projects/bioperl/
  61 + https://redmine.open-bio.org/projects/bioperl/
62 62
63 63 =head1 AUTHOR - Jason Stajich
64 64
2  Bio/Align/ProteinStatistics.pm
@@ -68,7 +68,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
68 68 of the bugs and their resolution. Bug reports can be submitted via the
69 69 web:
70 70
71   - http://redmine.open-bio.org/projects/bioperl/
  71 + https://redmine.open-bio.org/projects/bioperl/
72 72
73 73 =head1 AUTHOR - Jason Stajich
74 74
2  Bio/Align/StatisticsI.pm
@@ -51,7 +51,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
51 51 of the bugs and their resolution. Bug reports can be submitted via the
52 52 web:
53 53
54   - http://redmine.open-bio.org/projects/bioperl/
  54 + https://redmine.open-bio.org/projects/bioperl/
55 55
56 56 =head1 AUTHOR - Jason Stajich
57 57
2  Bio/Align/Utilities.pm
@@ -74,7 +74,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
74 74 of the bugs and their resolution. Bug reports can be submitted via the
75 75 web:
76 76
77   - http://redmine.open-bio.org/projects/bioperl/
  77 + https://redmine.open-bio.org/projects/bioperl/
78 78
79 79 =head1 AUTHOR - Jason Stajich
80 80
2  Bio/AlignIO.pm
@@ -254,7 +254,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
254 254 the bugs and their resolution. Bug reports can be submitted via the
255 255 web:
256 256
257   - http://redmine.open-bio.org/projects/bioperl/
  257 + https://redmine.open-bio.org/projects/bioperl/
258 258
259 259 =head1 AUTHOR - Peter Schattner
260 260
2  Bio/AlignIO/Handler/GenericAlignHandler.pm
@@ -562,7 +562,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
562 562 the bugs and their resolution. Bug reports can be submitted via the
563 563 web:
564 564
565   - http://redmine.open-bio.org/projects/bioperl/
  565 + https://redmine.open-bio.org/projects/bioperl/
566 566
567 567 =head1 AUTHOR - Chris Fields
568 568
2  Bio/AlignIO/arp.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
77 77 the bugs and their resolution. Bug reports can be submitted via the
78 78 web:
79 79
80   - http://redmine.open-bio.org/projects/bioperl/
  80 + https://redmine.open-bio.org/projects/bioperl/
81 81
82 82 =head1 AUTHORS
83 83
2  Bio/AlignIO/bl2seq.pm
@@ -87,7 +87,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
87 87 the bugs and their resolution. Bug reports can be submitted via the
88 88 web:
89 89
90   - http://redmine.open-bio.org/projects/bioperl/
  90 + https://redmine.open-bio.org/projects/bioperl/
91 91
92 92 =head1 AUTHOR - Peter Schattner
93 93
2  Bio/AlignIO/clustalw.pm
@@ -54,7 +54,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
54 54 the bugs and their resolution. Bug reports can be submitted via the
55 55 web:
56 56
57   - http://redmine.open-bio.org/projects/bioperl/
  57 + https://redmine.open-bio.org/projects/bioperl/
58 58
59 59 =head1 AUTHORS - Peter Schattner
60 60
2  Bio/AlignIO/emboss.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
59 59 of the bugs and their resolution. Bug reports can be submitted via the
60 60 web:
61 61
62   - http://redmine.open-bio.org/projects/bioperl/
  62 + https://redmine.open-bio.org/projects/bioperl/
63 63
64 64 =head1 AUTHOR - Jason Stajich
65 65
2  Bio/AlignIO/fasta.pm
@@ -41,7 +41,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
41 41 the bugs and their resolution. Bug reports can be submitted via the
42 42 web:
43 43
44   - http://redmine.open-bio.org/projects/bioperl/
  44 + https://redmine.open-bio.org/projects/bioperl/
45 45
46 46 =head1 AUTHORS
47 47
2  Bio/AlignIO/largemultifasta.pm
@@ -53,7 +53,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
53 53 the bugs and their resolution. Bug reports can be submitted via the
54 54 web:
55 55
56   - http://redmine.open-bio.org/projects/bioperl/
  56 + https://redmine.open-bio.org/projects/bioperl/
57 57
58 58 =head1 AUTHORS - Albert Vilella, Heikki Lehvaslaiho
59 59
2  Bio/AlignIO/maf.pm
@@ -64,7 +64,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
64 64 the bugs and their resolution. Bug reports can be submitted via the
65 65 web:
66 66
67   - http://redmine.open-bio.org/projects/bioperl/
  67 + https://redmine.open-bio.org/projects/bioperl/
68 68
69 69 =head1 AUTHORS - Allen Day
70 70
2  Bio/AlignIO/mase.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
46 46 the bugs and their resolution. Bug reports can be submitted via the
47 47 web:
48 48
49   - http://redmine.open-bio.org/projects/bioperl/
  49 + https://redmine.open-bio.org/projects/bioperl/
50 50
51 51 =head1 AUTHORS - Peter Schattner
52 52
2  Bio/AlignIO/mega.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
59 59 of the bugs and their resolution. Bug reports can be submitted the
60 60 web:
61 61
62   - http://redmine.open-bio.org/projects/bioperl/
  62 + https://redmine.open-bio.org/projects/bioperl/
63 63
64 64 =head1 AUTHOR - Jason Stajich
65 65
2  Bio/AlignIO/meme.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
59 59 the bugs and their resolution. Bug reports can be submitted via the
60 60 web:
61 61
62   - http://redmine.open-bio.org/projects/bioperl/
  62 + https://redmine.open-bio.org/projects/bioperl/
63 63
64 64 =head1 AUTHORS - Benjamin Berman
65 65
2  Bio/AlignIO/metafasta.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
58 58 the bugs and their resolution. Bug reports can be submitted via the
59 59 web:
60 60
61   - http://redmine.open-bio.org/projects/bioperl/
  61 + https://redmine.open-bio.org/projects/bioperl/
62 62
63 63 =head1 AUTHOR - Heikki Lehvaslaiho
64 64
2  Bio/AlignIO/msf.pm
@@ -45,7 +45,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
45 45 the bugs and their resolution. Bug reports can be submitted via the
46 46 web:
47 47
48   - http://redmine.open-bio.org/projects/bioperl/
  48 + https://redmine.open-bio.org/projects/bioperl/
49 49
50 50 =head1 AUTHORS - Peter Schattner
51 51
2  Bio/AlignIO/nexml.pm
@@ -38,7 +38,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
38 38 the bugs and their resolution. Bug reports can be submitted via the
39 39 web:
40 40
41   - http://redmine.open-bio.org/projects/bioperl/
  41 + https://redmine.open-bio.org/projects/bioperl/
42 42
43 43 =head1 AUTHORS
44 44
2  Bio/AlignIO/nexus.pm
@@ -49,7 +49,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
49 49 the bugs and their resolution. Bug reports can be submitted via the
50 50 web:
51 51
52   - http://redmine.open-bio.org/projects/bioperl/
  52 + https://redmine.open-bio.org/projects/bioperl/
53 53
54 54 =head1 AUTHORS - Heikki Lehvaslaiho
55 55
2  Bio/AlignIO/pfam.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
46 46 the bugs and their resolution. Bug reports can be submitted via the
47 47 web:
48 48
49   - http://redmine.open-bio.org/projects/bioperl/
  49 + https://redmine.open-bio.org/projects/bioperl/
50 50
51 51 =head1 AUTHORS - Peter Schattner
52 52
2  Bio/AlignIO/phylip.pm
@@ -71,7 +71,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
71 71 the bugs and their resolution. Bug reports can be submitted via the
72 72 web:
73 73
74   - http://redmine.open-bio.org/projects/bioperl/
  74 + https://redmine.open-bio.org/projects/bioperl/
75 75
76 76 =head1 AUTHORS - Heikki Lehvaslaiho and Jason Stajich
77 77
2  Bio/AlignIO/po.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
46 46 the bugs and their resolution. Bug reports can be submitted via the
47 47 web:
48 48
49   - http://redmine.open-bio.org/projects/bioperl/
  49 + https://redmine.open-bio.org/projects/bioperl/
50 50
51 51 =head1 AUTHORS - Matthew Betts
52 52
2  Bio/AlignIO/proda.pm
@@ -56,7 +56,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
56 56 the bugs and their resolution. Bug reports can be submitted via the
57 57 web:
58 58
59   - http://redmine.open-bio.org/projects/bioperl/
  59 + https://redmine.open-bio.org/projects/bioperl/
60 60
61 61 =head1 AUTHORS - Albert Vilella
62 62
2  Bio/AlignIO/prodom.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
46 46 the bugs and their resolution. Bug reports can be submitted via the
47 47 web:
48 48
49   - http://redmine.open-bio.org/projects/bioperl/
  49 + https://redmine.open-bio.org/projects/bioperl/
50 50
51 51 =head1 AUTHORS - Peter Schattner
52 52
2  Bio/AlignIO/psi.pm
@@ -51,7 +51,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
51 51 of the bugs and their resolution. Bug reports can be submitted via
52 52 the web:
53 53
54   - http://redmine.open-bio.org/projects/bioperl/
  54 + https://redmine.open-bio.org/projects/bioperl/
55 55
56 56 =head1 AUTHOR - Jason Stajich
57 57
2  Bio/AlignIO/selex.pm
@@ -55,7 +55,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
55 55 the bugs and their resolution. Bug reports can be submitted via the
56 56 web:
57 57
58   - http://redmine.open-bio.org/projects/bioperl/
  58 + https://redmine.open-bio.org/projects/bioperl/
59 59
60 60 =head1 AUTHORS - Peter Schattner
61 61
2  Bio/AlignIO/stockholm.pm
@@ -198,7 +198,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
198 198 the bugs and their resolution. Bug reports can be submitted via the
199 199 web:
200 200
201   - http://redmine.open-bio.org/projects/bioperl/
  201 + https://redmine.open-bio.org/projects/bioperl/
202 202
203 203 =head1 AUTHORS - Chris Fields, Peter Schattner
204 204
2  Bio/AlignIO/xmfa.pm
@@ -49,7 +49,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
49 49 the bugs and their resolution. Bug reports can be submitted via the
50 50 web:
51 51
52   - http://redmine.open-bio.org/projects/bioperl/
  52 + https://redmine.open-bio.org/projects/bioperl/
53 53
54 54 =head1 AUTHORS
55 55
2  Bio/AnalysisI.pm
@@ -55,7 +55,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
55 55 of the bugs and their resolution. Bug reports can be submitted via the
56 56 web:
57 57
58   - http://redmine.open-bio.org/projects/bioperl/
  58 + https://redmine.open-bio.org/projects/bioperl/
59 59
60 60 =head1 AUTHOR
61 61
2  Bio/AnalysisParserI.pm
@@ -108,7 +108,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
108 108 the bugs and their resolution. Bug reports can be submitted via the
109 109 web:
110 110
111   - http://redmine.open-bio.org/projects/bioperl/
  111 + https://redmine.open-bio.org/projects/bioperl/
112 112
113 113 =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
114 114
2  Bio/AnalysisResultI.pm
@@ -68,7 +68,7 @@ with code and data examples if at all possible.
68 68 Report bugs to the Bioperl bug tracking system to help us keep track
69 69 the bugs and their resolution. Bug reports can be submitted via the web:
70 70
71   - http://redmine.open-bio.org/projects/bioperl/
  71 + https://redmine.open-bio.org/projects/bioperl/
72 72
73 73 =head1 AUTHOR - Steve Chervitz, Hilmar Lapp
74 74
2  Bio/AnnotatableI.pm
@@ -62,7 +62,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
62 62 of the bugs and their resolution. Bug reports can be submitted via the
63 63 web:
64 64
65   - http://redmine.open-bio.org/projects/bioperl/
  65 + https://redmine.open-bio.org/projects/bioperl/
66 66
67 67 =head1 AUTHOR
68 68
2  Bio/Annotation/AnnotationFactory.pm
@@ -72,7 +72,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
72 72 of the bugs and their resolution. Bug reports can be submitted via
73 73 the web:
74 74
75   - http://redmine.open-bio.org/projects/bioperl/
  75 + https://redmine.open-bio.org/projects/bioperl/
76 76
77 77 =head1 AUTHOR - Hilmar Lapp
78 78
2  Bio/Annotation/Collection.pm
@@ -66,7 +66,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
66 66 the bugs and their resolution. Bug reports can be submitted via
67 67 the web:
68 68
69   - http://redmine.open-bio.org/projects/bioperl/
  69 + https://redmine.open-bio.org/projects/bioperl/
70 70
71 71 =head1 AUTHOR - Ewan Birney
72 72
2  Bio/Annotation/OntologyTerm.pm
@@ -85,7 +85,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
85 85 the bugs and their resolution. Bug reports can be submitted via
86 86 the web:
87 87
88   - http://redmine.open-bio.org/projects/bioperl/
  88 + https://redmine.open-bio.org/projects/bioperl/
89 89
90 90 =head1 AUTHOR - Hilmar Lapp
91 91
2  Bio/Annotation/Relation.pm
@@ -57,7 +57,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
57 57 the bugs and their resolution. Bug reports can be submitted via
58 58 the web:
59 59
60   - http://redmine.open-bio.org/projects/bioperl/
  60 + https://redmine.open-bio.org/projects/bioperl/
61 61
62 62 =head1 AUTHOR - Mira Han
63 63
2  Bio/Annotation/SimpleValue.pm
@@ -56,7 +56,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
56 56 the bugs and their resolution. Bug reports can be submitted via
57 57 the web:
58 58
59   - http://redmine.open-bio.org/projects/bioperl/
  59 + https://redmine.open-bio.org/projects/bioperl/
60 60
61 61 =head1 AUTHOR - Ewan Birney
62 62
2  Bio/Annotation/StructuredValue.pm
@@ -65,7 +65,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
65 65 the bugs and their resolution. Bug reports can be submitted via
66 66 or the web:
67 67
68   - http://redmine.open-bio.org/projects/bioperl/
  68 + https://redmine.open-bio.org/projects/bioperl/
69 69
70 70 =head1 AUTHOR - Hilmar Lapp
71 71
2  Bio/Annotation/TagTree.pm
@@ -99,7 +99,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
99 99 the bugs and their resolution. Bug reports can be submitted via
100 100 or the web:
101 101
102   - http://redmine.open-bio.org/projects/bioperl/
  102 + https://redmine.open-bio.org/projects/bioperl/
103 103
104 104 =head1 AUTHOR
105 105
2  Bio/Annotation/TypeManager.pm
@@ -60,7 +60,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
60 60 the bugs and their resolution.
61 61 Bug reports can be submitted via the web:
62 62
63   - http://redmine.open-bio.org/projects/bioperl/
  63 + https://redmine.open-bio.org/projects/bioperl/
64 64
65 65 =head1 AUTHOR - Ewan Birney
66 66
2  Bio/AnnotationCollectionI.pm
@@ -112,7 +112,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
112 112 the bugs and their resolution. Bug reports can be submitted via the
113 113 web:
114 114
115   - http://redmine.open-bio.org/projects/bioperl/
  115 + https://redmine.open-bio.org/projects/bioperl/
116 116
117 117 =head1 AUTHOR - Ewan Birney
118 118
2  Bio/AnnotationI.pm
@@ -100,7 +100,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
100 100 the bugs and their resolution. Bug reports can be submitted via the
101 101 web:
102 102
103   - http://redmine.open-bio.org/projects/bioperl/
  103 + https://redmine.open-bio.org/projects/bioperl/
104 104
105 105 =head1 AUTHOR - Ewan Birney
106 106
2  Bio/Assembly/Contig.pm
@@ -201,7 +201,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
201 201 the bugs and their resolution. Bug reports can be submitted via the
202 202 web:
203 203
204   - http://redmine.open-bio.org/projects/bioperl/
  204 + https://redmine.open-bio.org/projects/bioperl/
205 205
206 206 =head1 AUTHOR - Robson Francisco de Souza
207 207
2  Bio/Assembly/ContigAnalysis.pm
@@ -65,7 +65,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
65 65 the bugs and their resolution. Bug reports can be submitted via the
66 66 web:
67 67
68   - http://redmine.open-bio.org/projects/bioperl/
  68 + https://redmine.open-bio.org/projects/bioperl/
69 69
70 70 =head1 AUTHOR - Robson Francisco de Souza
71 71
2  Bio/Assembly/IO.pm
@@ -69,7 +69,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
69 69 the bugs and their resolution. Bug reports can be submitted via the
70 70 web:
71 71
72   - http://redmine.open-bio.org/projects/bioperl/
  72 + https://redmine.open-bio.org/projects/bioperl/
73 73
74 74 =head1 AUTHOR
75 75
2  Bio/Assembly/IO/ace.pm
@@ -136,7 +136,7 @@ with code and data examples if at all possible.
136 136 Report bugs to the Bioperl bug tracking system to help us keep track
137 137 the bugs and their resolution. Bug reports can be submitted via the web:
138 138
139   - http://redmine.open-bio.org/projects/bioperl/
  139 + https://redmine.open-bio.org/projects/bioperl/
140 140
141 141 =head1 AUTHOR - Robson Francisco de Souza
142 142
2  Bio/Assembly/IO/bowtie.pm
@@ -85,7 +85,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
85 85 of the bugs and their resolution. Bug reports can be submitted via
86 86 the web:
87 87
88   - http://redmine.open-bio.org/projects/bioperl/
  88 + https://redmine.open-bio.org/projects/bioperl/
89 89
90 90 =head1 AUTHOR - Dan Kortschak
91 91
2  Bio/Assembly/IO/maq.pm
@@ -117,7 +117,7 @@ the bugs and their resolution. Bug reports can be submitted via email
117 117 or the web:
118 118
119 119 bioperl-bugs@bio.perl.org
120   - http://redmine.open-bio.org/projects/bioperl/
  120 + https://redmine.open-bio.org/projects/bioperl/
121 121
122 122 =head1 AUTHOR - Mark A. Jensen
123 123
2  Bio/Assembly/IO/phrap.pm
@@ -139,7 +139,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
139 139 the bugs and their resolution. Bug reports can be submitted via the
140 140 web:
141 141
142   - http://redmine.open-bio.org/projects/bioperl/
  142 + https://redmine.open-bio.org/projects/bioperl/
143 143
144 144
145 145 =head1 AUTHOR - Robson Francisco de Souza
2  Bio/Assembly/IO/sam.pm
@@ -146,7 +146,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
146 146 of the bugs and their resolution. Bug reports can be submitted via
147 147 the web:
148 148
149   - http://redmine.open-bio.org/projects/bioperl/
  149 + https://redmine.open-bio.org/projects/bioperl/
150 150
151 151 =head1 AUTHOR - Mark A. Jensen
152 152
2  Bio/Assembly/IO/tigr.pm
@@ -212,7 +212,7 @@ the bugs and their resolution. Bug reports can be submitted via email
212 212 or the web:
213 213
214 214 bioperl-bugs@bio.perl.org
215   - http://redmine.open-bio.org/projects/bioperl/
  215 + https://redmine.open-bio.org/projects/bioperl/
216 216
217 217 =head1 AUTHOR - Florent E Angly
218 218
2  Bio/Assembly/Scaffold.pm
@@ -60,7 +60,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
60 60 the bugs and their resolution. Bug reports can be submitted via the
61 61 web:
62 62
63   - http://redmine.open-bio.org/projects/bioperl/
  63 + https://redmine.open-bio.org/projects/bioperl/
64 64
65 65 =head1 AUTHOR - Robson Francisco de Souza
66 66
2  Bio/Assembly/ScaffoldI.pm
@@ -52,7 +52,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
52 52 the bugs and their resolution. Bug reports can be submitted via the
53 53 web:
54 54
55   - http://redmine.open-bio.org/projects/bioperl/
  55 + https://redmine.open-bio.org/projects/bioperl/
56 56
57 57 =head1 AUTHOR - Robson Francisco de Souza
58 58
2  Bio/Assembly/Singlet.pm
@@ -70,7 +70,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
70 70 the bugs and their resolution. Bug reports can be submitted via the
71 71 web:
72 72
73   - http://redmine.open-bio.org/projects/bioperl/
  73 + https://redmine.open-bio.org/projects/bioperl/
74 74
75 75 =head1 AUTHOR - Chad S. Matsalla
76 76
2  Bio/Assembly/Tools/ContigSpectrum.pm
@@ -185,7 +185,7 @@ the bugs and their resolution. Bug reports can be submitted via email
185 185 or the web:
186 186
187 187 bioperl-bugs@bio.perl.org
188   - http://redmine.open-bio.org/projects/bioperl/
  188 + https://redmine.open-bio.org/projects/bioperl/
189 189
190 190 =head1 AUTHOR - Florent E Angly
191 191
2  Bio/Biblio.pm
@@ -151,7 +151,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
151 151 of the bugs and their resolution. Bug reports can be submitted via the
152 152 web:
153 153
154   - http://redmine.open-bio.org/projects/bioperl/
  154 + https://redmine.open-bio.org/projects/bioperl/
155 155
156 156 =head1 AUTHOR
157 157
2  Bio/Biblio/Article.pm
@@ -81,7 +81,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
81 81 of the bugs and their resolution. Bug reports can be submitted via the
82 82 web:
83 83
84   - http://redmine.open-bio.org/projects/bioperl/
  84 + https://redmine.open-bio.org/projects/bioperl/
85 85
86 86 =head1 AUTHORS
87 87
2  Bio/Biblio/BiblioBase.pm
@@ -72,7 +72,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
72 72 of the bugs and their resolution. Bug reports can be submitted via the
73 73 web:
74 74
75   - http://redmine.open-bio.org/projects/bioperl/
  75 + https://redmine.open-bio.org/projects/bioperl/
76 76
77 77 =head1 AUTHOR
78 78
2  Bio/Biblio/Book.pm
@@ -83,7 +83,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
83 83 of the bugs and their resolution. Bug reports can be submitted via the
84 84 web:
85 85
86   - http://redmine.open-bio.org/projects/bioperl/
  86 + https://redmine.open-bio.org/projects/bioperl/
87 87
88 88 =head1 AUTHORS
89 89
2  Bio/Biblio/BookArticle.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
77 77 of the bugs and their resolution. Bug reports can be submitted via the
78 78 web:
79 79
80   - http://redmine.open-bio.org/projects/bioperl/
  80 + https://redmine.open-bio.org/projects/bioperl/
81 81
82 82 =head1 AUTHORS
83 83
2  Bio/Biblio/IO.pm
@@ -192,7 +192,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
192 192 the bugs and their resolution. Bug reports can be submitted via the
193 193 web:
194 194
195   - http://redmine.open-bio.org/projects/bioperl/
  195 + https://redmine.open-bio.org/projects/bioperl/
196 196
197 197 =head1 AUTHOR
198 198
2  Bio/Biblio/IO/medline2ref.pm
@@ -48,7 +48,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
48 48 of the bugs and their resolution. Bug reports can be submitted via the
49 49 web:
50 50
51   - http://redmine.open-bio.org/projects/bioperl/
  51 + https://redmine.open-bio.org/projects/bioperl/
52 52
53 53 =head1 AUTHOR
54 54
2  Bio/Biblio/IO/medlinexml.pm
@@ -54,7 +54,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
54 54 of the bugs and their resolution. Bug reports can be submitted via the
55 55 web:
56 56
57   - http://redmine.open-bio.org/projects/bioperl/
  57 + https://redmine.open-bio.org/projects/bioperl/
58 58
59 59 =head1 AUTHOR
60 60
2  Bio/Biblio/IO/pubmed2ref.pm
@@ -48,7 +48,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
48 48 of the bugs and their resolution. Bug reports can be submitted via the
49 49 web:
50 50
51   - http://redmine.open-bio.org/projects/bioperl/
  51 + https://redmine.open-bio.org/projects/bioperl/
52 52
53 53 =head1 AUTHOR
54 54
2  Bio/Biblio/IO/pubmedxml.pm
@@ -54,7 +54,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
54 54 of the bugs and their resolution. Bug reports can be submitted via the
55 55 web:
56 56
57   - http://redmine.open-bio.org/projects/bioperl/
  57 + https://redmine.open-bio.org/projects/bioperl/
58 58
59 59 =head1 AUTHOR
60 60
2  Bio/Biblio/Journal.pm
@@ -79,7 +79,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
79 79 of the bugs and their resolution. Bug reports can be submitted via the
80 80 web:
81 81
82   - http://redmine.open-bio.org/projects/bioperl/
  82 + https://redmine.open-bio.org/projects/bioperl/
83 83
84 84 =head1 AUTHORS
85 85
2  Bio/Biblio/JournalArticle.pm
@@ -80,7 +80,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
80 80 of the bugs and their resolution. Bug reports can be submitted via the
81 81 web:
82 82
83   - http://redmine.open-bio.org/projects/bioperl/
  83 + https://redmine.open-bio.org/projects/bioperl/
84 84
85 85 =head1 AUTHORS
86 86
2  Bio/Biblio/MedlineArticle.pm
@@ -121,7 +121,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
121 121 of the bugs and their resolution. Bug reports can be submitted via the
122 122 web:
123 123
124   - http://redmine.open-bio.org/projects/bioperl/
  124 + https://redmine.open-bio.org/projects/bioperl/
125 125
126 126 =head1 AUTHORS
127 127
2  Bio/Biblio/MedlineBook.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
77 77 of the bugs and their resolution. Bug reports can be submitted via the
78 78 web:
79 79
80   - http://redmine.open-bio.org/projects/bioperl/
  80 + https://redmine.open-bio.org/projects/bioperl/
81 81
82 82 =head1 AUTHORS
83 83
2  Bio/Biblio/MedlineBookArticle.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
77 77 of the bugs and their resolution. Bug reports can be submitted via the
78 78 web:
79 79
80   - http://redmine.open-bio.org/projects/bioperl/
  80 + https://redmine.open-bio.org/projects/bioperl/
81 81
82 82 =head1 AUTHORS
83 83
2  Bio/Biblio/MedlineJournal.pm
@@ -80,7 +80,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
80 80 of the bugs and their resolution. Bug reports can be submitted via the
81 81 web:
82 82
83   - http://redmine.open-bio.org/projects/bioperl/
  83 + https://redmine.open-bio.org/projects/bioperl/
84 84
85 85 =head1 AUTHORS
86 86
2  Bio/Biblio/MedlineJournalArticle.pm
@@ -80,7 +80,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
80 80 of the bugs and their resolution. Bug reports can be submitted via the
81 81 web:
82 82
83   - http://redmine.open-bio.org/projects/bioperl/
  83 + https://redmine.open-bio.org/projects/bioperl/
84 84
85 85 =head1 AUTHORS
86 86
2  Bio/Biblio/Organisation.pm
@@ -74,7 +74,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
74 74 of the bugs and their resolution. Bug reports can be submitted via the
75 75 web:
76 76
77   - http://redmine.open-bio.org/projects/bioperl/
  77 + https://redmine.open-bio.org/projects/bioperl/
78 78
79 79 =head1 AUTHORS
80 80
2  Bio/Biblio/Patent.pm
@@ -79,7 +79,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
79 79 of the bugs and their resolution. Bug reports can be submitted via the
80 80 web:
81 81
82   - http://redmine.open-bio.org/projects/bioperl/
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83 83
84 84 =head1 AUTHORS
85 85
2  Bio/Biblio/Person.pm
@@ -83,7 +83,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
83 83 of the bugs and their resolution. Bug reports can be submitted via the
84 84 web:
85 85
86   - http://redmine.open-bio.org/projects/bioperl/
  86 + https://redmine.open-bio.org/projects/bioperl/
87 87
88 88 =head1 AUTHORS
89 89
2  Bio/Biblio/Proceeding.pm
@@ -74,7 +74,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
74 74 of the bugs and their resolution. Bug reports can be submitted via the
75 75 web:
76 76
77   - http://redmine.open-bio.org/projects/bioperl/
  77 + https://redmine.open-bio.org/projects/bioperl/
78 78
79 79 =head1 AUTHORS
80 80
2  Bio/Biblio/Provider.pm
@@ -76,7 +76,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
76 76 of the bugs and their resolution. Bug reports can be submitted via the
77 77 web:
78 78
79   - http://redmine.open-bio.org/projects/bioperl/
  79 + https://redmine.open-bio.org/projects/bioperl/
80 80
81 81 =head1 AUTHORS
82 82
2  Bio/Biblio/PubmedArticle.pm
@@ -85,7 +85,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
85 85 of the bugs and their resolution. Bug reports can be submitted via the
86 86 web:
87 87
88   - http://redmine.open-bio.org/projects/bioperl/
  88 + https://redmine.open-bio.org/projects/bioperl/
89 89
90 90 =head1 AUTHOR
91 91
2  Bio/Biblio/PubmedBookArticle.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
77 77 of the bugs and their resolution. Bug reports can be submitted via the
78 78 web:
79 79
80   - http://redmine.open-bio.org/projects/bioperl/
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81 81
82 82 =head1 AUTHOR
83 83
2  Bio/Biblio/PubmedJournalArticle.pm
@@ -90,7 +90,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
90 90 of the bugs and their resolution. Bug reports can be submitted via the
91 91 web:
92 92
93   - http://redmine.open-bio.org/projects/bioperl/
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94 94
95 95 =head1 AUTHOR
96 96
2  Bio/Biblio/Ref.pm
@@ -104,7 +104,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
104 104 of the bugs and their resolution. Bug reports can be submitted via the
105 105 web:
106 106
107   - http://redmine.open-bio.org/projects/bioperl/
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108 108
109 109 =head1 AUTHORS
110 110
2  Bio/Biblio/Service.pm
@@ -74,7 +74,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
74 74 of the bugs and their resolution. Bug reports can be submitted via the
75 75 web:
76 76
77   - http://redmine.open-bio.org/projects/bioperl/
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78 78
79 79 =head1 AUTHORS
80 80
2  Bio/Biblio/TechReport.pm
@@ -75,7 +75,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
75 75 of the bugs and their resolution. Bug reports can be submitted via the
76 76 web:
77 77
78   - http://redmine.open-bio.org/projects/bioperl/