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bioperl after 0.04

svn path=/bioperl-live/branches/bioperl/; revision=774
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0 parents commit 147a8dd5770ba8ee60ac21e4fa68d412e067c11c birney committed Dec 11, 1998
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  1. +528 −0 Bio/Parse.pm
  2. +1,137 −0 Bio/Root/Err.pm
  3. +206 −0 Bio/Root/Global.pm
  4. +1,141 −0 Bio/Root/IOManager.pm
  5. +2,680 −0 Bio/Root/Object.pm
  6. +947 −0 Bio/Root/Utilities.pm
  7. +1,052 −0 Bio/Root/Vector.pm
  8. +198 −0 Bio/Root/Xref.pm
  9. +3,634 −0 Bio/Seq.pm
  10. +1,486 −0 Bio/SimpleAlign.pm
  11. +155 −0 Bio/Tools/AlignFactory.pm
  12. +4,204 −0 Bio/Tools/Blast.pm
  13. +215 −0 Bio/Tools/Blast/CHANGES
  14. +1,745 −0 Bio/Tools/Blast/HSP.pm
  15. +749 −0 Bio/Tools/Blast/HTML.pm
  16. +453 −0 Bio/Tools/Blast/Run/LocalBlast.pm
  17. +8 −0 Bio/Tools/Blast/Run/Makefile.PL
  18. +1,112 −0 Bio/Tools/Blast/Run/Webblast.pm
  19. +241 −0 Bio/Tools/Blast/Run/postclient.pl
  20. +2,261 −0 Bio/Tools/Blast/Sbjct.pm
  21. +730 −0 Bio/Tools/Fasta.pm
  22. +818 −0 Bio/Tools/RestrictionEnzyme.pm
  23. +838 −0 Bio/Tools/SeqAnal.pm
  24. +846 −0 Bio/Tools/SeqPattern.pm
  25. +1,000 −0 Bio/Tools/WWW.pm
  26. +389 −0 Bio/Tools/pSW.pm
  27. +3,460 −0 Bio/UnivAln.pm
  28. +18 −0 Changes
  29. +167 −0 MANIFEST
  30. +8 −0 MANIFEST.SKIP
  31. +91 −0 Makefile.PL
  32. +49 −0 PLATFORMS
  33. +205 −0 README
  34. +36 −0 bioperl.lisp
  35. +404 −0 bioperl.pod
  36. +715 −0 examples/blast/blast_config.pl
  37. +141 −0 examples/blast/blast_seq.pl
  38. +8 −0 examples/blast/example.table1
  39. +7 −0 examples/blast/example.table2
  40. +127 −0 examples/blast/html.pl
  41. BIN examples/blast/out/blastn.2.gz
  42. BIN examples/blast/out/blastn.2.wu.gz
  43. BIN examples/blast/out/blastp.1.gcg.gz
  44. BIN examples/blast/out/blastp.1.gz
  45. BIN examples/blast/out/blastp.2.gz
  46. BIN examples/blast/out/blastp.2.nogap.gz
  47. +305 −0 examples/blast/out/blastp.2.wu
  48. BIN examples/blast/out/blastp.205.gz
  49. BIN examples/blast/out/blastp.2a.gz
  50. BIN examples/blast/out/blastp.2b.gz
  51. BIN examples/blast/out/blastp.email.html.gz
  52. +322 −0 examples/blast/out/blastx.2
  53. BIN examples/blast/out/blastx.2.email.gz
  54. +144 −0 examples/blast/parse.pl
  55. +179 −0 examples/blast/parse2.pl
  56. +223 −0 examples/blast/parse_multi.pl
  57. +154 −0 examples/blast/parse_positions.pl
  58. +142 −0 examples/blast/parse_stream.pl
  59. +148 −0 examples/blast/print_blasts.pl
  60. +141 −0 examples/blast/run.pl
  61. +61 −0 examples/blast/seq/seqs.fasta
  62. +33 −0 examples/blast/seq/yal011w.dna.fasta
  63. +6 −0 examples/blast/seq/yel009c.fasta
  64. +12 −0 examples/blast/seq/ymr284w.fasta
  65. +31 −0 examples/blosum62.bla
  66. +27 −0 examples/gon250.bla
  67. +113 −0 examples/psw.pl
  68. +109 −0 examples/restriction.pl
  69. +49 −0 examples/rev_and_trans.pl
  70. +93 −0 examples/root_object/Bar.pm
  71. +145 −0 examples/root_object/Foo.pm
  72. +95 −0 examples/root_object/Outer.pm
  73. +165 −0 examples/root_object/destroy.pl
  74. +155 −0 examples/root_object/error.out
  75. +166 −0 examples/root_object/error.pl
  76. +32 −0 examples/root_object/filehandle.out
  77. +75 −0 examples/root_object/filehandle.pl
  78. +29 −0 examples/root_object/io.out
  79. +70 −0 examples/root_object/io.pl
  80. +69 −0 examples/root_object/read.pl
  81. +3 −0 examples/root_object/read.test
  82. +3 −0 examples/root_object/read.test2
  83. +6 −0 examples/root_object/read.test3
  84. +40 −0 examples/root_object/utilities.pl
  85. +64 −0 examples/root_object/vector/Person.pm
  86. +143 −0 examples/root_object/vector/PersonManager.pm
  87. +183 −0 examples/root_object/vector/vector.out
  88. +127 −0 examples/root_object/vector/vector.pl
  89. +3 −0 examples/seq/id.list
  90. BIN examples/seq/seq.fasta.gz
  91. +115 −0 examples/seq/seq1.fasta
  92. +500 −0 examples/seq/seq2.fasta
  93. +44 −0 examples/seq/seqs1.pl
  94. +80 −0 examples/seq/seqs2.pl
  95. +70 −0 examples/seq/seqs3.pl
  96. +100 −0 examples/seq/seqs4.pl
  97. +699 −0 examples/seq/seqtools.pl
  98. +142 −0 examples/seq_pattern.pl
  99. +179 −0 examples/simplealign.pl
  100. +101 −0 t/Blast.t
  101. +42 −0 t/Fasta.t
  102. +42 −0 t/HSP.t
  103. +42 −0 t/HTML.t
  104. +70 −0 t/RestrictionEnzyme.t
  105. +42 −0 t/Sbjct.t
  106. +47 −0 t/Seq.t
  107. +42 −0 t/SeqAnal.t
  108. +42 −0 t/SimpleAlign.t
  109. +48 −0 t/UnivAln.t
  110. +42 −0 t/WWW.t
  111. +439 −0 t/blast.report
  112. +16 −0 t/expected.blast.out

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@@ -0,0 +1,206 @@
+#--------------------------------------------------------------------------------
+# PACKAGE : Bio::Root::Global.pm
+# PURPOSE : Provides global data, objects, and methods potentially useful to
+# many different modules and scripts.
+# AUTHOR : Steve A. Chervitz (sac@genome.stanford.edu)
+# CREATED : 3 Sep 1996
+# REVISION: $Id$
+#
+# INSTALLATION:
+# This module is included with the central Bioperl distribution:
+# http://bio.perl.org/Core/Latest
+# ftp://bio.perl.org/pub/DIST
+# Follow the installation instructions included in the README file.
+#
+# COMMENTS: Edit the $AUTHORITY string to a desired e-mail address.
+#
+# STRICTNESS, VERBOSITY, and variables containing the words WARN and FATAL
+# are considered experimental. The purpose & usage of these is explained
+# in Bio::Root::Object.pm.
+#
+# MODIFIED:
+# sac --- Tue Dec 1 1998
+# * Added $STRICTNESS and $VERBOSITY.
+# * Deprecated WARN_ON_FATAL, FATAL_ON_WARN, DONT_WARN and related methods.
+# These will eventually be removed.
+# sac --- Fri 5 Jun 1998: Added @DAYS.
+# sac --- Sun Aug 16 1998: Added $RECORD_ERR and &record_err().
+#--------------------------------------------------------------------------------
+package Bio::Root::Global;
+
+use Exporter ();
+use vars qw($BASE_YEAR @DAYS @MONTHS);
+
+@ISA = qw( Exporter );
+@EXPORT_OK = qw($AUTHORITY
+ $DEBUG $MONITOR $TESTING
+ $DONT_WARN $WARN_ON_FATAL $FATAL_ON_WARN $RECORD_ERR
+ $STRICTNESS $VERBOSITY
+ $CGI $GLOBAL
+ $BASE_YEAR %ROMAN_NUMS @MONTHS @DAYS
+ &roman2int &debug &monitor &testing &dont_warn &record_err
+ &warn_on_fatal &fatal_on_warn &strictness &verbosity
+ );
+
+%EXPORT_TAGS = (
+
+ std =>[qw($DEBUG $MONITOR $TESTING
+ $DONT_WARN $WARN_ON_FATAL $FATAL_ON_WARN $RECORD_ERR
+ $STRICTNESS $VERBOSITY
+ &debug &monitor &testing &dont_warn
+ &warn_on_fatal &fatal_on_warn &record_err
+ &strictness &verbosity
+ &roman2int $AUTHORITY $CGI $GLOBAL)],
+
+ obj =>[qw($GLOBAL)],
+
+ devel =>[qw($DEBUG $MONITOR $TESTING $DONT_WARN
+ $WARN_ON_FATAL $FATAL_ON_WARN $RECORD_ERR
+ $STRICTNESS $VERBOSITY
+ &debug &monitor &testing &dont_warn
+ &strictness &verbosity
+ &warn_on_fatal &fatal_on_warn)],
+
+ data =>[qw($BASE_YEAR %ROMAN_NUMS @MONTHS @DAYS)],
+
+ );
+
+# Note: record_err() is not included in the devel tag to allow Bio::Root:Object.pm
+# to define it without a name clash.
+
+######################################
+## Data ##
+######################################
+
+# Who should receive feedback from users and possibly automatic error messages.
+$AUTHORITY = 'sac@genome.stanford.edu';
+
+$DEBUG = 0;
+$MONITOR = 0;
+$TESTING = 0;
+$DONT_WARN = 0;
+$WARN_ON_FATAL = 0;
+$FATAL_ON_WARN = 0;
+$RECORD_ERR = 0;
+$STRICTNESS = 0;
+$VERBOSITY = 0;
+
+$BASE_YEAR = 1900;
+
+%ROMAN_NUMS = ('1'=>'I', '2'=>'II', '3'=>'III', '4'=>'IV', '5'=>'V',
+ '6'=>'VI', '7'=>'VII', '8'=>'VIII', '9'=>'IX', '10'=>'X',
+ '11'=>'XI', '12'=>'XII', '13'=>'XIII', '14'=>'XIV', '15'=>'XV',
+ '16'=>'XVI', '17'=>'XVII', '18'=>'XVIII', '19'=>'XIX', '20'=>'XX',
+ '21'=>'XXI', '22'=>'XXII',
+ );
+
+@MONTHS = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
+@DAYS = qw(Sun Mon Tue Wed Thu Fri Sat);
+
+$CGI = 0; # Boolean to indicate if the script is running as a CGI.
+ # Useful for conditionally producing HTML-formatted messages.
+
+# The implicit global object. Used for trapping miscellaneous errors/exceptions.
+# Created without using or requiring Bio::Root::Object.pm, because Object.pm uses Global.pm.
+# Just be sure to use Bio::Root::Object.pm, or a module that uses it.
+
+$GLOBAL = {};
+bless $GLOBAL, 'Bio::Root::Object';
+$GLOBAL->{'_name'} = 'Global object';
+
+
+######################################
+## Methods ##
+######################################
+
+sub roman2int {
+ my $roman = uc(shift);
+ foreach (keys %ROMAN_NUMS) {
+ return $_ if $ROMAN_NUMS{$_} eq $roman;
+ }
+# Alternatively:
+# my @int = grep $ROMAN_NUMS{$_} eq $roman, keys %ROMAN_NUMS;
+# return $int[0];
+ undef;
+}
+
+sub debug {
+ my $level = shift;
+ if( defined $level) { $DEBUG = $level }
+ else { $DEBUG = 0 }
+# $MONITOR and do{ print STDERR $DEBUG ? "Debug on ($DEBUG).\n\n" : "Debug off.\n\n"; };
+ $MONITOR and do{ print STDERR $DEBUG ? "Debug on ($DEBUG).\n\n" : ""; };
+ $DEBUG;
+}
+
+sub monitor {
+ my $level = shift;
+ if( defined $level) { $MONITOR = $level }
+ else { $MONITOR = 0 }
+ $DEBUG and (print STDERR "Monitor on ($MONITOR).\n\n");
+ $MONITOR;
+}
+
+sub testing {
+ my $level = shift;
+ if( defined $level) { $TESTING = $level }
+ else { $TESTING = 0 }
+ $TESTING ? ($MONITOR && print STDERR "Testing on ($TESTING).\n\n") : ($MONITOR && print STDERR "Testing off.\n\n");
+ $TESTING;
+}
+
+sub strictness {
+# Values can integers from -2 to 2
+# See Bio::Root::Object::strict() for more explanation.
+ my $arg = shift;
+ if( defined $arg) { $STRICTNESS = $arg}
+ $DEBUG && print STDERR "\n*** STRICTNESS: $arg ***\n\n";
+ $STRICTNESS;
+}
+
+sub verbosity {
+# Values can integers from -1 to 1
+# See Bio::Root::Object::verbose() for more explanation.
+ my $arg = shift;
+ if( defined $arg) { $VERBOSITY = $arg}
+ $DEBUG && print STDERR "\n*** VERBOSITY: $arg ***\n\n";
+ $VERBOSITY;
+}
+
+sub record_err {
+ if( defined shift) { $RECORD_ERR = 1}
+ else { $RECORD_ERR = 0 }
+ $RECORD_ERR ? ($DEBUG && print STDERR "\n*** RECORD_ERR on. ***\n\n") : ($DEBUG && print STDERR "RECORD_ERR off.\n\n");
+ $RECORD_ERR;
+}
+
+##
+## The following methods are deprecated and will eventually be removed.
+##
+
+sub dont_warn {
+ my $arg = shift;
+ print STDERR "\nDeprecated method dont_warn() called. Use verbosity(-1) instead\n";
+ if( $arg) { verbosity(-1)}
+ else { verbosity(0); }
+}
+
+sub warn_on_fatal {
+ my $arg = shift;
+ print STDERR "\nDeprecated method warn_on_fatal() called. Use strictness(-2) instead\n";
+ if( $arg) { strictness(-2)}
+ else { strictness(0); }
+}
+
+sub fatal_on_warn {
+ my $arg = shift;
+ print STDERR "\nDeprecated method fatal_on_warn() called. Use strictness(2) instead\n";
+ if( $arg) { strictness(2)}
+ else { strictness(0); }
+}
+
+#####################################################################################
+# END OF PACKAGE
+#####################################################################################
+
+1;
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