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added extensions

svn path=/bioperl-ext/branches/ewan/; revision=620
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0 parents commit cab3ef9de554774c998be081aed74043b80e1842 birney committed Sep 16, 1999
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  1. +51 −0 Bio/Ext/Align/Align.pm
  2. +3,313 −0 Bio/Ext/Align/Align.xs
  3. +21 −0 Bio/Ext/Align/Makefile.PL
  4. +31 −0 Bio/Ext/Align/blosum62.bla
  5. +2,587 −0 Bio/Ext/Align/libs/aln.c
  6. +977 −0 Bio/Ext/Align/libs/aln.h
  7. +586 −0 Bio/Ext/Align/libs/alnconvert.c
  8. +253 −0 Bio/Ext/Align/libs/alnconvert.h
  9. +908 −0 Bio/Ext/Align/libs/alnrange.c
  10. +297 −0 Bio/Ext/Align/libs/alnrange.h
  11. +464 −0 Bio/Ext/Align/libs/asciibtcanvas.c
  12. +126 −0 Bio/Ext/Align/libs/asciibtcanvas.h
  13. +370 −0 Bio/Ext/Align/libs/basematrix.c
  14. +274 −0 Bio/Ext/Align/libs/basematrix.h
  15. +361 −0 Bio/Ext/Align/libs/btcanvas.c
  16. +334 −0 Bio/Ext/Align/libs/btcanvas.h
  17. +743 −0 Bio/Ext/Align/libs/codon.c
  18. +462 −0 Bio/Ext/Align/libs/codon.h
  19. +226 −0 Bio/Ext/Align/libs/commandline.c
  20. +133 −0 Bio/Ext/Align/libs/commandline.h
  21. +677 −0 Bio/Ext/Align/libs/complexconsensi.c
  22. +327 −0 Bio/Ext/Align/libs/complexconsensi.h
  23. +437 −0 Bio/Ext/Align/libs/complexevalset.c
  24. +220 −0 Bio/Ext/Align/libs/complexevalset.h
  25. +1,004 −0 Bio/Ext/Align/libs/complexsequence.c
  26. +426 −0 Bio/Ext/Align/libs/complexsequence.h
  27. +708 −0 Bio/Ext/Align/libs/compmat.c
  28. +353 −0 Bio/Ext/Align/libs/compmat.h
  29. +30 −0 Bio/Ext/Align/libs/database.h
  30. +292 −0 Bio/Ext/Align/libs/dna.c
  31. +234 −0 Bio/Ext/Align/libs/dna.h
  32. +416 −0 Bio/Ext/Align/libs/dnamatrix.c
  33. +252 −0 Bio/Ext/Align/libs/dnamatrix.h
  34. +517 −0 Bio/Ext/Align/libs/dpenvelope.c
  35. +276 −0 Bio/Ext/Align/libs/dpenvelope.h
  36. +42 −0 Bio/Ext/Align/libs/dyna.h
  37. +81 −0 Bio/Ext/Align/libs/dynlibcross.c
  38. +54 −0 Bio/Ext/Align/libs/dynlibcross.h
  39. +1,565 −0 Bio/Ext/Align/libs/histogram.c
  40. +506 −0 Bio/Ext/Align/libs/histogram.h
  41. +1,441 −0 Bio/Ext/Align/libs/hscore.c
  42. +621 −0 Bio/Ext/Align/libs/hscore.h
  43. +230 −0 Bio/Ext/Align/libs/linesubs.c
  44. +50 −0 Bio/Ext/Align/libs/linesubs.h
  45. +51 −0 Bio/Ext/Align/libs/makefile
  46. +793 −0 Bio/Ext/Align/libs/packaln.c
  47. +328 −0 Bio/Ext/Align/libs/packaln.h
  48. +584 −0 Bio/Ext/Align/libs/probability.c
  49. +444 −0 Bio/Ext/Align/libs/probability.h
  50. +336 −0 Bio/Ext/Align/libs/protein.c
  51. +238 −0 Bio/Ext/Align/libs/protein.h
  52. +524 −0 Bio/Ext/Align/libs/proteindb.c
  53. +247 −0 Bio/Ext/Align/libs/proteindb.h
  54. +2,882 −0 Bio/Ext/Align/libs/proteinsw.c
  55. +343 −0 Bio/Ext/Align/libs/proteinsw.h
  56. +277 −0 Bio/Ext/Align/libs/seqaligndisplay.c
  57. +123 −0 Bio/Ext/Align/libs/seqaligndisplay.h
  58. +1,491 −0 Bio/Ext/Align/libs/sequence.c
  59. +613 −0 Bio/Ext/Align/libs/sequence.h
  60. +1,402 −0 Bio/Ext/Align/libs/sequencedb.c
  61. +445 −0 Bio/Ext/Align/libs/sequencedb.h
  62. +6,963 −0 Bio/Ext/Align/libs/sw.h
  63. +183 −0 Bio/Ext/Align/libs/sw_wrap.c
  64. +106 −0 Bio/Ext/Align/libs/sw_wrap.h
  65. +52 −0 Bio/Ext/Align/libs/wisebase.h
  66. +272 −0 Bio/Ext/Align/libs/wiseconfig.c
  67. +52 −0 Bio/Ext/Align/libs/wiseconfig.h
  68. +580 −0 Bio/Ext/Align/libs/wiseerror.c
  69. +323 −0 Bio/Ext/Align/libs/wiseerror.h
  70. +364 −0 Bio/Ext/Align/libs/wisefile.c
  71. +168 −0 Bio/Ext/Align/libs/wisefile.h
  72. +109 −0 Bio/Ext/Align/libs/wisememman.c
  73. +89 −0 Bio/Ext/Align/libs/wisememman.h
  74. +92 −0 Bio/Ext/Align/libs/wiseoverlay.c
  75. +74 −0 Bio/Ext/Align/libs/wiseoverlay.h
  76. +71 −0 Bio/Ext/Align/libs/wiserandom.c
  77. +72 −0 Bio/Ext/Align/libs/wiserandom.h
  78. +1,109 −0 Bio/Ext/Align/libs/wisestring.c
  79. +530 −0 Bio/Ext/Align/libs/wisestring.h
  80. +55 −0 Bio/Ext/Align/libs/wisetime.c
  81. +57 −0 Bio/Ext/Align/libs/wisetime.h
  82. +37 −0 Bio/Ext/Align/test.pl
  83. +351 −0 Bio/Ext/Align/typemap
  84. +24 −0 README
@@ -0,0 +1,51 @@
+
+
+
+package Bio::Ext::Align;
+
+use vars qw($AUTOLOAD @ISA @EXPORT_OK $dl_debug);
+use Exporter;
+use Carp;
+use strict;
+
+use DynaLoader;
+
+
+@ISA = qw(Exporter DynaLoader);
+# Items to export into callers namespace by default. Note: do not export
+# names by default without a very good reason. Use EXPORT_OK instead.
+# Do not simply export all your public functions/methods/constants.
+
+sub AUTOLOAD {
+ # This AUTOLOAD is used to 'autoload' constants from the constant()
+ # XS function. If a constant is not found then control is passed
+ # to the AUTOLOAD in AutoLoader.
+
+ my $constname;
+ ($constname = $AUTOLOAD) =~ s/.*:://;
+ my $val = constant($constname, @_ ? $_[0] : 0);
+ if ($! != 0) {
+ if ($! =~ /Invalid/) {
+ $AutoLoader::AUTOLOAD = $AUTOLOAD;
+ goto &AutoLoader::AUTOLOAD;
+ }
+ else {
+ croak "Your vendor has not defined Test macro $constname";
+ }
+ }
+ eval "sub $AUTOLOAD { $val }";
+ goto &$AUTOLOAD;
+}
+
+BEGIN {
+ $dl_debug = 40;
+}
+
+bootstrap Bio::Ext::Align; # hopefully has the correct things...
+
+# Preloaded methods go here.
+
+# Autoload methods go after __END__, and are processed by the autosplit program.
+
+1;
+__END__
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