Permalink
Browse files

Merge branch 'master' of github.com:bioperl/bioperl-live

  • Loading branch information...
2 parents 7344785 + fe79811 commit e0e6cf811b47946e4622f294ed7419f40b304491 @bosborne bosborne committed Mar 8, 2013
Showing with 1,675 additions and 14,551 deletions.
  1. +1 −0 .travis.yml
  2. +41 −41 Bio/Biblio.pm
  3. +6 −12 Bio/DB/Ace.pm
  4. +105 −111 Bio/DB/Biblio/biofetch.pm
  5. +182 −187 Bio/DB/Biblio/soap.pm
  6. +12 −12 Bio/DB/GenBank.pm
  7. +0 −372 Bio/DB/GenericWebAgent.pm
  8. +1 −1 Bio/DB/IndexedBase.pm
  9. +25 −25 Bio/DB/NCBIHelper.pm
  10. +24 −17 Bio/DB/SeqFeature/Store/berkeleydb.pm
  11. +2 −1 Bio/DB/SeqVersion/gi.pm
  12. +41 −41 Bio/DB/WebDBSeqI.pm
  13. +0 −533 Bio/FeatureIO.pm
  14. +0 −245 Bio/FeatureIO/bed.pm
  15. +0 −996 Bio/FeatureIO/gff.pm
  16. +0 −85 Bio/FeatureIO/gtf.pm
  17. +0 −217 Bio/FeatureIO/interpro.pm
  18. +0 −269 Bio/FeatureIO/ptt.pm
  19. +0 −186 Bio/FeatureIO/vecscreen_simple.pm
  20. +218 −225 Bio/Perl.pm
  21. +9 −9 Bio/Root/Test.pm
  22. +0 −354 Bio/SearchIO/Writer/BSMLResultWriter.pm
  23. +0 −315 Bio/SearchIO/XML/BlastHandler.pm
  24. +0 −312 Bio/SearchIO/XML/PsiBlastHandler.pm
  25. +0 −474 Bio/SearchIO/blastxml.pm
  26. +4 −4 Bio/SearchIO/hmmer2.pm
  27. +0 −1,381 Bio/SeqFeature/Annotated.pm
  28. +2 −1 Bio/SeqIO.pm
  29. +1 −1 Bio/SeqIO/chadoxml.pm
  30. +78 −35 Bio/SeqIO/fasta.pm
  31. +574 −590 Bio/SeqUtils.pm
  32. +4 −1 Bio/Tools/Geneid.pm
  33. +4 −2 Bio/Tools/GuessSeqFormat.pm
  34. +0 −3 Build.PL
  35. +24 −4 Changes
  36. +5 −2 examples/biblio/biblio-eutils-example.pl
  37. +2 −2 examples/db/getGenBank.pl
  38. +0 −106 scripts/Bio-DB-EUtilities/bp_einfo.pl
  39. +0 −1,065 scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl
  40. +6 −5 scripts/utilities/bp_download_query_genbank.pl
  41. +0 −70 scripts/utilities/bp_search2BSML.pl
  42. +1 −1 t/AlignIO/phylip.t
  43. +6 −6 t/Annotation/Annotation.t
  44. +1 −1 t/Assembly/ContigSpectrum.t
  45. +20 −20 t/RemoteDB/GenBank.t
  46. +7 −8 t/RemoteDB/GenPept.t
  47. +1 −1 t/RemoteDB/SwissProt.t
  48. +49 −40 t/RemoteDB/Taxonomy.t
  49. +0 −531 t/SearchIO/blastxml.t
  50. +24 −1 t/SearchIO/hmmer.t
  51. +0 −106 t/SeqFeature/Annotated.t
  52. +0 −363 t/SeqFeature/FeatureIO.t
  53. +15 −15 t/SeqIO/genbank.t
  54. +0 −1 t/data/1.bed
  55. +0 −7 t/data/directives.gff3
  56. +0 −610 t/data/ecoli_domains.rps.xml
  57. +74 −0 t/data/hmmpfam_HSPdashline.txt
  58. +106 −0 t/data/hmmpfam_multiresult.out
  59. +0 −11 t/data/hybrid1.gff3
  60. +0 −17 t/data/knownGene.gff3
  61. +0 −660 t/data/mus.bls.xml
  62. +0 −1,219 t/data/newblast.xml
  63. +0 −383 t/data/plague_yeast.bls.xml
  64. +0 −1,826 t/data/psiblast.xml
  65. +0 −370 t/data/test.ptt
  66. +0 −42 t/data/vecscreen_simple.test_output
View
@@ -36,3 +36,4 @@ notifications:
branches:
only:
- master
+ - v1
View
@@ -198,8 +198,8 @@ with an underscore _.
package Bio::Biblio;
use strict;
-
-use base qw(Bio::Root::Root Bio::DB::BiblioI);
+use warnings;
+use parent qw(Bio::Root::Root Bio::DB::BiblioI);
# -----------------------------------------------------------------------------
@@ -259,41 +259,41 @@ sub new {
# we want to call SUPER to create and bless an object
if ($class =~ /Bio::DB::Biblio::(\S+)/) {
- my ($self) = $class->SUPER::new (@args);
+ my ($self) = $class->SUPER::new (@args);
- # now the $self is an empty object - we will populate it from
- # the $caller - if $caller is an object
+ # now the $self is an empty object - we will populate it from
+ # the $caller - if $caller is an object
- if (ref ($caller)) {
- %{ $self } = %{ $caller };
- }
+ if (ref ($caller)) {
+ %{ $self } = %{ $caller };
+ }
- # and finally add values from '@args' into the newly created
- # object (the values will overwrite the values copied above)
+ # and finally add values from '@args' into the newly created
+ # object (the values will overwrite the values copied above)
- $self->_initialize (@args);
- return $self;
+ $self->_initialize (@args);
+ return $self;
# this is called only the first time when somebody calls: 'new
# Bio::Biblio (...)', and it actually loads a 'real-work-doing'
# module and call this new() method again (unless the loaded
# module has its own new() method)
} else {
- my %param = @args;
- @param { map { lc $_ } keys %param } = values %param; # lowercase keys
- my $access =
- $param {'-access'} ||
- $class->_guess_access ( $param {'-location'} ) ||
- 'soap';
- $access = "\L$access"; # normalize capitalization to lower case
-
- # load module with the real implementation - as defined in $access
- return unless (&_load_access_module ($access));
-
- # this will call this same method new() - but rather its the
- # upper (object) branche
- return "Bio::DB::Biblio::$access"->new (@args);
+ my %param = @args;
+ @param { map { lc $_ } keys %param } = values %param; # lowercase keys
+ my $access =
+ $param {'-access'} ||
+ $class->_guess_access ( $param {'-location'} ) ||
+ 'soap';
+ $access = "\L$access"; # normalize capitalization to lower case
+
+ # load module with the real implementation - as defined in $access
+ return unless (&_load_access_module ($access));
+
+ # this will call this same method new() - but rather its the
+ # upper (object) branche
+ return "Bio::DB::Biblio::$access"->new (@args);
}
}
@@ -316,27 +316,27 @@ It prints an error on STDERR if it fails to find and load the module
=cut
sub _load_access_module {
- my ($access) = @_;
- my ($module, $load, $m);
+ my ($access) = @_;
+ my ($module, $load, $m);
- $module = "_<Bio/DB/Biblio/$access.pm";
- $load = "Bio/DB/Biblio/$access.pm";
+ $module = "_<Bio/DB/Biblio/$access.pm";
+ $load = "Bio/DB/Biblio/$access.pm";
- return 1 if $main::{$module};
- eval {
- require $load;
- };
+ return 1 if $main::{$module};
+ eval {
+ require $load;
+ };
- if ( $@ ) {
- Bio::Root::Root->throw (<<END);
+ if ( $@ ) {
+ Bio::Root::Root->throw (<<END);
$load: $access cannot be found or loaded
Exception $@
For more information about the Biblio system please see the Bio::Biblio docs.
END
;
- return;
- }
- return 1;
+ return;
+ }
+ return 1;
}
# -----------------------------------------------------------------------------
@@ -361,8 +361,8 @@ CORBA).
# services
sub _guess_access {
-# my ($class, $location) = @_;
- return 'soap';
+# my ($class, $location) = @_;
+ return 'soap';
}
=head2 VERSION and Revision
View
@@ -2,7 +2,7 @@
#
# BioPerl module for Bio::DB::Ace
#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
@@ -20,7 +20,7 @@ Bio::DB::Ace - Database object interface to ACeDB servers
$db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
- $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
+ $seq = $db->get_Seq_by_id('J00522'); # Unique ID
# or ...
@@ -62,15 +62,15 @@ Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -208,9 +208,3 @@ sub _aceobj {
}
1;
-
-
-
-
-
-
Oops, something went wrong.

0 comments on commit e0e6cf8

Please sign in to comment.