bioruby/bioruby-blast-xmlparser

Commits on Jun 14, 2019

Supporting BioRuby version is 2.0.0; Change xmlparser version specifi…

ngoto committed Jun 14, 2019
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…cation
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0218194

Commits on Jun 13, 2019

no more rescue LoadError because "xmlparser" should be provided by a gem

ngoto committed Jun 13, 2019

19e7eca
import files for gem

ngoto committed Jun 13, 2019

4a9e23d

Commits on Sep 15, 2017

Bio::Blast::Report.xmlparser is moved from lib/bio/appl/blast/report.rb

ngoto committed Sep 15, 2017

0d4ce83
xml_set_parameter() is moved to lib/bio/appl/blast/report.rb in bioru…

ngoto committed Sep 15, 2017
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…by core

Because the method xml_set_parameter is also used from the REXML parser.
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8e6aa62

Support for BLAST XML format with multiple queries after blastall 2.2.14

ngoto committed Aug 28, 2008

 * BLAST XML format with multiple query sequences generated by
   blastall 2.2.14 or later is now supported.
 * New methods Bio::Blast::Report#reports, stores Bio::Blast::Report
   objects corresponding to the multiple query sequences.
 * New methods Bio::Blast::Report::Iteration#query_id, query_def,
   and query_len, which are available only for the new format.
 * New class Bio::Blast::Report::BlastXmlSplitter, flatfile splitter
   for Bio::FlatFile system.
 * Bug fix: Bio::Blast::Report#expect returned incorrect value.
 * Fixed typo and added tests in test/unit/bio/appl/blast/test_report.rb.
 * Some RDoc documents added/modified.

a0e55fc

Merging differences between 1.17 and 1.18 into xmplarser.rb and between

ngoto committed May 12, 2008
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1.12 and 1.13 into rexml.rb.
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b1f9d90
Standardize on The Ruby License

trevor authored and ngoto committed Apr 5, 2007

267af5d
s/Lisence/License

trevor authored and ngoto committed Dec 31, 2006

8ab5dc2
* minor doc fix

ktym authored and ngoto committed Sep 19, 2006

883da7f
* changed license to Ruby's

nakao authored and ngoto committed Apr 30, 2006

3607262
* expanded tab at the line head

ktym authored and ngoto committed Sep 8, 2005

277dd8b
fixed a bug : some data heve been truncated after reference in xml data

ngoto committed Sep 29, 2003

afbe449
* s/S/C/ for n

ktym authored and ngoto committed Jun 16, 2003

5da6c62

* changed to use common Bio::Blast::Report class (bio/appl/blast/repo…

ktym authored and ngoto committed Feb 5, 2003

…rt.rb)

* format (-m 7 or -m 8) are automatically determined/detected
* all the parsers can be loaded at the same time
* added Bio::Blast::Report.{xmlparser,rexml,tab} class methods
* fixed some typo in xmlparser.rb methods

92267c4

* direction method removed (not return unique result)

ktym authored and ngoto committed Nov 22, 2002

d38f7c0
* doc added

ktym authored and ngoto committed Jul 2, 2002

335f53c
* added query_def, target_def, query_seq, target_seq, midline methods…

ktym authored and ngoto committed Jun 25, 2002
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… to Hit
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5627b60
* Report#hits corrected (not iterator!)

ktym authored and ngoto committed Jun 25, 2002
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* Report#statistics actually not removed and will not. :)
* test code updated
* doc fix.
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997401f

* Report#each is changed to iterate on the hits of the last iteration's.

ktym authored and ngoto committed Jun 25, 2002
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  * behavior will not change for blastall (iterates once), just useful
    for the blastpgp users.
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1057f77
* each_iteration, each_hit, each methods are added in Report class.

ktym authored and ngoto committed Jun 24, 2002
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* compatible methods for Fasta::Report::Hit are added in Hit class.
* test code rewrited - common with rexml.rb :)
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b221201
* test code fix

ktym authored and ngoto committed Jun 22, 2002

6873b4a
* parser separated, API renewal

ktym authored and ngoto committed May 28, 2002
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* supports new genomenet outputs (seems not working though - fixme)
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8637709