Fixed failing DBD test
Restoring intended behaviour... I think
More thoroughly documented options and defaults
fixing bug 3421 and adding test (hmmer2 now correctly parses full line of dashes)
fix indentation (remove tabs, 3 space and 2 space indentation)
use until instead of while(1){last if...}
follow perl recommendations:

* always 'use warnings'
* 'use parent' instead of base
* declare package variables with our, do not use vars
* do not load unused Carp package
fix indentation (remove tabs, and weird 3 spaces indentation)
follow perl recommendations:

* always 'use warnings'
* 'use parent' instead of base
* declare package variables with our, do not use vars
Don't use a separate default scalar when there's a hash with default key
Merge branch 'topic/bug3302'

* topic/bug3302:
  fixing bug 3302 and adding test
updating Changes file
Bio::Perl - fix indentation (remove tabs, and weird 3 spaces indentation)
Fixed no-hit blast bug and faulty regexs, added tests
Revert "Fixed no-hit blast bug and faulty regexs, added tests"

This reverts commit dc5696bd3ea191d8142a765fce81bc8f7560ba82.
Fix for Bug #3251, plus fixed a couple of regular expressions. Also added tests.
All Blast tests pass.
Bio::AlignIO::fasta was not always using />\s*(\S+)/ as its primary id. Modified it back to the simplest expected behaviour
typo, removed ->

Fix Conflicts:

	Bio/SeqIO/genbank.pm
fix conflict
Per: http://www.bioperl.org/wiki/Bioperl_Best_Practices and
http://modernperlbooks.com/books/modern_perl/chapter_11.html, "new Class"
is to avoided. "Class->new()" should be used instead because bareword
indirect invocations can lead to subtle errors

Fix conflicts:

	Bio/SeqIO/genbank.pm