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bio::search::result::wabaresult(3pm) [debian man page]

Bio::Search::Result::WABAResult(3pm)			User Contributed Perl Documentation		      Bio::Search::Result::WABAResult(3pm)

NAME

       Bio::Search::Result::WABAResult - Result object for WABA alignment output

SYNOPSIS

       # use this object exactly as you would a GenericResult # the only extra method is query_database which is the # name of the file where the
       query sequence came from

DESCRIPTION

       This object is for WABA result output, there is little difference between this object and a GenericResult save the addition of one method
       query_database.	Expect many of the fields for GenericResult to be empty however as WABA was not intended to provide a lot of extra
       information other than the alignment.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       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 with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Search::Result::WABAResult->new();
	Function: Builds a new Bio::Search::Result::WABAResult object
	Returns : Bio::Search::Result::WABAResult
	Args	: -query_database => "name of the database where the query came from"

   query_database
	Title	: query_database
	Usage	: $obj->query_database($newval)
	Function: Data field for the database filename where the
		  query sequence came from
	Returns : value of query_database
	Args	: newvalue (optional)

   All other methods are inherited from Bio::Search::Result::GenericResult
       See the Bio::Search::Result::GenericResult for complete documentation of the rest of the methods that are available for this module.

perl v5.14.2							    2012-03-02				      Bio::Search::Result::WABAResult(3pm)

Check Out this Related Man Page

Bio::Search::HSP::FastaHSP(3pm) 			User Contributed Perl Documentation			   Bio::Search::HSP::FastaHSP(3pm)

NAME

       Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data

SYNOPSIS

	 # get a FastaHSP from a SearchIO stream
	 my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');

	 while( my $r = $in->next_result) {
	     while( my $hit = $r->next_result ) {
		  while( my $hsp = $hit->next_hsp ) {
		     print "smith-waterman score (if available): ",
			   $hsp->sw_score(),"
";
		  }
	     }
	 }

DESCRIPTION

       Describe the object here

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       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 with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Search::HSP::FastaHSP->new();
	Function: Builds a new Bio::Search::HSP::FastaHSP object
	Returns : Bio::Search::HSP::FastaHSP
	Args	: -swscore => smith-waterman score

   sw_score
	Title	: sw_score
	Usage	: $obj->sw_score($newval)
	Function: Get/Set Smith-Waterman score
	Returns : value of sw_score
	Args	: newvalue (optional)

   evalue2
	Title	: evalue2
	Usage	: $obj->evalue2($newval)
	Function: Get/Set E2() expectation value
	Returns : value of evalue2
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					   Bio::Search::HSP::FastaHSP(3pm)
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