Bio::Search::Hit::BlastHit man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Search::Hit::BlasUser(Contributed Perl DocumBio::Search::Hit::BlastHit(3)

NAME
       Bio::Search::Hit::BlastHit - Blast-specific subclass of
       Bio::Search::Hit::GenericHit

SYNOPSIS
	   use Bio::Search::Hit::BlastHit;
	   my $hit = Bio::Search::Hit::BlastHit->new(-algorithm => 'blastp');

       # See Bio::Search::Hit::GenericHit for information about working with
       Hits.

       # TODO: Describe how to configure a SearchIO stream so that it
       generates #	 GenericHit objects.

DESCRIPTION
       This object is a subclass of Bio::Search::Hit::GenericHit and provides
       some operations that facilitate working with BLAST and PSI-BLAST Hits.

       For general information about working with Hits, see
       Bio::Search::Hit::GenericHit.

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:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich and Steve Chervitz
       Email jason@bioperl.org Email sac@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::Hit::GenericHit->new();
	Function: Builds a new Bio::Search::Hit::GenericHit object
	Returns : Bio::Search::Hit::GenericHit
	Args	: See Bio::Search::Hit::GenericHit() for other args.
		  Here are the BLAST-specific args that can be used when
		  creating BlastHit objects:
		  -iteration	=> integer for the PSI-Blast iteration number
		  -found_again	=> boolean, true if hit appears in a
				   "previously found" section of a PSI-Blast report.

   iteration
	Usage	  : $hit->iteration( $iteration_num );
	Purpose	  : Gets the iteration number in which the Hit was found.
	Example	  : $iteration_num = $sbjct->iteration();
	Returns	  : Integer greater than or equal to 1
		    Non-PSI-BLAST reports will report iteration as 1, but this number
		    is only meaningful for PSI-BLAST reports.
	Argument  : iteration_num (optional, used when setting only)
	Throws	  : none

       See Also	  : found_again()

   found_again
	Title	  : found_again
	Usage	  : $hit->found_again;
		    $hit->found_again(1);
	Purpose	  : Gets a boolean indicator whether or not the hit has
		    been found in a previous iteration.
		    This is only applicable to PSI-BLAST reports.

		     This method indicates if the hit was reported in the
		     "Sequences used in model and found again" section of the
		     PSI-BLAST report or if it was reported in the
		     "Sequences not found previously or not previously below threshold"
		     section of the PSI-BLAST report. Only for hits in iteration > 1.

	Example	  : if( $hit->found_again()) { ... };
	Returns	  : Boolean, true (1) if the hit has been found in a
		    previous PSI-BLAST iteration.
		    Returns false (0 or undef) for hits that have not occurred in a
		    previous PSI-BLAST iteration.
	Argument  : Boolean (1 or 0). Only used for setting.
	Throws	  : none

       See Also	  : iteration()

perl v5.14.1			  2011-07-22	 Bio::Search::Hit::BlastHit(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net