bio::matrix::scoring(3pm) [debian man page]

Bio::Matrix::Scoring(3pm)				User Contributed Perl Documentation				 Bio::Matrix::Scoring(3pm)

NAME

       Bio::Matrix::Scoring - Object which can hold scoring matrix information

SYNOPSIS

	 use Bio::Matrix::Scoring;

DESCRIPTION

       An object which can handle AA or NT scoring matrix information.	Some transformation properties are available too.

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-dot-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::Matrix::Scoring->new();
	Function: Builds a new Bio::Matrix::Scoring object
	Returns : an instance of Bio::Matrix::Scoring
	Args	:

   entropy
	Title	: entropy
	Usage	: $obj->entropy($newval)
	Function:
	Example :
	Returns : value of entropy (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   expected_score
	Title	: expected_score
	Usage	: $obj->expected_score($newval)
	Function:
	Example :
	Returns : value of expected (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   scale
	Title	: scale
	Usage	: $obj->scale($newval)
	Function:
	Example :
	Returns : value of scale (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   scale_value
	Title	: scale_value
	Usage	: $obj->scale_value($newval)
	Function:
	Example :
	Returns : value of scale_value (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function:
	Example :
	Returns : value of description (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   database
	Title	: database
	Usage	: $obj->database($newval)
	Function:
	Example :
	Returns : value of database (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   lowest_score
	Title	: lowest_score
	Usage	: $obj->lowest_score($newval)
	Function:
	Example :
	Returns : value of lowest_score (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   highest_score
	Title	: highest_score
	Usage	: $obj->highest_score($newval)
	Function:
	Example :
	Returns : value of highest_score (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   lambda
	Title	: lambda
	Usage	: $obj->lambda($newval)
	Function:
	Example :
	Returns : value of lambda (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   H
	Title	: H
	Usage	: $obj->H($newval)
	Function:
	Example :
	Returns : value of H (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02						 Bio::Matrix::Scoring(3pm)

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NAME

       SVG::Frame - SVG::Frame object

METHODS

   new
	Title	: new
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   init
	Title	: init
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   add_glyph
	Title	: add_glyph
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   add_group
	Title	: add_group
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   groups
	Title	: groups
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   add_data
	Title	: add_data
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   all_data
	Title	: all_data
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   data
	Title	: data
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   glyphs
	Title	: glyphs
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   data_chunks
	Title	: data_chunks
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   draw
	Title	: draw
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _recalculate_stats
	Title	: _recalculate_stats
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _parent_svg
	Title	: _parent_svg
	Usage	: $obj->_parent_svg($newval)
	Function:
	Example :
	Returns : value of _parent_svg (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   _parent_group
	Title	: _parent_group
	Usage	: $obj->_parent_group($newval)
	Function:
	Example :
	Returns : value of _parent_group (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   svg
	Title	: svg
	Usage	: $obj->svg($newval)
	Function:
	Example :
	Returns : value of svg (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   xsize
	Title	: xsize
	Usage	: $obj->xsize($newval)
	Function:
	Example :
	Returns : value of xsize (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   ysize
	Title	: ysize
	Usage	: $obj->ysize($newval)
	Function:
	Example :
	Returns : value of ysize (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   xoffset
	Title	: xoffset
	Usage	: $obj->xoffset($newval)
	Function:
	Example :
	Returns : value of xoffset (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   yoffset
	Title	: yoffset
	Usage	: $obj->yoffset($newval)
	Function:
	Example :
	Returns : value of yoffset (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   xmin
	Title	: xmin
	Usage	: $obj->xmin($newval)
	Function:
	Example :
	Returns : value of xmin (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   xmax
	Title	: xmax
	Usage	: $obj->xmax($newval)
	Function:
	Example :
	Returns : value of xmax (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   ymin
	Title	: ymin
	Usage	: $obj->ymin($newval)
	Function:
	Example :
	Returns : value of ymin (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   ymax
	Title	: ymax
	Usage	: $obj->ymax($newval)
	Function:
	Example :
	Returns : value of ymax (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   xrange
	Title	: xrange
	Usage	: $obj->xrange($newval)
	Function:
	Example :
	Returns : value of xrange (a scalar)

   yrange
	Title	: yrange
	Usage	: $obj->yrange($newval)
	Function:
	Example :
	Returns : value of yrange (a scalar)

   stack
	Title	: stack
	Usage	: $obj->stack($newval)
	Function:
	Example :
	Returns : value of stack (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.10.0							    2009-01-07								Frame(3pm)

Linux and UNIX Man Pages

bio::matrix::scoring(3pm) [debian man page]

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