Christopher Fields > BioPerl-1.6.901 > Bio::Tools::EUtilities::Link::LinkSet

Download:
BioPerl-1.6.901.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  12
Open  4
View/Report Bugs
Module Version: 1.006901   Source  

NAME ^

Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets

SYNOPSIS ^

  # ...

DESCRIPTION ^

  # ...

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
  http://www.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 the bugs and their resolution. Bug reports can be submitted via the web.

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

AUTHOR ^

Email cjfields at bioperl dot org

APPENDIX ^

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

get_ids

 Title    : get_ids
 Usage    : my @ids = $linkset->get_ids
 Function : returns list of retrieved IDs
 Returns  : array of IDs
 Args     : none
 Notes    : Cmd                   Description
            acheck                same as get_submitted_ids
            lcheck                same as get_submitted_ids
            ncheck                same as get_submitted_ids
            prlinks               same as get_submitted_ids
            llinks                same as get_submitted_ids
            llinkslib             same as get_submitted_ids
            neighbor              linked IDs for database in get_database
            neighbor_history      linked IDs for database in get_database

get_database

 Title    : get_database
 Usage    : my $db = $info->get_database;
 Function : returns single database name (eutil-compatible).  This is the
            queried database. For elinks (which have 'db' and 'dbfrom')
            this is equivalent to db/dbto (use get_dbfrom() to for the latter).
            Note that this only returns the first db; in some cases this may
            not be what you want (when multiple dbs are queried, for instance)
 Returns  : string
 Args     : none
 Notes    : with all elink cmd arguments

get_db (alias for get_database)

get_dbto (alias for get_database)

get_databases

 Title    : get_databases
 Usage    : my $string = $linkset->get_databases;
 Function : retrieve databases referred to for this linkset
            these may be present as a single database or embedded in 
 Returns  : array of strings
 Args     : none

get_dbs (alias for get_databases)

get_dbfrom

 Title    : get_dbfrom
 Usage    : my $string = $linkset->get_dbfrom;
 Function : retrieve originating database for this linkset
 Returns  : string
 Args     : none

get_link_names

 Title    : get_link_names
 Usage    : my $string = $linkset->get_link_names;
 Function : retrieve eutil-compatible link names
 Returns  : array of strings
 Args     : none
 Notes    : Each LinkSet can hold multiple LinkInfo objects (each containing
            a link name). Also, some LinkSets define a single link name. This
            returns an array with all unique linknames globbed both sources, if
            present and defined

get_link_name

 Title    : get_link_name
 Usage    : my $string = $linkset->get_link_name;
 Function : retrieve eutil-compatible link name
 Returns  : single link name
 Args     : none

get_submitted_ids

 Title    : get_submitted_ids
 Usage    : my $string = $linkset->get_submitted_ids;
 Function : retrieve original ID list
 Returns  : string
 Args     : none

has_scores

 Title    : has_scores
 Usage    : if (my $linkset->has_scores) {...}
 Function : returns TRUE if score data is present 
 Returns  : Boolean 
 Args     : none

get_scores

 Title    : get_scores
 Usage    : %scores = $linkset->get_scores;
 Function : returns flattened list or hash ref containing ID => score pairs
 Returns  : hash or hash ref (based on list or scalar context)
 Args     : none

get_score_by_id

 Title    : get_score_by_id
 Usage    : $score = $linkset->get_score_by_id($id);
 Function : returns the score for a particular primary ID
 Returns  : integer
 Args     : [REQUIRED] Primary ID for the score lookup

has_linkout

 Title    : has_linkout
 Usage    : if ($linkset->has_linkout) {...}
 Function : returns TRUE if the single ID present in this linkset has a linkout
 Returns  : boolean
 Args     : none
 Notes    : this checks cmd=lcheck (boolean for a linkout) and also backchecks
            cmd=acheck for databases with name 'LinkOut'

has_neighbor

 Title    : has_neighbor
 Usage    : if ($linkset->has_neighbor) {...}
 Function : returns TRUE if the single ID present in this linkset has a neighbor
            in the same database
 Returns  : boolean
 Args     : none
 Notes    : this checks cmd=ncheck (boolean for a neighbor in same database); no
            other checks performed at this time

next_UrlLink

 Title    : next_UrlLink
 Usage    : while (my $url = $linkset->next_UrlLink) {...}
 Function : iterate through UrlLink objects
 Returns  : Bio::Tools::EUtilities::Link::UrlLink
 Args     : 

get_UrlLinks

 Title    : get_UrlLinks
 Usage    : my @urls = $linkset->get_UrlLinks
 Function : returns all UrlLink objects
 Returns  : list of Bio::Tools::EUtilities::Link::UrlLink
 Args     : 

next_LinkInfo

 Title    : next_LinkInfo
 Usage    : while (my $info = $linkset->next_LinkInfo) {...}
 Function : iterate through LinkInfo objects
 Returns  : Bio::Tools::EUtilities::Link::LinkInfo
 Args     : 

get_LinkInfo

 Title    : get_LinkInfo
 Usage    : my @links = $linkset->get_LinkInfo
 Function : returns all LinkInfo objects
 Returns  : list of Bio::Tools::EUtilities::Link::LinkInfo
 Args     : 

rewind

 Title    : rewind
 Usage    : $info->rewind() # rewinds all (default)
            $info->rewind('links') # rewinds only links
 Function : 'rewinds' (resets) specified interators (all if no arg)
 Returns  : none
 Args     : [OPTIONAL] String: 
            'all'       - all iterators (default)
            'linkinfo' or 'linkinfos'  - LinkInfo objects only
            'urllinks'   - UrlLink objects only

to_string

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting
 Note     : Used generally for debugging and for various print methods
syntax highlighting: