Search results for "distribution:BioPerl Bio::Search::Result::ResultI"
Bio::Search::Result::ResultI - Abstract interface to Search Result objects
Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few funda...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for 'pull' parsers
Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few funda...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects
This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser depending on what format report we are parsing. This object is for creating new Results....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects
The SearchUtils.pm module is a collection of subroutines used primarily by Bio::Search::Hit::HitI objects for some of the additional functionality, such as HSP tiling. Right now, the SearchUtils is just a collection of methods, not an object....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
This object is an implementation of the Bio::Search::Result::ResultI interface and provides a generic place to store results from a sequence database search. Unless you're writing a parser, you won't ever need to create a GenericResult or any other R...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::axt - a parser for axt format reports
This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those f...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::psl - A parser for PSL output (UCSC)
This is a SearchIO driver for PSL format. PSL format is documented here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL By default it assumes PSL output came from BLAT you can override that by specifying -program_name => 'BLASTZ' when in...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML
This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface. See Bio::SearchIO::SearchWriterI for more info on the filter method....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::wise - Parsing of wise output as alignments
This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output
This parser will process the waba output (NOT the human readable format)....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::sim4 - parser for Sim4 alignments
This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html Cannot parse LAV or 'exon file' formats (A=2 or A=5)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers.
This object handles the hit data from a database sequence search. PullHitI is for fast implementations that only do parsing work on the hit data when you actually request information by calling one of the HitI methods. Many methods of HitI are implem...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AnalysisParserI - Generic analysis output parser interface
AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derive...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::erpin - SearchIO-based ERPIN parser
This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::fasta - A SearchIO parser for FASTA results
This object contains the event based parsing code for FASTA format reports. It creates Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP objects. This module will parse -m 9 -d 0 output as well as default m 1 outp...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::blast - Event generator for event based parsing of blast reports
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a BLAST report file. Read the Bio::SearchIO for more information about how to use this. This driver can parse: * NCBI produced plain t...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the Bio::SearchIO for more information about how to use this. REVERSE STR...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO
This object is a subclass of Bio::SearchIO and provides some operations that facilitate working with CrossMatch and CrossMatch results. For general information about working with Results, see Bio::Search::Result::GenericResult....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC