Search results for "distribution:FAST Bio::Search::HSP::HSPI"
FAST::Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
FAST::Bio::Search::HSP::HSPI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the FAST::Bio::Search::HSP::HSPI interface, you can do the following things with it:...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::PullHSPI - FAST::Bio::Search::HSP::HSPI interface for pull parsers.
PullHSP is for fast implementations that only do parsing work on the hsp data when you actually request information by calling one of the HSPI methods. Many methods of HSPI are implemented in a way suitable for inheriting classes that use FAST::Bio::...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::HSPFactory - A factory to create FAST::Bio::Search::HSP::HSPI 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 HSPs....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for FAST::Bio::Search::HSP::HSPI objects
FAST::Bio::SearchIO::Writer::HSPTableWriter generates output at the finest level of granularity for data within a search result. Data for each HSP within each hit in a search result is output in tab-delimited format, one row per HSP. Available Column...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::PullHitI - FAST::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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
FAST::Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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 FAST::Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For peopl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
This object implements a parser for hmmpfam hsp output, a program in the HMMER package....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::GenericHit - A generic implementation of the FAST::Bio::Search::Hit::HitI interface
This object handles the hit data from a Database Sequence Search such as FASTA or BLAST. Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects ar...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
This object implements a parser for BlastN hsp output....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't eve...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits
This object implements a parser for hmmpfam hit output, a program in the HMMER package....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
This object implements a parser for BLASTN hit output....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a FAST::Bio::Search::ResultI in Text.
This object implements the SearchWriterI interface which will produce a set of Text for a specific FAST::Bio::Search::Report::ReportI interface. You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %has...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC