Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module

SYNOPSIS

       Not used directly. Useful POD here for developers, however.

       The interface is designed to make the following code conversion as simple as possible:

       From:

        # Bio::Search::SearchUtils-based
        while ( local $_ = $result->next_hit ) {
           printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
             $hit->significance, $hit->frac_aligned_query, $hit->num_identical);
        }

       To:

        # TilingI-based
        while ( local $_ = $result->next_hit ) {
           my $tiling = Bio::Search::Tiling::MyTiling($_);
           printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n",
             $hit->significance, $tiling->frac_aligned_query, $tiling->num_identical);
        }

DESCRIPTION

       This module provides strong suggestions for any intended HSP tiling object implementation.
       An object subclassing TilingI should override the methods defined here according to their
       descriptions below.

       See the section STATISTICS METHODS for hints on implementing methods that are valid across
       different algorithms and report types.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen

       Email maj@fortinbras.us

APPENDIX

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

   STATISTICS METHODS
       The tiling statistics can be thought of as global counterparts to similar statistics
       defined for the individual HSPs. We therefore prescribe definitions for many of the
       synonymous methods defined in Bio::Search::HSP::HSPI.

       The tiling statistics must be able to keep track of the coordinate systems in which both
       the query and subject sequences exist; i.e., either nucleotide or amino acid. This
       information is typically inferred from the name of the algorithm used to perform the
       original search (contained in "$hit_object->algorithm"). Here is a table of algorithm
       information that may be useful (if you trust us).

        algorithm   query on hit   coordinates(q/h)
        ---------   ------------   ---------------
         blastn      dna on dna         dna/dna
         blastp      aa  on aa           aa/aa
         blastx      xna on aa          dna/aa
        tblastn      aa  on xna          aa/dna
        tblastx      xna on xna         dna/dna
          fasta      dna on dna         dna/dna
          fasta      aa  on aa           aa/aa
          fastx      xna on aa          dna/aa
          fasty      xna on aa          dna/aa
         tfasta      aa  on xna          aa/dna
         tfasty      aa  on xna          aa/dna
        megablast    dna on dna         dna/dna

         xna: translated nucleotide data

       Statistics methods must also be aware of differences in reporting among the algorithms.
       Hit attributes are not necessarily normalized over all algorithms. Devs, please feel free
       to add examples to the list below.

       NCBI BLAST vs WU-BLAST (AB-BLAST) lengths
           The total length of the alignment is reported differently between these two flavors.
           "$hit_object->length()" will contain the number in the denominator of the stats line;
           i.e., 120 in

            Identical = 34/120 Positives = 67/120

           NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a.
           "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the
           algorithm (a.k.a. "without gaps").

       Finally, developers should remember that sequence data may or may not be associated with
       the HSPs contained in the hit object. This will typically depend on whether a full report
       (e.g, "blastall -m0") or a summary (e.g., "blastall -m8") was parsed. Statistics methods
       that depend directly on the sequence data will need to check that that data is present.

   identities
        Title   : identities
        Alias   : num_identical
        Usage   : $num_identities = $tiling->identities()
        Function: Return the estimated or exact number of identities in the
                  tiling, accounting for overlapping HSPs
        Example :
        Returns : number of identical residue pairs
        Args    :

   conserved
        Title   : conserved
        Alias   : num_conserved
        Usage   : $num_conserved = $tiling->conserved()
        Function: Return the estimated or exact number of conserved sites in the
                  tiling, accounting for overlapping HSPs
        Example :
        Returns : number of conserved residue pairs
        Args    :

   length
        Title   : length
        Usage   : $max_length = $tiling->length($type)
        Function: Return the total number of residues of the subject or query
                  sequence covered by the tiling
        Returns : number of "logical" residues covered
        Args    : scalar $type, one of 'hit', 'subject', 'query'

   frac_identical
        Title   : frac_identical
        Usage   : $tiling->frac_identical($type)
        Function: Return the fraction of sequence length consisting
                  of identical pairs
        Returns : scalar float
        Args    : scalar $type, one of 'hit', 'subject', 'query'
        Note    : This method must take account of the $type coordinate
                  system and the length reporting method (see STATISTICS
                  METHODS above)

   percent_identity
        Title   : percent_identity
        Usage   : $tiling->percent_identity($type)
        Function: Return the fraction of sequence length consisting
                  of identical pairs as a percentage
        Returns : scalar float
        Args    : scalar $type, one of 'hit', 'subject', 'query'

   frac_conserved
        Title   : frac_conserved
        Usage   : $tiling->frac_conserved($type)
        Function: Return the fraction of sequence length consisting
                  of conserved pairs
        Returns : scalar float
        Args    : scalar $type, one of 'hit', 'subject', 'query'
        Note    : This method must take account of the $type coordinate
                  system and the length reporting method (see STATISTICS
                  METHODS above)

   percent_conserved
        Title   : percent_conserved
        Usage   : $tiling->percent_conserved($type)
        Function: Return the fraction of sequence length consisting
                  of conserved pairs as a percentage
        Returns : scalar float
        Args    : scalar $type, one of 'hit', 'subject', 'query'

   frac_aligned
        Title   : frac_aligned
        Usage   : $tiling->frac_aligned($type)
        Function: Return the fraction of B<input> sequence length consisting
                  that was aligned by the algorithm
        Returns : scalar float
        Args    : scalar $type, one of 'hit', 'subject', 'query'
        Note    : This method must take account of the $type coordinate
                  system and the length reporting method (see STATISTICS
                  METHODS above)

   range
        Title   : range
        Usage   : $tiling->range($type)
        Function: Returns the extent of the longest tiling
                  as ($min_coord, $max_coord)
        Returns : array of two scalar integers
        Args    : scalar $type, one of 'hit', 'subject', 'query'

TILING ITERATORS

   next_tiling
        Title   : next_tiling
        Usage   : @hsps = $self->next_tiling($type);
        Function: Obtain a tiling of HSPs over the $type ('hit', 'subject',
                  'query') sequence
        Example :
        Returns : an array of HSPI objects
        Args    : scalar $type: one of 'hit', 'subject', 'query', with
                  'subject' an alias for 'hit'

   rewind_tilings
        Title   : rewind_tilings
        Usage   : $self->rewind_tilings($type)
        Function: Reset the next_tilings($type) iterator
        Example :
        Returns : True on success
        Args    : scalar $type: one of 'hit', 'subject', 'query', with
                  'subject' an alias for 'hit'

INFORMATIONAL ACCESSORS

   algorithm
        Title   : algorithm
        Usage   : $tiling->algorithm
        Function: Retrieve the algorithm name associated with the
                  invocant's hit object
        Returns : scalar string
        Args    :