NAME

       Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of      sequence based
       on quality.

SYNOPSIS

         use Bio::Tools::Alignment::Trim;
         $o_trim = Bio::Tools::Alignment::Trim->new();
         $o_trim->set_reverse_designator("R");
         $o_trim->set_forward_designator("F");

DESCRIPTION

       This is a specialized module designed by Chad for Chad to trim sequences based on a highly
       specialized list of requirements. In other words, write something that will trim sequences
       'just like the people in the lab would do manually'.

       I settled on a sliding-window-average style of search which is ugly and slow but does
       _exactly_ what I want it to do.

       Mental note: rewrite this.

       It is very important to keep in mind the context in which this module was written:
       strictly to support the projects for which Consed.pm was designed.

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@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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

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

AUTHOR - Chad Matsalla

       Email bioinformatics-at-dieselwurks.com

APPENDIX

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

   new()
        Title   : new()
        Usage   : $o_trim = Bio::Tools::Alignment::Trim->new();
        Function: Construct the Bio::Tools::Alignment::Trim object. No parameters
                  are required to create this object. It is strictly a bundle of
                  functions, as far as I am concerned.
        Returns : A reference to a Bio::Tools::Alignment::Trim object.
        Args    : (optional)
                  -windowsize (default 10)
                  -phreds (default 20)

   set_designators($forward_designator,$reverse_designator)
        Title   : set_designators(<forward>,<reverse>)
        Usage   : $o_trim->set_designators("F","R")
        Function: Set the string by which the system determines whether a given
               sequence represents a forward or a reverse read.
        Returns : Nothing.
        Args    : two scalars: one representing the forward designator and one
               representing the reverse designator

   set_forward_designator($designator)
        Title   : set_forward_designator($designator)
        Usage   : $o_trim->set_forward_designator("F")
        Function: Set the string by which the system determines if a given
               sequence is a forward read.
        Returns : Nothing.
        Args    : A string representing the forward designator of this project.

   set_reverse_designator($reverse_designator)
        Title   : set_reverse_designator($reverse_designator)
        Function: Set the string by which the system determines if a given
               sequence is a reverse read.
        Usage   : $o_trim->set_reverse_designator("R")
        Returns : Nothing.
        Args    : A string representing the forward designator of this project.

   get_designators()
        Title   : get_designators()
        Usage   : $o_trim->get_designators()
        Returns : A string describing the current designators.
        Args    : None
        Notes   : Really for informational purposes only. Duh.

   trim_leading_polys()
        Title   : trim_leading_polys()
        Usage   : $o_trim->trim_leading_polys()
        Function: Not implemented. Does nothing.
        Returns : Nothing.
        Args    : None.
        Notes   : This function is not implemented. Part of something I wanted to
               do but never got around to doing.

   dump_hash()
        Title   : dump_hash()
        Usage   : $o_trim->dump_hash()
        Function: Unimplemented.
        Returns : Nothing.
        Args    : None.
        Notes   : Does nothing.

   trim_singlet($sequence,$quality,$name,$class)
        Title   : trim_singlet($sequence,$quality,$name,$class)
        Usage   : ($r_trim_points,$trimmed_sequence) =
               @{$o_trim->trim_singlet($sequence,$quality,$name,$class)};
        Function: Trim a singlet based on its quality.
        Returns : a reference to an array containing the forward and reverse
               trim points and the trimmed sequence.
        Args    : $sequence : A sequence (SCALAR, please)
                  $quality : A _scalar_ of space-delimited quality values.
                  $name : the name of the sequence
                  $class : The class of the sequence. One of qw(singlet
                       singleton doublet pair multiplet)
        Notes   : At the time this was written the bioperl objects SeqWithQuality
               and PrimaryQual did not exist. This is what is with the clumsy
               passing of references and so on. I will rewrite this next time I
               have to work with it. I also wasn't sure whether this function
               should return just the trim points or the points and the sequence.
               I decided that I always wanted both so that's how I implemented
               it.
            - Note that the size of the sliding windows is set during construction of
              the Bio::Tools::Alignment::Trim object.

   trim_doublet($sequence,$quality,$name,$class)
        Title   : trim_doublet($sequence,$quality,$name,$class)
        Usage   : ($r_trim_points,$trimmed_sequence) =
                   @{$o_trim->trim_singlet($sequence,$quality,$name,$class)};
        Function: Trim a singlet based on its quality.
        Returns : a reference to an array containing the forward and reverse
        Args    : $sequence : A sequence
                  $quality : A _scalar_ of space-delimited quality values.
                  $name : the name of the sequence
                  $class : The class of the sequence. One of qw(singlet
                       singleton doublet pair multiplet)
        Notes   : At the time this was written the bioperl objects SeqWithQuality
               and PrimaryQual did not exist. This is what is with the clumsy
               passing of references and so on. I will rewrite this next time I
               have to work with it. I also wasn't sure whether this function
               should return just the trim points or the points and the sequence.
               I decided that I always wanted both so that's how I implemented
               it.

   chop_sequence($name,$class,$sequence,@points)
        Title   : chop_sequence($name,$class,$sequence,@points)
        Usage   : ($start_point,$end_point,$chopped_sequence) =
               $o_trim->chop_sequence($name,$class,$sequence,@points);
        Function: Chop a sequence based on its name, class, and sequence.
        Returns : an array containing three scalars:
               1- the start trim point
               2- the end trim point
               3- the chopped sequence
        Args    :
                  $name : the name of the sequence
                  $class : The class of the sequence. One of qw(singlet
                       singleton doublet pair multiplet)
                  $sequence : A sequence
                  @points : An array containing two elements- the first contains
                       the start trim point and the second conatines the end trim
                       point.

   _get_start($r_quals,$windowsize,$phreds,$offset)
        Title   : _get_start($r_quals,$windowsize,$phreds,$offset)
        Usage   : $start_base = $self->_get_start($r_windows,5,20);
        Function: Provide the start trim point for this sequence.
        Returns : a scalar representing the start of the sequence
        Args    :
               $r_quals : A reference to an array containing quality values. In
                       context, this array of values has been smoothed by then
                       sliding window-look ahead algorithm.
               $windowsize : The size of the window used when the sliding window
                       look-ahead average was calculated.
               $phreds : <fill in what this does here>
               $offset : <fill in what this does here>

   _get_end($r_qual,$windowsize,$phreds,$count)
        Title   : _get_end($r_qual,$windowsize,$phreds,$count)
        Usage   : my $end_base = &_get_end($r_windows,20,20,$start_base);
        Function: Get the end trim point for this sequence.
        Returns : A scalar representing the end trim point for this sequence.
        Args    :
               $r_qual : A reference to an array containing quality values. In
                       context, this array of values has been smoothed by then
                       sliding window-look ahead algorithm.
               $windowsize : The size of the window used when the sliding window
                       look-ahead average was calculated.
               $phreds : <fill in what this does here>
               $count : Start looking for the end of the sequence here.

   count_doublet_trailing_zeros($r_qual)
        Title   : count_doublet_trailing_zeros($r_qual)
        Usage   : my $start_of_trailing_zeros = &count_doublet_trailing_zeros(\@qual);
        Function: Find out when the trailing zero qualities start.
        Returns : A scalar representing where the zeros start.
        Args    : A reference to an array of quality values.
        Notes   : Again, this should be rewritten to use PrimaryQual objects.
               A more detailed explanation of why phrap puts these zeros here should
               be written and placed here. Please email and hassle the author.

   _sliding_window($r_quals,$windowsize)
        Title   : _sliding_window($r_quals,$windowsize)
        Usage   : my $r_windows = &_sliding_window(\@qual,$windowsize);
        Function: Create a sliding window, look-forward-average on an array
               of quality values. Used to smooth out differences in qualities.
        Returns : A reference to an array containing the smoothed values.
        Args    : $r_quals: A reference to an array containing quality values.
                  $windowsize : The size of the sliding window.
        Notes   : This was written before PrimaryQual objects existed. They
                  should use that object but I haven't rewritten this yet.

   _print_formatted_qualities
        Title   : _print_formatted_qualities(\@quals)
        Usage   : &_print_formatted_qualities(\@quals);
        Returns : Nothing. Prints.
        Args    : A reference to an array containing quality values.
        Notes   : An internal procedure used in debugging. Prints out an array nicely.

   _get_end_old($r_qual,$windowsize,$phreds,$count)
        Title   : _get_end_old($r_qual,$windowsize,$phreds,$count)
        Usage   : Deprecated. Don't use this!
        Returns : Deprecated. Don't use this!
        Args    : Deprecated. Don't use this!