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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

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

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!