Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace

SYNOPSIS

           # get a Bio::Seq::Qual compliant object somehow
                 $st = &get_object_somehow();

           # to test this is a seq object
                 $st->isa("Bio::Seq::TraceI")
                      || $obj->throw("$obj does not implement the Bio::Seq::TraceI interface");

                 # set the trace for T to be @trace_points
            my $arrayref = $st->trace("T",\@trace_points);
                 # get the trace points for "C"
            my $arrayref = $st->trace("C");
                 # get a subtrace for "G" from 10 to 100
            $arrayref = $st->subtrace("G",10,100);
                 # what is the trace value for "A" at position 355?
            my $trace_calue = $st->traceat("A",355);
                 # create a false trace for "A" with $accuracy
            $arrayref = $st->false_trace("A",Bio::Seq::Quality, $accuracy);
                 # does this trace have entries for each base?
            $bool = $st->is_complete();
                 # how many entries are there in this trace?
            $length = $st->length();

DESCRIPTION

       This object defines an abstract interface to basic trace information. This information may
       have come from an ABI- or scf- formatted file or may have been made up.

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

AUTHOR - Chad Matsalla

       Email bioinformatics@dieselwurks.com

APPENDIX

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

Implementation Specific Functions

       These functions are the ones that a specific implementation must define.

   trace($base,\@new_values)
        Title   : trace($base,\@new_values)
        Usage   : @trace_Values  = @{$obj->trace($base,\@new_values)};
        Function: Returns the trace values as a reference to an array containing the
            trace values. The individual elements of the trace array are not validated
            and can be any numeric value.
        Returns : A reference to an array.
        Status  :
       Arguments: $base : which color channel would you like the trace values for?
                      - $base must be one of "A","T","G","C"
                 \@new_values : a reference to an array of values containing trace
                      data for this base

   subtrace($base,$start,$end)
        Title   : subtrace($base,$start,$end)
        Usage   : @subset_of_traces = @{$obj->subtrace("A",10,40)};
        Function: returns the trace values from $start to $end, where the
               first value is 1 and the number is inclusive, ie 1-2 are the first
               two trace values of this base. Start cannot be larger than end but can
               be equal.
        Returns : A reference to an array.
        Args    : $base: "A","T","G" or "C"
                 $start: a start position
                 $end  : an end position

   can_call_new()
        Title   : can_call_new()
        Usage   : if( $obj->can_call_new ) {
                    $newobj = $obj->new( %param );
                }
        Function: can_call_new returns 1 or 0 depending on whether an
               implementation allows new constructor to be called. If a new
               constructor is allowed, then it should take the followed hashed
               constructor list.
                  $myobject->new( -qual => $quality_as_string,
                                  -display_id  => $id,
                                  -accession_number => $accession,
                                  );
        Example :
        Returns : 1 or 0
        Args    :

   traceat($channel,$position)
        Title   : qualat($channel,$position)
        Usage   : $trace = $obj->traceat(500);
        Function: Return the trace value at the given location, where the
               first value is 1 and the number is inclusive, ie 1-2 are the first
               two bases of the sequence. Start cannot be larger than end but can
               be equal.
        Returns : A scalar.
        Args    : A base and a position.

   length()
        Title   : length()
        Usage   : $length = $obj->length("A");
        Function: Return the length of the array holding the trace values for the "A"
            channel. A check should be done to make sure that this Trace object
            is_complete() before doing this to prevent hazardous results.
        Returns : A scalar (the number of elements in the quality array).
        Args    : If used, get the traces from that channel. Default to "A"

   trace_indices($new_indices)
        Title   : trace_indices($new_indices)
        Usage   : $indices = $obj->trace_indices($new_indices);
        Function: Return the trace iindex points for this object.
        Returns : A scalar
        Args    : If used, the trace indices will be set to the provided value.