Bio::Seq TraceI
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Summary
Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Carp
Dumpvalue
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 = $st->length();
Description
This object defines an abstract interface to basic trace information. This
information may have come from an ABI- or scf- formatted file or may have been
made up.
Methods
traceDescriptionCode
subtraceDescriptionCode
can_call_newDescriptionCode
traceatDescriptionCode
lengthDescriptionCode
trace_indicesDescriptionCode
Methods description
trace($base,\@new_values)code    nextTop
 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)codeprevnextTop
 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()codeprevnextTop
 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,$position)codeprevnextTop
 Title   : qualat($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()codeprevnextTop
 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)codeprevnextTop
 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.
Methods code
tracedescriptionprevnextTop
sub trace {
   my ($self) = @_;
   if( $self->can('throw') ) {
       $self->throw("Bio::Seq::TraceI definition of trace - implementing class did not provide this method");
   } else {
       confess("Bio::Seq::TraceI definition of trace - implementing class did not provide this method");
   }
}
subtracedescriptionprevnextTop
sub subtrace {
   my ($self) = @_;

   if( $self->can('throw') ) {
       $self->throw("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method");
   } else {
       confess("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method");
   }
}
can_call_newdescriptionprevnextTop
sub can_call_new {
   my ($self,@args) = @_;
   # we default to 0 here
return 0;
}
traceatdescriptionprevnextTop
sub traceat {
   my ($self,$value) = @_;
   if( $self->can('warn') ) {
       $self->warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method");
   } else {
       warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method");
   }
   return '';
}
lengthdescriptionprevnextTop
sub length {
   my ($self)= @_;
   if( $self->can('throw') ) {
       $self->throw("Bio::Seq::TraceI definition of length - implementing class did not provide this method");
   } else {
       confess("Bio::Seq::TraceI definition of length - implementing class did not provide this method");
   }
}
trace_indicesdescriptionprevnextTop
sub trace_indices {
   my ($self)= @_;
   if( $self->can('throw') ) {
       $self->throw("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method");
   } else {
       confess("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method");
   }
}




1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 MatsallaTop
Email bioinformatics@dieselwurks.com
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Implementation Specific FunctionsTop
These functions are the ones that a specific implementation must
define.