NAME

       Bio::LiveSeq::Transcript - Transcript class for LiveSeq

SYNOPSIS

         # documentation needed

DESCRIPTION

       This stores information about coding sequences (CDS).  The implementation is that a
       Transcript object accesses a collection of Exon objects, inferring from them the
       nucleotide structure and sequence.

AUTHOR - Joseph A.L. Insana

       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

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

   new
         Title   : new
         Usage   : $transcript = Bio::LiveSeq::Transcript->new(-exons => \@obj_refs);

         Function: generates a new Bio::LiveSeq::Transcript
         Returns : reference to a new object of class Transcript
         Errorcode -1
         Args    : reference to an array of Exon object references

   all_Exons
        Title   : all_Exons
        Usage   : $transcript_obj->all_Exons()
        Function: returns references to all Exon objects the Transcript is composed of
        Example : foreach $exon ($transcript->all_Exons()) { do_something }
        Returns : array of object references
        Args    : none

   downstream_seq
        Title   : downstream_seq
        Usage   : $transcript_obj->downstream_seq()
                : $transcript_obj->downstream_seq(64)
        Function: returns a string of nucleotides downstream of the end of the
                  CDS. If there is some information of the real mRNA, from features in
                  an attached Gene object, it will return up to those boundaries.
                  Otherwise it will return 1000 nucleotides.
                  If an argument is given it will override the default 1000 number
                  and return instead /that/ requested number of nucleotides.
                  But if a Gene object is attached, this argument will be ignored.
        Returns : string
        Args    : an optional integer number of nucleotides to be returned instead of
                  the default if no gene attached

   upstream_seq
        Title   : upstream_seq
        Usage   : $transcript_obj->upstream_seq()
                : $transcript_obj->upstream_seq(64)
        Function: just like downstream_seq but returns nucleotides before the ATG
        Note    : the default, if no Gene information present and no nucleotides
                  number given, is to return up to 400 nucleotides.

   get_Translation
         Title   : valid
         Usage   : $translation = $obj->get_Translation()
         Function: retrieves the reference to the object of class Translation (if any)
                   attached to a LiveSeq object
         Returns : object reference
         Args    : none

   translation_table
        Title   : translation_table
        Usage   : $name = $obj->translation_table;
                : $name = $obj->translation_table(11);
        Function: Returns or sets the translation_table used for translating the
                  transcript.
                  If it has never been set, it will return undef.
        Returns : an integer

   frame
        Title   : frame
        Usage   : $frame = $transcript->frame($label);
        Function: Returns the frame of a particular nucleotide.
                  Frame can be 0 1 or 2 and means the position in the codon triplet
                  of the particulat nucleotide. 0 is the first codon_position.
                  Codon_position (1 2 3) is simply frame+1.
                  If the label asked for is not inside the Transcript, -1 will be
                  returned.
        Args    : a label
        Returns : 0 1 or 2
        Errorcode -1