Bio::Variation::SeqDiff(3pm)

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new

  Title   : new
  Usage   : $seqDiff = Bio::Variation::SeqDiff->new;
  Function: generates a new Bio::Variation::SeqDiff
  Returns : reference to a new object of class SeqDiff
  Args    :

id

 Title   : id
 Usage   : $obj->id(H0001); $id = $obj->id();
 Function: 
           Sets or returns the id of the seqDiff.
           Should be used to give the collection of variants a UID
           without semantic associations.
 Example : 
 Returns : value of id, a scalar
 Args    : newvalue (optional)

sysname

 Title   : sysname
 Usage   : $obj->sysname('5C>G'); $sysname = $obj->sysname();
 Function: 
           Sets or returns the systematic name of the seqDiff.  The
           name should follow the HUGO Mutation Database Initiative
           approved nomenclature. If called without first setting the
           value, will generate it from L<Bio::Variation::DNAMutation>
           objects attached.
 Example : 
 Returns : value of sysname, a scalar
 Args    : newvalue (optional)

trivname

 Title   : trivname
 Usage   : $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname();
 Function: 
           Sets or returns the trivial name of the seqDiff.
           The name should follow the HUGO Mutation Database Initiative
           approved nomenclature. If called without first setting the
           value, will generate it from L<Bio::Variation::AAChange>
           objects attached.
 Example : 
 Returns : value of trivname, a scalar
 Args    : newvalue (optional)

chromosome

 Title   : chromosome
 Usage   : $obj->chromosome('X'); $chromosome = $obj->chromosome();
 Function: 
           Sets or returns the chromosome ("linkage group") of the seqDiff.
 Example : 
 Returns : value of chromosome, a scalar
 Args    : newvalue (optional)

gene_symbol

 Title   : gene_symbol
 Usage   : $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol;
 Function: 
           Sets or returns the gene symbol for the studied CDS.
 Example : 
 Returns : value of gene_symbol, a scalar
 Args    : newvalue (optional)

description

 Title   : description
 Usage   : $obj->description('short description'); $descr = $obj->description();
 Function: 
           Sets or returns the short description of the seqDiff.
 Example : 
 Returns : value of description, a scalar
 Args    : newvalue (optional)

alphabet

 Title   : alphabet
 Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
 Function: Returns the type of primary reference sequence being one of 
           'dna', 'rna' or 'protein'. This is case sensitive.
 Returns : a string either 'dna','rna','protein'. 
 Args    : none

numbering

 Title   : numbering
 Usage   : $obj->numbering('coding'); $numbering = $obj->numbering();
 Function: 
           Sets or returns the string giving the numbering schema used
           to describe the variants.
 Example : 
 Returns : value of numbering, a scalar
 Args    : newvalue (optional)

offset

 Title   : offset
 Usage   : $obj->offset(124); $offset = $obj->offset();
 Function: 
           Sets or returns the offset from the beginning of the DNA sequence 
           to the coordinate start used to describe variants. Typically
           the beginning of the coding region of the gene. 
           The cds_start should be 1 + offset.
 Example : 
 Returns : value of offset, a scalar
 Args    : newvalue (optional)

cds_start

 Title   : cds_start
 Usage   : $obj->cds_start(123); $cds_start = $obj->cds_start();
 Function: 
           Sets or returns the cds_start from the beginning of the DNA
           sequence to the coordinate start used to describe
           variants. Typically the beginning of the coding region of
           the gene. Needs to be and is implemented as 1 + offset.
 Example : 
 Returns : value of cds_start, a scalar
 Args    : newvalue (optional)

cds_end

 Title   : cds_end
 Usage   : $obj->cds_end(321); $cds_end = $obj->cds_end();
 Function: 
           Sets or returns the position of the last nucleotitide of the
           termination codon. The coordinate system starts from cds_start.
 Example : 
 Returns : value of cds_end, a scalar
 Args    : newvalue (optional)

rna_offset

 Title   : rna_offset
 Usage   : $obj->rna_offset(124); $rna_offset = $obj->rna_offset();
 Function: 
           Sets or returns the rna_offset from the beginning of the RNA sequence 
           to the coordinate start used to describe variants. Typically
           the beginning of the coding region of the gene. 
 Example : 
 Returns : value of rna_offset, a scalar
 Args    : newvalue (optional)

rna_id

 Title   : rna_id
 Usage   : $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id();
 Function: 
            Sets or returns the ID for original RNA sequence of the seqDiff.
 Example : 
 Returns : value of rna_id, a scalar
 Args    : newvalue (optional)

add_Variant

 Title   : add_Variant
 Usage   : $obj->add_Variant($variant)
 Function: 
           Pushes one Bio::Variation::Variant into the list of variants.
           At the same time, creates a link from the Variant to SeqDiff
           using its SeqDiff method.
 Example : 
 Returns : 1 when succeeds, 0 for failure.
 Args    : Variant object

each_Variant

 Title   : each_Variant
 Usage   : $obj->each_Variant();
 Function: 
            Returns a list of Variants.
 Example : 
 Returns : list of Variants
 Args    : none

add_Gene

 Title   : add_Gene
 Usage   : $obj->add_Gene($gene)
 Function: 
           Pushes one L<Bio::LiveSeq::Gene> into the list of genes.
 Example : 
 Returns : 1 when succeeds, 0 for failure.
 Args    : Bio::LiveSeq::Gene object

See Bio::LiveSeq::Gene for more information.

each_Gene

 Title   : each_Gene
 Usage   : $obj->each_Gene();
 Function: 
            Returns a list of L<Bio::LiveSeq::Gene>s.
 Example : 
 Returns : list of Genes
 Args    : none

dna_ori

 Title   : dna_ori
 Usage   : $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori();
 Function: 
            Sets or returns the original DNA sequence string of the seqDiff.
 Example : 
 Returns : value of dna_ori, a scalar
 Args    : newvalue (optional)

dna_mut

 Title   : dna_mut
 Usage   : $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut();
 Function: 
            Sets or returns the mutated DNA sequence of the seqDiff.
            If sequence has not been set generates it from the
            original sequence and DNA mutations.
 Example : 
 Returns : value of dna_mut, a scalar
 Args    : newvalue (optional)

rna_ori

 Title   : rna_ori
 Usage   : $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori();
 Function: 
            Sets or returns the original RNA sequence of the seqDiff.
 Example : 
 Returns : value of rna_ori, a scalar
 Args    : newvalue (optional)

rna_mut

 Title   : rna_mut
 Usage   : $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut();
 Function: 
            Sets or returns the mutated RNA sequence of the seqDiff.
 Example : 
 Returns : value of rna_mut, a scalar
 Args    : newvalue (optional)

aa_ori

 Title   : aa_ori
 Usage   : $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori();
 Function: 
            Sets or returns the original protein sequence of the seqDiff.
 Example : 
 Returns : value of aa_ori, a scalar
 Args    : newvalue (optional)

aa_mut

 Title   : aa_mut
 Usage   : $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut();
 Function: 
            Sets or returns the mutated protein sequence of the seqDiff.
 Example : 
 Returns : value of aa_mut, a scalar
 Args    : newvalue (optional)

seqobj

 Title   : seqobj
 Usage   : $dnaobj = $obj->seqobj('dna_mut');
 Function: 
            Returns the any original or mutated sequences as a
            Bio::PrimarySeq object.
 Example : 
 Returns : Bio::PrimarySeq object for the requested sequence
 Args    : string, method name for the sequence requested

See Bio::PrimarySeq for more information.

alignment

 Title   : alignment
 Usage   : $obj->alignment
 Function: 
           Returns a pretty RNA/AA sequence alignment from linked
           objects.  Under construction: Only simple coding region
           point mutations work.
 Example : 
 Returns : 
 Args    : none