Modware::Feature::CHROMOSOME - Modware representation of a chromosome

  NEVER INSTANTIATE THIS OBJECT, USE Modware::Feature or Modware::Chromosome

  ANOTHER INTERFACE TO CREATE THESE OBJECTS IS IN Modware::Chromosome where you can specify
    -chromosome_name or -chromosome_no as arguments

  USE CASE: write a fasta file for the chromsome

     my $chromosome = new Modware::Chromosome( -chromosome_name => '2' );
     print $chromosome->sequence( -format => 'fasta' );

 *********** COMING SOON ***********************************************
  USE CASE: write a genbank file WITH FEATURE ANNOTATIONS
     my $chromosome = new Modware::Chromosome( -chromosome_name => '2' );

     print $chromosome->to_file( -format => 'genbank' );

  THis object represents a chromosome.  

  The bioperl method returns a Bio::Seq object representing the chromosome.
  
  --------------------------------------------------
              Sequence editing
  --------------------------------------------------

  This is also the object where, currenlty, all sequence editing takes place.

  Contig reshuffling edits should use remove_contig and insert_contig.
  They both try to take care of things like inserting and removing adjacent gaps accordingly.

  change_bases is used for smaller scale sequence edits where you want to insert, delete, or replace some bases:
  
   CONTIGS UPSTREAM OF THE CHANGE WILL REMAIN UNCHANGED
   CONTIGS DOWNSTREAM OF THE CHANGE WILL BE SHIFTED BY THE APPROPRIATE AMOUNT
   THE CONTIG OVERLAPPING THIS CONTIG WILL HAVE ITS END MOVED BY THE APPROPRIATE AMOUNT
   CDS FEATURES DOWNSTREAM OF THE CHANGE WILL BE SHIFTED BY THE APPROPRIATE AMOUNT
   CDS FEATURES ENCLOSED BY CHANGE WILL BE DELETED!
   CDS FEATURES OVERLAPPING, BUT NOT ENCLOSED BY THE CHANGE WILL BE MARKED 'Corrupted' and otherwise be unchnaged

 Examples:
        $obj->change_bases('',   10);      delete nucleotide #10     
        $obj->change_bases('',   10, 2);   delete two nucleotides starting from #10
        $obj->change_bases('G',  10);      change nuc #10 to 'G'
        $obj->change_bases('GA', 10, 4);   replace #10 and 3 following with 'GA'
        $obj->change_bases('GA', 10, 2));  is same as $obj->change_bases('GA',  10);
        $obj->change_bases('GA', 10, 0 );  insert 'GA' before nucleotide at #10
        $obj->change_bases('GA', 10, 1);   GA inserted before #10, #10 deleted
        $obj->change_bases('GATC', 10, 2); GATC inserted before #10, #10&#11 deleted
        $obj->change_bases('GATC', 10, 6); GATC inserted before #10, #10-#15 deleted

  
  --------------------------------------------------
              Sequence dumping
  --------------------------------------------------

   The sequence can be dumped in any format through the 'sequence' method which takes one argument: -format
   if Bio::SeqIO can do it, you can specify it.  THIS WILL ONLY DUMP 

   The 'to_file' method is similar but it makes sure that all seqFeatures are included in the to_file, so that 
   annotated files ( embl, genbank, game ) can include all of these.

   Eric Just e-just@northwestern.edu

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