made documentation more contig based

docs/ensembl.txt

 
 Ensembl is a software system to automatically analyses and maintain
 the analysis on genomic DNA. It is entirely open source (BSD style
-license) and is run openly from http://ensembl.ebi.ac.uk/. Please go
+license) and is run openly from http://www.ensembl.org/. Please go
 the web site for the most up to date documentation, code and
 discussion.
 
@@ -49,9 +49,15 @@ objects are as follows:
 
    Bio::EnsEMBL::DBSQL::Obj    - The Ensembl database object
    Bio::EnsEMBL::DBSQL::Clone  - A Clone (sequencing unit) 
-   Bio::EnsEMBL::DBSQL::Contig - A Contig, being continuous DNA sequenced together.
-                                 A Clone has a number of contigs: finished clones
-                                 have one Contig, working draft clones have more than one.
+   Bio::EnsEMBL::DBSQL::RawContig - 
+                        
+	           A Contig, being continuous DNA sequenced together.
+                   A Clone has a number of contigs: finished clones
+                   have one Contig, working draft clones have more than one.
+
+   Bio::EnsEMBL::DB::VirtualContig - A in-software contig made from a number
+                  of RawContigs put together due to overlap or sized gapped
+                  information
 
 NB. We call contigs of DNA which span across a number of clones
 "CloneContigs". The Contig object above refers to what comes out of
@@ -64,19 +70,20 @@ the assembly process in working draft data.
 
 The gene objects can hold the following cases:
   
-   a) Gene structures across pieces of DNA sequence where the interveaning sequence is
-not known (nor do we have to assumme a length to them)
+   a) Gene structures across pieces of DNA sequence where the
+interveaning sequence is not known (nor do we have to assumme a length
+to them)
 
-   b) Alternative transcripts of a Gene. A distinction is made between alternative
-transcripts producing unique cDNAs and alternative protein coding products. In other
-words, a Gene could produce 5 unique cDNA structures, but only 3 unique protein 
-structures, with 3 of the 5 cDNAs making the same protein but differing in their
-UTRs.
+   b) Alternative transcripts of a Gene. A distinction is made between
+alternative transcripts producing unique cDNAs and alternative protein
+coding products. In other words, a Gene could produce 5 unique cDNA
+structures, but only 3 unique protein structures, with 3 of the 5
+cDNAs making the same protein but differing in their UTRs.
 
    Ensembl also reuses a number of Bioperl objects, in particular 
 
    Bio::Seq                 - Sequence object 
-   Bio::AnnSeq              - Annotated sequence object
+   Bio::PrimarySeq          - Light weight, "just the sequence" object
    Bio::SeqFeature::Generic - Generic seq feature base class 
    Bio::SeqFeature::Homol   - seq feature class representing a similarity hit.
 
@@ -109,22 +116,31 @@ Bio::EnsEMBL::DBSQL::Clone  - A Clone (sequencing unit)
   @contigs = $clone->get_all_Contigs(); - All contigs in a clone
   $version = $clone->version();         - Version of the clone, from Ensembl's perspective
   $version = $clone->embl_version();    - Version of the data in the clone
-  $seq     = $clone->seq                - Bio::Seq of DNA data, with N's between contigs
-  $annseq  = $clone->get_AnnSeq();      - Bio::AnnSeq, with Genes attached on Clone
-                                          Able to dump the clone in EMBL/GenBank format
 
-Bio::EnsEMBL::DBSQL::Contig - A Contig (contingous DNA in one sequencing unit)
------------------------------------------------------------------------------
+Available on all contigs (whether Raw or Virtual)
+-------------------------------------------------
 
   @genes    = $contig->get_all_Genes()       - Gets all the genes attached to this contig
-  $seq      = $contig->seq()                 - The Bio::Seq of this contig
   @features = $contig->get_all_SeqFeatures() - All the computed sequence features for this
                                                contig
-  $length   = $contig->length();             - Length of the contig (far better than $seq->seq_len)
-  $order    = $contig->order();              - Which contig order this is thought to be
-  $strand   = $contig->orientation();        - Which strand this contig is on
-  $offset   = $contig->offset();             - Offset of the contig 
+  $length   = $contig->length();             - Length of the contig
+
+  Contigs also inheriet from Bio::SeqI this means that the following
+methods work:
+
+   @sf = $contig->top_SeqFeatures(); # genes map to virtual genes
+   $seq = $contig->seq(); # sequence as a string
+   $seq = $contig->subseq(100,200); # sequence as a string
 
+They can also be used to provide EMBL/GenBank flat files
+
+   $seqio = Bio::SeqIO->new('-format' => 'EMBL', -fh => \*STDOUT);
+   $seqio->write_seq($contig);
+
+They can also provide extensions to the left and right
+
+   # produces a new contig 1000 base pairs to the 3' of this contig
+   $newcontig = $contig->extend(1000,-1000); 
 
 Bio::EnsEMBL::Gene - A gene structure
 -------------------------------------
@@ -153,5 +169,14 @@ Methods inherieted from Bio::SeqFeature::Generic
 
   $start  = $exon->start()  - start position in bio coordinates. 
   $end    = $exon->end()    - end position in bio coordinates
-  $strand = $exon->strand() - 
+  $strand = $exon->strand() - 1 or -1
+
+
+
+
+
+
+
+
+