static_golden_path
Gives coordinates for the same piece of DNA in 3 ways:
fpcctg_name  fpcctg_start  fpcctg_end 
raw_id       raw_start    raw_end      raw_ori
chr_name     chr_start    chr_end

raw_id points to the contig.internal_id

so usually raw_start is 1, and raw_end is the length of the contig

(fpcctg_ori is 1 by the construction of the fpcctg,
chr_ori is 1 by definition)

If it's not  in static_golden_path, then it's not viewable (at least 
not by the contig viewer).


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If put stuff back in contigview to allow negative positions and
use cluck in DBAdaptor::prepare then the following query results in an
error in Carp::Heavy  :
http://gruyere.cshl.org/perl/contigview?chr=R6_AP003714&vc_start=68028&vc_end=168027&vc_pix=588&vc_left=106&click_to_move_window.x=417&click_to_move_window.y=32

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The labels on the DNA(contigs) line are the clone names.
    ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/contig.pm
Can add links from contigs or clones there (see 'zmenu')

======================================================================

/protein_id="BAB40083.1"
http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi?val=BAB40083.1

/db_xref="GI:13486852"
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=13486852

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We probably should use id's
Exon = GRME+number instead of Exon+number
Transcript GRMT ... transc
Gene GRMG ... Gene
Translation GRMP ... transl
and the number should be 11 digits w/ leading 0's
But this has been fixed by adding the variables
$ENSEMBL_PREFIXE $ENSEMBL_PREFIXT $ENSEMBL_PREFIXG $ENSEMBL_PREFIXP
and making a few changes - the original lines are in
id_prefix.txt

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Color of Genes and transcripts depends on whether the gene ->is_known()
which = either the Gene or on of its transcripts has a DBLink
Known   rust
unknown black
ext     pine
hi      green
pseudo  grey2

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geneview requires the dna-fetching bug to be fixed

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"Prediction Method" has been commented out of geneview because it is
wrong now - we have imported external genes as internal.

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In order to indicate pseudo-genes, set type='pseudo'
They will appear gray on the transcript track

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Since we don't have supporting evidence yet, links to transview
are commented out of perl/geneview, perl/protview, perl/unisearch, 
and ensembl-draw/modules/Bio/EnsEMBL/GlyphSet/transcript.pm

======================================================================

The Region stuff in dumpcfgview has been commented out because we
don't have an assembly - clone is good enough

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Set debug=4 to get queries written to error_log

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Added to Clone:
->site  (Sequencing Site)     (and ->seqsite_html($site) to DBAdaptor)
->gi	(for GenBank Access)
->name  (BAC or PAC name)


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Right now in the clone table, modified=created=when submitted to Genbank

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prepare:
we may have  ' ... \' ... '
which should be changed to 
             ' ... '' ... '


======================================================================

added ->get_all_clones() to
Bio/EnsEMBL/Virtual/StaticContig.pm
which returns an array of Clone objects - all clones for the
contigs the virtual contig is built from.

======================================================================

