Hello Again,
I may have spoke to soon. The problem describe below occurs whenever I
search a feature that doesn't belong to the reference class. I've tried
it with both features of types that are automatic classes and those that
are not. If the feature name doesn't exist it provides a proper error
page but if it does it throw the 'missing FROM-clause entry for table
"sub_f"' error.
below is the general section of my conf as Cyril requested.
----- BEGIN ----------------
[GENERAL]
# ---------------------------- #
# --- Database Information --- #
# ---------------------------- #
description = S. salar Physical Map
db_adaptor = Bio::DB::Das::Chado
database = dbi:Pg:dbname=XXXXXX
user = XXXXX
pass = XXXXXX
db_args = -dsn yourConnectString
-enable_seqscan 0
-srcfeatureslice 1
-do2Level 1
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
js = /gbrowse/js
tmpimages = /gbrowse/tmp /home/asalbase/dev/htdocs/gbrowse/tmp
# where to link to when user clicks in detailed view
link = AUTO
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
default features = FPC_Contigs PCR_Markers BAC_Clones
# The class of the feature that is used as the reference for all others
reference class = ultracontig
# This option controls what feature to show when the user first visits
initial landmark = fps1
# max default and min segment sizes for detailed view
max segment = 10000000
default segment = 500000
min segment = 20
# zoom levels
zoom levels = 50 100 200 1000 2000 5000 10000 20000 50000 100000
200000 500000 1000000 2000000 5000000
# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources = 1
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
# ------------------------------ #
# --- Searching The Database --- #
# ------------------------------ #
# "automatic" classes to try when an unqualified identifier is given
automatic classes = contig BAC_cloned_genomic_insert STS
instructions = "Type in the name of a contig, clone or marker."
# "automatic" classes to try when an unqualified identifier is given
automatic classes = contig BAC_cloned_genomic_insert STS
instructions = "Type in the name of a contig, clone or marker."
# ---------------------- #
# --- HTML Insertion --- #
# ---------------------- #
# inside the <head></head> section
head = <link rel="stylesheet" type="text/css" href="/css/asalbase.css" />
# at the top...
header =
# a footer
footer = <p>Footer PlaceMarker</p>
# Various places where you can insert your own HTML -- see configuration
docs
html1 = sub { use lib '/home/asalbase/dev/perl-lib'; }
html2 =
html3 =
html4 =
html5 =
html6 =
-------------- END ------------------------
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