Thanks Cyril, that did the trick.
Cyril Pommier wrote:
> You should try to remove do2Level, it might be that this speed
> improvment does not work anymore
>
> Keith Anthony Boroevich a écrit :
>> 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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>
>
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