# The standard options file for Artemis

# (Note that comment lines start with a hash (#) symbol)

# $Header: /nfs/disk222/yeastpub/Repository/powmap/etc/options,v 1.41 2000/08/31 10:10:48 kmr Exp $

# This file should contain option settings that look like this:
# 
# option_name = option_value
# 
# If the value of an options is too long to fit on one line it can be split
# over several lines by ending each line with a backslash like this:
# 
# option_name = option_value another_option_value \
#     a_third_option_value a_forth_option_value


# This option will set the font size for all the Artemis windows.

font_size = 14


# This option is used to set the default minimum size of a "large" open
# reading frame, which controls which ORFS are marked by the "Mark Open
# Reading Frames" menu item.

minimum_orf_size = 100


# This option gives the bases of the possible start codons

start_codons = atg


# This is the setting for S.coelicolor:
#   start_codons = atg gtg ttg


# The translation_table option is used to lookup codon translations.  The
# table must have exactly 64 entries, and there is one entry for each codon.
# The entries should appear in this order: 
#   TTT, TTC, TTA, TTG,
#   TCT, TCC, ...,
#   ...

# this is the default table:
#
# translation_table = \
#     f f l l \
#     s s s s \
#     y y # + \
#     c c * w \
#             \
#     l l l l \
#     p p p p \
#     h h q q \
#     r r r r \
#             \
#     i i i m \
#     t t t t \
#     n n k k \
#     s s r r \
#             \
#     v v v v \
#     a a a a \
#     d d e e \
#     g g g g

# this is the eukaryotic mitochondrial table:
#
# translation_table = \
#     f f l l \
#     s s s s \
#     y y * * \
#     c c w w \
#             \
#     l l l l \
#     p p p p \
#     h h q q \
#     r r r r \
#             \
#     i i m m \
#     t t t t \
#     n n k k \
#     s s * * \
#             \
#     v v v v \
#     a a a a \
#     d d e e \
#     g g g g


# the sequence of colour numbers must not have any gaps - if for example
# colour_5 is missing then all colours with higher numbers will be ignored

# the three numbers for each colour correspond to red, green and blue
# respectively.  each number is an intensity from 0 to 255

# white
colour_0 = 255 255 255
# dark grey
colour_1 = 100 100 100
# red
colour_2 = 255 0 0
# green
colour_3 = 0 255 0
# blue
colour_4 = 0 0 255
# cyan
colour_5 = 0 255 255
# magenta
colour_6 = 255 0 255
# yellow
colour_7 = 255 255 0
# pale green
colour_8 = 152 251 152
# light sky blue
colour_9 = 135 206 250
# orange
colour_10 = 255 165 0
# brown
colour_11 = 200 150 100
# pink
colour_12 = 255 200 200
# light grey
colour_13 = 170 170 170
# black
colour_14 = 0 0 0
# reds:
colour_15 = 255  63  63
colour_16 = 255 127 127
colour_17 = 255 191 191

colour_of_CDS = 5
colour_of_cds? = 7
colour_of_BLASTCDS = 2
colour_of_BLASTN_HIT = 6
colour_of_CRUNCH_D = 2
colour_of_source = 0
colour_of_prim_tran = 0
colour_of_stem_loop = 2
colour_of_misc_feature = 3
colour_of_misc_RNA = 12
colour_of_delta = 3
colour_of_LTR = 4
colour_of_repeat_region = 9
colour_of_repeat_unit = 9
colour_of_terminator = 3
colour_of_promoter = 3
colour_of_intron = 1
colour_of_exon = 7
colour_of_mRNA = 1
colour_of_tRNA = 8
colour_of_TATA = 3
colour_of_bldA = 2
colour_of_GFF = 11

colour_of_start_codon = 6


# this is the URL that contains the IOR of the EMBL server
embl_ior_url = http://corba.ebi.ac.uk/EMBL/IOR/Embl.IOR

# this is the URL that contains the IOR of the EnsEMBL server
# ensembl_ior_url = file:///nfs/disk12/kmr/powmap/db.ior


# if this option is "yes" the feature list will be displayed on startup (this
# is the default)
show_list = yes


# if this option is "yes" Sanger specific menu items and functions will be
# visible in the display
sanger_options = no


# the full path to the editor used for editing the qualifiers 
#external_editor = emacs


# this list is added to the keys from the feature_keys file
extra_keys = \
           BLASTN_HIT CDS_BEFORE CDS_AFTER CDS_before CDS_after \
           CDS_motif BLASTCDS polymorphism GFF WUBLASTN_HIT \
           WUBLASTX_HIT BLASTX_HIT TBLASTX_HIT BLASTN_HIT CRUNCH_D

# this list is added to the qualifiers from the qualifier_types file
extra_qualifiers = \
    fasta_file "text" \
    blast_file "text" \
    blastx_file "text" \
    blastn_file "text" \
    blastp_file "text" \
    tblastn_file "text" \
    tblastx_file "text" \
    bicsw_file "text" \
    hth_file "text" \
    sigcleave_file "text" \
    label text \
    colour text \
    class "text" \
    gene "text" \
    gff_seqname text \
    gff_feature text \
    gff_source text \
    gff_group text \
    blast_score text \
    subject_id text \
    query_id text \
    subject_start text \
    subject_end text \
    percent_id text \
    score text \
    hp_match "text" \
    fasta_match "text" \
    blastp_match "text" \
    pfam_match "text" \
    prosite_match "text"

# These pairs consist of a program name and a parameter string
feature_protein_programs = \
    fasta %SNTU \
    sigcleave 0 \
    blast swir \
    blastp swir \
    tblastn embl_other \
    hth -

feature_dna_programs = \
    tblastx embl_other \
    blastn embl_other \
    blastx swir

application_programs = \
    jalview
                     

# this is the list of keys that should be displayed by default in the edit
# window 
common_keys = \
    allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \
    mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \
    repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \
    tRNA unsure variation -10_signal -35_signal CDS_motif gene \
    BLASTN_HIT CDS_BEFORE CDS_AFTER BLASTCDS
