# Sample tiers file (a simplified version of fly.tiers)

# This file describes to Apollo how different feature types should be
# displayed.
# Tiers files have two types of records: tier records and type records.
# Tiers are groupings of one or more types to be displayed together.
# [Tier] fields and the default values are:
# label :  false  (Group tier label)
# visible : true
# expanded : false
# sorted : false
# maxrows : maximum number of rows to show for this tier--default 0 means all
# labeled : false
# curated : false  [Whether to display in blue annotation zone]
# warnonedit : false  [Can also be used as a Type parameter to tag
#              individual types]
# number_of_levels : 3 [The default is 1, for one-level annotation types;
#                    use 3 for gene-like annotations (gene/transcript/exon)]
#
# The order in which tiers are listed in this file determines their
# vertical display order (the first tier is displayed closest to the
# central axis).
#
# TYPE fields:
#  tiername : the tier this type appears in
#  typename : label for this type
#  resulttype : data type(s) to be included this type
#  color : can be a standard color name (e.g. red) or an R,G,B triplet (default gray)
#  utr_color : color used for utr regions. Only works with
#              DrawableGeneFeatureSet. (default black)
#  usescore : default true  # use score to set the height of this glyph
#  minscore : 0 # minimum score for scaling height
#  maxscore : 100 # maximum score for scaling height
#  glyph : what glyph to use (mandatory).  Current choices include
# DrawableGeneFeatureSet (exons connected by peaked introns),
# DrawableResultFeatureSet (exons connected by straight lines),
# DoubleHeadedArrow, Triangle, Zigzag, ThinRectangle (a rectangular outline).
#  column : names of column(s) in detail table.  Choices include
# GENOMIC_RANGE, GENOMIC_LENGTH, MATCH_RANGE, MATCH_LENGTH,
# SCORE, NAME, READS.  You can also specify column names not in all caps
# that correspond to properties of the features present in the data (e.g.
# query_frame).
#  sortbycolumn : row order in table determined by this column
#  reversesort : Sort table rows in reverse order?  (default false)
#  groupby : GENE method to use for grouping features (GENE, SINGLE, HOMOLOGY)
#  weburl : optional, URL for pulling up web pages about this type of result
#  freshdate : date after which sequences of this type are considered "new"
# (the dates are found in the sequence descriptions)
#  idformat : format of IDs for this kind of annotation (regexp, e.g. CG\d+)
#  annot_type : when this result is promoted to an annotation, annot_type says
#  which type of annotation it should become.
#  warnonedit : false  [Overrides value of warnonedit setting, if any,
# for the parent tier]
#
# The fields for a Type or Tier record can appear in any order, one per
# line.  Be sure that none of the lines get broken up by inserted newlines.

[Tier]
tiername : Annotation
expanded : true
labeled : true
curated : true
warnonedit : false

# Default utr_color is "transparent" (same as AnnotationBackgroundColor defined in game.style)
# (So if you change AnnotationBackgroundColor, be sure to change utr_color to match!)
[Type]
label : gene
tiername : Annotation
datatype : gene
datatype : transcript
datatype : exon
glyph : DrawableGeneFeatureSet
color : 51,102,255
idformat : FBgn\d{7}
utr_color : 176,224,230
name_method : FlyNameAdapter
overlap_method : ORF_Overlap
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
number_of_levels : 3

[Type]
label : tRNA
tiername : Annotation
datatype : tRNA
glyph : DrawableResultFeatureSet
color : 0,204,0
idformat : FBgn\d{7}
name_method : FlyNameAdapter
overlap_method : ORF_Overlap
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE

[Type]
label : snRNA
tiername : Annotation
datatype : snRNA
glyph : DrawableResultFeatureSet
color : 0,204,0
idformat : FBgn\d{7}
name_method : FlyNameAdapter
overlap_method : ORF_Overlap
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE

[Type]
label : pseudogene
tiername : Annotation
datatype : pseudogene
glyph : DrawableResultFeatureSet
color : 153,153,255
idformat : FBgn\d{7}
name_method : FlyNameAdapter
overlap_method : ORF_Overlap
column : GENOMIC_RANGE
column : ID
number_of_levels : 3


[Tier]
tiername : Other annotated features
# expand while testing
expanded : true
labeled : true
curated : true
warnonedit : true

[Type]
label : P insertion_site
tiername : Other annotated features
datatype : p_insertion
datatype : P insertion_site
datatype : transposable_element_insertion_site
# There's an insertion_site in CG9884: P{PZ}oaf[E-32].  I assume it
# belongs in this tier.
datatype : insertion_site
glyph : Triangle
# Now hot pink--turquoise was too hard to see on aqua annotation background
color : 255,0,203
idformat : FBti\d{7}
name_method : FlyNameAdapter
overlap_method : NoOverlap
# column : SCORE
column : ID
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
label : promoter
tiername : Other annotated features
datatype : promoter
datatype : CAAT_signal
datatype : TATA_signal
datatype : -35_signal
datatype : -10_signal
datatype : GC_signal
glyph : PromoterGlyph
color : 255,255,51
idformat : CG\d+
name_method : FlyNameAdapter
overlap_method : NoOverlap
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
label : remark
tiername : Other annotated features
datatype : miscellaneous curator's observation
datatype : remark
glyph : Zigzag
color : 255,255,204
idformat : CR\d+
name_method : FlyNameAdapter
overlap_method : NoOverlap
column : GENOMIC_RANGE
column : ID

# ARGS types
[Type]
label : rescue fragment
tiername : Other annotated features
datatype : rescue_fragment
glyph : ThinRectangle
color : 153,51,255
name_method : FlyNameAdapter
overlap_method : NoOverlap
column : ID
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
label : point mutation
tiername : Other annotated features
datatype : point_mutation
glyph : Triangle
color : 0,102,204
name_method : FlyNameAdapter
overlap_method : NoOverlap
column : ID
column : GENOMIC_RANGE
sortbycolumn : GENOMIC_RANGE

# This tier is for showing new analysis results that you layer on with
# "Add analysis result".  I tried putting it at the beginning (before the
# Annotation tier) but that led to a weird display bug.
[Tier]
tiername : New analysis results
expanded : true
labeled : true

[Type]
label : New analysis results
tiername : New analysis results
glyph : DrawableResultFeatureSet
color : 255,255,0
usescore : true
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : Previous Releases
expanded : true

[Type]
label : Release 2 GadFly
tiername : Previous Releases
datatype : sim4:na_gadfly.dros
datatype : sim4:na_gadfly.dros.RELEASE2
glyph : DrawableResultFeatureSet
color : 153,255,255
usescore : true
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
label : Release 3.1 GadFly
tiername : Previous Releases
datatype : sim4:na_transcript.dmel.RELEASE31
glyph : DrawableResultFeatureSet
color : 0,204,255
usescore : true
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : Gene Prediction
expanded : true

[Type]
label : Genie
tiername : Gene Prediction
datatype : piecegenie
datatype : piecegenie:dummy
datatype : genie_masked:dummy
glyph : DrawableResultFeatureSet
color : 153,51,255
usescore : true
minscore : 100.0
column : SCORE
column : GENOMIC_RANGE
column : query_frame
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
weburl : http://www.fruitfly.org/seq_tools/genie.html#

[Type]
label : Genscan
tiername : Gene Prediction
datatype : genscan:dummy
datatype : genscan_masked:dummy
datatype : genscan
glyph : DrawableResultFeatureSet
color : 204,153,255
usescore : true
minscore : -1.0
maxscore : 50.0
column : SCORE
column : GENOMIC_RANGE
column : query_frame
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
weburl : http://genes.mit.edu/GENSCAN.html#

[Type]
label : Fgenesh
tiername : Gene Prediction
datatype : fgenesh:dummy
glyph : DrawableResultFeatureSet
color : 255,153,255
usescore : true
minscore : 100.0
column : SCORE
column : GENOMIC_RANGE
column : query_frame
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
weburl : http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind#

[Tier]
tiername : Fly EST
expanded : true

[Type]
label : Fly EST All
tiername : Fly EST
datatype : sim4:na_EST.complete.dros
datatype : sim4:na_EST.all_nr.dros
glyph : DrawableResultFeatureSet
color : 153,255,153
usescore : true
column : NAME
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=

[Type]
label : EST Same Strain
tiername : Fly EST
datatype : sim4:na_dbEST.same.dmel
glyph : DrawableResultFeatureSet
color : 153,255,153
usescore : true
column : NAME
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=
freshdate : Fri Jan 31 00:00:00 PST 2003

[Tier]
tiername : TBLASTX to Insects
expanded : true

[Type]
label : Ecore Agam
tiername : TBLASTX to Insects
datatype : ecore:intron
glyph : DrawableResultFeatureSet
color : 255,153,102
usescore : true
column : NAME
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY

[Type]
label : Dpse genomic
tiername : TBLASTX to Insects
datatype : tblastxwrap_masked:na_baylorf1_scfchunk.dpse
glyph : DrawableResultFeatureSet
color : 255,102,51
usescore : true
column : SCORE
column : identity
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY

[Tier]
tiername : BLASTX Similarity to Other Species
expanded : true

[Type]
label : Worm
tiername : BLASTX Similarity to Other Species
datatype : blastx_masked:aa_SPTR.worm
datatype : blastx:aa_SPTR.worm
glyph : DrawableResultFeatureSet
color : 255,153,0
usescore : true
column : SCORE
column : identity
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl : http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[swall-acc:__ID__]+-e
freshdate : Fri Jan 31 00:00:00 PST 2003

[Type]
label : Primate
tiername : BLASTX Similarity to Other Species
datatype : blastx_masked:aa_SPTR.primate
datatype : blastx:aa_SPTR.primate
glyph : DrawableResultFeatureSet
color : 255,153,0
usescore : true
column : SCORE
column : identity
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl : http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[swall-acc:__ID__]+-e
freshdate : Fri Jan 31 00:00:00 PST 2003

[Tier]
tiername : Start Codon

[Type]
label : startcodon_frame1
tiername : Start Codon
datatype : codons
datatype : startcodon_frame1
glyph : SiteCodon
color : 34,220,34
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
label : startcodon_frame2
tiername : Start Codon
datatype : codons
datatype : startcodon_frame2
glyph : SiteCodon
color : 34,220,34
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
label : startcodon_frame3
tiername : Start Codon
datatype : codons
datatype : startcodon_frame3
glyph : SiteCodon
color : 34,220,34
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Tier]
tiername : Stop Codon

[Type]
label : stopcodon_frame1
tiername : Stop Codon
datatype : codons
datatype : stopcodon_frame1
glyph : SiteCodon
color : red
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
label : stopcodon_frame2
tiername : Stop Codon
datatype : codons
datatype : stopcodon_frame2
glyph : SiteCodon
color : red
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
label : stopcodon_frame3
tiername : Stop Codon
datatype : codons
datatype : stopcodon_frame3
glyph : SiteCodon
color : red
column : NAME
column : GENOMIC_RANGE
sortbycolumn : NAME

[Tier]
tiername : Sequence selection

[Type]
label : Sequence selection
tiername : Sequence selection
datatype : Sequence selection
glyph : DrawableResultFeatureSet
color : orange
column : NAME
sortbycolumn : NAME

[Tier]
tiername : Do Not Show
visible : false

// Gaps (runs of Ns) can be shown as red squiggles at the axis
[Type]
tiername : Do Not Show
typename : Gap
resulttype : gap:gap
color : white
usescore : false
glyph : DrawableResultFeatureSet
column : SCORE
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE