[Gmod-apollo-cmts] CVS: apollo/conf rice.tiers,NONE,1.1

[Guanming Wu <gua...@us...>]

Update of /cvsroot/gmod/apollo/conf
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6511/apollo/conf

Added Files:
	rice.tiers 
Log Message:
rice tiers file: more work needed

--- NEW FILE: rice.tiers ---
# This file describes to Apollo how different features should be displayed.  
# There are two types of records: tier records and type lines.
# Tiers are groupings of one or more types to be displayed together.

# [Tier] fields and the default values
# 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

# 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).
# The fields for a Type or Tier record can appear in any order, one per line.

# 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.
#  column : names of column(s) in detail table.  Choices include
# 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 : for annotations, the result types that generate this type of annotation

[Tier]
tiername : Annotation
visible : true
expanded : true
maxrows : 0
labeled : true

[Type]
tiername : Annotation
typename : gene
resulttype : gene
resulttype : transcript
resulttype : exon
color : 51,102,255
# Default utr_color is "transparent" (same as AnnotationBackgroundColor defined in game.style)
utr_color : 176,224,230
usescore : false
glyph : DrawableGeneFeatureSet
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
overlap_method : ORF_Overlap
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : transposable_element
resulttype : transposable_element
color : 255,0,203
usescore : false
minscore : 0
maxscore : 0
glyph : DoubleHeadedArrow
column : GENOMIC_RANGE 
column : ID
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : tRNA
resulttype : tRNA
color : 0,204,0
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : snRNA
resulttype : snRNA
color : 0,204,0
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : snoRNA
resulttype : snoRNA
color : 0,204,0
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : ncRNA
resulttype : misc. non-coding RNA
resulttype : ncRNA
color : 0,204,0
usescore : false
glyph :	DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : rRNA
resulttype : rRNA
color : 0,204,0
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : miRNA
resulttype : microRNA
resulttype : miRNA
color : 0,204,0
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE
column : ID
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : pseudogene
resulttype : pseudogene
glyph : DrawableGeneFeatureSet
color : 153,153,255
usescore : false
scorethreshold : -1.0
column : GENOMIC_RANGE
column : ID
reversesort : false
groupby : GENE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : remark
resulttype : miscellaneous curator's observation
resulttype : remark
glyph : Zigzag 
color : 255,255,204
usescore : false
scorethreshold : -1.0
column : GENOMIC_RANGE
column : ID
reversesort : false
groupby : GENE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : promoter
resulttype : promoter
resulttype : CAAT_signal
resulttype : TATA_signal
resulttype : -35_signal
resulttype : -10_signal
resulttype : GC_signal
color : 255,255,51
usescore : false
glyph : PromoterGlyph
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : P insertion_site
resulttype : p_insertion
resulttype : P insertion_site
color : 0,204,204
usescore : false
glyph : Triangle
column : SCORE
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Type]
tiername : Annotation
typename : piggyBAC insertion_site
resulttype : piggyBAC_insertion
resulttype : piggyBAC insertion_site
color : 102,102,255
usescore : false
glyph : Triangle
column : SCORE
column : GENOMIC_RANGE
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
name_method : FlyNameAdapter

[Tier]
tiername : Gene Prediction
visible : true
expanded : true

[Type]
tiername : Gene Prediction
typename : Genie
resulttype : piecegenie
resulttype : piecegenie:dummy
color : 153,51,255
usescore : true
minscore : 100
maxscore 500
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : query_frame
sortbycolumn : GENOMIC_RANGE
weburl : http://www.fruitfly.org/seq_tools/genie.html#

[Type]
tiername : Gene Prediction
typename : Genscan
resulttype : genscan:dummy
resulttype : genscan
color : 204,153,255
usescore : true
minscore : -1
maxscore : 50
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : query_frame
sortbycolumn : GENOMIC_RANGE
weburl : http://genes.mit.edu/GENSCAN.html#

[Type]
tiername : Gene Prediction
typename : FgenesH
resulttype : FgenesH:na
color : 255,153,255
usescore : true
minscore : 100
maxscore 500
glyph : DrawableResultFeatureSet
column : SCORE
column : GENOMIC_RANGE
column : query_frame
sortbycolumn : GENOMIC_RANGE
weburl : http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind#

[Type]
tiername : Gene Prediction
typename : Heidelberg 
resulttype : HDP:dummy
color : 153,153,255
usescore : true
minscore : 100
maxscore 500
glyph : DrawableResultFeatureSet
column : SCORE
column : GENOMIC_RANGE
column : query_frame
sortbycolumn : GENOMIC_RANGE
weburl : http://HDFlyArray.zmbh.uni-heidelberg.de/cgi-bin/gbrowse#

[Tier]
tiername : Transposon result
visible : true
expanded : true

[Type]
tiername : Transposon result
typename : Transposon result
resulttype : JOSHTRANSPOSON:Sept
resulttype : BDGP_TE:092002
resulttype : transposable_element
color : 255,0,203
usescore : false
glyph : DoubleHeadedArrow
column : NAME 
column : SCORE 
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl : http://www.fruitfly.org/p_disrupt/TE.html#
annot_type : transposable_element

[Tier]
tiername : Non-coding RNA
visible : true

[Type]
tiername : Non-coding RNA
typename : tRNA-result
resulttype : trnascan-se:dummy
resulttype : tRNAscan-se
color : 204,255,51
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : trna_type 
column : anticodon
sortbycolumn : SCORE
annot_type : tRNA

[Type]
tiername : Non-coding RNA
typename : Non-coding RNA
resulttype : sim4:na_smallRNA.dros
color : 50,255,10
usescore :true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
sortbycolumn : SCORE
groupby : HOMOLOGY
weburl : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=

[Tier]
tiername : blat
visible : true

[Type]
tiername : blat
typename : Rice_EST
resulttype : blat:Rice_EST
color : 255,20,0
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
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: 15-MAY-2002

[Type]
tiername : blat
typename : Rice_cDNA
resulttype : blat:Rice_cDNA
color : 204,0,51
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE
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: 15-MAY-2002

[Type]
tiername : blat
typename : Rice_protein
resulttype : blat:Rice_protein
color : 255,250,10
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : GENOMIC_LENGTH 
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : Synteny

[Type]
typename : Putative Ortholog
tiername : Synteny
resulttype : syntenicblock:dummy
glyph : DrawableResultFeatureSet
color : 255,102,153
usescore : false
scorethreshold : -1.0
column : GENOMIC_LENGTH
column : MATCH_LENGTH
column : GENOMIC_RANGE
column : MATCH_RANGE
column : SCORE
reversesort : false
groupby : GENE

[Tier]
tiername : Comparative
visible : true

[Type]
tiername : Comparative
typename : Maize_EST
resulttype : blat:Maize_EST
color : 255,165,0
usescore : true
minscore : 0
maxscore 100
glyph : DrawableResultFeatureSet
column : NAME
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY

[Type]
tiername : Comparative
typename : Maize_genome
resulttype : blat:Maize_genome
glyph : DrawableResultFeatureSet
color : 255,204,51
minscore : 0
maxscore : 100
column : SCORE
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH

[Tier]
tiername : Insertion Site
visible : true

[Type]
tiername : Insertion Site
typename : P Element Insertion
resulttype : sim4:na_pe.dros
resulttype : pinsertion:dummy
resulttype : pinsertion
color : 64,224,208
usescore : false
minscore : 0
maxscore : 100
glyph : Triangle
column : SCORE 
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
annot_type : P insertion_site

[Type]
tiername : Insertion Site
typename : piggyBAC Insertion
resulttype : sim4:na_piggyBAC.dros
resulttype : piggyBACinsertion:dummy
color : 102,102,255
usescore : false
minscore : 0
maxscore : 100
glyph : Triangle
column : SCORE 
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
annot_type : piggyBAC insertion_site

[Tier]
tiername : Affymetrix Oligo
visible : true

[Type]
tiername : Affymetrix Oligo
typename : Oligo
resulttype : sim4:na_affy_oligo.dros
color : 102,51,255
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : score 
column : GENOMIC_RANGE 
column : query_frame 
column : probability
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : BAC Scaffold
expanded : true
visible  : false

[Type]
tiername : BAC Scaffold
typename : BAC Scaffold
resulttype : clonelocator:scaffoldBACs
color : 153,153,153
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY

[Tier]
tiername : Tiling Path
expanded : true
visible  : false

[Type]
tiername : Tiling Path
typename : Tiling Path
resulttype : assembly:path
color : 204,204,204
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY

[Tier]
tiername : Start Codon
visible : true

[Type]
tiername : Start Codon
typename : startcodon_frame1
resulttype : codons
resulttype : startcodon_frame1
color : 34,220,34
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
tiername : Start Codon
typename : startcodon_frame2
resulttype : codons
resulttype : startcodon_frame2
color : 34,220,34
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
tiername : Start Codon
typename : startcodon_frame3
resulttype : codons
resulttype : startcodon_frame3
color : 34,220,34
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Tier]
tiername : Stop Codon
visible : true

[Type]
tiername : Stop Codon
typename : stopcodon_frame1
resulttype : codons
resulttype : stopcodon_frame1
color : red
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
tiername : Stop Codon
typename : stopcodon_frame2
resulttype : codons
resulttype : stopcodon_frame2
color : red
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Type]
tiername : Stop Codon
typename : stopcodon_frame3
resulttype : codons
resulttype : stopcodon_frame3
color : red
usescore : false
glyph : SiteCodon
column : NAME 
column : GENOMIC_RANGE
sortbycolumn : NAME

[Tier]
tiername : Repeat
expanded : true
visible  : false

[Type]
tiername : Repeat
typename : Repeat
resulttype : repeatmasker
resulttype : repeatmasker:dummy
resulttype : RepeatMasker:dummy
color : 255,0,255
usescore : true
glyph : DoubleHeadedArrow
column : NAME 
column : SCORE 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : GENOMIC_LENGTH 
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : Promoter prediction
expanded : true
visible  : false

[Type]
tiername : Promoter prediction
typename : Promoter prediction
resulttype : promoter:dummy
resulttype : sim4:promoter_all_1941.fa
color : 255,255,51
usescore : true
minscore : 0
maxscore : 1
glyph : PromoterGlyph
column : NAME 
column : SCORE 
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : SCORE
annot_type : promoter

[Tier]
tiername : Cytology
expanded : true
visible  : false

[Type]
tiername : Cytology
typename : Cytology
resulttype : locator:cytology
color : 102,102,102
usescore : false
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Tier]
tiername : Sequence selection

[Type]
tiername : Sequence selection
typename : Sequence selection
resulttype : Sequence selection
color : orange
usescore : false
glyph : DrawableResultFeatureSet
column : NAME
sortbycolumn : NAME

[Tier]
tiername : Do Not Show
visible  : false

// Gaps (runs of Ns) are now 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

tiername : Do Not Show
typename : DGC Gold
resulttype : sim4:na_DGC_gold.dros
color : white
usescore : false
glyph : DrawableResultFeatureSet
column : SCORE
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE

# The result types that follow are just in example.xml.  If we change
# example.xml, we may be able to delete these.
[Type]
tiername : Do Not Show
typename : gaasterland
resulttype : sim4:gaasterland.272partialmatch.fst
resulttype : sim4:gaasterland.771bestnovel.fst
color : 153,153,153
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
tiername : Do Not Show
typename : Ensembl
resulttype : ensembl:Sept
resulttype : ensembl1:Sept
resulttype : ensembl2:Sept
color : 204,153,255
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
typename : BLASTX Similarity to All Dmel
tiername : Do Not Show
resulttype : blastx:aa_SPTR.dros
glyph : DrawableResultFeatureSet
color : 255,20,0
usescore : false
scorethreshold : -1.0
column : SCORE
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : null
reversesort : false
groupby : GENE
weburl : http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[swall-acc:__ID__]+-e

[Type]
tiername : Do Not Show
typename : STS
resulttype : sim4:na_sts.dros
color : 218,112,214
usescore : false
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : GENOMIC_LENGTH 
column : MATCH_LENGTH
sortbycolumn : SCORE

[Type]
tiername : Do Not Show
typename : EST group
resulttype : groupest:na_DGC.dros
resulttype : groupest:dummy
resulttype : groupest:na_est.dros
resulttype : groupest:na_EST.all_nr.dros
resulttype : groupest:na_EST.complete.dros
resulttype : groupest:na_DGC_EST_nr.dros
resulttype : groupest:na_DGC.in_process.dros
color : 255,255,255
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : NAME 
column : SCORE 
column : READS 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : GENOMIC_LENGTH 
column : MATCH_LENGTH
sortbycolumn : MATCH_RANGE

[Type]
tiername : Do Not Show
typename : snRNA-result
resulttype : sim4:na_snRNA.dros
resulttype : snRNA
color : 50,255,10
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : query_frame
sortbycolumn : SCORE
groupby : HOMOLOGY
weburl : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=

// These two are in gadfly3 (but not gadflyx)
[Type]
tiername : Do Not Show
typename : NCBI
resulttype : ncbi:Sept
color : 153,51,255
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : GENOMIC_RANGE 
column : GENOMIC_LENGTH
sortbycolumn : GENOMIC_RANGE

[Type]
tiername : Do Not Show
typename : dbP
resulttype : sim4:dbP.fa
color : 131,192,255
usescore : true
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE 
column : GENOMIC_RANGE 
column : MATCH_RANGE 
column : GENOMIC_LENGTH 
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE