# 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 : unmasked_sequence [Type] typename : unmasked_sequence tiername : unmasked_sequence datatype : un-RepeatMasked_sequence glyph : DrawableResultFeatureSet color : 255,255,204 [Type] typename : low_complexity tiername : unmasked_sequence datatype : RepeatMasker_low_complexity glyph : DoubleHeadedArrow color : 102,102,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE [Tier] tiername : REannotate_repeat [Type] typename : LTR tiername : REannotate_repeat datatype : REannotate_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : LTR_internal tiername : REannotate_repeat datatype : REannotate_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : DNA_transposon tiername : REannotate_repeat datatype : REannotate_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : non-LTR_retrotransposon tiername : REannotate_repeat datatype : REannotate_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : repeat_element tiername : REannotate_repeat datatype : REannotate_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : satellite tiername : REannotate_repeat datatype : REannotate_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 1-nested_REannotate_repeat [Type] typename : 1-nested_LTR tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 1-nested_LTR_internal tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 1-nested_DNA_transposon tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 1-nested_non-LTR_retrotransposon tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 1-nested_repeat tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 1-nested_satellite tiername : 1-nested_REannotate_repeat datatype : REannotate_1-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 2-nested_REannotate_repeat [Type] typename : 2-nested_LTR tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 2-nested_LTR_internal tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 2-nested_DNA_transposon tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 usescore : true minscore : 1.0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 2-nested_non-LTR_retrotransposon tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 2-nested_repeat tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 2-nested_satellite tiername : 2-nested_REannotate_repeat datatype : REannotate_2-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 3-nested_REannotate_repeat [Type] typename : 3-nested_LTR tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 3-nested_LTR_internal tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 3-nested_DNA_transposon tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 3-nested_non-LTR_retrotransposon tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 3-nested_repeat tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 3-nested_satellite tiername : 3-nested_REannotate_repeat datatype : REannotate_3-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 4-nested_REannotate_repeat [Type] typename : 4-nested_LTR tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 4-nested_LTR_internal tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 4-nested_DNA_transposon tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 usescore : true minscore : 1.0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 4-nested_non-LTR_retrotransposon tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 4-nested_repeat tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 4-nested_satellite tiername : 4-nested_REannotate_repeat datatype : REannotate_4-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 5-nested_REannotate_repeat [Type] typename : 5-nested_LTR tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 5-nested_LTR_internal tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 5-nested_DNA_transposon tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 5-nested_non-LTR_retrotransposon tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 5-nested_repeat tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 5-nested_satellite tiername : 5-nested_REannotate_repeat datatype : REannotate_5-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Tier] tiername : 6-nested_REannotate_repeat [Type] typename : 6-nested_LTR tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_LTR glyph : DrawableResultFeatureSet color : 255,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 6-nested_LTR_internal tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_LTR_internal glyph : DrawableResultFeatureSet color : 255,51,50 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 6-nested_DNA_transposon tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_DNA_transposon glyph : DrawableResultFeatureSet color : 0,153,0 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 6-nested_non-LTR_retrotransposon tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_non-LTR_retrotransposon glyph : DrawableResultFeatureSet color : 0,102,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE [Type] typename : 6-nested_repeat tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_repeat glyph : DrawableResultFeatureSet color : 255,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE column : NAME sortbycolumn : GENOMIC_RANGE [Type] typename : 6-nested_satellite tiername : 6-nested_REannotate_repeat datatype : REannotate_6-nested_satellite glyph : DrawableResultFeatureSet color : 25,0,255 column : NAME column : MATCH_RANGE column : MATCH_LENGTH column : GENOMIC_RANGE column : GENOMIC_LENGTH column : SCORE sortbycolumn : GENOMIC_RANGE