From WormBaseWiki
WormBase Models
Curator Comments/Description
Model
///////////////////////////////////////////////////////////////////////////////////////////
//
// Method class
//
// Used a lot by acedb code for displaying data (on the FMap) and dumping data (via GFF)
//
///////////////////////////////////////////////////////////////////////////////////////////
?Method Remark ?Text #Evidence
// the Display information controls how the column looks.
Display No_display
Colour #Colour
CDS_colour #Colour
Frame_sensitive
Strand_sensitive Show_up_strand #Colour
Score Score_by_offset // has priority over width, for Jean
Score_by_width
Score_by_histogram UNIQUE Float // baseline value
Score_bounds UNIQUE Float UNIQUE Float
// limits for squashing
Percent // '%' in text, + default bounds 25, 100
Overlap_mode UNIQUE Overlap // draw on top - default
Bumpable // bump to avoid overlap
Cluster // one column per homol target
Width UNIQUE Float
Symbol UNIQUE Text // first char only is used
Right_priority UNIQUE Float // the greater the more right
Max_mag UNIQUE Float // don't show if more bases per line
Min_mag UNIQUE Float // don't show if fewer bases per line
Show_text // only put text in right-hand column if set
Gapped // draw sequences or homols with gaps
Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override.
Join_blocks // link up all blocks of a single feature with lines
Blastn // can calculate percent from score if blastn
Blixem Blixem_X
Blixem_N
Blixem_P
Belvu
Gene_assemble Gene_assemble_method ?Method UNIQUE Float
// Float factor to multiply score by
Intron_min UNIQUE Int
Exon_min UNIQUE Int
Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
// base cost, cost per log bp beyond min
// Int is min for this if not Intron_min
Inter_gene_cost UNIQUE Float
GF_parameters GF_range UNIQUE Int
// +- range for genefinder feature calculation
GF_ATG_cutoff UNIQUE Float
GF_5_cutoff UNIQUE Float
GF_3_cutoff UNIQUE Float
EMBL_dump_info #EMBL_dump_info
EMBL_dump EMBL_feature UNIQUE Text // require this
EMBL_threshold UNIQUE Float // apply to score unless overridden
EMBL_qualifier Text UNIQUE Text
// if 1 Text, it is the entire qualifier including '/'
// if 2 Texts, 1st is an sprintf format and 2nd is
// an argument. If this is "score", "note", "y1", "y2" or "target"
// then use the corresponding field of the Feature or Homol line.
// multiple formats will be concatenated until one starts with '/'.
GFF GFF_source UNIQUE Text
GFF_feature UNIQUE ?SO_term
Proposed Changes
?Method Remark ?Text #Evidence
Display No_display
.
.
Display_gaps // draw the gaps for gapped sequences or homols
Join_blocks // link up all blocks for any one feature in a column with connecting lines
// Alignment options (default is map with gaps but no misaligns or clipping).
Align_mapping Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override.
Allow_clipping // Map even if alignment gets clipped.
Map_gaps // Map gaps for gapped aligns.
.
.
GFF GFF_source UNIQUE Text
GFF_feature UNIQUE Text
GFF_align_gaps UNIQUE Coords // Export in Attribute format: Gaps "ref_start ref_end match_start match_end, ..."
String // Export original align string in Attribute format: Match_string <string type> "<match string>"
