Brian Fristensky wrote :
Whoa -- I guess I missed something. What is a ?Method object, and
can these be defined within ACeDB or Blixem? Where are ?Method
objects documented?
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Hello
What I have understood is that ?Method object correspond to the display definition. Following is a copy of the ?Method as defined in the ACEDB 4_7g model. I do not know where it is documented. If somebody knows, I am interested.
?Method Remark ?Text
// the Display information controls how the column looks.
Display 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
Blastn // can calculate percent from score if blastn
Blixem Blixem_X
Blixem_N
Blixem_P
Belvu
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 '/'.
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
GFF GFF_source UNIQUE Text
GFF_feature UNIQUE Text
EMBL_dump_info #EMBL_dump_info // when used for controlling dump
