Blixem_X in the ?Method

laminaria.EST est at sb-roscoff.fr
Fri Jun 4 06:57:12 EST 1999

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?


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
		Strand_sensitive Show_up_strand #Colour
		Score	Score_by_offset	// has priority over width, for Jean
			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
	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

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