WormBase Model:Method

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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>"