Difference between revisions of "WormBase Model:Method"
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== Model == | == Model == | ||
<pre> | <pre> | ||
+ | /////////////////////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // 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 | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == | ||
+ | <pre> | ||
+ | ?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>" | ||
+ | </pre> |
Latest revision as of 15:09, 1 November 2010
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>"