Difference between revisions of "WS224 Models.wrm"
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<pre>This cycle there were 2 proposed model changes to the ?Strain Class and some acedb magic tags added/moved. | <pre>This cycle there were 2 proposed model changes to the ?Strain Class and some acedb magic tags added/moved. | ||
− | + | This will effect groups that have an old version of the methods loaded into their databases. | |
− | ?Strain | + | 1/2) ?Strain Class |
− | |||
− | |||
− | |||
− | |||
− | + | Addition of inbreeding states Selfed, Isofemale, Multifemale and Inbred. | |
− | + | ||
− | + | Addition of more landscapes, Botanical_garden_zoo, Wet_shrubland and Dry_shrubland. | |
− | + | Change for Wild_forest -> Forest. | |
− | + | ||
− | + | 3) ?Method | |
− | + | Addition of the top level tag Align_mapping and downstream tags. | |
− | + | These additions/changes were take from the core ACeDB models.wrm as these are used by more modern binaries. | |
− | + | ||
+ | == Model Changes == | ||
+ | |||
+ | Human readable diff: | ||
+ | |||
+ | ?Strain | ||
+ | ------- | ||
+ | |||
+ | > Inbreeding_state UNIQUE Selfed Text | ||
+ | > Isofemale Text | ||
+ | > Multifemale Text | ||
+ | > Inbred Text | ||
+ | |||
+ | < Wild_forest | ||
+ | --- | ||
+ | > Forest | ||
+ | |||
+ | > Botanical_garden_zoo | ||
+ | > Wet_shrubland | ||
+ | > Dry_shrubland | ||
+ | |||
+ | |||
+ | ?Method | ||
+ | ------- | ||
+ | |||
+ | Descriptions and text: | ||
+ | |||
+ | < Display No_display | ||
+ | --- | ||
+ | > Display No_display // column is not displayed at all. | ||
+ | |||
+ | < CDS_colour #Colour | ||
+ | --- | ||
+ | > CDS_colour #Colour // CDS outlined in this colour. | ||
+ | |||
+ | < Percent // '%' in text, + default bounds 25, 100 | ||
+ | --- | ||
+ | > Percent // Score will be displayed as a '%' in fmap reportline + bounds default to 25 & 100. | ||
+ | |||
+ | < Symbol UNIQUE Text // first char only is used | ||
+ | --- | ||
+ | > Symbol UNIQUE Text // first char only is used | ||
+ | |||
+ | < 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 | ||
+ | < Join_blocks // link up all blocks of a single feature with lines | ||
+ | --- | ||
+ | > 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 | ||
+ | > Join_blocks // link up all blocks of a single feature with lines | ||
+ | > Display_gaps // draw sequences or homols with gaps | ||
+ | |||
+ | |||
+ | > 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 '/'. | ||
+ | > EMBL_dump_info #EMBL_dump_info // when used for controlling dump | ||
+ | |||
+ | < 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 '/'. | ||
+ | |||
+ | |||
+ | Alignment Method update: | ||
+ | < Gapped // draw sequences or homols with gaps | ||
+ | < Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. | ||
+ | --- | ||
+ | > Display_gaps // draw sequences or homols with gaps | ||
+ | > Gapped // draw sequences or homols with gaps //leaving this is preserved backwards compatibility | ||
+ | > // Alignment options (default is map only with no misaligns or clipping and do not map gaps). | ||
+ | > Align_mapping Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. | ||
+ | > Allow_clipping // Map gaps even if they need to be clipped. | ||
+ | > Map_gaps // Map gaps for gapped aligns. | ||
+ | </pre> |
Revision as of 14:19, 12 January 2011
Models Tagged for WS224
This cycle there were 2 proposed model changes to the ?Strain Class and some acedb magic tags added/moved. This will effect groups that have an old version of the methods loaded into their databases. 1/2) ?Strain Class Addition of inbreeding states Selfed, Isofemale, Multifemale and Inbred. Addition of more landscapes, Botanical_garden_zoo, Wet_shrubland and Dry_shrubland. Change for Wild_forest -> Forest. 3) ?Method Addition of the top level tag Align_mapping and downstream tags. These additions/changes were take from the core ACeDB models.wrm as these are used by more modern binaries. == Model Changes == Human readable diff: ?Strain ------- > Inbreeding_state UNIQUE Selfed Text > Isofemale Text > Multifemale Text > Inbred Text < Wild_forest --- > Forest > Botanical_garden_zoo > Wet_shrubland > Dry_shrubland ?Method ------- Descriptions and text: < Display No_display --- > Display No_display // column is not displayed at all. < CDS_colour #Colour --- > CDS_colour #Colour // CDS outlined in this colour. < Percent // '%' in text, + default bounds 25, 100 --- > Percent // Score will be displayed as a '%' in fmap reportline + bounds default to 25 & 100. < Symbol UNIQUE Text // first char only is used --- > Symbol UNIQUE Text // first char only is used < 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 < Join_blocks // link up all blocks of a single feature with lines --- > 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 > Join_blocks // link up all blocks of a single feature with lines > Display_gaps // draw sequences or homols with gaps > 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 '/'. > EMBL_dump_info #EMBL_dump_info // when used for controlling dump < 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 '/'. Alignment Method update: < Gapped // draw sequences or homols with gaps < Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. --- > Display_gaps // draw sequences or homols with gaps > Gapped // draw sequences or homols with gaps //leaving this is preserved backwards compatibility > // Alignment options (default is map only with no misaligns or clipping and do not map gaps). > Align_mapping Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. > Allow_clipping // Map gaps even if they need to be clipped. > Map_gaps // Map gaps for gapped aligns.