WS224 Models.wrm

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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 '/'.

< 		GFF_feature UNIQUE ?SO_term
---
> 		GFF_feature UNIQUE Text


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.