Quality metrics.

administration.rst

@@ -1215,6 +1215,19 @@ exclamation mark (!) next to them:
   functions by default - this can be overridden by user preference.
 
   * Allowed: true/false.
+
+* recommended - Sets whether the scheme will appear in a list of recommended
+  schemes for use in some analysis plugins. Selecting this option makes the
+  scheme easier to select when there are a lot of schemes defined. It should 
+  be used sparingly.
+
+* quality_metric - Sets whether the scheme can be used to help assess the 
+  quality of a genome assembly. For a well annotated genome it would be 
+  expected for all loci in the scheme to have an allele designated. The
+  annotation status can be searched in an isolate query. This can be used in
+  conjunction with the quality_metric_good and quality_metric_bad attributes
+  that can be used to set the thresholds for what constitutes a good or bad
+  annotation.
 
 * dbase_name - Name of seqdef database (system name) containing scheme 
   profiles (optional).
@@ -1246,6 +1259,15 @@ exclamation mark (!) next to them:
 
   * Allowed: any integer.
 
+* quality_metric_good - threshold number of loci that must have allele 
+  designations for a genome annotation to be considered good for this scheme.
+  If this isn't set then the number of loci in the scheme is used.
+
+* quality_metric_bad - threshold number of loci that must have allele
+  designations below which a genome annotation is to be considered bad for this
+  scheme. If this isn't set then the value used for quality_metric_good is 
+  used (or the number of scheme loci if this also is not set).
+
 * view - Restrict this scheme to only isolates contained in the specified
   database view. This option will only appear if the views attribute is set
   in the system tag. The view needs to have been defined in the database as

conf.py

@@ -47,16 +47,16 @@
 
 # General information about the project.
 project = u'BIGSdb'
-copyright = u'2014-2020, Keith Jolley'
+copyright = u'2014-2021, Keith Jolley'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.29.0'
+version = '1.30.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.29.0'
+release = '1.30.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

dbase_setup.rst

@@ -560,13 +560,6 @@ Any value set here can be overridden in a
     'authenticated_users' for anybody who has been able to log in. 
     Default 'public'.  
 
-* recommended_schemes
-
-  * Comma-separated list of recommended schemes to suggest to Genome Comparator
-    users. If lots of schemes are defined, a user may be tempted to click 'All
-    loci' and this may not be the best option. Populating this attribute, 
-    results in an additional list of preferred schemes that can be chosen.
-
 * related_databases
 
   * Semi-colon separated list of links to related BIGSdb databases on the