+ <ul>
+ <li><em>label</em><br> Indicates that the feature
+ description should be used to create a colour for features of
+ this type.<br> <em>Note: if no threshold value is
+ needed then only 'label' is required.<br> This
+ keyword was added in Jalview 2.6
+ </em></li>
+
+ <li><em>score</em><br> Indicates that the feature
+ score should be used to create a graduated colour for features of
+ this type, in conjunction with mincolor, maxcolor.<br><em>This keyword was added in Jalview 2.11.
+ It may be omitted (score is the default) if mincolor and maxcolor are specified.
+ </em></li>
+
+ <li><em>attribute|attName</em><br> Indicates that the value of feature
+ attribute 'attName' should be used to create a colour for features of
+ this type.
+ <br>For example, <em>attribute|clinical_significance</em> to colour by clinical_significance.
+ <br>To colour by range of a numeric attribute, include <em>mincolor</em> and <em>maxcolor</em>, or omit to colour by text (category).
+ <br>(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.)
+ <br>A sub-attribute should be written as, for example, CSQ:IMPACT.
+ <br><em>This keyword was added in Jalview 2.11</em></li>
+
+ <li><em>mincolor</em> and <em>maxcolor</em><br> Colour
+ triplets specified as hexadecimal or comma separated values
+ (may be left blank for a <em>label</em> style colourscheme,
+ but remember to specify the remaining fields)</li>
+
+ <li><em>absolute</em><br> An optional switch
+ indicating that the <em>minvalue</em> and <em>maxvalue</em>
+ parameters should be left as is, rather than rescaled
+ according to the range of scores for this feature type.</li>
+
+ <li><em>minvalue</em> and <em>maxvalue</em><br>
+ Minimum and maximum values defining the range of scores for
+ which the colour range will be defined over.<br>If minvalue is
+ greater than maxvalue then the linear mapping will have
+ negative gradient.</li>
+
+ <li><em>novalue</em> <br>
+ Specifies the colour to use if colouring by attribute, when the attribute is absent.
+ Valid options are <em>novaluemin, novaluemax, novaluenone</em>, to use mincolor, maxcolor, or no colour.
+ <br>If not specified this will default to novaluemin.</li>
+
+ <li><em>thresholdtype</em><br> Either
+ "none", "below", or "above". <em>below</em>
+ and <em>above</em> require an additional <em>threshold
+ value</em> which is used to control the display of features with
+ a score either below or above the value.</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
+
+ <p>
+ <strong>Feature Filters</strong>
+ </p>
+ <p>This section is optional, and allows one or more filters to be defined for each feature type.
+ <br>Only features that satisfy the filter conditions will be displayed.
+ <br>Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+ <br>Each line has the format:
+ <pre>featureType <em><tab></em> (filtercondition1) [and|or] (filtercondition2) [and|or]...<br></pre>
+ The parentheses are not needed if there is only one condition.
+ Combine multiple conditions with either <em>and</em> or <em>or</em> (but not a mixture).
+ <br>Each condition is written as:
+ <pre>Label|Score|AttributeName condition [value]</pre>
+ where <em>condition</em> is not case sensitive, and should be one of
+ <ul>
+ <li><em>Contains</em> - value should contain the given text (not case sensitive); example <em>clinical_significance contains Pathogenic</em></li>
+ <li><em>NotContains</em> - value should not contain the given text</li>
+ <li><em>Matches</em> - value should match the given text (not case sensitive)</li>
+ <li><em>NotMatches</em> - value should not match the given text (not case sensitive)</li>
+ <li><em>Present</em> - specified attribute is present on the feature (no value required); example <em>CSQ:SIFT present</em></li>
+ <li><em>NotPresent</em> - specified attribute is not present on the feature (no value required)</li>
+ <li><em>EQ</em> - feature score, or specified attribute, is equal to the (numeric) value</li>
+ <li><em>NE, LT, LE, GT, GE</em> - tests for not equal to / less than / less than or equal to / greater than / greater than or equal to the value</li>
+ </ul>
+ A non-numeric value always fails a numeric test.<br>If either attribute name, or value to compare, contains spaces, then enclose in single quotes:
+ <em>'mutagenesis site' contains 'decreased affinity'</em>
+ <br>Tip: to see examples of valid syntax, first configure colours and filters in Jalview, then <em>File | Export Features</em> to Textbox in Jalview Format.
+ <br><em>Feature filters were added in Jalview 2.11</em>
+ </p>
+
+ <p>
+ <strong>Feature Instances</strong>
+ </p>