From 77bcd1f60d9c26328d8859445f4225cd0ef571a9 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 20 Sep 2018 12:23:14 +0100
Subject: [PATCH] JAL-2843 tweaks to help text for filters

---
 help/html/features/featuresFormat.html |   19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index 171a3d0..4d13dcd 100755
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -148,21 +148,22 @@
      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
+     <pre>Label <em>or</em> Score <em>or</em> AttributeName condition [value]</pre>
+     where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition.
+     <br><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>Contains</em> - description (or attribute) should contain the given value (not case sensitive); example <em>clinical_significance contains Pathogenic</em></li> 
+     <li><em>NotContains</em> - description (or attribute) should not contain the given value</li> 
+     <li><em>Matches</em> - description (or attribute)  should match the given value (not case sensitive)</li> 
+     <li><em>NotMatches</em> - description (or attribute) should not match the given value (not case sensitive)</li> 
+     <li><em>Present</em> - attribute is present on the feature (no value required); example <em>CSQ:SIFT present</em></li> 
+     <li><em>NotPresent</em> - 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>Tip: some examples of filter syntax are given below; or to see more, 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>
 
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1.7.10.2