2.2 documentation

[jalview.git] / help / html / features / search.html

diff --git a/help/html/features/search.html b/help/html/features/search.html
index 5fedf33..3d60858 100755 (executable)
--- a/help/html/features/search.html
+++ b/help/html/features/search.html
@@ -13,23 +13,27 @@ td {
 <p><strong>Search</strong></p>\r
 <p>The search box is displayed by pressing Control and F or\r
   selecting &quot;Find...&quot; from the &quot;Search&quot; menu.</p>\r
-<img src="search.gif">\r
-<p>&quot;Find next&quot; will find the next occurence of the specified\r
-  and adjust the alignment window view to show it, and &quot;Find\r
-  all&quot; highlights all matches for a pattern. The &quot;Create new\r
-  group&quot; is a quick way to highlight and group residues matching\r
-  the specified search pattern throughout the alignment.</p> \r
+<img src="search.gif" width="339" height="110">\r
+<p>&quot;Find next&quot; will find the next occurence of the specified and adjust \r
+  the alignment window view to show it, and &quot;Find all&quot; highlights all \r
+  matches for a pattern. The &quot;New Feature&quot; is a quick way to highlight \r
+  and group residues matching the specified search pattern throughout the alignment. \r
 <ul>\r
-<li>The search uses regular expressions. (understands a mixture of\r
-  posix and perl style regex - see below for a summary)</li>\r
-<li>Gaps are ignored when matching the query to the sequences in the\r
-  alignment.</li>\r
-<li>The search is applied to both sequences and their IDs but the &quot;Find next&quot;\r
-  and &quot;Find all&quot; buttons only count the sequence matches.</li>\r
-  <li>If a region is selected, then search will <strong>only</strong>\r
-  be performed on that region. </li>\r
+  <li>The search uses regular expressions. (understands a mixture of posix and \r
+    perl style regex - see below for a summary)</li>\r
+  <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>\r
+  <li>The search is applied to both sequences and their IDs but the &quot;Find \r
+    next&quot; and &quot;Find all&quot; buttons only count the sequence matches.</li>\r
+  <li>If a region is selected, then search will <strong>only</strong> be performed \r
+    on that region. </li>\r
   <li>To quickly clear the current selection, press the &quot;Escape&quot; key.</li>\r
+  <li>Tick the &quot;Match Case&quot; box to perform a case sensitive search.</li>\r
 </ul>\r
+<p><strong>Creating Features from Search Results</strong></p>\r
+<p>\r
+  If &quot;New Feature&quot; is selected, the feature can be given a name from \r
+  a popup input box. Use the &quot;Feature Settings&quot; under the &quot;View&quot; \r
+  menu to change the visibility and colour of the new sequence feature.</p> \r
 <p><strong>A quick Regular Expression Guide</strong></p>\r
 <p>A regular expression is not just a simple text query - although it\r
 can be used like one, the query is not parsed literally, but\r
@@ -83,12 +87,13 @@ below describes some of the regular expression syntax:<br></p>
   </tr>\r
   <tr>\r
     <td>{min,}</td>\r
-    <td> Matches at least the specified number of the preceding element.</td>\r
+    <td> Matches of the preceding element matched at least the\r
+    specified number of times</td>\r
   </tr>\r
   <tr>\r
     <td>{min,max} </td>\r
-    <td>Matches if the preceding element matches between min and max\r
-    number of times.</td>\r
+    <td>Matches if the preceding element matches min or at most max\r
+    number of times</td>\r
   </tr>\r
 </table>\r
 </body>\r