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JAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction...
[jalview.git] / help / html / features / clarguments.html
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 3e56f7c..fa273a5 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -67,8 +67,8 @@
         <div align="center">-annotations FILE/URL</div>
       </td>
       <td>Add precalculated annotations to the alignment. See <a
-        href="annotationsFormat.html" target="NEW"
-      >Annotation File</a> description.
+        href="annotationsFormat.html" target="NEW">Annotation
+          File</a> description.
       </td>
     </tr>
     <tr>
@@ -96,41 +96,28 @@
     </tr>
     <tr>
       <td>
-        <div align="center">-nousagestats</div>
-      <td>
-        <div align="left">Turn off google analytics usage tracking</div>
-      </td>
-    </tr>
-    <tr>
+        <div align="center">-nonews</div>
       <td>
-        <div align="center">-[no]sortbytree</div>
-      <td>
-        <div align="left">Enable or disable automatic sorting of
-          associated view when a new tree is displayed</div>
+        <div align="left">
+          Disable check for <a href="../webServices/newsreader.html">Jalview
+            news</a> on startup (not recommended other than for classroom /
+          demo usage)
+        </div>
       </td>
     </tr>
     <tr>
       <td>
-        <div align="center">-dasserver nickname=URL</div>
+        <div align="center">-nousagestats</div>
       <td>
-        <div align="left">
-          Add and enable a <a href="dassettings.html">DAS server</a>
-          with given nickname (alphanumeric or underscores only) for
-          retrieval of features for all alignments<br> Sources that
-          also support the sequence command may be specified by
-          prepending the URL with 'sequence:'<br> <em>e.g.</em>
-          sequence:http://localdas.somewhere.org/das/source
-        </div>
+        <div align="left">Turn off google analytics usage tracking</div>
       </td>
     </tr>
     <tr>
       <td>
-        <div align="center">-fetchfrom nickname</div>
+        <div align="center">-[no]sortbytree</div>
       <td>
-        <div align="left">
-          Query a <a href="dassettings.html">DAS source</a> called
-          nickname for features for the alignments and display them
-        </div>
+        <div align="left">Enable or disable automatic sorting of
+          associated view when a new tree is displayed</div>
       </td>
     </tr>
     <tr>
@@ -247,6 +234,14 @@
       <td><div align="left">Create Scalable Vector Graphics
           file FILE from alignment.</div></td>
     </tr>
+    <tr>
+      <td><div align="center">-biojsMSA FILE</div></td>
+      <td><div align="left">Write an HTML page to display
+          the alignment with the <a href="biojsmsa.html">
+          BioJS MSAviewer MSA</a>
+          </div>
+      </td>
+    </tr>
   </table>
 </body>
 </html>