JAL-3384 Added -out to showUsage and clarguments help text

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 60db069..3674dcc 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -47,6 +47,16 @@
       <td><div align="left">Use the given Jalview properties
           file instead of users default.</div></td>
     </tr>
+
+    <tr>
+      <td><div align="center">-out FILE</div></td>
+      <td><div align="left">
+          Redirect all output and error messaging to FILE.
+          <br/>
+          If FILE is a relative path, this will be relative to the Jalview app directory.
+      </div></td>
+    </tr>
+
     <tr>
       <td><div align="center">-features FILE/URL</div></td>
       <td><div align="left">

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0fc92f9..61d81c2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -797,6 +797,7 @@ public class Jalview
             "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                     + "-nodisplay\tRun Jalview without User Interface.\n"
                     + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+                    + "-out FILE\tRedirect output and error messages to FILE.\n"
                     + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                     + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                     + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"