From ee037b551494b3c8095d51bb3075f6fafb592c70 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Wed, 7 Aug 2013 17:23:58 +0100
Subject: [PATCH] Describe new parameters of Jpred

---
 conf/settings/JpredParameters.xml |    9 +++++++++
 conf/settings/JpredPresets.xml    |   10 ++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml
index 03c6906..ec4f167 100644
--- a/conf/settings/JpredParameters.xml
+++ b/conf/settings/JpredParameters.xml
@@ -12,6 +12,15 @@
         <furtherDetails>prog_docs/jpred.txt</furtherDetails>
     </options>
 
+    <options>
+        <name>JABAWS configuration</name>
+        <description>
+            Configure Jpred to worik within JABAWS
+        </description>
+        <optionNames>-jabaws</optionNames>
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>
+    </options>
+
     <prmSeparator> </prmSeparator>
 
     <parameters isRequired="false">
diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml
index 51f3d30..3f9b72b 100644
--- a/conf/settings/JpredPresets.xml
+++ b/conf/settings/JpredPresets.xml
@@ -8,8 +8,9 @@
             Dundee cluser configuration
         </description>
         <optlist>
-            <option>-dbpath /homes/www-jpred/databases </option>
-            <option>-dbname uniref90</option>
+			<option>-dbpath /homes/www-jpred/databases </option>
+			<option>-dbname uniref90</option>
+			<option>-jabaws</option>
         </optlist>
     </preset>
 
@@ -19,9 +20,10 @@
             My 4-core laptop configuration
         </description>
         <optlist>
-            <option>-dbpath /data/UNIREFdb</option>
+            <option>-dbpath /data/UNIREFdb/</option>
             <option>-dbname ported_db</option>
-            <option>-ncpu 4</option>
+            <option>-ncpu 3</option>
+            <option>-jabaws</option>
         </optlist>
     </preset>
 
-- 
1.7.10.2