From 77c2047d3b2cb8839784b29f5f2a659101dafd67 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 13 Sep 2013 16:45:35 +0100
Subject: [PATCH] New set of presets for Jpred

---
 conf/settings/JpredPresets.xml |   35 +++++++++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 4 deletions(-)

diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml
index 3f9b72b..5407708 100644
--- a/conf/settings/JpredPresets.xml
+++ b/conf/settings/JpredPresets.xml
@@ -3,21 +3,48 @@
     <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>
 
     <preset>
-        <name>cluser configuration</name>
+        <name>cluser-single</name>
         <description>
-            Dundee cluser configuration
+            Dundee cluser configuration for single sequence prediction
         </description>
         <optlist>
 			<option>-dbpath /homes/www-jpred/databases </option>
 			<option>-dbname uniref90</option>
 			<option>-jabaws</option>
+			<option>-seq</option>
         </optlist>
     </preset>
 
     <preset>
-        <name>laptop configuration</name>
+        <name>cluster-alignment</name>
         <description>
-            My 4-core laptop configuration
+            Dundee cluser configuration for multiple sequence alignment prediction
+        </description>
+        <optlist>
+			<option>-dbpath /homes/www-jpred/databases </option>
+			<option>-dbname uniref90</option>
+			<option>-jabaws</option>
+        </optlist>
+    </preset>
+
+    <preset>
+        <name>single</name>
+        <description>
+            4-core laptop configuration for single sequence prediction
+        </description>
+        <optlist>
+            <option>-dbpath /data/UNIREFdb/</option>
+            <option>-dbname ported_db</option>
+            <option>-ncpu 3</option>
+            <option>-jabaws</option>
+            <option>-seq</option>
+        </optlist>
+    </preset>
+
+    <preset>
+        <name>alignemnt</name>
+        <description>
+            4-core laptop configuration for multiple sequence alignment prediction
         </description>
         <optlist>
             <option>-dbpath /data/UNIREFdb/</option>
-- 
1.7.10.2