From 2a2a8850288820f9059fd071eba4bb50b4b3fb3c Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 24 Nov 2010 13:12:35 +0000
Subject: [PATCH] Dundee specific settings from JWS2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3384 e3abac25-378b-4346-85de-24260fe3988d
---
 dundee-conf/settings/ClustalLimits.xml  |    2 +-
 dundee-conf/settings/MafftLimits.xml    |   32 ++++++++++++++++++++++++++++++-
 dundee-conf/settings/MuscleLimits.xml   |   17 +++++++++++++++-
 dundee-conf/settings/ProbconsLimits.xml |    2 +-
 dundee-conf/settings/TcoffeeLimits.xml  |   10 ++++++++--
 5 files changed, 57 insertions(+), 6 deletions(-)

diff --git a/dundee-conf/settings/ClustalLimits.xml b/dundee-conf/settings/ClustalLimits.xml
index ebbe206..28adf27 100644
--- a/dundee-conf/settings/ClustalLimits.xml
+++ b/dundee-conf/settings/ClustalLimits.xml
@@ -12,7 +12,7 @@
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>40</seqNumber>
+		<seqNumber>30</seqNumber>
 		<seqLength>500</seqLength>
 	</limit>
 </limits>
diff --git a/dundee-conf/settings/MafftLimits.xml b/dundee-conf/settings/MafftLimits.xml
index 7db541e..4cd787f 100644
--- a/dundee-conf/settings/MafftLimits.xml
+++ b/dundee-conf/settings/MafftLimits.xml
@@ -6,8 +6,38 @@
 		<seqLength>1000</seqLength>
 	</limit>
 	<limit isDefault="false">
+		<preset>L-INS-i (Accuracy-oriented)</preset>
+		<seqNumber>500</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>G-INS-i (Accuracy-oriented)</preset>
+		<seqNumber>500</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>E-INS-i (Accuracy-oriented)</preset>
+		<seqNumber>500</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>FFT-NS-i (Speed oriented)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>FFT-NS-1 (Speed oriented)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>NW-NS-PartTree-1 (Speed oriented)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>40</seqNumber>
+		<seqNumber>20</seqNumber>
 		<seqLength>500</seqLength>
 	</limit>
 </limits>
diff --git a/dundee-conf/settings/MuscleLimits.xml b/dundee-conf/settings/MuscleLimits.xml
index 88cfc61..75d66d9 100644
--- a/dundee-conf/settings/MuscleLimits.xml
+++ b/dundee-conf/settings/MuscleLimits.xml
@@ -6,8 +6,23 @@
 		<seqLength>1000</seqLength>
 	</limit>
 	<limit isDefault="false">
+		<preset>Protein alignment(Fastest speed)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>Nucleotide alignment(Fastest speed)</preset>
+		<seqNumber>1000</seqNumber>
+		<seqLength>3000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>Huge alignments (speed-oriented)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>3000</seqLength>
+	</limit>
+	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>40</seqNumber>
+		<seqNumber>20</seqNumber>
 		<seqLength>500</seqLength>
 	</limit>
 </limits>
diff --git a/dundee-conf/settings/ProbconsLimits.xml b/dundee-conf/settings/ProbconsLimits.xml
index 96c8b31..e530fb9 100644
--- a/dundee-conf/settings/ProbconsLimits.xml
+++ b/dundee-conf/settings/ProbconsLimits.xml
@@ -7,7 +7,7 @@
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>30</seqNumber>
+		<seqNumber>20</seqNumber>
 		<seqLength>500</seqLength>
 	</limit>
 </limits>
diff --git a/dundee-conf/settings/TcoffeeLimits.xml b/dundee-conf/settings/TcoffeeLimits.xml
index f21fb03..84b3f50 100644
--- a/dundee-conf/settings/TcoffeeLimits.xml
+++ b/dundee-conf/settings/TcoffeeLimits.xml
@@ -6,8 +6,14 @@
 		<seqLength>1000</seqLength>
 	</limit>
 	<limit isDefault="false">
+		<preset>Quick align. Very fast approximate (Speed-oriented)</preset>
+		<seqNumber>1000</seqNumber>
+		<seqLength>3000</seqLength>
+	</limit>
+	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>40</seqNumber>
-		<seqLength>500</seqLength>
+		<seqNumber>15</seqNumber>
+		<seqLength>400</seqLength>
 	</limit>
 </limits>
+
-- 
1.7.10.2