From b5ed73498a3f12da3f6f8465ec115065ec98e931 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Mon, 14 Feb 2011 18:22:55 +0000
Subject: [PATCH 1/1] Add limits for presets from jws2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3752 e3abac25-378b-4346-85de-24260fe3988d
---
 conf/settings/ClustalLimits.xml  |   22 ++++++++++++---------
 conf/settings/MafftLimits.xml    |   39 ++++++++++++++++++++++++++++++++++++--
 conf/settings/MuscleLimits.xml   |   26 ++++++++++++++++++++++---
 conf/settings/ProbconsLimits.xml |    8 ++++----
 conf/settings/TcoffeeLimits.xml  |   17 +++++++++++++----
 5 files changed, 90 insertions(+), 22 deletions(-)

diff --git a/conf/settings/ClustalLimits.xml b/conf/settings/ClustalLimits.xml
index d490402..52b0ef3 100644
--- a/conf/settings/ClustalLimits.xml
+++ b/conf/settings/ClustalLimits.xml
@@ -1,18 +1,22 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
 <limits>
  <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>
-	<limit isDefault="false">
-		<preset>Disable gap weighting (Speed-oriented)</preset>
-		<seqNumber>2000</seqNumber>
-		<seqLength>1000</seqLength>
-	</limit>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>500</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
+	</limit>
+
+	<!-- Uncomment/edit these if you would like to have separate limits for presets	-->
+	<!-- 
+	<limit isDefault="false">
+		<preset>Disable gap weighting (Speed-oriented)</preset>
+		<seqNumber>1000</seqNumber>
+		<seqLength>3000</seqLength>
 	</limit>
+	 -->
 </limits>
diff --git a/conf/settings/MafftLimits.xml b/conf/settings/MafftLimits.xml
index 06a6324..7067ff5 100644
--- a/conf/settings/MafftLimits.xml
+++ b/conf/settings/MafftLimits.xml
@@ -2,12 +2,47 @@
 <limits>
  <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
+	</limit>
+	
+	<!-- Uncomment/edit these if you would like to have separate limits for presets	--> 
+	<!-- 
+	<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>
+	 -->
+	
 </limits>
diff --git a/conf/settings/MuscleLimits.xml b/conf/settings/MuscleLimits.xml
index feb6fc7..2aceb46 100644
--- a/conf/settings/MuscleLimits.xml
+++ b/conf/settings/MuscleLimits.xml
@@ -2,12 +2,32 @@
 <limits>
  <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>500</seqNumber>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
+	</limit>
+	
+	<!-- Uncomment/edit these if you would like to have separate limits for presets	-->
+	<!-- 
+	<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>
+	 -->
+	 
 </limits>
diff --git a/conf/settings/ProbconsLimits.xml b/conf/settings/ProbconsLimits.xml
index 179d0dc..1d871d7 100644
--- a/conf/settings/ProbconsLimits.xml
+++ b/conf/settings/ProbconsLimits.xml
@@ -2,12 +2,12 @@
 <limits>
  <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>500</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 </limits>
diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml
index 3416ca3..660d27c 100644
--- a/conf/settings/TcoffeeLimits.xml
+++ b/conf/settings/TcoffeeLimits.xml
@@ -2,12 +2,21 @@
 <limits>
  <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>
 	<limit isDefault="true">
-		<seqNumber>1000</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
 	</limit>
 	<limit isDefault="false">
 		<preset># LocalEngineExecutionLimit #</preset>
-		<seqNumber>500</seqNumber>
-		<seqLength>1000</seqLength>
+		<seqNumber>100000</seqNumber>
+		<seqLength>100000</seqLength>
+	</limit>
+	
+	<!-- Uncomment/edit these if you would like to have separate limits for presets	-->
+	<!-- 
+	<limit isDefault="false">
+		<preset>Quick align. Very fast approximate (Speed-oriented)</preset>
+		<seqNumber>1000</seqNumber>
+		<seqLength>3000</seqLength>
 	</limit>
+	 -->
 </limits>
-- 
1.7.10.2