From 566113028e37ad49c91f7f87238658ed5019d101 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 9 Feb 2011 11:04:49 +0000
Subject: [PATCH] Disable jronn parameter

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3723 e3abac25-378b-4346-85de-24260fe3988d
---
 conf/Executable.properties                        |    2 +-
 conf/settings/JronnParameters.xml                 |    5 +++++
 datamodel/compbio/data/sequence/SequenceUtil.java |    1 +
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 99b9c6c..fcd6057 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -65,7 +65,7 @@ local.jronn.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe
 local.jronn.bin=/sw/java/latest/bin/java
 cluster.jronn.bin=/sw/java/latest/bin/java
 jronn.jar.file=binaries/jronn3.1.jar
-jronn.parameters.file=conf/settings/JronnParameters.xml
+# jronn.parameters.file=conf/settings/JronnParameters.xml
 jronn.limits.file=conf/settings/JronnLimits.xml
 #TODO jronn.jvm.options=-Xms32M -Xmx512M
 jronn.cluster.cpunum=4
diff --git a/conf/settings/JronnParameters.xml b/conf/settings/JronnParameters.xml
index 27e7a86..bfe02e6 100644
--- a/conf/settings/JronnParameters.xml
+++ b/conf/settings/JronnParameters.xml
@@ -1,4 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+
+<!-- Although it is perfectly possible to specify this parameter, its not clear what it means
+	none of the original RONN web sites allow changing this -> so disable. 
+ 
 <runnerConfig>
 	<runnerClassName>compbio.runner.disorder.Jronn</runnerClassName>
 	<prmSeparator>=</prmSeparator>
@@ -15,3 +19,4 @@
 		</validValue>
 	</parameters>
 </runnerConfig>
+-->
\ No newline at end of file
diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index 7e6c672..754cf5f 100644
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -365,6 +365,7 @@ public final class SequenceUtil {
 		infasta.close();
 		return seqs;
 	}
+		
 	private static float[] convertToNumber(String[] annotValues)
 			throws UnknownFileFormatException {
 		float[] annotation = new float[annotValues.length];
-- 
1.7.10.2