Disable jronn parameter

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3723 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 99b9c6c..fcd6057 100644 (file)
--- 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\r
 cluster.jronn.bin=/sw/java/latest/bin/java\r
 jronn.jar.file=binaries/jronn3.1.jar\r
-jronn.parameters.file=conf/settings/JronnParameters.xml\r
+# jronn.parameters.file=conf/settings/JronnParameters.xml\r
 jronn.limits.file=conf/settings/JronnLimits.xml\r
 #TODO jronn.jvm.options=-Xms32M -Xmx512M\r
 jronn.cluster.cpunum=4\r

diff --git a/conf/settings/JronnParameters.xml b/conf/settings/JronnParameters.xml
index 27e7a86..bfe02e6 100644 (file)
--- a/conf/settings/JronnParameters.xml
+++ b/conf/settings/JronnParameters.xml
@@ -1,4 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+\r
+<!-- Although it is perfectly possible to specify this parameter, its not clear what it means\r
+       none of the original RONN web sites allow changing this -> so disable. \r
+ \r
 <runnerConfig>\r
        <runnerClassName>compbio.runner.disorder.Jronn</runnerClassName>\r
        <prmSeparator>=</prmSeparator>\r
@@ -15,3 +19,4 @@
                </validValue>\r
        </parameters>\r
 </runnerConfig>\r
+-->
\ 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 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -365,6 +365,7 @@ public final class SequenceUtil {
                infasta.close();\r
                return seqs;\r
        }\r
+               \r
        private static float[] convertToNumber(String[] annotValues)\r
                        throws UnknownFileFormatException {\r
                float[] annotation = new float[annotValues.length];\r