From c9f7971449a47c55a05742cfcb93157e30dd385a Mon Sep 17 00:00:00 2001
From: =?utf8?q?F=C3=A1bio=20Madeira?= <fmmarquesmadeira@dundee.ac.uk>
Date: Wed, 8 Feb 2017 10:17:06 +0000
Subject: [PATCH] JWS-113 Commented Jpred entries in various configuration
 files.

---
 WEB-INF/sun-jaxws.xml       |    6 +++---
 WEB-INF/web.xml             |   18 +++++++++---------
 binaries/src/setexecflag.sh |    4 ++--
 conf/Executable.properties  |   32 ++++++++++++++++----------------
 wsbuild.xml                 |   26 +++++++++++++-------------
 5 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
index 13d6fac..eff3279 100644
--- a/WEB-INF/sun-jaxws.xml
+++ b/WEB-INF/sun-jaxws.xml
@@ -42,9 +42,9 @@
 	<endpoint name='IUPredWS'
 		implementation='compbio.ws.server.IUPredWS'
 		url-pattern='/IUPredWS'/>
-	<endpoint name='JpredWS'
-		implementation='compbio.ws.server.JpredWS'
-		url-pattern='/JpredWS'/>
+	<!--<endpoint name='JpredWS'-->
+		<!--implementation='compbio.ws.server.JpredWS'-->
+		<!--url-pattern='/JpredWS'/>-->
 	<endpoint name='RNAalifoldWS'
 		implementation='compbio.ws.server.RNAalifoldWS'
 		url-pattern='/RNAalifoldWS'/>
diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index cec1884..6ec75a1 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -174,11 +174,11 @@
 		<load-on-startup>1</load-on-startup>
 	</servlet>
 
-	<servlet>
-		<servlet-name>JpredWS</servlet-name>
-		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
+	<!--<servlet>-->
+		<!--<servlet-name>JpredWS</servlet-name>-->
+		<!--<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>-->
+		<!--<load-on-startup>1</load-on-startup>-->
+	<!--</servlet>-->
 	<servlet>
 		<servlet-name>RNAalifoldWS</servlet-name>
 		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
@@ -296,10 +296,10 @@
 		<url-pattern>/IUPredWS</url-pattern>
 	</servlet-mapping>
 
-	<servlet-mapping>
-		<servlet-name>JpredWS</servlet-name>
-		<url-pattern>/JpredWS</url-pattern>
-	</servlet-mapping>
+	<!--<servlet-mapping>-->
+		<!--<servlet-name>JpredWS</servlet-name>-->
+		<!--<url-pattern>/JpredWS</url-pattern>-->
+	<!--</servlet-mapping>-->
 
 	<servlet-mapping>
 		<servlet-name>RNAalifoldWS</servlet-name>
diff --git a/binaries/src/setexecflag.sh b/binaries/src/setexecflag.sh
index 38ad0fa..7e300ed 100644
--- a/binaries/src/setexecflag.sh
+++ b/binaries/src/setexecflag.sh
@@ -32,8 +32,8 @@ chmod +x globplot/GlobPlot.py globplot/sav_gol
 echo "Setting executable flag for IUPred..."
 chmod +x iupred/iupred
 
-echo "Setting executable flag for Jpred..."
-chmod +x jpred/i686/* jpred/x86_64/*
+#echo "Setting executable flag for Jpred..."
+#chmod +x jpred/i686/* jpred/x86_64/*
 
 echo "Setting executable flag for ViennaRNA..."
 chmod +x ViennaRNA/Progs/RNAalifold
diff --git a/conf/Executable.properties b/conf/Executable.properties
index cbc8474..cfacc2f 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -215,22 +215,22 @@ aacon.limits.file        = conf/settings/AAConLimits.xml
 ###########################################################################################
 #                               JPRED CONFIGURATION                                       #
 ###########################################################################################
-local.jpred.bin        = binaries/src/jpred/jpred.pl
-#cluster.jpred.bin      = /home/jabaws/binaries/src/jpred/jpred.pl
-# These paths will be converted to absolute if relative.
-jpred.bin.env          = BLASTMAT#binaries/src/jpred/data/blast
-# The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If 
-# you install the database to a different path chenge the variable here
-jpred.data.uniref.path = /data/UNIREFdb
-# WARNING!!! 
-# Redefine jpred.data.uniref.name if you do undestand what the variable means
-jpred.data.uniref.name = cluster
-### This parameters specifies the directory where the matrices files are stored
-jpred.presets.file     = conf/settings/JpredPresets.xml
-jpred.parameters.file  = conf/settings/JpredParameters.xml
-jpred.limits.file      = conf/settings/JpredLimits.xml
-jpred.cluster.cpunum   = 4
-#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
+#local.jpred.bin        = binaries/src/jpred/jpred.pl
+##cluster.jpred.bin      = /home/jabaws/binaries/src/jpred/jpred.pl
+## These paths will be converted to absolute if relative.
+#jpred.bin.env          = BLASTMAT#binaries/src/jpred/data/blast
+## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If
+## you install the database to a different path chenge the variable here
+#jpred.data.uniref.path = /data/UNIREFdb
+## WARNING!!!
+## Redefine jpred.data.uniref.name if you do undestand what the variable means
+#jpred.data.uniref.name = cluster
+#### This parameters specifies the directory where the matrices files are stored
+#jpred.presets.file     = conf/settings/JpredPresets.xml
+#jpred.parameters.file  = conf/settings/JpredParameters.xml
+#jpred.limits.file      = conf/settings/JpredLimits.xml
+#jpred.cluster.cpunum   = 4
+##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
 
 ###########################################################################################
 #                               RNAALIFOLD CONFIGURATION                                  #
diff --git a/wsbuild.xml b/wsbuild.xml
index c8aa0e5..c6966f6 100644
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@ -18,7 +18,7 @@
 	</path>
 
 	<property name="wsdl.dir" location="${basedir}/webservices/compbio/ws/server/resource" />
-	<property name="jpred.wsdl" location="${wsdl.dir}/JpredWS.wsdl" />
+	<!--<property name="jpred.wsdl" location="${wsdl.dir}/JpredWS.wsdl" />-->
 	<property name="aacon.wsdl" location="${wsdl.dir}/AAConWS.wsdl" />
 	<property name="clustal.wsdl" location="${wsdl.dir}/ClustalWS.wsdl" />
 	<property name="muscle.wsdl" location="${wsdl.dir}/MuscleWS.wsdl" />
@@ -56,18 +56,18 @@
 		<!-- destdir - Where to put generated classes -->
 		<!-- sourcedestdir -  Where to put generated source files -->
 		<!-- resourcedestdir - Where to put generated source files -->
-		<wsgen sei="compbio.ws.server.JpredWS"
-				sourcedestdir="${basedir}/webservices"
-				destdir="${classes}"
-				resourcedestdir="${wsdl.dir}"
-				keep="true"
-				genwsdl="true"
-				extension="false"
-				xendorsed="true"
-				verbose="true">
-				<classpath refid="classes.path" />
-				<classpath refid="project.classpath" />
-		</wsgen>
+		<!--<wsgen sei="compbio.ws.server.JpredWS"-->
+				<!--sourcedestdir="${basedir}/webservices"-->
+				<!--destdir="${classes}"-->
+				<!--resourcedestdir="${wsdl.dir}"-->
+				<!--keep="true"-->
+				<!--genwsdl="true"-->
+				<!--extension="false"-->
+				<!--xendorsed="true"-->
+				<!--verbose="true">-->
+				<!--<classpath refid="classes.path" />-->
+				<!--<classpath refid="project.classpath" />-->
+		<!--</wsgen>-->
 		<wsgen sei="compbio.ws.server.AAConWS"
 				sourcedestdir="${basedir}/webservices"
 				destdir="${classes}"
-- 
1.7.10.2