From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Mon, 27 Jun 2011 15:33:31 +0000 (+0000)
Subject: Minor tweaks
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c6a81e764710c10a6ee8b6c9fbac287d2abd2dfa;p=jabaws.git

Minor tweaks

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4340 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/conf/Executable.properties b/conf/Executable.properties
index d43ff97..f345f86 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -78,8 +78,7 @@ local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe
 local.jronn.bin=/sw/java/latest/bin/java
 cluster.jronn.bin=/sw/java/latest/bin/java
 jronn.jar.file=binaries/windows/jronn3.1.jar
-#jronn.parameters.file=conf/settings/JronnParameters.xml
-#jronn.limits.file=conf/settings/JronnLimits.xml
+jronn.limits.file=conf/settings/JronnLimits.xml
 #jronn.cluster.cpunum=4
 #jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
 
@@ -94,7 +93,7 @@ cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMB
 local.globplot.bin=binaries/src/globplot/GlobPlot.py
 cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
 #globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 
-#globplot.limits.file=conf/settings/GlobPlotLimits.xml
+globplot.limits.file=conf/settings/GlobPlotLimits.xml
 #globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
 ### IUPred configuration ### 
diff --git a/datamodel/compbio/metadata/LimitsManager.java b/datamodel/compbio/metadata/LimitsManager.java
index 9e8dfb4..94de517 100644
--- a/datamodel/compbio/metadata/LimitsManager.java
+++ b/datamodel/compbio/metadata/LimitsManager.java
@@ -54,8 +54,14 @@ public class LimitsManager<T> {
 
 	@Override
 	public String toString() {
-		return "LimitsManager [limits=" + limit + ", runnerClassName="
-				+ runnerClassName + "]";
+		if (limit == null) {
+			return "";
+		}
+		String value = "";
+		for (Limit<T> lim : limit) {
+			value += lim.toString();
+		}
+		return value;
 	}
 
 	/**
diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index 7091f02..4f721fe 100644
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@ -209,7 +209,7 @@ public class WSTester {
 	 *             executable does not exists for a server platform
 	 */
 	@SuppressWarnings("unchecked")
-	private <T> boolean checkService(JABAService wservice) {
+	private <T> boolean checkService(JABAService wservice, Services service) {
 		try {
 			if (wservice == null) {
 				throw new NullPointerException(
@@ -219,7 +219,8 @@ public class WSTester {
 			if (wservice instanceof MsaWS) {
 				return testMsaWS((MsaWS<T>) wservice);
 			} else if (wservice instanceof SequenceAnnotation) {
-				return testSequenceAnnotationWS((SequenceAnnotation<T>) wservice);
+				return testSequenceAnnotationWS(
+						(SequenceAnnotation<T>) wservice, service);
 			} else {
 				throw new UnsupportedOperationException("The service: "
 						+ wservice.getClass() + " is not supported! ");
@@ -230,11 +231,15 @@ public class WSTester {
 		}
 	}
 
-	private <T> boolean testSequenceAnnotationWS(SequenceAnnotation<T> wservice)
-			throws Exception {
+	private <T> boolean testSequenceAnnotationWS(
+			SequenceAnnotation<T> wservice, Services service) throws Exception {
 		writer.print("Calling analyse.........");
-		boolean success = testDefaultAnalyse(loadAlignment(), wservice, null,
-				null);
+
+		List<FastaSequence> input = loadSeqs();
+		if (service == Services.AAConWS) {
+			input = loadAlignment();
+		}
+		boolean success = testDefaultAnalyse(input, wservice, null, null);
 
 		PresetManager<T> presetman = wservice.getPresets();
 		if (presetman != null) {
@@ -242,8 +247,7 @@ public class WSTester {
 			if (presets != null && !presets.isEmpty()) {
 				Preset<T> preset = presets.get(0);
 				writer.print("Calling analyse with Preset.........");
-				success = testDefaultAnalyse(loadAlignment(), wservice, preset,
-						null);
+				success = testDefaultAnalyse(input, wservice, preset, null);
 			}
 		}
 		testMetadata(wservice);
@@ -304,6 +308,7 @@ public class WSTester {
 		LimitsManager<T> limits = msaws.getLimits();
 		if (limits != null && limits.getLimits().size() > 0) {
 			writer.println(OK);
+			// writer.println("Limits details: \n" + limits.toString());
 		} else {
 			writer.println(UNSUPPORTED);
 		}
@@ -408,7 +413,7 @@ public class WSTester {
 		boolean succeed = false;
 		try {
 			writer.println("Checking service " + service.toString());
-			succeed = checkService(ws);
+			succeed = checkService(ws, service);
 		} finally {
 			FileUtil.closeSilently(((Closeable) ws));
 		}