From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 14 Oct 2013 09:58:40 +0000 (+0100)
Subject: Define path to UNIREF database in conf/Executable.properties
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d32ee68d6295b36d77bd115b1fb0af2068f29837;p=jabaws.git

Define path to UNIREF database in conf/Executable.properties
---

diff --git a/conf/Executable.properties b/conf/Executable.properties
index a4f1aa3..cbc8474 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -218,7 +218,13 @@ aacon.limits.file        = conf/settings/AAConLimits.xml
 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;UNIREFDB#binaries/src/jpred/unirefdb;
+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
diff --git a/runner/compbio/runner/predictors/Jpred.java b/runner/compbio/runner/predictors/Jpred.java
index 12f9487..0e08e0a 100644
--- a/runner/compbio/runner/predictors/Jpred.java
+++ b/runner/compbio/runner/predictors/Jpred.java
@@ -40,7 +40,8 @@ import compbio.metadata.ResultNotAvailableException;
 /**
  * Command line
  * 
- * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb -ncpu 4
+ * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath
+ * /data/UNIREFdb -ncpu 4
  * 
  * @author asherstnev
  * 
@@ -59,15 +60,17 @@ public class Jpred extends SkeletalExecutable<Jpred> {
 	public static final String STAT_FILE = "stat.txt";
 
 	public Jpred() {
+		String dbpath = ph.getProperty("jpred.data.uniref.path");
+		String dbname = ph.getProperty("jpred.data.uniref.name");
 		addParameters(Arrays.asList("-logfile " + STAT_FILE));
-		addParameters(Arrays.asList("-jabaws"));
+		addParameters(Arrays.asList("-dbpath " + dbpath));
+		addParameters(Arrays.asList("-dbname " + dbname));
 	}
 
 	// HashMap<Method, float[]>
 	@SuppressWarnings("unchecked")
 	@Override
-	public JpredAlignment getResults(String workDirectory)
-			throws ResultNotAvailableException {
+	public JpredAlignment getResults(String workDirectory) throws ResultNotAvailableException {
 		JpredAlignment annotations = null;
 		try {
 			InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));
@@ -129,7 +132,8 @@ public class Jpred extends SkeletalExecutable<Jpred> {
 
 	@Override
 	public CommandBuilder<Jpred> getParameters(ExecProvider provider) {
-		// If number of cores is provided, set it for the cluster execution only!
+		// If number of cores is provided, set it for the cluster execution
+		// only!
 		if (provider == Executable.ExecProvider.Cluster) {
 			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
 			cpunum = (cpunum == 0) ? 1 : cpunum;
diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 095d8fd..daeb8fa 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -467,8 +467,8 @@ public class Jws2Client {
 				jobId = msaws.align(fastalist);
 			}
 			System.out.println("\ncalling program.........");
-			long startTime = System.nanoTime();
 			/*
+			long startTime = System.nanoTime();
 			while (JobStatus.RUNNING == msaws.getJobStatus(jobId)) {
 				Thread.sleep(1000);
 				long endTime = System.nanoTime();