From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 4 Jun 2012 16:06:13 +0000 (+0100)
Subject: JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for... 
X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=commitdiff_plain;h=63193df50e954f74c63611a1176034491b4615a1

JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for large sets of sequences in multithreaded mode
---

diff --git a/binaries/windows/bj3.0.4p-jronn.jar b/binaries/windows/bj3.0.4p-jronn.jar
new file mode 100644
index 0000000..9e09b30
Binary files /dev/null and b/binaries/windows/bj3.0.4p-jronn.jar differ
diff --git a/binaries/windows/bj3.0.4p-jronn.jar.readme b/binaries/windows/bj3.0.4p-jronn.jar.readme
new file mode 100644
index 0000000..41eb6c9
--- /dev/null
+++ b/binaries/windows/bj3.0.4p-jronn.jar.readme
@@ -0,0 +1,4 @@
+This is a patched version of the biojava3-protein-disorder v3.0.4 build of JRonn.
+See these bugs: 
+http://issues.jalview.org/browse/JWS-27
+https://redmine.open-bio.org/issues/3362
diff --git a/binaries/windows/bj3.0.4p-jronn.patch b/binaries/windows/bj3.0.4p-jronn.patch
new file mode 100644
index 0000000..f043b19
--- /dev/null
+++ b/binaries/windows/bj3.0.4p-jronn.patch
@@ -0,0 +1,23 @@
+Index: src/main/java/org/biojava3/ronn/ORonn.java
+===================================================================
+--- src/main/java/org/biojava3/ronn/ORonn.java	(revision 9674)
++++ src/main/java/org/biojava3/ronn/ORonn.java	(working copy)
+@@ -102,7 +102,9 @@
+ 		timer = new Timer(TimeUnit.MILLISECONDS);
+ 	}
+ 
+-	synchronized void writeResults(final float[] meanScores, final char[] seqs) {
++	void writeResults(final float[] meanScores, final char[] seqs) {
++		synchronized (out)
++		{
+ 		out.println(">" + sequence.getId());
+ 		if (layout == ResultLayout.VERTICAL) {
+ 			for (int i = 0; i < meanScores.length; i++) {
+@@ -124,6 +126,7 @@
+ 		}
+ 		out.println();
+ 		out.flush();
++		}
+ 	}
+ 
+ 	static boolean isValidSequence(final FastaSequence fsequence) {
diff --git a/binaries/windows/jronn3.1.jar b/binaries/windows/jronn3.1.jar
deleted file mode 100644
index fa39e98..0000000
Binary files a/binaries/windows/jronn3.1.jar and /dev/null differ
diff --git a/conf/Executable.properties b/conf/Executable.properties
index dcb5d5a..114ac18 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -55,7 +55,7 @@
 ## local.<execname>.bin.windows properties are optional for these, if not 
 ## provided they will be replaced to the java executable path from JAVA_HOME 
 ## environmental variable. 
-#<execname>.jar.file=binaries/windows/jronn3.1.jar
+#<execname>.jar.file=binaries/windows/bj3.0.4p-jronn.jar