--- /dev/null
+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
--- /dev/null
+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) {
## local.<execname>.bin.windows properties are optional for these, if not \r
## provided they will be replaced to the java executable path from JAVA_HOME \r
## environmental variable. \r
-#<execname>.jar.file=binaries/windows/jronn3.1.jar\r
+#<execname>.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
\r
\r
\r