JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for...

diff --git a/binaries/windows/bj3.0.4p-jronn.jar b/binaries/windows/bj3.0.4p-jronn.jar
new file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -55,7 +55,7 @@
 ## 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