From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Tue, 1 Oct 2019 09:53:36 +0000 (+0200)
Subject: JAL-3437 issue with
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=e9672febde14edb7392d321b1b5748bbcda4d542;p=jalview.git

JAL-3437 issue with
System.getProperty("javax.xml.datatype.DatatypeFactory")

1/2 ?
---

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
index f51640c..fde0115 100644
--- a/_j2sclasslist.txt
+++ b/_j2sclasslist.txt
@@ -672,10 +672,12 @@ javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
 javax/xml/bind/annotation/adapters/XmlAdapter.js
 javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
 javax/xml/bind/helpers/DefaultValidationEventHandler.js
+javax/xml/datatype/DatatypeFactory.js
 javax/xml/datatype/XMLGregorianCalendar.js
 javax/xml/namespace/QName.js
 javax/xml/stream/XMLInputFactory.js
 javax/xml/stream/XMLStreamReader.js
+org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js
 org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
 org/json/simple/parser/JSONParser.js
 org/json/simple/parser/ParseException.js
@@ -810,6 +812,7 @@ swingjs/xml/JSJAXBField.js
 swingjs/xml/JSJAXBUnmarshaller.js
 swingjs/xml/JSSAXAttributes.js
 swingjs/xml/JSSAXParser.js
+swingjs/xml/JSXMLDatatypeFactoryImpl.js
 swingjs/xml/JSXMLGregorianCalendarImpl.js
 swingjs/xml/JSXMLInputFactory.js
 swingjs/xml/JSXMLStreamReader.js
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index cb61740..df76c61 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -29,6 +29,21 @@ import java.io.IOException;
 
 public enum FileFormat implements FileFormatI
 {
+  BSML("BSML", "bbb", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new BSMLFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 621cfac..fc9938f 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -179,6 +179,15 @@ public class IdentifyFile
             break;
           }
         }
+        if (data.startsWith("<?xml"))
+        {
+          data = source.nextLine();
+          if (data.startsWith("<Bsml>"))
+          {
+            reply = FileFormat.BSML;
+            break;
+          }
+        }
         data = data.toUpperCase();
 
         if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 76474a0..72900a8 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index fccfaec..9b20eae 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20190929051131 
+20191001111303 
diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip
index 76474a0..72900a8 100644
Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
index fccfaec..9b20eae 100644
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20190929051131 
+20191001111303