Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop

diff --git a/.classpath b/.classpath
index cad9e2b..d973eeb 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -12,7 +12,6 @@
        <classpathentry kind="lib" path="lib/regex.jar"/>
        <classpathentry kind="lib" path="lib/saaj.jar"/>
        <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-       <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
        <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
@@ -39,7 +38,7 @@
        <classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
        <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
-       <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
+       <classpathentry kind="lib" path="/Users/jprocter/git/jalview/lib/groovy-all-2.4.6-indy.jar"/>
        <classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
        <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
        <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>

diff --git a/lib/groovy-all-1.8.2.jar b/lib/groovy-all-1.8.2.jar
deleted file mode 100755 (executable)
index 85af249..0000000
Binary files a/lib/groovy-all-1.8.2.jar and /dev/null differ

diff --git a/lib/groovy-all-2.4.6-indy.jar b/lib/groovy-all-2.4.6-indy.jar
new file mode 100644 (file)
index 0000000..5f3d51c
Binary files /dev/null and b/lib/groovy-all-2.4.6-indy.jar differ

diff --git a/lib/xercesImpl.jar b/lib/xercesImpl.jar
deleted file mode 100755 (executable)
index 0aaa990..0000000
Binary files a/lib/xercesImpl.jar and /dev/null differ

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6c8750f..d0b3232 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -90,6 +90,7 @@ public class Jalview
    */
   public static void main(String[] args)
   {
+    System.setSecurityManager(null);
     System.out.println("Java version: "
             + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index 83d1a98..428b998 100755 (executable)
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2025,7 +2025,7 @@ and any path to a file to save to the file]]></string>
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@ -2043,7 +2043,7 @@ and any path to a file to save to the file]]></string>
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
                                                                <long>6149494</long>