Adding Jama for Ryan.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -28,6 +28,9 @@
     <dependency org="com.google.collections" name="google-collections" rev="1.0"/>
     <dependency org="dom4j" name="dom4j" rev="1.6"/>
 
+    <!-- Matrix package from math.nist.gov -->
+    <dependency org="gov.nist" name="Jama" rev="1.0.2" conf="default"/>
+
     <!-- Dependencies for the graph aligner -->  
     <dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3" conf="default"/>
      

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -39,6 +39,7 @@ import java.util.List;
  * PackageUtils contains some useful methods for package introspection.
  */
 public class PackageUtils {
+    
     /**
      * A reference into our introspection utility.
      */

settings/ivysettings.xml

@@ -14,5 +14,6 @@
     <module organisation="net.sf" module="samtools" resolver="projects" />
     <module organisation="org.reflections" module="reflections" resolver="projects" />
     <module organisation="org.broad" module="tribble" resolver="projects" />
+    <module organisation="gov.nist" module="Jama" resolver="projects" />
   </modules>
 </ivysettings>

settings/repository/gov.nist/Jama-1.0.2.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="gov.nist" module="Jama" revision="1.0.2" status="release" />
+</ivy-module>