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a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-27 04:49:49 +00:00
parent bf3dbd8401
commit f6468f9143
5 changed files with 18 additions and 13 deletions
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15
ivy.xml
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@ -18,15 +18,22 @@
<dependency org="org.broad" name="tribble" rev="latest.integration" conf="default"/>
<!-- Dependencies for reflections mvn repository -->
<dependency org="org.reflections" name="reflections" rev="0.9.2" conf="default"/>
<dependency org="org.reflections" name="reflections" rev="0.9.5-svnversion79" conf="default"/>
<dependency org="com.google.collections" name="google-collections" rev="0.9" conf="default"/>
<dependency org="javassist" name="javassist" rev="3.8.0.GA"/>
<dependency org="ch.qos.logback" name="logback-core" rev="0.9.9"/>
<dependency org="ch.qos.logback" name="logback-classic" rev="0.9.9"/>
<dependency org="org.slf4j" name="slf4j-api" rev="1.5.6"/>
<dependency org="xml-apis" name="xml-apis" rev="1.0.b2"/>
<dependency org="com.google.collections" name="google-collections" rev="1.0"/>
<dependency org="dom4j" name="dom4j" rev="1.6"/>
<!-- Dependencies for the graph aligner -->
<dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3" conf="default"/>
<dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3" conf="default"/>
<!-- Dependencies for VariantFiltration -->
<dependency org="commons-jexl" name="commons-jexl" rev="1.1" conf="default"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1" conf="default"/>
<dependency org="commons-jexl" name="commons-jexl" rev="1.1" conf="default"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1" conf="default"/>
<!-- Scala dependancies -->
<dependency org="org.scala-lang" name="scala-compiler" rev="2.7.7" conf="scala->default"/>

14
java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
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@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.classloader;
import org.reflections.Reflections;
import org.reflections.scanners.SubTypesScanner;
import org.reflections.util.AbstractConfiguration;
import org.reflections.util.ClasspathHelper;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.reflections.util.ConfigurationBuilder;
import org.slf4j.LoggerFactory;
import java.util.Set;
import java.util.ArrayList;
@ -45,13 +45,11 @@ public class PackageUtils {
private static Reflections reflections = null;
static {
// Initialize general-purpose source tree reflector.
reflections = new Reflections( new AbstractConfiguration() {
{
setUrls(ClasspathHelper.getUrlsForCurrentClasspath());
setScanners(new SubTypesScanner());
}
});
reflections = new Reflections( new ConfigurationBuilder()
.setUrls(ClasspathHelper.getUrlsForCurrentClasspath())
.setScanners(new SubTypesScanner()));
}
/**

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settings/repository/org.reflections/reflections-0.9.2.jar
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settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar 100644
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2
settings/repository/org.reflections/reflections-0.9.2.xml → settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.reflections" module="reflections" revision="0.9.2" status="release" />
<info organisation="org.reflections" module="reflections" revision="0.9.5-svnversion79" status="release" />
</ivy-module>