Subject: use log4j v1.X
Description: upstream use log4j v2.X which is not yet available in Debian.
There is no specific v2 API usage, so applying a patch to use the log4j 
version available in Debian waiting for new version availability.
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2014-02-01
Forwarded: no
--- a/biojava3-structure/pom.xml
+++ b/biojava3-structure/pom.xml
@@ -29,9 +29,9 @@
 		</dependency>
 
 		<dependency>
-			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-core</artifactId>
-			<version>2.0-beta7</version>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>1.2.17</version>
 		</dependency>
 		
 		<!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId> 
--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
@@ -23,8 +23,8 @@
 import java.io.InputStream;
 import java.net.URL;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
@@ -25,8 +25,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
@@ -31,8 +31,8 @@
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
@@ -28,8 +28,8 @@
 import java.util.Set;
 import java.util.TreeSet;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
 
 /**
  * Provides programmatic access to ASTRAL representative sets. See the paper by <a
