Add log4J configuration file

src/main/java/groupId/IsoMet/ParseSbml.java

@@ -26,7 +26,7 @@ import java.util.stream.Collectors;
 
 public class ParseSbml {
 
-	private static final Logger logger = LogManager.getLogger(ParseSbml.class.getName());
+	private static final Logger logger = LogManager.getLogger(ParseSbml.class);
 
 	/*
 	 * parse SBML using JSBML library

src/main/java/groupId/IsoMet/SmilesFromInchiAnnot.java

@@ -23,7 +23,7 @@ import java.util.regex.Pattern;
 
 public class SmilesFromInchiAnnot {
 
-    private static final Logger logger = LogManager.getLogger(SmilesFromInchiAnnot.class.getName());
+    private static final Logger logger = LogManager.getLogger(SmilesFromInchiAnnot.class);
 
     //Our data of interest, molecular structure, can be extracted from InChIs.
     //InChIs are molecular descriptor

src/main/java/groupId/IsoMet/data/Compound.java

@@ -20,7 +20,7 @@ import org.sbml.jsbml.Species;
 
 public class Compound{
 
-	private static final Logger logger = LogManager.getLogger(Compound.class.getName());
+	private static final Logger logger = LogManager.getLogger(Compound.class);
 
 
 	private final Species sbmlSpecie;

src/main/resources/log4j2.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<Configuration status="ALL">
+    <Appenders>
+        <Console name="Console" target="SYSTEM_OUT">
+            <PatternLayout pattern="%d{HH:mm} %logger{1} : %highlight{%-5level} - %msg%n" />
+        </Console>
+        <File name="GSAMLOG" fileName="gsam.log" immediateFlush="false" append="false">
+            <PatternLayout pattern="%d{yyy-MM-dd HH:mm} %logger{1}, %-5level - %msg%n"/>
+        </File>
+    </Appenders>
+    <Loggers>
+        <Logger name="groupId.IsoMet" level="debug" additivity="false">
+            <AppenderRef ref="GSAMLOG"/>
+        </Logger>
+        <Root level="warn">
+            <AppenderRef ref="Console"/>
+        </Root>
+    </Loggers>
+</Configuration>