Important fix for biojava#155, was not specifying runtime scope corre…

…ctly
josemduarte · Aug 29, 2014 · 8e7c44f · 8e7c44f
1 parent feccb19
commit 8e7c44f
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Showing 2 changed files with 13 additions and 17 deletions.
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureSequenceMatcher.java
@@ -46,6 +46,8 @@
 import org.biojava3.core.sequence.compound.AminoAcidCompound;
 import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava3.core.sequence.template.CompoundSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 /**
@@ -55,6 +57,8 @@
  *
  */
 public class StructureSequenceMatcher {
+
+	private static final Logger logger = LoggerFactory.getLogger(StructureSequenceMatcher.class);
 
 	/**
 	 * Get a substructure of {@code wholeStructure} containing only the {@link Group Groups} that are included in
@@ -203,10 +207,10 @@ public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Stru
 
 				Group g = atomIndexPosition.get(structIndex);
 
-				System.err.format("Warning: chain %s residue %s in the Structure %s has no corresponding amino acid in the sequence.\n",
+				logger.warn(String.format("Warning: chain %s residue %s in the Structure %s has no corresponding amino acid in the sequence.",
 						g.getChainId(),
 						g.getResidueNumber().toString(),
-						g.getChain().getParent().getPDBCode());
+						g.getChain().getParent().getPDBCode()) );
 				continue;
 			}
 

diff --git a/pom.xml b/pom.xml
@@ -379,36 +379,28 @@
         		<artifactId>slf4j-api</artifactId>
         		<version>${slf4j.version}</version>
     		</dependency>
-    		<!-- binding for log4j 1.2
-			<dependency>
-  				<groupId>org.slf4j</groupId>
-  				<artifactId>slf4j-log4j12</artifactId>
-  				<version>1.7.7</version>  				
-  				<scope>runTime</scope>
-			</dependency>
-			 -->
-			 <!-- binding for log4j 2 -->
+			<!-- binding for log4j 2 -->
   			<dependency>
     			<groupId>org.apache.logging.log4j</groupId>
     			<artifactId>log4j-slf4j-impl</artifactId>
     			<version>${log4j.version}</version>
-    			<!-- runTime scope includes the test scope as well -->
-    			<scope>runTime</scope>
+    			<!-- runtime scope includes the test scope as well -->
+    			<scope>runtime</scope>
   			</dependency>
   			<!-- Log4j API and Core implementation required for binding -->
   			<dependency>
     			<groupId>org.apache.logging.log4j</groupId>
     			<artifactId>log4j-api</artifactId>
     			<version>${log4j.version}</version>
-    			<!-- runTime scope includes the test scope as well -->
-    			<scope>runTime</scope>    			
+    			<!-- runtime scope includes the test scope as well -->
+    			<scope>runtime</scope>    			
   			</dependency>
   			<dependency>
     			<groupId>org.apache.logging.log4j</groupId>
     			<artifactId>log4j-core</artifactId>
     			<version>${log4j.version}</version>
-    			<!-- runTime scope includes the test scope as well -->
-    			<scope>runTime</scope>    			
+    			<!-- runtime scope includes the test scope as well -->
+    			<scope>runtime</scope>    			
   			</dependency>			
 		</dependencies>
 	</dependencyManagement>