Removing almost all warnings in structure module, some logging changes

josemduarte · josemduarte · commit bb14709958f8 · 2017-11-16T08:54:26.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -28,6 +28,9 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 
 public class BioAssemblyIdentifier implements StructureIdentifier {
+
+	private static final long serialVersionUID = -356206725119993449L;
+	
 	private String pdbCode;
 	private int biolNr;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -25,7 +25,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.text.DateFormat;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java
@@ -671,8 +671,8 @@ private void getPdbRegions(Atom[] ca1, Atom[] ca2){
 			Chain c1 = p1.getChain();
 			Chain c2 = p2.getChain();
 
-			String cid1 = c1.getChainID();
-			String cid2 = c2.getChainID();
+			String cid1 = c1.getId();
+			String cid2 = c2.getId();
 
 			String pdb1 = p1.getResidueNumber().toString();
 			String pdb2 = p2.getResidueNumber().toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -338,6 +338,7 @@ public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int
 		int     i;
 		int eqr = 0;
 
+		@SuppressWarnings("unused")
 		int count = 0;
 		for(i = 0; i < alnLength; i ++) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -731,7 +731,8 @@ private static String complement(String sequence, boolean RNA) {
      * @param b An array of length 3 or 4 (4th component is ignored)
      * @return The cross product of the vectors (just the first three components
      */
-    private static double[] cross(double[] a, double[] b) {
+    @SuppressWarnings("unused")
+	private static double[] cross(double[] a, double[] b) {
         assert a.length >= 3 && b.length >= 3;
         double[] result = new double[4];
         result[0] = a[1]*b[2]-a[2]*b[1];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java
@@ -41,7 +41,9 @@
  */
 public class MismatchedBasePairParameters extends BasePairParameters {
 
-    public static final double DEFAULT_MAX_STAGGER = 2.0;
+	private static final long serialVersionUID = 2837124340169886674L;
+	
+	public static final double DEFAULT_MAX_STAGGER = 2.0;
     public static final double DEFAULT_MAX_PROPELLER = 60.0;
     public static final double DEFAULT_MAX_SHEAR = 5.0;
     public static final double DEFAULT_MAX_STRETCH = 5.0;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java
@@ -42,7 +42,9 @@
  */
 public class TertiaryBasePairParameters extends BasePairParameters {
 
-    public static final double DEFAULT_MAX_STAGGER = 2.0;
+	private static final long serialVersionUID = 2556427111533466577L;
+	
+	public static final double DEFAULT_MAX_STAGGER = 2.0;
     public static final double DEFAULT_MAX_PROPELLER = 60.0;
     // These are the criteria used to select proper base pairs.
     private double maxStagger = DEFAULT_MAX_STAGGER,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -33,8 +33,11 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 
 public class PDPDomain implements StructureIdentifier {
-	String identifier;
-	SubstructureIdentifier canonical;
+	private static final long serialVersionUID = 6894463080739943026L;
+	
+	private String identifier;
+	private SubstructureIdentifier canonical;
+	
 	public static final Pattern PDP_NAME_PATTERN = Pattern.compile("^(?:PDP:)([0-9][a-z0-9]{3})(\\w)(\\w)$",Pattern.CASE_INSENSITIVE);
 
 	public PDPDomain(String pdpDomainName, List<ResidueRange> ranges) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
@@ -194,8 +194,8 @@ private static EntityInfo findNonPolyEntityWithDescription(String description, L
 
 	private static boolean areResNumbersAligned(Chain c1, Chain c2) {
 
-		boolean isC1prot = StructureTools.isProtein(c1);
-		boolean isC2prot = StructureTools.isProtein(c2);
+		boolean isC1prot = c1.isProtein();
+		boolean isC2prot = c2.isProtein();
 
 		// different kind of chain: we won't try to align them
 		if (isC1prot != isC2prot ) return false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -3140,10 +3140,10 @@ private void assignChainsAndEntities(){
 			for (Chain c:model) {
 
 				// we only have entities for polymeric chains, all others are ignored for assigning entities
-				if (StructureTools.isChainWaterOnly(c)) {
+				if (c.isWaterOnly()) {
 					waterChains.add(c);
 
-				} else if (StructureTools.isChainPureNonPolymer(c)) {
+				} else if (c.isPureNonPolymer()) {
 					nonPolyChains.add(c);
 
 				} else {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
@@ -15,7 +15,7 @@
 public class MetalBondConsumer implements MMcifConsumer{
 
 
-    Map<String,List<MetalBondDistance>> definitions = new HashMap();
+    Map<String,List<MetalBondDistance>> definitions = new HashMap<>();
 
     @Override
     public void documentStart() {
@@ -28,7 +28,7 @@ public void documentEnd() {
         // minimize memory consumption
 
         for  (List<MetalBondDistance> d : definitions.values()){
-            ArrayList<MetalBondDistance> a = (ArrayList)d;
+            ArrayList<MetalBondDistance> a = (ArrayList<MetalBondDistance>)d;
 
             a.trimToSize();
         }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -931,7 +931,7 @@ private void linkEntities() {
 					entityInfo = new EntityInfo();
 					entityInfo.setMolId(eId);
 					entityInfo.addChain(chain);
-					if (StructureTools.isChainWaterOnly(chain)) {
+					if (chain.isWaterOnly()) {
 						entityInfo.setType(EntityType.WATER);
 					} else {
 						entityInfo.setType(EntityType.NONPOLYMER);
@@ -970,10 +970,10 @@ private void linkEntities() {
 				for (Chain c:model) {
 
 					// we only have entities for polymeric chains, all others are ignored for assigning entities
-					if (StructureTools.isChainWaterOnly(c)) {
+					if (c.isWaterOnly()) {
 						waterChains.add(c);
 
-					} else if (StructureTools.isChainPureNonPolymer(c)) {
+					} else if (c.isPureNonPolymer()) {
 						nonPolyChains.add(c);
 
 					} else {
@@ -1730,13 +1730,8 @@ private StructRef getStructRef(String ref_id){
 	 */
 	@Override
 	public void newStructRefSeq(StructRefSeq sref) {
-		//if (DEBUG)
-		//	System.out.println(sref);
 		DBRef r = new DBRef();
 
-
-		//if (DEBUG)
-		//	System.out.println( " " + sref.getPdbx_PDB_id_code() + " " + sref.getPdbx_db_accession());
 		r.setIdCode(sref.getPdbx_PDB_id_code());
 		r.setDbAccession(sref.getPdbx_db_accession());
 		r.setDbIdCode(sref.getPdbx_db_accession());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -1048,7 +1048,7 @@ private void produceWarning(String key, String val, Class<?> c, Set<String> warn
 		if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
 			logger.debug(warning);
 		} else {
-			logger.warn(warning);
+			logger.info(warning);
 		}
 
 		if(warnings != null) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -29,7 +29,6 @@
 import javax.vecmath.Matrix4d;
 
 import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.multiple.Block;
