Merge pull request biojava#566 from andviane/master

andreasprlic · web-flow · commit 87a76448af30 · 2016-08-22T07:10:09.000-07:00
GenericInsdcHeaderFormat: Fixed formatting codes.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
@@ -186,7 +186,7 @@ private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<
 				if(f.getLocations().getStrand() != Strand.NEGATIVE) {
 					StringBuilder sb = new StringBuilder();
 					Formatter formatter = new Formatter(sb,Locale.US);
-					formatter.format("Inconsistent strands: %r for parent, %r for child", feature.getLocations().getStrand(), f.getLocations().getStrand());
+					formatter.format("Inconsistent strands: %s for parent, %s for child", feature.getLocations().getStrand(), f.getLocations().getStrand());
 					String output = formatter.toString();
 					formatter.close();
 					throw new RuntimeException(output);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -106,7 +106,7 @@ private static double getResetVal(double unpenalizedScore,
 			double nResFromMainDiag, double[] gradientPolyCoeff,
 			double gradientExpCoeff) {
 
-		if (unpenalizedScore == Double.NaN)
+		if (Double.isNaN(unpenalizedScore))
 			return 0; // what else?
 
 		// We can actually return a positive value if this is high enough
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
@@ -25,6 +25,7 @@
 
 
 import org.biojava.nbio.structure.EntityInfo;
+import org.biojava.nbio.structure.EntityType;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -92,7 +93,7 @@ private void checkPDB(String pdbId, String organismTaxId) throws IOException, St
 		assertTrue(s.getEntityInfos().size() > 0);
 
 		for ( EntityInfo c : s.getEntityInfos()) {
-			if(c.getType().equals("polymer")) { 
+			if(EntityType.POLYMER.equals(c.getType())) { 
 				assertNotNull(c.getOrganismTaxId());
 				if(pdbId.equals("3zd6")){
 					if(c.getMolId()==2) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -287,7 +287,7 @@ public String getCoefficientText(boolean header, String beginLine, String beginC
 	public static String fmt(Double d, int precision, int pad) {
 		if(d == null)
 			return "";
-		if(d == Double.NaN)
+		if(Double.isNaN(d))
 			return "";
 		String value = "";
 		DecimalFormat dfe = new DecimalFormat("0.00E0");
