Merge branch 'bugfixes-4.2' into master

sbliven · sbliven · commit 637aee6866a2 · 2017-02-15T21:56:09.000+01:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
@@ -403,7 +403,7 @@ public void testGetSubRangesExtended() throws StructureException {
 		assertEquals("Wrong number of chains in "+range, 1, substr.size());
 		chain = substr.getChainByIndex(0);
 		assertEquals("Did not find the expected number of residues in "+range, 4, chain.getAtomLength() );
-		
+
 		range = "A:--1";
 		substr = StructureTools.getSubRanges(structure2, range);
 		assertEquals("Wrong number of chains in "+range, 1, substr.size());
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
@@ -103,7 +103,7 @@ public void destroy(){
 	public void setAtoms(Atom[] atoms){
 		Structure s = new StructureImpl();
 		Chain c = new ChainImpl();
-		c.setId("A");
+		c.setChainID("A");
 		for (Atom a: atoms){
 			c.addGroup(a.getGroup());
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -782,6 +782,10 @@ public static final Atom getCentroid(Atom[] atomSet) {
 		if (atomSet.length==0) 
 			throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
 
+		// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
+		if (atomSet.length==0) 
+			throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
+		
 		double[] coords = new double[3];
 
 		coords[0] = 0;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -613,7 +613,7 @@ private void calcReferenceVector() {
 		referenceVector = getReferenceAxisCylic();
 
 		if (referenceVector == null) {
-			System.err.println("Warning: no reference vector found. Using y-axis.");
+			logger.warn("no reference vector found. Using y-axis.");
 			referenceVector = new Vector3d(Y_AXIS);
 		}
 		// make sure reference vector is perpendicular principal roation vector
@@ -629,7 +629,7 @@ private Vector3d orthogonalize(Vector3d vector1, Vector3d vector2) {
 			vector2.negate();
 		}
 		if (Math.abs(dot) < 0.00001) {
-			System.out.println("HelixAxisAligner: Warning: reference axis parallel");
+			logger.info("HelixAxisAligner: reference axis parallel");
 		}
 		vector2.cross(vector1, vector2);
 //		System.out.println("Intermed. refVector: " + vector2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -331,7 +331,7 @@ private List<Integer> alignWithReferenceAxis(List<Integer> orbit) {
 		}
 		Collections.reverse(orbit.subList(1,  orbit.size()));
 		if (orbit.get(1) != index2) {
-			System.err.println("Warning: alignWithReferenceAxis failed");
+			logger.warn("alignWithReferenceAxis failed");
 		}
 //		System.out.println("Orbit2: " + orbit);
 		return orbit;
@@ -644,7 +644,7 @@ private List<Integer> deconvolute(List<Integer> orbit) {
 			int index = p0.indexOf(current);
 			int next = p1.get(index);
 			if (!orbit.contains(next)) {
-				System.err.println("deconvolute: inconsistency in permuation. Returning original order");
+				logger.warn("deconvolute: inconsistency in permuation. Returning original order");
 				return orbit;
 			}
 			inRotationOrder.add(next);
@@ -687,7 +687,7 @@ private void calcReferenceVector() {
 		}
 
 		if (referenceVector == null) {
-			System.err.println("Warning: no reference vector found. Using y-axis.");
+			logger.warn("no reference vector found. Using y-axis.");
 			referenceVector = new Vector3d(Y_AXIS);
 		}
 		// make sure reference vector is perpendicular principal roation vector
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -23,14 +23,15 @@
 
 import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
 /**
  *
  * @author Peter
  */
-public class PermutationGroup {
+public class PermutationGroup implements Iterable<List<Integer>> {
 	List<List<Integer>> permutations = new ArrayList<List<Integer>>();
 
 	public void addPermutation(List<Integer> permutation) {
@@ -140,6 +141,11 @@ public int hashCode() {
 	    return getGroupTable().hashCode();
 	}
 
+	@Override
+	public Iterator<List<Integer>> iterator() {
+		return permutations.iterator();
+	}
+
 	@Override
 	public boolean equals(Object obj) {
 	    if (this == obj) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -27,13 +27,14 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.Iterator;
 import java.util.List;
 
 /**
  * @see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
  * @author Peter
  */
-public class RotationGroup {
+public class RotationGroup implements Iterable<Rotation> {
 	private List<Rotation> rotations = new ArrayList<Rotation>();
 	private int principalAxisIndex = 0;
 	private int higherOrderRotationAxis = 0;
@@ -369,4 +370,9 @@ public int compare(Rotation o1, Rotation o2) {
 			}
 		});
 	}
+
+	@Override
+	public Iterator<Rotation> iterator() {
+		return rotations.iterator();
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java

Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@ public void destroy(){`
`103`	`103`	`public void setAtoms(Atom[] atoms){`
`104`	`104`	`Structure s = new StructureImpl();`
`105`	`105`	`Chain c = new ChainImpl();`
`106`		`- c.setId("A");`
	`106`	`+ c.setChainID("A");`
`107`	`107`	`for (Atom a: atoms){`
`108`	`108`	`c.addGroup(a.getGroup());`
`109`	`109`	`}`
Original file line number	Diff line number	Diff line change
`@@ -613,7 +613,7 @@ private void calcReferenceVector() {`
`613`	`613`	`referenceVector = getReferenceAxisCylic();`
`614`	`614`
`615`	`615`	`if (referenceVector == null) {`
`616`		`- System.err.println("Warning: no reference vector found. Using y-axis.");`
	`616`	`+ logger.warn("no reference vector found. Using y-axis.");`
`617`	`617`	`referenceVector = new Vector3d(Y_AXIS);`
`618`	`618`	`}`
`619`	`619`	`// make sure reference vector is perpendicular principal roation vector`
`@@ -629,7 +629,7 @@ private Vector3d orthogonalize(Vector3d vector1, Vector3d vector2) {`
`629`	`629`	`vector2.negate();`
`630`	`630`	`}`
`631`	`631`	`if (Math.abs(dot) < 0.00001) {`
`632`		`- System.out.println("HelixAxisAligner: Warning: reference axis parallel");`
	`632`	`+ logger.info("HelixAxisAligner: reference axis parallel");`
`633`	`633`	`}`
`634`	`634`	`vector2.cross(vector1, vector2);`
`635`	`635`	`// System.out.println("Intermed. refVector: " + vector2);`
Original file line number	Diff line number	Diff line change
`@@ -331,7 +331,7 @@ private List<Integer> alignWithReferenceAxis(List<Integer> orbit) {`
`331`	`331`	`}`
`332`	`332`	`Collections.reverse(orbit.subList(1, orbit.size()));`
`333`	`333`	`if (orbit.get(1) != index2) {`
`334`		`- System.err.println("Warning: alignWithReferenceAxis failed");`
	`334`	`+ logger.warn("alignWithReferenceAxis failed");`
`335`	`335`	`}`
`336`	`336`	`// System.out.println("Orbit2: " + orbit);`
`337`	`337`	`return orbit;`
`@@ -644,7 +644,7 @@ private List<Integer> deconvolute(List<Integer> orbit) {`
`644`	`644`	`int index = p0.indexOf(current);`
`645`	`645`	`int next = p1.get(index);`
`646`	`646`	`if (!orbit.contains(next)) {`
`647`		`- System.err.println("deconvolute: inconsistency in permuation. Returning original order");`
	`647`	`+ logger.warn("deconvolute: inconsistency in permuation. Returning original order");`
`648`	`648`	`return orbit;`
`649`	`649`	`}`
`650`	`650`	`inRotationOrder.add(next);`
`@@ -687,7 +687,7 @@ private void calcReferenceVector() {`
`687`	`687`	`}`
`688`	`688`
`689`	`689`	`if (referenceVector == null) {`
`690`		`- System.err.println("Warning: no reference vector found. Using y-axis.");`
	`690`	`+ logger.warn("no reference vector found. Using y-axis.");`
`691`	`691`	`referenceVector = new Vector3d(Y_AXIS);`
`692`	`692`	`}`
`693`	`693`	`// make sure reference vector is perpendicular principal roation vector`