biojava · josemduarte · Dec 19, 2019 · Nov 10, 2019 · Nov 10, 2019 · Nov 12, 2019
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -163,7 +163,8 @@ public interface Atom extends Cloneable, PDBRecord {
 
 	/**
 	 * Get alternate Location.
-	 * @return a Character object representing the alt loc value
+	 * @return a Character object representing the alt loc value. Default altLoc ('.' in mmCIF files)
+	 * is represented by ' ' (space character, ascii 32).
 	 * @see #setAltLoc
 	 */
 	public Character getAltLoc();

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
@@ -157,10 +157,6 @@ public void setZ(double z) {
 	@Override
 	public double getZ() { return coords.z; }
 
-	/**
-	 * Set alternate Location.
-	 * @see #getAltLoc
-	 */
 	@Override
 	public void setAltLoc(Character c) {
 		// after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
@@ -170,11 +166,6 @@ public void setAltLoc(Character c) {
 			altLoc = c ;
 	}
 
-	/**
-	 * Get alternate Location.
-	 * @return a Character object representing the alt loc value
-	 * @see #setAltLoc
-	 */
 	@Override
 	public Character getAltLoc() {
 		// after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
@@ -309,7 +300,7 @@ public void setBonds(List<Bond> bonds) {
 	@Override
 	public void addBond(Bond bond) {
 		if (bonds==null) {
-			bonds = new ArrayList<Bond>(BONDS_INITIAL_CAPACITY);
+			bonds = new ArrayList<>(BONDS_INITIAL_CAPACITY);
 		}
 		bonds.add(bond);
 	}

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -103,12 +103,13 @@ public interface Group extends Serializable {
 
 	/**
 	 * Set the atoms of this group.
-	 * @see {@link Atom}
+	 * @see Atom
 	 * @param atoms a list of atoms
 	 */
 	public void setAtoms(List<Atom> atoms);
 
-	/** Remove all atoms from this group.
+	/**
+	 * Remove all atoms from this group.
 	 *
 	 */
 	public void clearAtoms();
@@ -118,13 +119,14 @@ public interface Group extends Serializable {
 	 * Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium),
 	 * ambiguities should not occur within the same group though. To solve these ambiguities
 	 * one would need to check the atom returned for the required element with {@link Atom#getElement()}
+	 * <p>
+	 * Note this method will return only the atom in the default alternative location (be it '.' or a letter).
 	 *
 	 * @param name  a trimmed String representing the atom's PDB name, e.g. "CA"
 	 * @return an Atom object or null if no such atom exists within this group
 	 */
 	public Atom getAtom(String name) ;
-
-
+
 	/**
 	 * Get at atom by position.
 	 *

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -77,7 +77,7 @@ public class HetatomImpl implements Group {
 	 * Behaviors for how to balance memory vs. performance.
 	 * @author Andreas Prlic
 	 */
-	public static enum PerformanceBehavior {
+	public enum PerformanceBehavior {
 
 		/** use a built-in HashMap for faster access to memory, at the price of more memory consumption */
 		BETTER_PERFORMANCE_MORE_MEMORY,
@@ -87,7 +87,7 @@ public static enum PerformanceBehavior {
 
 	}
 
-	public static PerformanceBehavior performanceBehavior=PerformanceBehavior.LESS_MEMORY_SLOWER_PERFORMANCE;
+	private static PerformanceBehavior performanceBehavior=PerformanceBehavior.LESS_MEMORY_SLOWER_PERFORMANCE;
 
 	private Map<String,Atom> atomNameLookup;
 
@@ -105,42 +105,28 @@ public HetatomImpl() {
 		pdb_name = null ;
 
 		residueNumber = null;
-		atoms    = new ArrayList<Atom>();
-		properties = new HashMap<String,Object>();
+		atoms    = new ArrayList<>();
+		properties = new HashMap<>();
 		parent = null;
 		chemComp = null;
 		altLocs = null;
 
 		if ( performanceBehavior == PerformanceBehavior.BETTER_PERFORMANCE_MORE_MEMORY)
-			atomNameLookup = new HashMap<String,Atom>();
+			atomNameLookup = new HashMap<>();
 		else
 			atomNameLookup = null;
 	}
 
-
-	/**
-	 *  returns true or false, depending if this group has 3D coordinates or not.
-	 * @return true if Group has 3D coordinates
-	 */
 	@Override
 	public boolean has3D() {
 		return pdb_flag;
 	}
 
-	/** flag if group has 3D data.
-	 *
-	 * @param flag  true to set flag that this Group has 3D coordinates
-	 */
 	@Override
 	public void setPDBFlag(boolean flag){
 		pdb_flag = flag ;
 	}
 
-	/** Set three character name of Group .
-	 *
-	 * @param s  a String specifying the PDBName value
-	 * @see #getPDBName
-	 */
 	@Override
 	public void setPDBName(String s) {
 		// hetatoms can have pdb_name length < 3. e.g. CU (see 1a4a position 1200 )
@@ -152,12 +138,6 @@ public void setPDBName(String s) {
 
 	}
 
-	/**
-	 * Returns the PDBName.
-	 *
-	 * @return a String representing the PDBName value
-	 * @see #setPDBName
-	 */
 	@Override
 	public String getPDBName() { return pdb_name;}
 
@@ -187,12 +167,8 @@ public void addAtom(Atom atom){
 				logger.warn("An atom with name " + atom.getName() + " " + altLocStr + " is already present in group: " + this.toString() + ". The atom with serial " + atom.getPDBserial() + " will be ignored in look-ups.");
 			}
 		}
-	};
-
+	}
 
-	/** remove all atoms
-	 *
-	 */
 	@Override
 	public void clearAtoms() {
 		atoms.clear();
@@ -245,8 +221,7 @@ public Atom getAtom(String name) {
 		if ( atomNameLookup != null)
 			return atomNameLookup.get(name);
 		else {
-			/** This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
-			 */
+			// This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
 			for (Atom a : atoms) {
 				if (a.getName().equals(name)) {
 					return a;
@@ -279,16 +254,13 @@ public boolean hasAtom(String fullName) {
 			Atom a = atomNameLookup.get(fullName.trim());
 			return a != null;
 		} else {
-			/** This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
-			 */
+			// This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
 			for (Atom a : atoms) {
 				if (a.getName().equals(fullName)) {
 					return true;
 				}
 			}
 			return false;
-
-
 		}
 
 	}
@@ -400,42 +372,21 @@ public void setProperties(Map<String,Object> props) {
 		properties =  props ;
 	}
 
-	/** return properties.
-	 *
-	 * @return a HashMap object representing the properties value
-	 * @see #setProperties
-	 */
 	@Override
 	public Map<String, Object> getProperties() {
 		return properties ;
 	}
 
-	/** set a single property .
-	 *
-	 * @see #getProperties
-	 * @see #getProperty
-	 */
 	@Override
 	public void setProperty(String key, Object value){
 		properties.put(key,value);
 	}
 
-	/** get a single property .
-	 * @param key  a String
-	 * @return an Object
-	 * @see #setProperty
-	 * @see #setProperties
-	 */
 	@Override
 	public Object getProperty(String key){
 		return properties.get(key);
 	}
 
-
-	/** return an AtomIterator.
-	 *
-	 * @return an Iterator object
-	 */
 	@Override
 	public Iterator<Atom> iterator() {
 		return new AtomIterator(this);
@@ -588,7 +539,7 @@ public boolean hasAltLoc() {
 	@Override
 	public List<Group> getAltLocs() {
 		if ( altLocs == null)
-			return new ArrayList<Group>();
+			return new ArrayList<>();
 		return altLocs;
 	}
 
@@ -629,7 +580,7 @@ public Group getAltLocGroup(Character altLoc) {
 	@Override
 	public void addAltLoc(Group group) {
 		if ( altLocs == null) {
-			altLocs = new ArrayList<Group>();
+			altLocs = new ArrayList<>();
 		}
 		altLocs.add(group);
 
@@ -640,10 +591,6 @@ public boolean isWater() {
 		return GroupType.WATERNAMES.contains(pdb_name);
 	}
 
-	/** attempts to reduce the memory imprint of this group by trimming
-	 * all internal Collection objects to the required size.
-	 *
-	 */
 	@Override
 	public void trimToSize(){
 
@@ -663,10 +610,10 @@ public void trimToSize(){
 		}
 
 		// now let's fit the hashmaps to size
-		properties = new HashMap<String, Object>(properties);
+		properties = new HashMap<>(properties);
 
 		if ( atomNameLookup != null)
-			atomNameLookup = new HashMap<String,Atom>(atomNameLookup);
+			atomNameLookup = new HashMap<>(atomNameLookup);
 
 	}