Clarifying docs and some more cleanup

josemduarte · josemduarte · commit 0ff1823543a1 · 2019-11-11T21:39:04.000-08:00
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
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
@@ -254,16 +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;
-
-
 		}
 
 	}
@@ -375,42 +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);
@@ -615,10 +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(){
 
