Back-porting cloning fix (see #541) into bugfixes-4.2

josemduarte · josemduarte · commit 46b30b35f409 · 2016-07-27T17:46:48.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
@@ -183,6 +183,10 @@ public Object clone() {
 				n.addAltLoc(nAltLocGroup);
 			}
 		}
+		
+		if (chemComp!=null)
+			n.setChemComp(chemComp);
+
 
 		return n;
 	}
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
@@ -88,7 +88,7 @@ public static enum PerformanceBehavior {
 
 	private Map<String,Atom> atomNameLookup;
 
-	private ChemComp chemComp ;
+	protected ChemComp chemComp ;
 
 	private List<Group> altLocs;
 
@@ -402,6 +402,9 @@ public Object clone() {
 				n.addAltLoc(nAltLocGroup);
 			}
 		}
+		
+		if (chemComp!=null)
+			n.setChemComp(chemComp);
 
 		return n;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
@@ -27,10 +27,9 @@
 
 
 /**
- *
- *  A nucleotide group is almost the same as a Hetatm group.
- *  @see HetatomImpl
- *  @see AminoAcidImpl
+ * A nucleotide group is almost the same as a Hetatm group.
+ * @see HetatomImpl
+ * @see AminoAcidImpl
  * @author Andreas Prlic
  * @since 1.4
  * @version %I% %G%
@@ -94,29 +93,5 @@ public Atom getP() {
 
 	}
 
-	@Override
-	public Object clone(){
-		NucleotideImpl n = new NucleotideImpl();
-
-		n.setPDBFlag(has3D());
-		n.setResidueNumber(getResidueNumber());
-
-		n.setPDBName(getPDBName());
-
-		// copy the atoms
-		for (Atom atom1 : atoms) {
-			Atom atom = (Atom) atom1.clone();
-			n.addAtom(atom);
-			atom.setGroup(n);
-		}
-
-		// copying the alt loc groups if present, otherwise they stay null
-		if (getAltLocs()!=null && !getAltLocs().isEmpty()) {
-			for (Group altLocGroup:this.getAltLocs()) {
-				Group nAltLocGroup = (Group)altLocGroup.clone();
-				n.addAltLoc(nAltLocGroup);
-			}
-		}
-		return n;
-	}
+	// no need to implement clone here, it's already in super class
 }

Original file line number	Diff line number	Diff line change
`@@ -183,6 +183,10 @@ public Object clone() {`
`183`	`183`	`n.addAltLoc(nAltLocGroup);`
`184`	`184`	`}`
`185`	`185`	`}`
	`186`	`+`
	`187`	`+ if (chemComp!=null)`
	`188`	`+ n.setChemComp(chemComp);`
	`189`	`+`
`186`	`190`
`187`	`191`	`return n;`
`188`	`192`	`}`
Original file line number	Diff line number	Diff line change
`@@ -88,7 +88,7 @@ public static enum PerformanceBehavior {`
`88`	`88`
`89`	`89`	`private Map<String,Atom> atomNameLookup;`
`90`	`90`
`91`		`- private ChemComp chemComp ;`
	`91`	`+ protected ChemComp chemComp ;`
`92`	`92`
`93`	`93`	`private List<Group> altLocs;`
`94`	`94`
`@@ -402,6 +402,9 @@ public Object clone() {`
`402`	`402`	`n.addAltLoc(nAltLocGroup);`
`403`	`403`	`}`
`404`	`404`	`}`
	`405`	`+`
	`406`	`+ if (chemComp!=null)`
	`407`	`+ n.setChemComp(chemComp);`
`405`	`408`
`406`	`409`	`return n;`
`407`	`410`	`}`