Merge pull request #402 from SynBioDex/develop

Develop

core2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.sbolstandard</groupId>
 		<artifactId>libSBOLj-parent</artifactId>
-		<version>2.1.0</version>
+		<version>2.1.1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>libSBOLj</artifactId>
@@ -126,5 +126,5 @@
 		</plugins>
 	</build>
 
-	<version>2.1.0</version>
+	<version>2.1.1-SNAPSHOT</version>
 </project>

core2/src/main/java/org/sbolstandard/core2/AccessType.java

@@ -20,7 +20,7 @@ public enum AccessType {
 	PRIVATE("private");
 	private final String accessType;
 
-	AccessType(String accessType) {
+	private AccessType(String accessType) {
 		this.accessType = accessType;
 	}
 
@@ -64,19 +64,11 @@ else if (access.equals(AccessType.PRIVATE)) {
 		}
 	}
 
-	/**
-	 * Returns the access type.
-	 * @return access type.
-	 */
-	String getAccessType() {
-		return accessType;
-	}
-
 	@Override
 	public String toString() {
 		return accessType;
 	}
 
-	static final URI publicURI = URI.create(Sbol2Terms.sbol2.getNamespaceURI() + "public");
-	static final URI privateURI = URI.create(Sbol2Terms.sbol2.getNamespaceURI() + "private");
+	private static final URI publicURI = URI.create(Sbol2Terms.sbol2.getNamespaceURI() + "public");
+	private static final URI privateURI = URI.create(Sbol2Terms.sbol2.getNamespaceURI() + "private");
 }

core2/src/main/java/org/sbolstandard/core2/Annotation.java

@@ -20,7 +20,7 @@
 import uk.ac.ncl.intbio.core.datatree.NestedDocument;
 
 /**
- * Represents the SBOL Annotation data model.
+ * Represents an Annotation object in the cSBOL data model.
  * 
  * @author Zhen Zhang
  * @author Matthew Pocock
@@ -376,7 +376,7 @@ NamedProperty<QName> getValue() {
 	/**
 	 * Sets the value of this Annotation instance to the specified argument.
 	 */
-	void setValue(NamedProperty<QName> value) {
+	private void setValue(NamedProperty<QName> value) {
 		this.value = value;
 	}
 

core2/src/main/java/org/sbolstandard/core2/Collection.java

@@ -7,7 +7,7 @@
 import java.util.Set;
 
 /**
- * Represents the SBOL Collection data model.
+ * Represents an Collection object in the SBOL data model.
  * 
  * @author Zhen Zhang
  * @author Nicholas Roehner
@@ -19,6 +19,11 @@ public class Collection extends TopLevel{
 
 	private Set<URI> members;
 
+	/**
+	 * @param identity
+	 * @throws SBOLValidationException if an SBOL validation rule was violated in the following constructor:
+	 * {@link TopLevel#TopLevel(URI)}. 
+	 */
 	Collection(URI identity) throws SBOLValidationException {
 		super(identity);
 		this.members = new HashSet<>();
@@ -37,11 +42,16 @@ private Collection(Collection collection) throws SBOLValidationException {
 		//super(collection.getIdentity());
 		super(collection);
 		this.members = new HashSet<>();
-		Set<URI> newMembers = new HashSet<>();
 		for (URI member : collection.getMemberURIs()) {
-			newMembers.add(member);
+			this.addMember(member);
+		}
+	}
+
+	void copy(Collection collection) throws SBOLValidationException {
+		((TopLevel)this).copy((TopLevel)collection);
+		for (URI member : collection.getMemberURIs()) {
+			this.addMember(member);
 		}
-		this.setMembers(newMembers);
 	}
 
 	/**
@@ -54,8 +64,8 @@ private Collection(Collection collection) throws SBOLValidationException {
 	 * @throws SBOLValidationException if the following SBOL validation rule was violated: 12103.
 	 */
 	public boolean addMember(URI memberURI) throws SBOLValidationException {
-		if (sbolDocument != null && sbolDocument.isComplete()) {
-			if (sbolDocument.getTopLevel(memberURI)==null) {
+		if (this.getSBOLDocument() != null && this.getSBOLDocument().isComplete()) {
+			if (this.getSBOLDocument().getTopLevel(memberURI)==null) {
 				throw new SBOLValidationException("sbol-12103", this);
 			}
 		}
@@ -106,7 +116,7 @@ public Set<URI> getMemberURIs() {
 	public Set<TopLevel> getMembers() {
 		Set<TopLevel> result = new HashSet<>();
 		for (URI memberURI : members) {
-			TopLevel member = sbolDocument.getTopLevel(memberURI);
+			TopLevel member = this.getDocument().getTopLevel(memberURI);
 			result.add(member);
 		}
 		return result;
@@ -169,7 +179,7 @@ public boolean equals(Object obj) {
 	 * @throws SBOLValidationException if an SBOL validation rule violation occurred in {@link #Collection(Collection)}.
 	 */
 	@Override
-	protected Collection deepCopy() throws SBOLValidationException {
+	Collection deepCopy() throws SBOLValidationException {
 		return new Collection(this);
 	}
 
@@ -207,17 +217,14 @@ Collection copy(String URIprefix, String displayId, String version) throws SBOLV
 	 * @see org.sbolstandard.core2.abstract_classes.TopLevel#checkDescendantsURIcompliance()
 	 */
 	@Override
-	protected void checkDescendantsURIcompliance() throws SBOLValidationException {
-		URIcompliance.isTopLevelURIformCompliant(this.getIdentity());
+	void checkDescendantsURIcompliance() {//throws SBOLValidationException {
+		//URIcompliance.isTopLevelURIformCompliant(this.getIdentity());
 	}
 
 	@Override
 	public String toString() {
 		return "Collection ["
-				+ "identity=" + identity 
-				+ (this.isSetDisplayId()?", displayId=" + displayId:"") 
-				+ (this.isSetName()?", name=" + name:"")
-				+ (this.isSetDescription()?", description=" + description:"") 
+				+ super.toString()
 				+ (members.size()>0?", members=" + members:"")  
 				+ "]";
 	}

core2/src/main/java/org/sbolstandard/core2/ComparableVersion.java

@@ -357,12 +357,12 @@ public String toString()
         }
     }
 
-    public ComparableVersion( String version )
+    ComparableVersion( String version )
     {
         parseVersion( version );
     }
 
-    public final void parseVersion( String version )
+    private final void parseVersion( String version )
     {
         this.value = version;