#6 predefining PROPERTY if empty

+ unit tests
CIDARLAB · Jul 26, 2017 · 42163ea · 42163ea
1 parent b7eb74f
commit 42163ea
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diff --git a/src/main/java/org/cidarlab/eugene/dom/ComponentType.java b/src/main/java/org/cidarlab/eugene/dom/ComponentType.java
@@ -26,150 +26,160 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
  * POSSIBILITY OF SUCH DAMAGE.
  */
-
 package org.cidarlab.eugene.dom;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.cidarlab.eugene.constants.EugeneConstants;
 import org.cidarlab.eugene.exception.EugeneException;
 
 /**
- * A ComponentType represents an abstract genetic component, such as part type. 
- * In Eugene, every Component has a ComponentType. A ComponentType has a list of 
+ * A ComponentType represents an abstract genetic component, such as part type.
+ * In Eugene, every Component has a ComponentType. A ComponentType has a list of
  * properties that the Component instantiates (so-called Property Values).
- *  
+ *
  * @author Ernst Oberortner
  *
  */
-public class ComponentType 
-	extends NamedElement {
+public class ComponentType
+  extends NamedElement {
 
-	private static final long serialVersionUID = 1242448556255896751L;
+    private static final long serialVersionUID = 1242448556255896751L;
 
-	/*
+    /*
 	 * LIST OF PROPERTIES
 	 * 
 	 * Every ComponentType has two pre-defined properties: PIGEON and SEQUENCE
 	 * both pre-defined properties are appended at the 
 	 * end of the user-defined list of properties.
 	 * 
-	 */
-	protected List<Property> properties; 
-	
-	/**
-	 * Constructor w/ name
-	 * 
-	 * @param name   ... the name of the ComponentType
-	 */
-	protected ComponentType(String name) {
-		super(name);
-		this.properties = new ArrayList<Property>();
-
-		this.addPredefinedProperties();
-	}
-	
-	private void addPredefinedProperties() {
-		/*
+     */
+    protected List<Property> properties;
+
+    /**
+     * Constructor w/ name
+     *
+     * @param name ... the name of the ComponentType
+     */
+    protected ComponentType(String name) {
+        super(name);
+        this.properties = new ArrayList<Property>();
+
+        this.addPredefinedProperties();
+    }
+
+    private void addPredefinedProperties() {
+        /*
 		 * check if the list of properties contains 
-		 * the PIGEON and SEQUENCE Property
-		 */
-		boolean bPigeon = false;
-		boolean bSequence = false;
-		for(Property prop : this.getProperties()) {
-			if(EugeneConstants.SEQUENCE_PROPERTY.equals(prop.getName().toUpperCase())) {
-				bSequence = true;
-			} else if(EugeneConstants.PIGEON_PROPERTY.equals(prop.getName().toUpperCase())) {
-				bPigeon = true;
-			}
-		}
-
-		if(!bPigeon) {
-			this.properties.add(
-					new Property(EugeneConstants.PIGEON_PROPERTY, EugeneConstants.TXT));
-		}
-
-		if(!bSequence) {
-			this.properties.add(
-					new Property(EugeneConstants.SEQUENCE_PROPERTY, EugeneConstants.TXT));
-		}
-	}
-
-	/**
-	 * Constructor w/ name and properties
-	 * 
-	 * @param name   ... the name of the ComponentType
-	 * @param properties ... a list of properties of the type
-	 */
-	public ComponentType(String name, List<Property> properties) {
-		super(name);
-		this.properties = properties;
-
-		this.addPredefinedProperties();
-	}
-
-
-	/**
-	 * The getProperties() method returns the list of properties 
-	 * of the ComponentType
-	 * 
-	 * @return  the of the ComponentType's properties
-	 */
-	public List<Property> getProperties() {
-		return this.properties;
-	}
-
-	/**
-	 * The getProperty(String) method returns a property of 
-	 * a given name. If the property does not exist, then 
-	 * it returns NULL.
-	 *  
-	 * @param name   ... the name of the desired Property
-	 * @return   ... the Property if it exists, NULL otherwise
-	 */
-	public Property getProperty(String name) {
-
-		for (Property p : this.getProperties()) {
-			if (p.getName().equals(name)) {
-				return p;
-			}
-		}
-
-		return (Property) null;
-	}
-
-	@Override
-	public String toString() {
-		StringBuilder sb = new StringBuilder();
-		sb.append("Type ").append(this.getName()).append("(");
-		for(int i=0; i<this.getProperties().size(); i++) {
-			sb.append(".").append(this.getProperties().get(i).getName()).append("(")
-				.append(this.getProperties().get(i).getType()).append(")");
-
-			if(i < this.getProperties().size() -1 ) {
-				sb.append(", ");
-			}
-		}
-		sb.append(");");
-		return sb.toString();
-	}
-
-	@Override
-	public NamedElement getElement(String name) {
-		/*
+		 * the PIGEON, SEQUENCE, SEQUENCE_ONTOLOGY Properties
+         */
+
+        List<String> requiredProps = Arrays.asList(
+          EugeneConstants.SEQUENCE_ONTOLOGY_PROPERTY,
+          EugeneConstants.PIGEON_PROPERTY,
+          EugeneConstants.SEQUENCE_PROPERTY);
+
+        List<String> props = this.getPropertyNames();
+
+        for (String rProp : requiredProps) {
+            if (!props.contains(rProp)) {
+                this.properties.add(new Property(rProp, EugeneConstants.TXT));
+            }
+        }
+    }
+
+    /**
+     * Constructor w/ name and properties
+     *
+     * @param name ... the name of the ComponentType
+     * @param properties ... a list of properties of the type
+     */
+    public ComponentType(String name, List<Property> properties) {
+        super(name);
+        this.properties = properties;
+
+        this.addPredefinedProperties();
+    }
+
+    /**
+     * The getProperties() method returns the list of properties of the
+     * ComponentType
+     *
+     * @return the of the ComponentType's properties
+     */
+    public List<Property> getProperties() {
+        return this.properties;
+    }
+
+    /**
+     * The getProperty(String) method returns a property of a given name. If the
+     * property does not exist, then it returns NULL.
+     *
+     * @param name ... the name of the desired Property
+     * @return ... the Property if it exists, NULL otherwise
+     */
+    public Property getProperty(String name) {
+
+        for (Property p : this.getProperties()) {
+            if (p.getName().equals(name)) {
+                return p;
+            }
+        }
+
+        return (Property) null;
+    }
+
+    /**
+     * The getProperties() method returns the list of properties of the
+     * ComponentType
+     *
+     * @return the of the ComponentType's properties
+     */
+    public List<String> getPropertyNames() {
+
+        List<String> names = new ArrayList<>();
+
+        for (Property prop : this.getProperties()) {
+            names.add(prop.getName());
+        }
+
+        return names;
+
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        sb.append("Type ").append(this.getName()).append("(");
+        for (int i = 0; i < this.getProperties().size(); i++) {
+            sb.append(".").append(this.getProperties().get(i).getName()).append("(")
+              .append(this.getProperties().get(i).getType()).append(")");
+
+            if (i < this.getProperties().size() - 1) {
+                sb.append(", ");
+            }
+        }
+        sb.append(");");
+        return sb.toString();
+    }
+
+    @Override
+    public NamedElement getElement(String name) {
+        /*
 		 * here, we iterate over the properties
-		 */
-		return this.getProperty(name);
-	}
-
-	@Override
-	public NamedElement getElement(int idx) 
-			throws EugeneException {
-		if(idx < 0 || idx >= this.getProperties().size()) {
-			throw new EugeneException(idx + " is out of bounds in the " + this.getName() +" type!");
-		}
-		return this.getProperties().get(idx);
-	}
+         */
+        return this.getProperty(name);
+    }
+
+    @Override
+    public NamedElement getElement(int idx)
+      throws EugeneException {
+        if (idx < 0 || idx >= this.getProperties().size()) {
+            throw new EugeneException(idx + " is out of bounds in the " + this.getName() + " type!");
+        }
+        return this.getProperties().get(idx);
+    }
 
 }