Merge pull request #5 from ProgrammingLife3/NodeSplit

"TomBrouws confirmed fixes on slack"

Author: Delfil

pom.xml

@@ -14,6 +14,11 @@
       <version>4.12</version>
       <scope>test</scope>
     </dependency>
+      <dependency>
+          <groupId>org.graphstream</groupId>
+          <artifactId>gs-core</artifactId>
+          <version>1.2</version>
+      </dependency>
   </dependencies>
   <build>
     <plugins>

src/main/java/tudelft/ti2806/pl3/data/AminoAcid.java

@@ -9,7 +9,7 @@ public enum AminoAcid {
 	Arg, Gly, Ochre, Amber, Opal;
 
 	private static final int CODON_SIZE = 3;
-	private static final int CODONS = (int) Math.pow(Gene.values().length - 1,
+	private static final int CODONS = (int) Math.pow(BasePair.MAX_GENE,
 			CODON_SIZE);
 	private static final AminoAcid[] TRANSLATION_TABLE = fillTranslationTable();
 	private static final String TRANSLATION_TABLE_FILE = "data/translationTable";
@@ -26,7 +26,6 @@ public static AminoAcid get(int index) {
 		if (index == -1) {
 			return null;
 		}
-		System.out.println(CODONS + " - " + CODON_SIZE);
 		return TRANSLATION_TABLE[index];
 	}
 
@@ -43,7 +42,7 @@ private static AminoAcid[] fillTranslationTable() {
 			for (int i = 0; i < CODONS; i++) {
 				String[] data = scanner.nextLine().split(" ");
 				if (!data[0].startsWith("#")) {
-					table[Gene.getCodon(Gene.getGeneString(data[0]))]
+					table[BasePair.getCodon(BasePair.toEnumString(data[0]))]
 							= valueOf(data[1]);
 				}
 			}
@@ -61,11 +60,11 @@ private static AminoAcid[] fillTranslationTable() {
 	 *            an array of the genes to be read
 	 * @return an array of all acids read
 	 */
-	public static AminoAcid[] getAcids(Gene[] gene) {
+	public static AminoAcid[] getAcids(BasePair[] gene) {
 		int size = gene.length / 3;
 		AminoAcid[] array = new AminoAcid[size];
 		for (int i = 0; i < size; i++) {
-			array[i] = get(Gene.getCodon(gene, i * 3));
+			array[i] = get(BasePair.getCodon(gene, i * 3));
 		}
 		return array;
 	}

src/main/java/tudelft/ti2806/pl3/data/BasePair.java

@@ -0,0 +1,82 @@
+package tudelft.ti2806.pl3.data;
+
+public enum BasePair {
+	N(0, -1), T(1, 0), U(2, 0), C(3, 1), A(4, 2), G(5, 3);
+	
+	private int value;
+	public byte storeByte;
+	private static BasePair[] storeByteToBasePair = new BasePair[] { N, T, U, C, A, G };
+	public static final int MAX_GENE = 4;
+	
+	BasePair(int storeByte, int value) {
+		this.value = value;
+		this.storeByte = (byte) storeByte;
+	}
+	
+	/**
+	 * Translates a three bit string of quaternary numbers into a six bit string
+	 * of binary numbers.
+	 * 
+	 * @param basePair
+	 *            the string of basePairs
+	 * @return the encoding of the three given basePair bits <br>
+	 *         -1 if the codon contains an unknown basePair (N)
+	 */
+	public static int getCodon(BasePair[] basePair) {
+		if (basePair[0] == N || basePair[1] == N || basePair[2] == N) {
+			return -1;
+		}
+		return (basePair[0].value << 4) + (basePair[1].value << 2) + basePair[2].value;
+	}
+	
+	/**
+	 * Translates the first three bits of the basePair string from the given index.
+	 * 
+	 * @param basePair
+	 *            the array of basePairs to be read
+	 * @param index
+	 *            index from where to read
+	 * @return encoding of the three basePair bits
+	 * @return -1 if the codon contains an unknown basePair (N)
+	 */
+	public static int getCodon(BasePair[] basePair, int index) {
+		return getCodon(new BasePair[] { basePair[index], basePair[index + 1],
+				basePair[index + 2] });
+	}
+	
+	/**
+	 * Reads a string and translates it into a byte array.
+	 * 
+	 * @param string
+	 *            string of basePair characters
+	 * @return an array of basePairs
+	 */
+	public static byte[] getBasePairString(String string) {
+		String[] charArray = string.split("");
+		byte[] array = new byte[charArray.length];
+		for (int i = 0; i < charArray.length; i++) {
+			array[i] = valueOf(charArray[i]).storeByte;
+		}
+		return array;
+	}
+
+	/**
+	 * Reads a string and translates it into a basePair array.
+	 * 
+	 * @param string
+	 *            string of basePair characters
+	 * @return an array of basePairs
+	 */
+	public static BasePair[] toEnumString(String string) {
+		byte[] str = getBasePairString(string);
+		BasePair[] result = new BasePair[str.length];
+		for (int i = 0; i < str.length; i++) {
+			result[i] = getBasePair(str[i]);
+		}
+		return result;
+	}
+	
+	private static BasePair getBasePair(byte pair) {
+		return storeByteToBasePair[pair];
+	}
+}

src/main/java/tudelft/ti2806/pl3/data/Gene.java

@@ -0,0 +1,41 @@
+package tudelft.ti2806.pl3.data;
+
+public class Genome {
+	public final String identifier;
+	
+	public Genome(String identifier) {
+		this.identifier = identifier;
+	}
+	
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result
+				+ ((identifier == null) ? 0 : identifier.hashCode());
+		return result;
+	}
+	
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj) {
+			return true;
+		}
+		if (obj == null) {
+			return false;
+		}
+		if (getClass() != obj.getClass()) {
+			return false;
+		}
+		Genome other = (Genome) obj;
+		if (identifier == null) {
+			if (other.identifier != null) {
+				return false;
+			}
+		} else if (!identifier.equals(other.identifier)) {
+			return false;
+		}
+		return true;
+	}
+	
+}

src/main/java/tudelft/ti2806/pl3/data/Genome.java

@@ -0,0 +1,30 @@
+package tudelft.ti2806.pl3.data.filter;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Filter is an interface for filters. The filter is supposed to be calculated
+ * on initialising of the instance over the entire data set, so the filters can
+ * be applied individually in any order.
+ * 
+ * @author Sam Smulders
+ *
+ * @param <T>
+ *            the element type to filter
+ */
+public abstract class Filter<T> {
+	protected List<T> filter = new ArrayList<T>();
+	
+	/**
+	 * Calculates what elements have to be removed from the list and stores it.
+	 * 
+	 * @param list
+	 *            a list of the entire data set to filter
+	 */
+	public abstract void calculateFilter(List<T> list);
+	
+	public final void filter(List<T> list) {
+		list.removeAll(filter);
+	}
+}

src/main/java/tudelft/ti2806/pl3/data/GraphParser.java

@@ -0,0 +1,25 @@
+package tudelft.ti2806.pl3.data.filter;
+
+import tudelft.ti2806.pl3.data.Genome;
+import tudelft.ti2806.pl3.data.graph.Node;
+
+import java.util.List;
+
+public class GenomeFilter extends Filter<Node> {
+	protected final String genome;
+	
+	public GenomeFilter(String genome) {
+		this.genome = genome;
+	}
+	
+	@Override
+	public void calculateFilter(List<Node> list) {
+		for (Node node : list) {
+			for (Genome source : node.getSource()) {
+				if (source.equals(genome)) {
+					filter.add(node);
+				}
+			}
+		}
+	}
+}