Added parsing of missing values and never clause.

src/mltk/core/Instance.java

@@ -288,9 +288,15 @@ public String toString() {
 			}
 		} else {
 			double[] values = getValues();
-			sb.append(values[0]);
+			if (Double.isNaN(values[0])) 
+				sb.append("?");
+			else	
+				sb.append(values[0]);
 			for (int i = 1; i < values.length; i++) {
-				sb.append("\t").append(values[i]);
+				if (Double.isNaN(values[i])) 
+					sb.append("\t?");
+				else	
+					sb.append("\t").append(values[i]);
 			}
 			if (!Double.isNaN(getTarget())) {
 				sb.append("\t").append(getTarget());

src/mltk/core/Instances.java

@@ -5,6 +5,7 @@
 import java.util.Iterator;
 import java.util.List;
 
+import mltk.core.io.AttrInfo;
 import mltk.util.Random;
 
 /**
@@ -48,6 +49,15 @@ public Instances(List<Attribute> attributes, Attribute targetAtt) {
 		this(attributes, targetAtt, 1000);
 	}
 
+	/**
+	 * Constructs a dataset from attributes and target attribute.
+	 * 
+	 * @param ainfo container for attributes and target attribute.
+	 */	
+	public Instances(AttrInfo ainfo) {
+		this(ainfo.attributes, ainfo.clsAttr);
+	}
+
 	/**
 	 * Constructs a dataset from attributes and target attribute, with specified capacity.
 	 * 

src/mltk/core/io/AttrInfo.java

@@ -0,0 +1,46 @@
+package mltk.core.io;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import mltk.core.Attribute;
+
+/**
+ * Structure for information on attributes in the data: 
+ * list of active attributes, class attributes,  
+ * columns corresponding to the active attributes in the data file
+ * 
+ * @author Daria Sorokina
+ * 
+ */
+
+public class AttrInfo {
+	public List<Attribute> attributes;
+	public Attribute clsAttr;
+	public List<Integer> columns;
+
+	/**
+	 * Default constructor 
+	 */
+	public AttrInfo() {
+		this.attributes = new ArrayList<Attribute>();
+		this.columns = new ArrayList<Integer>();
+	}
+
+	/**
+	 * Maps names of attributes into their ids
+	 * 
+	 * @param names names of attributes
+	 * @return a list of corresponding attribute ids.
+	 */
+	public List<Integer> getIds(List<String> names)	{
+		List<Integer> ids = new ArrayList<>();
+		for(String name: names)
+			for(Attribute att: attributes)
+				if(att.getName().equals(name)) {
+					ids.add(att.getIndex());
+					break;
+				}
+		return ids;
+	}
+}

src/mltk/core/io/AttributesReader.java

@@ -3,19 +3,21 @@
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.HashSet;
+import java.util.Set;
 
 import mltk.core.Attribute;
 import mltk.core.BinnedAttribute;
 import mltk.core.NominalAttribute;
 import mltk.core.NumericalAttribute;
-import mltk.util.tuple.Pair;
+
 
 /**
- * Class for reading attributes. It only reads in a list of attributes from the attribute file.
+ * Class for reading attributes information. 
+ * It reads in a list of attributes, list of inactive attributes and a class attribute
+ *  from the attribute file.
  * 
- * @author Yin Lou
+ * @author Yin Lou, modified by Daria Sorokina
  * 
  */
 public class AttributesReader {
@@ -24,18 +26,40 @@ public class AttributesReader {
 	 * Reads attributes and class attribute from attribute file.
 	 * 
 	 * @param attFile the attribute file.
-	 * @return a pair of attributes and class attribute (null if no class attribute).
+	 * @return attribute information instance.
 	 * @throws IOException
 	 */
-	public static Pair<List<Attribute>, Attribute> read(String attFile) throws IOException {
-		BufferedReader br = new BufferedReader(new FileReader(attFile), 65535);
-		List<Attribute> attributes = new ArrayList<Attribute>();
-		Attribute clsAttr = null;
-		for (int i = 0;; i++) {
-			String line = br.readLine();
-			if (line == null) {
+	public static AttrInfo read(String attFile) throws IOException {
+
+		Set<String> neverNames = new HashSet<String>();
+		AttrInfo ainfo = new AttrInfo();
+
+		BufferedReader br1 = new BufferedReader(new FileReader(attFile), 65535);
+		String line = br1.readLine();		
+		while ((line != null) && (line.indexOf("contexts:") == -1)) {
+			line = br1.readLine();
+		}
+		if (line != null) {
+			line = br1.readLine();
+		}
+		while (line != null) {
+			neverNames.add(line.split(" ")[0]);
+			line = br1.readLine();
+		}
+		br1.close();
+
+		BufferedReader br2 = new BufferedReader(new FileReader(attFile), 65535);
+		ainfo.clsAttr = null;
+		for (int i = 0, col = 0;; i++, col++) {
+			line = br2.readLine();
+			if ((line == null) || (line.indexOf("contexts:") != -1)) {
 				break;
 			}
+			String aname = line.split(": ")[0];
+			if(neverNames.contains(aname)) {
+				i--;
+				continue;
+			}
 			Attribute att = null;
 			if (line.indexOf("binned") != -1) {
 				att = BinnedAttribute.parse(line);
@@ -44,17 +68,19 @@ public static Pair<List<Attribute>, Attribute> read(String attFile) throws IOExc
 			} else {
 				att = NumericalAttribute.parse(line);
 			}
-			att.setIndex(i);
 			if (line.indexOf("(class)") != -1) {
-				clsAttr = att;
+				att.setIndex(col);
+				ainfo.clsAttr = att;
 				i--;
 			} else {
-				attributes.add(att);
+				att.setIndex(i);
+				ainfo.attributes.add(att);
+				ainfo.columns.add(col);
 			}
 		}
-		br.close();
+		br2.close();
 
-		return new Pair<List<Attribute>, Attribute>(attributes, clsAttr);
+		return ainfo;
 	}
 
 }