LMS-1883 FeatureVector extended to carry also vocabulary-based features

SVN: 18932

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVector.java

 package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
 
 import java.io.Serializable;
-import java.util.Arrays;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Feature vector for one well.
@@ -15,28 +16,101 @@ public class FeatureVector implements Serializable
     private final WellPosition wellPosition;
 
     private final double[] values;
+    
+    private final boolean[] vocabularyFeatureFlags;
+    
+    private final String[] vocabularyTerms;
 
+    /**
+     * Creates an instance for the specified well assuming all features are numbers.
+     */
     public FeatureVector(WellPosition well, double[] values)
+    {
+        this(well, values, new boolean[values.length], new String[values.length]);
+    }
+
+    /**
+     * Creates an instance for the specified well.
+     * 
+     * @param values Array with values of numerical features.
+     * @param vocabularyFeatureFlags Array telling which feature is a numerical one (
+     *            <code>false</code>) or a vocabulary term (<code>true</code>).
+     * @param vocabularyTerms Array with values of vocabulary-based features.
+     * @throws IllegalArgumentException if all arrays have not the same length.
+     */
+    public FeatureVector(WellPosition well, double[] values, boolean[] vocabularyFeatureFlags,
+            String[] vocabularyTerms)
     {
         this.wellPosition = well;
         this.values = values;
+        this.vocabularyFeatureFlags = vocabularyFeatureFlags;
+        this.vocabularyTerms = vocabularyTerms;
+        if (values.length != vocabularyFeatureFlags.length
+                || values.length != vocabularyTerms.length)
+        {
+            throw new IllegalArgumentException("Array lengths different: " + values.length + " "
+                    + vocabularyFeatureFlags.length + " " + vocabularyTerms.length);
+        }
     }
 
-    /** well position on a plate */
+    /** Returns the well position on a plate. */
     public WellPosition getWellPosition()
     {
         return wellPosition;
     }
 
-    /** feature vector values */
+    /** 
+     * Returns the array of numerical features. If the value is {@link Double#NaN} it means either
+     * an unknown value of the numerical feature or a vocabulary-based feature. 
+     */
     public double[] getValues()
     {
         return values;
     }
+    
+    /**
+     * Return the array of flags specifying the type of feature where <code>true</code> means
+     * vocabulary-based feature and <code>false</code> numerical feature.
+     */
+    public final boolean[] getVocabularyFeatureFlags()
+    {
+        return vocabularyFeatureFlags;
+    }
+
+    /**
+     * Returns the array of vocabulary-based features. If the value is <code>null</code> it means
+     * either an unknown value of the vocabulary-base feature or a numerical feature.
+     */
+    public final String[] getVocabularyTerms()
+    {
+        return vocabularyTerms;
+    }
+
+    /**
+     * Returns the feature vector as a list of objects. The list element is either an instance of
+     * String (vocabulary-based feature), an instance of Double (numerical feature), or
+     * <code>null</code> if the feature is unknown.
+     */
+    public List<Object> getValueObjects()
+    {
+        ArrayList<Object> result = new ArrayList<Object>();
+        for (int i = 0; i < values.length; i++)
+        {
+            if (vocabularyFeatureFlags[i])
+            {
+                result.add(vocabularyTerms[i]);
+            } else
+            {
+                double number = values[i];
+                result.add(Double.isNaN(number) ? null : number);
+            }
+        }
+        return result;
+    }
 
     @Override
     public String toString()
     {
-        return "wellPosition: " + wellPosition + ", values: " + Arrays.toString(values);
+        return "wellPosition: " + wellPosition + ", values: " + getValueObjects();
     }
 }
\ No newline at end of file

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java

@@ -449,22 +449,12 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
     }
     
     private void assertFeatureVector(int expectedRowNumber, int expectedColumnNumber,
-            FeatureVector featureVector, double... expectedValues)
+            FeatureVector featureVector, Object... expectedValues)
     {
         assertEquals(expectedRowNumber, featureVector.getWellPosition().getWellRow());
         assertEquals(expectedColumnNumber, featureVector.getWellPosition().getWellColumn());
 
-        assertEquals(asList(expectedValues), asList(featureVector.getValues()));
-    }
-
-    private List<Double> asList(double[] values)
-    {
-        List<Double> list = new ArrayList<Double>();
-        for (double value : values)
-        {
-            list.add(value);
-        }
-        return list;
+        assertEquals(Arrays.asList(expectedValues).toString(), featureVector.getValueObjects().toString());
     }
 
     private void prepareGetHomeDatabaseInstance()