public void testChildAddition() {
    // Test child addition
    CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter5");
    testCmpFilter.addChild(locationFilter);
    testCmpFilter.setRelation(Relation.AND);
    testCmpFilter.setNetwork(cyNetwork);

    testCmpFilter.apply();

    BitSet expectedNodeBitSet = new BitSet(4);
    expectedNodeBitSet.set(0, false);
    expectedNodeBitSet.set(1, false);
    expectedNodeBitSet.set(2, true);
    expectedNodeBitSet.set(3, true);

    assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());

    // Add new child
    testCmpFilter.addChild(rankFilter);

    testCmpFilter.apply();

    expectedNodeBitSet.set(0, false);
    expectedNodeBitSet.set(1, false);
    expectedNodeBitSet.set(2, true);
    expectedNodeBitSet.set(3, false);

    assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
  }
  public void testChildDeletion() {
    // Test child deletion
    CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter4");
    testCmpFilter.addChild(locationFilter);
    testCmpFilter.addChild(rankFilter);
    testCmpFilter.setRelation(Relation.AND);
    testCmpFilter.setNetwork(cyNetwork);

    testCmpFilter.apply();

    // Before deletion
    BitSet expectedBitSet4 = new BitSet();
    expectedBitSet4.set(2, true);

    assertEquals(expectedBitSet4.toString(), testCmpFilter.getNodeBits().toString());

    testCmpFilter.removeChild(locationFilter);
    testCmpFilter.apply();

    // after deletion
    expectedBitSet4.set(0, true);
    expectedBitSet4.set(1, false);
    expectedBitSet4.set(2, true);
    expectedBitSet4.set(3, false);

    assertEquals(expectedBitSet4.toString(), testCmpFilter.getNodeBits().toString());
  }
  /**
   * DOCUMENT ME!
   *
   * @throws Exception DOCUMENT ME!
   */
  public void testAND1() {
    CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter1");
    testCmpFilter.addChild(locationFilter);
    testCmpFilter.addChild(rankFilter);
    testCmpFilter.setRelation(Relation.AND);
    testCmpFilter.setNetwork(cyNetwork);
    testCmpFilter.apply();

    BitSet expectedNodeBitSet = new BitSet(4);
    expectedNodeBitSet.set(2, true);

    assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
  }
  public void testAND2() {
    // (node filter) AND (edge filter) ==> return empty bitSet -- false for all bits
    CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter2");
    testCmpFilter.addChild(locationFilter); // node filter
    testCmpFilter.addChild(pmidFilter); // edge filter
    testCmpFilter.setRelation(Relation.AND);
    testCmpFilter.setNetwork(cyNetwork);
    testCmpFilter.apply();

    BitSet expectedBitSet = new BitSet(4);

    assertEquals(expectedBitSet.toString(), testCmpFilter.getNodeBits().toString());
    assertEquals(expectedBitSet.toString(), testCmpFilter.getEdgeBits().toString());
  }
  public void testOR1() {
    CompositeFilter testCmpFilter = new CompositeFilter("testCmpFilter3");
    testCmpFilter.addChild(locationFilter);
    testCmpFilter.addChild(rankFilter);
    testCmpFilter.setRelation(Relation.OR);
    testCmpFilter.setNetwork(cyNetwork);

    testCmpFilter.apply();
    // System.out.println("testCmpFilter.toString() ="+ testCmpFilter.toString());

    BitSet expectedNodeBitSet = new BitSet(4);
    expectedNodeBitSet.set(0, true);
    expectedNodeBitSet.set(2, true);
    expectedNodeBitSet.set(3, true);

    assertEquals(expectedNodeBitSet.toString(), testCmpFilter.getNodeBits().toString());
  }
  public void setUp() {
    // Create a sample network and add sample node/edge attributes
    initNetwork();

    // Index this network by all the related Node attributes
    TaskMonitorBase monitor = new TaskMonitorBase();
    QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance();
    quickFind.addNetwork(cyNetwork, monitor);

    //  Try indexing all attributes
    // quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, LOCATION, new TaskMonitorBase());
    // TextIndex index_by_location = (TextIndex) quickFind.getIndex(cyNetwork);

    // quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, RANK, new TaskMonitorBase());
    // NumberIndex integerIndex_rank = (NumberIndex) quickFind.getIndex(cyNetwork);

    // quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_NODES, SCORE, new TaskMonitorBase());
    // NumberIndex doubleIndex_score = (NumberIndex) quickFind.getIndex(cyNetwork);

    // quickFind.reindexNetwork(cyNetwork, QuickFind.INDEX_EDGES, PMID, new TaskMonitorBase());
    // TextIndex textIndex_pmid = (TextIndex) quickFind.getIndex(cyNetwork);

    // Create a list of atomic filters
    locationFilter = new StringFilter();
    locationFilter.setName("locationFilter");
    locationFilter.setControllingAttribute(LOCATION);
    locationFilter.setSearchStr("cy*");
    locationFilter.setIndexType(QuickFind.INDEX_NODES);

    locationFilter.setNetwork(cyNetwork);

    rankFilter = new NumericFilter<Integer>();
    rankFilter.setName("rankFilter");
    rankFilter.setControllingAttribute(RANK);
    rankFilter.setLowBound(2);
    rankFilter.setHighBound(3);
    rankFilter.setIndexType(QuickFind.INDEX_NODES);
    rankFilter.setNetwork(cyNetwork);

    scoreFilter = new NumericFilter<Double>();
    scoreFilter.setName("scoreFilter");
    scoreFilter.setControllingAttribute(SCORE);
    scoreFilter.setLowBound(1.0);
    scoreFilter.setHighBound(5.0);
    scoreFilter.setIndexType(QuickFind.INDEX_NODES);
    scoreFilter.setNetwork(cyNetwork);

    pmidFilter = new StringFilter();
    pmidFilter.setName("edgeFilter");
    pmidFilter.setControllingAttribute(PMID);
    pmidFilter.setSearchStr("123");
    pmidFilter.setIndexType(QuickFind.INDEX_EDGES);
    pmidFilter.setNetwork(cyNetwork);

    // Create a composite filter 1
    compositeFilter1 = new CompositeFilter("firstCompositeFilter");
    compositeFilter1.addChild(locationFilter);
    compositeFilter1.addChild(rankFilter);
    compositeFilter1.setRelation(Relation.AND);

    // Create a composite filter 2
    compositeFilter2 = new CompositeFilter("secondCompositeFilter");
    compositeFilter2.addChild(locationFilter);
    compositeFilter2.addChild(pmidFilter);
    compositeFilter2.setRelation(Relation.AND);
  }