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);
}