Author: laylaoesper
Date: 2010-07-21 12:45:23 -0700 (Wed, 21 Jul 2010)
New Revision: 20983
Added:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/SemanticSummaryClusterBuilderUnitTest.java
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/AllTests.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/CloudParametersUnitTest.java
Log:
Updates to the unit tests.
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/AllTests.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/AllTests.java
2010-07-21 19:41:16 UTC (rev 20982)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/AllTests.java
2010-07-21 19:45:23 UTC (rev 20983)
@@ -37,7 +37,8 @@
Class[] testClasses = {
SemanticSummaryParametersUnitTest.class,
WordFilterUnitTest.class,
- CloudParametersUnitTest.class};
+ CloudParametersUnitTest.class,
+ SemanticSummaryClusterBuilderUnitTest.class};
TestSuite suite = new TestSuite(testClasses);
suite.setName("SemanticSummaryPlugin Test");
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/CloudParametersUnitTest.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/CloudParametersUnitTest.java
2010-07-21 19:41:16 UTC (rev 20982)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/CloudParametersUnitTest.java
2010-07-21 19:45:23 UTC (rev 20983)
@@ -119,6 +119,8 @@
cloudParams.setSelectedNodes(selNodeNames);
cloudParams.setSelectedNumNodes(7);
cloudParams.setNetworkNumNodes(13);
+ cloudParams.setNetWeightFactor(1.0);
+ cloudParams.setDisplayStyle("No Clustering");
//Register Cloud
parentParams.addCloud(cloudName, cloudParams);
@@ -227,7 +229,7 @@
cloudParams.updateRatios();
- //Test Ratios (with default k = 1)
+ //Test Ratios (with k = 1)
HashMap<String,Double> ratios = cloudParams.getRatios();
assertEquals((Double)ratios.get("node"),new
Double((5.0*13)/(7*9)));
assertEquals((Double)ratios.get("onenode"),new
Double((2.0*13)/(7*4)));
Added:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/SemanticSummaryClusterBuilderUnitTest.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/SemanticSummaryClusterBuilderUnitTest.java
(rev 0)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/test/SemanticSummaryClusterBuilderUnitTest.java
2010-07-21 19:45:23 UTC (rev 20983)
@@ -0,0 +1,157 @@
+package cytoscape.csplugins.semanticsummary.test;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import junit.framework.TestCase;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.csplugins.semanticsummary.CloudParameters;
+import cytoscape.csplugins.semanticsummary.CloudWordInfo;
+import cytoscape.csplugins.semanticsummary.SemanticSummaryClusterBuilder;
+import cytoscape.csplugins.semanticsummary.SemanticSummaryParameters;
+import cytoscape.csplugins.semanticsummary.SingleWordCluster;
+import cytoscape.csplugins.semanticsummary.WordClusters;
+import cytoscape.csplugins.semanticsummary.WordPair;
+
+public class SemanticSummaryClusterBuilderUnitTest extends TestCase
+{
+
+ //Variables
+ String cloudName = "CloudName";
+ SemanticSummaryParameters parentParams;
+ CloudParameters cloudParams;
+
+ @Before
+ public void setUp() throws Exception
+ {
+ //Create parent parameters
+ parentParams = new SemanticSummaryParameters();
+
+ //Create a set of CyNodes
+ List<CyNode> allNodes = new ArrayList<CyNode>();
+ CyNode node1 = Cytoscape.getCyNode("Regulation of apoptosis",
true);
+ CyNode node2 = Cytoscape.getCyNode("Positive regulation of
apoptosis", true);
+ CyNode node3 = Cytoscape.getCyNode("Positive regulation of
programmed cell death", true);
+ CyNode node4 = Cytoscape.getCyNode("Immune response",
true);//only one count
+ CyNode node5 = Cytoscape.getCyNode("Activation of immune
response", true);
+ CyNode node6 = Cytoscape.getCyNode("Activation of humoral
immune response", true);
+
+ //Add nodes to list
+ allNodes.add(node1);
+ allNodes.add(node2);
+ allNodes.add(node3);
+ allNodes.add(node4);
+ allNodes.add(node5);
+ allNodes.add(node6);
+
+ //Create CloudParameters object
+ cloudParams = new CloudParameters();
+ cloudParams.setCloudName(cloudName);
+ cloudParams.setNetworkParams(parentParams);
+
+ //Set Lists in Params
+ List<String> nodeNames = new ArrayList<String>();
+ for(Iterator<CyNode> iter = allNodes.iterator();
iter.hasNext();)
+ nodeNames.add(iter.next().toString());
+
+ parentParams.setNetworkNodes(nodeNames);
+
+ cloudParams.setSelectedNodes(nodeNames);
+ cloudParams.setSelectedNumNodes(6);
+ cloudParams.setNetworkNumNodes(6);
+
+ //Register Cloud
+ parentParams.addCloud(cloudName, cloudParams);
+ }
+
+ @Test
+ public void testInitialize()
+ {
+ SemanticSummaryClusterBuilder builder = new
SemanticSummaryClusterBuilder();
+ builder.initialize(cloudParams);
+
+ //Test queue stuff
+ ArrayList<WordPair> pair = builder.getQueue().getQueue();
+ WordPair firstPair = pair.get(0);
+ String word1 = firstPair.getFirstWord();
+ String word2 = firstPair.getSecondWord();
+ Double val = firstPair.getProbability();
+ assertTrue(word1.equals("programmed"));
+ assertTrue(word2.equals("cell"));
+ assertTrue(val == 6.0);
+
+ //Test Cluster stuff
+ WordClusters clusters = builder.getClusters();
+ ArrayList<SingleWordCluster> wordClusters =
clusters.getClusters();
+ int size = wordClusters.size();
+ assertTrue(size == 10);
+ }
+
+ @Test
+ public void testClusterData()
+ {
+ SemanticSummaryClusterBuilder builder = new
SemanticSummaryClusterBuilder();
+ builder.initialize(cloudParams);
+ builder.clusterData(3.0);
+
+ //Test queue stuff
+ ArrayList<WordPair> pair = builder.getQueue().getQueue();
+ WordPair firstPair = pair.get(0);
+ String word1 = firstPair.getFirstWord();
+ String word2 = firstPair.getSecondWord();
+ Double val = firstPair.getProbability();
+ assertTrue(word1.equals("immune"));
+ assertTrue(word2.equals("response"));
+ assertTrue(val == 2.0);
+
+ //Test Cluster stuff
+ WordClusters clusters = builder.getClusters();
+ ArrayList<SingleWordCluster> wordClusters =
clusters.getClusters();
+ int size = wordClusters.size();
+ assertTrue(size == 7);
+
+ }
+
+ @Test
+ public void testBuildCloudWords()
+ {
+ SemanticSummaryClusterBuilder builder = new
SemanticSummaryClusterBuilder();
+ builder.initialize(cloudParams);
+ builder.clusterData(3.0);
+ builder.buildCloudWords();
+
+ //Test build cloudWordInfo objects
+ ArrayList<CloudWordInfo> info = builder.getCloudWords();
+
+ CloudWordInfo first = info.get(0);
+ int firstSize = first.getFontSize();
+ String firstWord = first.getWord();
+ int firstCluster = first.getCluster();
+ Color firstColor = first.getTextColor();
+ assertTrue(firstSize == 56);
+ assertTrue(firstWord.equals("regulation"));
+ assertTrue(firstCluster == 0);
+ assertTrue(firstColor.equals(Color.BLACK));
+
+ int lastSize = info.size() - 1;
+ CloudWordInfo last = info.get(lastSize);
+ int lastFontSize = last.getFontSize();
+ String lastWord = last.getWord();
+ int lastCluster = last.getCluster();
+ Color lastColor = last.getTextColor();
+ assertTrue(lastFontSize == 12);
+ assertTrue(lastWord.equals("death"));
+ assertTrue(lastCluster == 6);
+ assertTrue(lastColor.equals(Color.GRAY));
+ }
+
+}
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