edu.iastate.biocyc.test
Class RiceReaderTest

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          edu.iastate.biocyc.test.RiceReaderTest

All Implemented Interfaces:

junit.framework.Test

public class RiceReaderTest
extends junit.framework.TestCase

this is only used for ricecyc data

Author:

Jie Li

Field Summary

(package private) static org.apache.log4j.Logger

logger log4j facility

Constructor Summary

RiceReaderTest(java.lang.String arg0)

Method Summary

protected void	setUp()
protected void	tearDown()
void	testBigMap() put all maps together, there should be 109417 instances
void	testBiologicalType() test the biological type
void	testClassNetwork() test the class network
void	testCollectClassType() test our interesting classes
void	testConvertGraph() test the graph conversion
void	testDuplicatedClassName() get duplicated class name
void	testDuplicatedCompoundName() get duplicated compound name
void	testDuplicatedGeneName() get duplicated gene name
void	testDuplicatedProteinName() get duplicated protein name
void	testGeneLocation()
void	testNestedNetwork() test the nested network
void	testProteinType() test the protein, if it is a polypeptide or a protein complex
void	testReactionNetwork() test the reaction network
void	testReadClass() read compound data
void	testReadEnzrxn() read the control interaction
void	testReadGene() test the read of gene.
void	testReadPathway() read the pathway test
void	testReadProtein() read the protein data
void	testReadReaction() read the reaction data
void	testRewriteGraph() test the rewrite graph
void	testTrimString() test the string trim feature
void	testVisualization() visualize the whole graph in the cytoscape

Methods inherited from class junit.framework.TestCase

countTestCases, createResult, getName, run, run, runBare, runTest, setName, toString

Methods inherited from class junit.framework.Assert

assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertFalse, assertFalse, assertNotNull, assertNotNull, assertNotSame, assertNotSame, assertNull, assertNull, assertSame, assertSame, assertTrue, assertTrue, fail, fail

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

Constructor Detail

RiceReaderTest

public RiceReaderTest(java.lang.String arg0)

Method Detail

setUp

protected void setUp()
              throws java.lang.Exception

Overrides:

setUp in class junit.framework.TestCase

Throws:

java.lang.Exception

tearDown

protected void tearDown()
                 throws java.lang.Exception

Overrides:

tearDown in class junit.framework.TestCase

Throws:

java.lang.Exception

testReadProtein

public void testReadProtein()

read the protein data

testReadClass

public void testReadClass()

read compound data

testReadGene

public void testReadGene()

test the read of gene. XXX Before this is tested, the maximum memory should be large enough.

testReadPathway

public void testReadPathway()

read the pathway test

testReadEnzrxn

public void testReadEnzrxn()

read the control interaction

testReadReaction

public void testReadReaction()

read the reaction data

testBigMap

public void testBigMap()

put all maps together, there should be 109417 instances

testGeneLocation

public void testGeneLocation()

testClassNetwork

public void testClassNetwork()

test the class network

testCollectClassType

public void testCollectClassType()

test our interesting classes

testBiologicalType

public void testBiologicalType()

test the biological type

testProteinType

public void testProteinType()

test the protein, if it is a polypeptide or a protein complex

testNestedNetwork

public void testNestedNetwork()

test the nested network

testReactionNetwork

public void testReactionNetwork()

test the reaction network

testDuplicatedClassName

public void testDuplicatedClassName()

get duplicated class name

testDuplicatedCompoundName

public void testDuplicatedCompoundName()

get duplicated compound name

testDuplicatedGeneName

public void testDuplicatedGeneName()

get duplicated gene name

testDuplicatedProteinName

public void testDuplicatedProteinName()

get duplicated protein name

testTrimString

public void testTrimString()

test the string trim feature

testRewriteGraph

public void testRewriteGraph()

test the rewrite graph

testConvertGraph

public void testConvertGraph()

test the graph conversion

testVisualization

public void testVisualization()

visualize the whole graph in the cytoscape