org.fhcrc.cpl.viewer.test.commandline
Class PeptideArrayTest

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          org.fhcrc.cpl.toolbox.test.BaseCommandTest
              org.fhcrc.cpl.toolbox.test.commandline.BaseCommandLineTest
                  org.fhcrc.cpl.viewer.test.commandline.PeptideArrayTest

All Implemented Interfaces:

junit.framework.Test

public class PeptideArrayTest
extends BaseCommandLineTest
implements junit.framework.Test

Note: since this test calls out to R, it is dependent on the version of R on the path. Currently, the MD5 sums are calculated using R 2.0.1

Field Summary

protected static java.lang.String	sumMassPoint1Scan75Normalize
protected static java.lang.String	sumMassPoint2Scan50
protected static java.lang.String	sumMassPoint2Scan50Details

Fields inherited from class org.fhcrc.cpl.toolbox.test.commandline.BaseCommandLineTest

commandLineModule

Constructor Summary

PeptideArrayTest()

Method Summary

protected CommandLineModule	createCommandLineModule() Return an instance of the FindPeptidesCommandLineModule
protected void	doCleanup() Each implementing class can do special cleanup here
protected void	doRun(junit.framework.TestResult result) Strategy is to filter a set of features in various ways and then compare MD5 sums of the resulting feature files (with whitespace removed) with sums computed when the tests were written

Methods inherited from class org.fhcrc.cpl.toolbox.test.commandline.BaseCommandLineTest

clearArgumentValues, executeCommandLineModule, getCommandLineModule, renewCommandLineModule, setArgumentValue, setUnnamedArgumentValue, setUnnamedSeriesArgumentValue, unsetArgumentValue, unsetUnnamedArgumentValue

Methods inherited from class org.fhcrc.cpl.toolbox.test.BaseCommandTest

cleanup, constructTempFilePath, getTempDirName, log, run

Methods inherited from class junit.framework.TestCase

countTestCases, createResult, getName, run, runBare, runTest, setName, setUp, tearDown, 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, failNotEquals, failNotSame, failSame, format

Methods inherited from class java.lang.Object

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

Methods inherited from interface junit.framework.Test

countTestCases, run

Field Detail

sumMassPoint1Scan75Normalize

protected static final java.lang.String sumMassPoint1Scan75Normalize

See Also:

Constant Field Values

sumMassPoint2Scan50

protected static final java.lang.String sumMassPoint2Scan50

See Also:

Constant Field Values

sumMassPoint2Scan50Details

protected static final java.lang.String sumMassPoint2Scan50Details

See Also:

Constant Field Values

Constructor Detail

PeptideArrayTest

public PeptideArrayTest()

Method Detail

createCommandLineModule

protected CommandLineModule createCommandLineModule()

Return an instance of the FindPeptidesCommandLineModule

Specified by:

createCommandLineModule in class BaseCommandLineTest

Returns:

doCleanup

protected void doCleanup()

Description copied from class: BaseCommandTest

Each implementing class can do special cleanup here

Specified by:

doCleanup in class BaseCommandTest

doRun

protected void doRun(junit.framework.TestResult result)

Strategy is to filter a set of features in various ways and then compare MD5 sums of the resulting feature files (with whitespace removed) with sums computed when the tests were written

Specified by:

doRun in class BaseCommandTest

Parameters:

result -