org.algernon.test
Class PharmGKBTest1

java.lang.Object
  org.algernon.test.PharmGKBTest1

public class PharmGKBTest1

extends Object

Tests basic execution functionality of Algernon. Does not test the compiler. Example:

 java -classpath ${CLASSES}:${PHARMGEN}/lib/protege.jar:${PHARMGEN}/lib/ojdbc14.jar org.algernon.test.PharmGKBTest1
 

See Also:

Algernon

Field Summary

protected Algernon	m_algy
protected String	m_defaultProject
protected AlgernonKB	m_kb

Constructor Summary

PharmGKBTest1()

Method Summary

void	findIllegalSequences()
void	findIllegalSNPPositions()
void	findSubmittedGenesNotOnWatchlist()
static long	getCurrentTime() Returns the current time in milliseconds.
static long	getElapsedTime(long startTime) Returns the elapsed time since the startTime in milliseconds.
Boolean	illegalSequence(LispString s)
String	illegalSequence(String s)
void	init() Reads in the parameters and tries to open the KB.
Boolean	invalidPosition(LispInteger position, LispInteger start, LispInteger end)
boolean	invalidPosition(long position, long start, long end)
static void	main(String[] args)
protected void	processSNDQuery(String query, String title)
void	start() Executes some small code snippets.
void	stop() Halts the program nicely.

Methods inherited from class java.lang.Object

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

Field Detail

m_kb

protected AlgernonKB m_kb

m_algy

protected Algernon m_algy

m_defaultProject

protected String m_defaultProject

Constructor Detail

PharmGKBTest1

public PharmGKBTest1()

Method Detail

main

public static void main(String[] args)

init

public void init()

Reads in the parameters and tries to open the KB.

stop

public void stop()

Halts the program nicely.

start

public void start()

Executes some small code snippets.

findIllegalSNPPositions

public void findIllegalSNPPositions()

processSNDQuery

protected void processSNDQuery(String query,
                               String title)

invalidPosition

public Boolean invalidPosition(LispInteger position,
                               LispInteger start,
                               LispInteger end)

invalidPosition

public boolean invalidPosition(long position,
                               long start,
                               long end)

findIllegalSequences

public void findIllegalSequences()

illegalSequence

public Boolean illegalSequence(LispString s)

illegalSequence

public String illegalSequence(String s)

findSubmittedGenesNotOnWatchlist

public void findSubmittedGenesNotOnWatchlist()

getCurrentTime

public static long getCurrentTime()

Returns the current time in milliseconds. Useful for timing method calls.

getElapsedTime

public static long getElapsedTime(long startTime)

Returns the elapsed time since the startTime in milliseconds. Useful for timing method calls.