org.biojava.bio.structure.align.client
Class JFatCatClient

java.lang.Object
  org.biojava.bio.structure.align.client.JFatCatClient

public class JFatCatClient
extends java.lang.Object

Constructor Summary

JFatCatClient()

Method Summary

static java.lang.String	convertStreamToString(java.io.InputStream stream)
static AFPChain	getAFPChainFromServer(java.lang.String serverLocation, java.lang.String name1, java.lang.String name2, Atom[] ca1, Atom[] ca2)
static AFPChain	getAFPChainFromServer(java.lang.String serverLocation, java.lang.String method, java.lang.String name1, java.lang.String name2, Atom[] ca1, Atom[] ca2, int timeout)
static PdbPairsMessage	getPdbPairs(java.lang.String url, int nrPair, java.lang.String username)
int	getPositionInQueue(java.lang.String serverLocation, java.lang.String method, java.lang.String name1, java.lang.String name2)
int	getPositionInQueue(java.lang.String serverLocation, java.lang.String method, java.lang.String name1, java.lang.String name2, int timeout)
static int	getRandomSleepTime()
static java.util.SortedSet<java.lang.String>	getRepresentatives(java.lang.String serverLocation, int cutoff)
static int	getTimeout()
static boolean	hasPrecalculatedResult(java.lang.String serverLocation, java.lang.String method, java.lang.String name1, java.lang.String name2)
static boolean	hasPrecalculatedResult(java.lang.String serverLocation, java.lang.String method, java.lang.String name1, java.lang.String name2, int timeout)
static void	main(java.lang.String[] args)
static void	sendAFPChainToServer(java.lang.String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static java.lang.String	sendMultiAFPChainToServer(java.lang.String serverLocation, java.lang.String multiXML, java.lang.String username)
static java.lang.String	sendMultiAFPChainToServer(java.lang.String serverLocation, java.lang.String multiXML, java.lang.String username, java.lang.String version)

Methods inherited from class java.lang.Object

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

Constructor Detail

JFatCatClient

public JFatCatClient()

Method Detail

main

public static void main(java.lang.String[] args)

hasPrecalculatedResult

public static boolean hasPrecalculatedResult(java.lang.String serverLocation,
                                             java.lang.String method,
                                             java.lang.String name1,
                                             java.lang.String name2)

hasPrecalculatedResult

public static boolean hasPrecalculatedResult(java.lang.String serverLocation,
                                             java.lang.String method,
                                             java.lang.String name1,
                                             java.lang.String name2,
                                             int timeout)

getPositionInQueue

public int getPositionInQueue(java.lang.String serverLocation,
                              java.lang.String method,
                              java.lang.String name1,
                              java.lang.String name2)

getPositionInQueue

public int getPositionInQueue(java.lang.String serverLocation,
                              java.lang.String method,
                              java.lang.String name1,
                              java.lang.String name2,
                              int timeout)

getAFPChainFromServer

public static AFPChain getAFPChainFromServer(java.lang.String serverLocation,
                                             java.lang.String name1,
                                             java.lang.String name2,
                                             Atom[] ca1,
                                             Atom[] ca2)

getAFPChainFromServer

public static AFPChain getAFPChainFromServer(java.lang.String serverLocation,
                                             java.lang.String method,
                                             java.lang.String name1,
                                             java.lang.String name2,
                                             Atom[] ca1,
                                             Atom[] ca2,
                                             int timeout)

convertStreamToString

public static java.lang.String convertStreamToString(java.io.InputStream stream)

sendMultiAFPChainToServer

public static java.lang.String sendMultiAFPChainToServer(java.lang.String serverLocation,
                                                         java.lang.String multiXML,
                                                         java.lang.String username)
                                                  throws JobKillException

Throws:

JobKillException

sendMultiAFPChainToServer

public static java.lang.String sendMultiAFPChainToServer(java.lang.String serverLocation,
                                                         java.lang.String multiXML,
                                                         java.lang.String username,
                                                         java.lang.String version)
                                                  throws JobKillException

Throws:

JobKillException

getRandomSleepTime

public static int getRandomSleepTime()

sendAFPChainToServer

public static final void sendAFPChainToServer(java.lang.String serverLocation,
                                              AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2)

getTimeout

public static final int getTimeout()

getPdbPairs

public static final PdbPairsMessage getPdbPairs(java.lang.String url,
                                                int nrPair,
                                                java.lang.String username)
                                         throws java.net.MalformedURLException,
                                                java.io.IOException,
                                                JobKillException

Throws:

java.net.MalformedURLException

java.io.IOException

JobKillException

getRepresentatives

public static final java.util.SortedSet<java.lang.String> getRepresentatives(java.lang.String serverLocation,
                                                                             int cutoff)