org.biojava.nbio.structure.align.client

Class JFatCatClient

java.lang.Object

org.biojava.nbio.structure.align.client.JFatCatClient

public class JFatCatClient
extends Object

Constructor Summary

Constructors

Constructor and Description
JFatCatClient()

Method Summary

Modifier and Type	Method and Description
static String	convertStreamToString(InputStream stream)
static AFPChain	getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2)
static AFPChain	getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
static PdbPairsMessage	getPdbPairs(String url, int nrPair, String username)
int	getPositionInQueue(String serverLocation, String method, String name1, String name2)
int	getPositionInQueue(String serverLocation, String method, String name1, String name2, int timeout)
static int	getRandomSleepTime()
static SortedSet<String>	getRepresentatives(String serverLocation, int cutoff)
static int	getTimeout()
static boolean	hasPrecalculatedResult(String serverLocation, String method, String name1, String name2)
static boolean	hasPrecalculatedResult(String serverLocation, String method, String name1, String name2, int timeout)
static void	main(String[] args)
static void	sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String	sendMultiAFPChainToServer(String serverLocation, String multiXML, String username)
static String	sendMultiAFPChainToServer(String serverLocation, String multiXML, String username, 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(String[] args)
                 throws Exception

Throws:

Exception

hasPrecalculatedResult

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

hasPrecalculatedResult

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

getPositionInQueue

public int getPositionInQueue(String serverLocation,
                              String method,
                              String name1,
                              String name2)

getPositionInQueue

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

getAFPChainFromServer

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

getAFPChainFromServer

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

convertStreamToString

public static String convertStreamToString(InputStream stream)

sendMultiAFPChainToServer

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

Throws:

JobKillException

sendMultiAFPChainToServer

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

Throws:

JobKillException

getRandomSleepTime

public static int getRandomSleepTime()

sendAFPChainToServer

public static final void sendAFPChainToServer(String serverLocation,
                                              AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2)
                                       throws JobKillException

Throws:

JobKillException

getTimeout

public static final int getTimeout()

getPdbPairs

public static final PdbPairsMessage getPdbPairs(String url,
                                                int nrPair,
                                                String username)
                                         throws IOException,
                                                JobKillException

Throws:

IOException

JobKillException

getRepresentatives

public static final SortedSet<String> getRepresentatives(String serverLocation,
                                                         int cutoff)