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

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

public class JFatCatClient
extends Object


Constructor Summary
JFatCatClient()
           
 
Method Summary
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)

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)

getTimeout

public static final int getTimeout()

getPdbPairs

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

getRepresentatives

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