compbio.ws.server

Class WSUtil

java.lang.Object

compbio.ws.server.WSUtil

public final class WSUtil
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
WSUtil()

Method Summary

Modifier and Type	Method and Description
static <T> java.lang.String	align(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, java.lang.String callingMethod, Limit<T> limit)
static <T> java.lang.String	analize(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
static boolean	cancelJob(java.lang.String jobId)
static <T> java.lang.String	fold(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
static <T> ScoreManager	getAnnotation(java.lang.String jobId, org.apache.log4j.Logger log)
static <T> java.util.List<java.lang.String>	getCommands(java.util.List<Option<T>> options, java.lang.String keyValueSeparator)
static AsyncExecutor	getEngine(ConfiguredExecutable<?> confClustal)
static JobStatus	getJobStatus(java.lang.String jobId)
static byte	getProgress(java.lang.String jobId)
static ChunkHolder	pullFile(java.lang.String file, long position)
(package private) static <T> void	reportUsage(ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger)
static void	validateAAConInput(java.util.List<FastaSequence> sequences)
static void	validateFastaInput(java.util.List<FastaSequence> sequences)
static void	validateJobId(java.lang.String jobId)

Methods inherited from class java.lang.Object

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

Constructor Detail

WSUtil

public WSUtil()

Method Detail

validateJobId

public static final void validateJobId(java.lang.String jobId)
                                throws java.security.InvalidParameterException

Throws:

java.security.InvalidParameterException

validateFastaInput

public static final void validateFastaInput(java.util.List<FastaSequence> sequences)
                                     throws JobSubmissionException

Throws:

JobSubmissionException

getJobStatus

public static JobStatus getJobStatus(java.lang.String jobId)

pullFile

public static ChunkHolder pullFile(java.lang.String file,
                                   long position)

getProgress

public static byte getProgress(java.lang.String jobId)

getEngine

public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)

cancelJob

public static boolean cancelJob(java.lang.String jobId)

align

public static <T> java.lang.String align(java.util.List<FastaSequence> sequences,
                                         ConfiguredExecutable<T> confExec,
                                         org.apache.log4j.Logger logger,
                                         java.lang.String callingMethod,
                                         Limit<T> limit)
                                  throws LimitExceededException,
                                         JobSubmissionException

Throws:

LimitExceededException

JobSubmissionException

reportUsage

static <T> void reportUsage(ConfiguredExecutable<T> confExec,
                            org.apache.log4j.Logger logger)

analize

public static <T> java.lang.String analize(java.util.List<FastaSequence> sequences,
                                           ConfiguredExecutable<T> confExec,
                                           org.apache.log4j.Logger log,
                                           java.lang.String method,
                                           Limit<T> limit)
                                    throws JobSubmissionException

Throws:

JobSubmissionException

fold

public static <T> java.lang.String fold(java.util.List<FastaSequence> sequences,
                                        ConfiguredExecutable<T> confExec,
                                        org.apache.log4j.Logger log,
                                        java.lang.String method,
                                        Limit<T> limit)
                                 throws JobSubmissionException

Throws:

JobSubmissionException

getCommands

public static final <T> java.util.List<java.lang.String> getCommands(java.util.List<Option<T>> options,
                                                                     java.lang.String keyValueSeparator)

validateAAConInput

public static void validateAAConInput(java.util.List<FastaSequence> sequences)
                               throws JobSubmissionException

Throws:

JobSubmissionException

getAnnotation

public static <T> ScoreManager getAnnotation(java.lang.String jobId,
                                             org.apache.log4j.Logger log)
                                      throws ResultNotAvailableException

Throws:

ResultNotAvailableException