compbio.ws.server
Class WSUtil

java.lang.Object
  compbio.ws.server.WSUtil

public final class WSUtil
extends java.lang.Object

Constructor Summary

WSUtil()

Method Summary

static <T> java.lang.String	align(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger statLog, javax.xml.ws.WebServiceContext wsContext, java.lang.String callingMethod, Limit<T> limit)
static boolean	cancelJob(java.lang.String jobId)
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 java.lang.String	getRemoteAddress(javax.xml.ws.WebServiceContext wsContext)
static void	log(org.apache.log4j.Logger statLog, javax.xml.ws.WebServiceContext wsContext, java.lang.String activity)
static void	log(org.apache.log4j.Logger statLog, javax.xml.ws.WebServiceContext wsContext, java.lang.String jobId, java.lang.String activity)
static ChunkHolder	pullFile(java.lang.String jobId, long position)
static void	validateFastaInput(java.util.List<FastaSequence> sequences)
static void	validateJobId(java.lang.String jobId)

Methods inherited from class java.lang.Object

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

Constructor Detail

WSUtil

public WSUtil()

Method Detail

log

public static void log(org.apache.log4j.Logger statLog,
                       javax.xml.ws.WebServiceContext wsContext,
                       java.lang.String activity)

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 java.security.InvalidParameterException

Throws:

java.security.InvalidParameterException

log

public static void log(org.apache.log4j.Logger statLog,
                       javax.xml.ws.WebServiceContext wsContext,
                       java.lang.String jobId,
                       java.lang.String activity)

getJobStatus

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

pullFile

public static ChunkHolder pullFile(java.lang.String jobId,
                                   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)

getRemoteAddress

public static java.lang.String getRemoteAddress(javax.xml.ws.WebServiceContext wsContext)

align

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

Throws:

LimitExceededException

JobSubmissionException

getCommands

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