+C-Index +

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-3.html;fp=website%2Ffull_javadoc%2Findex-files%2Findex-3.html;h=e656e094ad0f5d1ba614234e1bc7e54724f67bbc;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-3.html b/website/full_javadoc/index-files/index-3.html new file mode 100644 index 0000000..e656e09 --- /dev/null +++ b/website/full_javadoc/index-files/index-3.html @@ -0,0 +1,426 @@ + + + + + + +C-Index + + + + + + + + + + + + +

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+ + + +A B C D E F G H I J K L M N O P R S T U V W _

+C

call() - +Method in class compbio.engine.local.ExecutableWrapper +: It is vital that output and error streams are captured immediately for + this call() to succeed. +
canAcceptMoreWork() - +Method in class compbio.engine.local.LocalExecutorService +: If the Executor queue is empty +
CancelJob - Class in compbio.data.msa.jaxws
CancelJob() - +Constructor for class compbio.data.msa.jaxws.CancelJob +: +
cancelJob(String) - +Method in interface compbio.data.msa.JManagement +: Stop running the job jobId but leave its output untouched +
cancelJob(String) - +Method in interface compbio.engine.AsyncExecutor +: Stop running job. +
cancelJob(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +: +
cancelJob(String, ClusterSession) - +Static method in class compbio.engine.cluster.drmaa.ClusterUtil +: +
cancelJob() - +Method in class compbio.engine.cluster.drmaa.JobRunner +: +
cancelJob(String) - +Method in class compbio.engine.local.AsyncLocalRunner +: +
cancelJob(Future<ConfiguredExecutable<?>>, String) - +Static method in class compbio.engine.local.LocalEngineUtil +: +
cancelJob() - +Method in class compbio.engine.local.LocalRunner +: +
cancelJob() - +Method in interface compbio.engine.SyncExecutor +: Stops running job. +
cancelJob(String) - +Method in class compbio.ws.server.ClustalOWS +: +
cancelJob(String) - +Method in class compbio.ws.server.ClustalWS +: +
cancelJob(String) - +Method in class compbio.ws.server.GenericMetadataService +: +
cancelJob(String) - +Method in class compbio.ws.server.MafftWS +: +
cancelJob(String) - +Method in class compbio.ws.server.MuscleWS +: +
cancelJob(String) - +Method in class compbio.ws.server.ProbconsWS +: +
cancelJob(String) - +Method in class compbio.ws.server.TcoffeeWS +: +
cancelJob(String) - +Static method in class compbio.ws.server.WSUtil +: +
CancelJobResponse - Class in compbio.data.msa.jaxws
CancelJobResponse() - +Constructor for class compbio.data.msa.jaxws.CancelJobResponse +: +
Category - Class in compbio.data.msa: Class that splits Services to categories.
CATEGORY_ALIGNMENT - +Static variable in class compbio.data.msa.Category +: All of the Category names +
CATEGORY_CONSERVATION - +Static variable in class compbio.data.msa.Category +: +
CATEGORY_DISORDER - +Static variable in class compbio.data.msa.Category +: +
checkService(Services) - +Method in class compbio.ws.client.WSTester +: Test JABA web service +
ChunkHolder - Class in compbio.metadata: Represents a chunk of a string data together with the position in a file for + the next read operation.
ChunkHolder(String, long) - +Constructor for class compbio.metadata.ChunkHolder +: +
Cleaner - Class in compbio.engine: Deprecated.
Cleaner() - +Constructor for class compbio.engine.Cleaner +: Deprecated. +
cleanProteinSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +: Remove all non AA chars from the sequence +
cleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +: Removes all whitespace chars in the sequence string +
cleanup(String) - +Method in interface compbio.engine.AsyncExecutor +: Remove all files and a job directory for a jobid. +
cleanup(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +: +
cleanup() - +Method in class compbio.engine.cluster.drmaa.JobRunner +: +
cleanup(String) - +Method in class compbio.engine.local.AsyncLocalRunner +: +
cleanup(ConfiguredExecutable<?>) - +Static method in class compbio.engine.local.LocalEngineUtil +: +
cleanup() - +Method in class compbio.engine.local.LocalRunner +: +
cleanup() - +Method in interface compbio.engine.SyncExecutor +: Clean up after the job +
close() - +Method in class compbio.data.sequence.FastaReader +: Call this method to close the connection to the input file if you want to + free up the resources. +
close() - +Method in class compbio.engine.cluster.drmaa.ClusterSession +: +
closeSilently(Logger, Closeable) - +Static method in class compbio.data.sequence.SequenceUtil +: Closes the Closable and logs the exception if any +
CLUSTAL_INFO - +Static variable in enum compbio.ws.client.Services +: +
CLUSTAL_OMEGA_INFO - +Static variable in enum compbio.ws.client.Services +: +
ClustalAlignmentUtil - Class in compbio.data.sequence: Tools to read and write clustal formated files
ClustalAlignmentUtil() - +Constructor for class compbio.data.sequence.ClustalAlignmentUtil +: +
ClustalO - Class in compbio.runner.msa
ClustalO() - +Constructor for class compbio.runner.msa.ClustalO +: --threads= Number of processors to use + + -l, --log= Log all non-essential output to this file +
ClustalOWS - Class in compbio.ws.server
ClustalOWS() - +Constructor for class compbio.ws.server.ClustalOWS +: +
ClustalW - Class in compbio.runner.msa
ClustalW() - +Constructor for class compbio.runner.msa.ClustalW +: +
ClustalWS - Class in compbio.ws.server
ClustalWS() - +Constructor for class compbio.ws.server.ClustalWS +: +
CLUSTER_STAT_IN_SEC - +Static variable in class compbio.engine.cluster.drmaa.ClusterUtil +: +
CLUSTER_TASK_ID_PREFIX - +Static variable in class compbio.engine.client.ConfExecutable +: +
CLUSTER_WORK_DIRECTORY - +Static variable in class compbio.engine.Configurator +: +
ClusterJobId - Class in compbio.engine
ClusterJobId(String) - +Constructor for class compbio.engine.ClusterJobId +: +
ClusterSession - Class in compbio.engine.cluster.drmaa
ClusterUtil - Class in compbio.engine.cluster.drmaa
ClusterUtil() - +Constructor for class compbio.engine.cluster.drmaa.ClusterUtil +: +
COILS_EXPECTATION_THRESHOLD - +Variable in class compbio.runner.disorder.Disembl +: For the region to be considered disordered the values must exceed these +
CommandBuilder<T> - Class in compbio.engine.client
CommandBuilder(String) - +Constructor for class compbio.engine.client.CommandBuilder +: +
compare(Hit, Hit) - +Method in class compbio.pipeline._jpred.Hit.EvalueComporator +: +
compare(Hit, Hit) - +Method in class compbio.pipeline._jpred.Hit.NumberComporator +: +
compareTo(Range) - +Method in class compbio.data.sequence.Range +: +
compareTo(Score) - +Method in class compbio.data.sequence.Score +: +
compareTo(Delayed) - +Method in class compbio.engine.FilePuller +: +
compbio.data._structure - package compbio.data._structure
compbio.data.msa.jaxws - package compbio.data.msa.jaxws
compbio.pipeline._jpred - package compbio.pipeline._jpred
compbio.runner._jpred - package compbio.runner._jpred
confDir - +Static variable in class compbio.engine.conf.PropertyHelperManager +: +
ConfExecutable<T> - Class in compbio.engine.client
ConfExecutable(Executable<T>, String) - +Constructor for class compbio.engine.client.ConfExecutable +: +
Configurator - Class in compbio.engine
Configurator() - +Constructor for class compbio.engine.Configurator +: +
ConfiguredExecutable<T> - Interface in compbio.engine.client
configureExecutable(Executable<T>) - +Static method in class compbio.engine.Configurator +: +
configureExecutable(Executable<T>, List<FastaSequence>) - +Static method in class compbio.engine.Configurator +: +
configureExecutable(Executable<T>, Executable.ExecProvider) - +Static method in class compbio.engine.Configurator +: +
connect() - +Static method in class compbio.ws.client.AAConClient +: Connects to a AACon web service by the host and the service name +
connect(String, Services) - +Static method in class compbio.ws.client.Jws2Client +: Connects to a web service by the host and the service name web service + type +
connectToRegistry(String) - +Static method in class compbio.ws.client.Jws2Client +: Get a connection of JABAWS registry +
ConservationMethod - Enum in compbio.data.sequence: Enumeration listing of all the supported methods.
contextDestroyed(ServletContextEvent) - +Method in class compbio.stat.servlet.StatisticCollector +: +
contextDestroyed(ServletContextEvent) - +Method in class compbio.ws.server.SetExecutableFlag +: +
contextDestroyed(ServletContextEvent) - +Method in class compbio.ws.server.ShutdownEngines +: +
contextInitialized(ServletContextEvent) - +Method in class compbio.stat.servlet.StatisticCollector +: +
contextInitialized(ServletContextEvent) - +Method in class compbio.ws.server.SetExecutableFlag +: This listener is designed to run only once when the web application is + deployed to set executable flag for binaries. +
contextInitialized(ServletContextEvent) - +Method in class compbio.ws.server.ShutdownEngines +: +
convertToAbsolute(String) - +Static method in class compbio.engine.client.Util +: +
copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +: +
countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +: +
CustomAlign - Class in compbio.data.msa.jaxws
CustomAlign() - +Constructor for class compbio.data.msa.jaxws.CustomAlign +: +
customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +: Align a list of sequences with options. +
customAlign(List<FastaSequence>, List<Option<T>>) - +Method in class compbio.ws.server._MsaService +: +
customAlign(List<FastaSequence>, List<Option<ClustalO>>) - +Method in class compbio.ws.server.ClustalOWS +: +
customAlign(List<FastaSequence>, List<Option<ClustalW>>) - +Method in class compbio.ws.server.ClustalWS +: +
customAlign(List<FastaSequence>, List<Option<Mafft>>) - +Method in class compbio.ws.server.MafftWS +: +
customAlign(List<FastaSequence>, List<Option<Muscle>>) - +Method in class compbio.ws.server.MuscleWS +: +
customAlign(List<FastaSequence>, List<Option<Probcons>>) - +Method in class compbio.ws.server.ProbconsWS +: +
customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - +Method in class compbio.ws.server.TcoffeeWS +: +
CustomAlignResponse - Class in compbio.data.msa.jaxws
CustomAlignResponse() - +Constructor for class compbio.data.msa.jaxws.CustomAlignResponse +: +
CustomAnalize - Class in compbio.data.msa.jaxws
CustomAnalize() - +Constructor for class compbio.data.msa.jaxws.CustomAnalize +: +
customAnalize(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.SequenceAnnotation +: Analyse the sequences according to custom settings defined in options + list. +
customAnalize(List<FastaSequence>, List<Option<Disembl>>) - +Method in class compbio.ws.server.DisemblWS +: +
customAnalize(List<FastaSequence>, List<Option<GlobPlot>>) - +Method in class compbio.ws.server.GlobPlotWS +: +
customAnalize(List<FastaSequence>, List<Option<T>>) - +Method in class compbio.ws.server.SequenceAnnotationService +: +
CustomAnalizeResponse - Class in compbio.data.msa.jaxws
CustomAnalizeResponse() - +Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse +: +