X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-3.html;h=a980810ee2acde93720bf2197b8ba3b97a03b2a5;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=02682d7477bb22710972b2a2268c5dbb99f40529;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-3.html b/website/full_javadoc/index-files/index-3.html index 02682d7..a980810 100644 --- a/website/full_javadoc/index-files/index-3.html +++ b/website/full_javadoc/index-files/index-3.html @@ -2,12 +2,12 @@ - + C-Index - + @@ -92,9 +92,9 @@ Method in class compbio.engine.local.CancelJob - Class in compbio.data.msa.jaxws
 
CancelJob() - Constructor for class compbio.data.msa.jaxws.CancelJob
  -
cancelJob(String) - -Method in interface compbio.data.msa.MsaWS -
Stop running job but leave its output untouched +
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. @@ -119,9 +119,15 @@ Method in class compbio.engine.local.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
  @@ -140,13 +146,19 @@ Static method in class compbio.ws.server.CancelJobResponse - Class in compbio.data.msa.jaxws
 
CancelJobResponse() - Constructor for class compbio.data.msa.jaxws.CancelJobResponse
  -
ChunkHolder - Class in compbio.metadata
Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
ChunkHolder(String, long) - +
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
 
Cleaner() - +
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 @@ -171,12 +183,27 @@ Method in class compbio.engine.local.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
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
  @@ -195,16 +222,31 @@ Static variable in class compbio.engine.ClusterJobId - Class in compbio.engine
 
ClusterJobId(String) - Constructor for class compbio.engine.ClusterJobId
  -
ClusterNativeSpecExecutable<T> - Interface in compbio.engine.client
 
ClusterSession - Class in compbio.engine.cluster.drmaa
 
ClusterUtil - Class in compbio.engine.cluster.drmaa
 
ClusterUtil() - +
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 - package compbio.data.msa
 
compbio.data.msa.jaxws - package compbio.data.msa.jaxws
 
compbio.pipeline._jpred - package compbio.pipeline._jpred
 
compbio.runner._jpred - package compbio.runner._jpred
 
compbio.runner.psiblast - package compbio.runner.psiblast
 
compbio.ws.client - package compbio.ws.client
 
compbio.ws.server - package compbio.ws.server
 
confDir - +
compbio.data._structure - package compbio.data._structure
 
compbio.data.msa - package compbio.data.msa
Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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) - @@ -222,9 +264,28 @@ Static method in class compbio.engine.configureExecutable(Executable<T>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
  -
connect(String, Jws2Client.Services) - +
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 -
Connects to a web service by the host and the service name +
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.ShutdownEngines +
  +
contextInitialized(ServletContextEvent) - +Method in class compbio.stat.servlet.StatisticCollector +
  +
contextInitialized(ServletContextEvent) - +Method in class compbio.ws.server.ShutdownEngines +
 
convertToAbsolute(String) - Static method in class compbio.engine.client.Util
  @@ -240,6 +301,12 @@ Constructor for class compbio.data.msa.jaxws.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
  @@ -258,6 +325,25 @@ Method in class compbio.ws.server.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 +