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.msaWeb 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
+