X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-6.html;h=113b47f40b3057a0970f22b2ff0239f3a8ecbe6c;hb=faac303bf9ad8c17b71a55d23b7a2c0a9e6e2efa;hp=970991cb4dee817934cda9921c12cee69f005362;hpb=02ace2e4cf6d29a70be3dd799f84e3f14333cdbb;p=jabaws.git
diff --git a/website/dm_javadoc/index-files/index-6.html b/website/dm_javadoc/index-files/index-6.html
index 970991c..113b47f 100644
--- a/website/dm_javadoc/index-files/index-6.html
+++ b/website/dm_javadoc/index-files/index-6.html
@@ -2,12 +2,12 @@
-
+
G-Index
-
+
@@ -85,9 +85,39 @@ function windowTitle()
gapchar -
Static variable in class compbio.data.sequence.ClustalAlignmentUtil
Dash char to be used as gap char in the alignments
+ getActualNumberofSequences() -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
getActualNumberofSequences() -
Method in exception compbio.metadata.LimitExceededException
+ GetAnnotation - Class in compbio.data.msa.jaxws GetAnnotation() -
+Constructor for class compbio.data.msa.jaxws.GetAnnotation
+
+ getAnnotation(String) -
+Method in interface compbio.data.msa.SequenceAnnotation
+Return the result of the job.
+ getAnnotationForSequence(String) -
+Method in class compbio.data.sequence.ScoreManager
+
+ GetAnnotationResponse - Class in compbio.data.msa.jaxws GetAnnotationResponse() -
+Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse
+
+ getArg0() -
+Method in class compbio.data.msa.jaxws.GetLastTested
+
+ getArg0() -
+Method in class compbio.data.msa.jaxws.GetLastTestedOn
+
+ getArg0() -
+Method in class compbio.data.msa.jaxws.GetServiceDescription
+
+ getArg0() -
+Method in class compbio.data.msa.jaxws.IsOperating
+
+ getArg0() -
+Method in class compbio.data.msa.jaxws.TestService
+
getArgument(String) -
Method in class compbio.metadata.RunnerConfig
Returns the argument by its name if found, NULL otherwise.
@@ -107,6 +137,9 @@ Method in class compbio.metadata.getAvgSequenceLength(List<FastaSequence>) -
Static method in class compbio.metadata.Limit
Calculates an average sequence length of the dataset
+ getCategories() -
+Static method in class compbio.data.msa.Category
+
getChunk() -
Method in class compbio.metadata.ChunkHolder
@@ -128,6 +161,24 @@ Method in class compbio.metadata.getDescription() -
Method in class compbio.metadata.Preset
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.Align
+
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.Analize
+
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.CustomAlign
+
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.CustomAnalize
+
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.PresetAlign
+
+ getFastaSequences() -
+Method in class compbio.data.msa.jaxws.PresetAnalize
+
getFormatedSequence(int) -
Method in class compbio.data.sequence.FastaSequence
Format sequence per width letter in one string.
@@ -143,36 +194,105 @@ Method in class compbio.metadata.getGapchar() -
Method in class compbio.data.sequence.AlignmentMetadata
- getHost(String[]) -
-Static method in class compbio.ws.client.Jws2Client
-Extracts host name from the command line
getId() -
Method in class compbio.data.sequence.FastaSequence
Gets the value of id
- getJobStatus(String) -
-Method in interface compbio.data.msa.MsaWS
+getJobId() -
+Method in class compbio.data.msa.jaxws.CancelJob
+
+ getJobId() -
+Method in class compbio.data.msa.jaxws.GetAnnotation
+
+ getJobId() -
+Method in class compbio.data.msa.jaxws.GetJobStatus
+
+ getJobId() -
+Method in class compbio.data.msa.jaxws.GetResult
+
+ getJobId() -
+Method in class compbio.data.msa.jaxws.PullExecStatistics
+
+ GetJobStatus - Class in compbio.data.msa.jaxws GetJobStatus() -
+Constructor for class compbio.data.msa.jaxws.GetJobStatus
+
+ getJobStatus(String) -
+Method in interface compbio.data.msa.JManagement
Return the status of the job.
+ GetJobStatusResponse - Class in compbio.data.msa.jaxws GetJobStatusResponse() -
+Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse
+
+ GetLastTested - Class in compbio.data.msa.jaxws GetLastTested() -
+Constructor for class compbio.data.msa.jaxws.GetLastTested
+
+ getLastTested(Services) -
+Method in interface compbio.data.msa.RegistryWS
+Number of seconds since the last test.
+ GetLastTestedOn - Class in compbio.data.msa.jaxws GetLastTestedOn() -
+Constructor for class compbio.data.msa.jaxws.GetLastTestedOn
+
+ getLastTestedOn(Services) -
+Method in interface compbio.data.msa.RegistryWS
+The date and time the service has been verified to work last time
+ GetLastTestedOnResponse - Class in compbio.data.msa.jaxws GetLastTestedOnResponse() -
+Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse
+
+ GetLastTestedResponse - Class in compbio.data.msa.jaxws GetLastTestedResponse() -
+Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse
+
getLength() -
Method in class compbio.data.sequence.FastaSequence
- getLimit(String) -
-Method in interface compbio.data.msa.MsaWS
+GetLimit - Class in compbio.data.msa.jaxws GetLimit() -
+Constructor for class compbio.data.msa.jaxws.GetLimit
+
+ getLimit(String) -
+Method in interface compbio.data.msa.Metadata
Get a Limit for a preset.
getLimitByName(String) -
Method in class compbio.metadata.LimitsManager
- getLimits() -
-Method in interface compbio.data.msa.MsaWS
+GetLimitResponse - Class in compbio.data.msa.jaxws GetLimitResponse() -
+Constructor for class compbio.data.msa.jaxws.GetLimitResponse
+
+ GetLimits - Class in compbio.data.msa.jaxws GetLimits() -
+Constructor for class compbio.data.msa.jaxws.GetLimits
+
+ getLimits() -
+Method in interface compbio.data.msa.Metadata
List Limits supported by a web service.
getLimits() -
Method in class compbio.metadata.LimitsManager
+ GetLimitsResponse - Class in compbio.data.msa.jaxws GetLimitsResponse() -
+Constructor for class compbio.data.msa.jaxws.GetLimitsResponse
+
getMax() -
Method in class compbio.metadata.ValueConstrain
+ getMessage() -
+Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean
+
+ getMessage() -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
+ getMessage() -
+Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
+
+ getMessage() -
+Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
+
+ getMessage() -
+Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean
+
getMetadata() -
Method in class compbio.data.sequence.Alignment
+ getMethod(String) -
+Static method in enum compbio.data.sequence.ConservationMethod
+
+ getMethod() -
+Method in class compbio.data.sequence.Score
+Returns the ConservationMethod
getMin() -
Method in class compbio.metadata.ValueConstrain
@@ -188,6 +308,15 @@ Method in class compbio.metadata.getNextPosition() -
Method in class compbio.metadata.ChunkHolder
+ getNumberOfScores() -
+Method in class compbio.data.sequence.ScoreManager.ScoreHolder
+
+ getNumberOfSeq() -
+Method in class compbio.data.sequence.ScoreManager
+
+ getNumberOfSequencesAllowed() -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
getNumberOfSequencesAllowed() -
Method in exception compbio.metadata.LimitExceededException
@@ -200,6 +329,12 @@ Method in class compbio.metadata.getOptionNames() -
Method in class compbio.metadata.Option
+ getOptions() -
+Method in class compbio.data.msa.jaxws.CustomAlign
+
+ getOptions() -
+Method in class compbio.data.msa.jaxws.CustomAnalize
+
getOptions() -
Method in class compbio.metadata.Preset
@@ -209,6 +344,9 @@ Method in class compbio.metadata.getParameters() -
Method in class compbio.metadata.RunnerConfig
Returns the list of parameters supported executable of type T.
+ getPosition() -
+Method in class compbio.data.msa.jaxws.PullExecStatistics
+
getPossibleValues() -
Method in interface compbio.metadata.Argument
@@ -218,45 +356,156 @@ Method in class compbio.metadata.getPossibleValues() -
Method in class compbio.metadata.Parameter
List is more convenient to work with
+ getPreset() -
+Method in class compbio.data.msa.jaxws.PresetAlign
+
+ getPreset() -
+Method in class compbio.data.msa.jaxws.PresetAnalize
+
getPreset() -
Method in class compbio.metadata.Limit
getPresetByName(String) -
Method in class compbio.metadata.PresetManager
- getPresets() -
-Method in interface compbio.data.msa.MsaWS
+getPresetName() -
+Method in class compbio.data.msa.jaxws.GetLimit
+
+ GetPresets - Class in compbio.data.msa.jaxws GetPresets() -
+Constructor for class compbio.data.msa.jaxws.GetPresets
+
+ getPresets() -
+Method in interface compbio.data.msa.Metadata
Get presets supported by a web service
getPresets() -
Method in class compbio.metadata.PresetManager
+ GetPresetsResponse - Class in compbio.data.msa.jaxws GetPresetsResponse() -
+Constructor for class compbio.data.msa.jaxws.GetPresetsResponse
+
getPrmSeparator() -
Method in class compbio.metadata.RunnerConfig
getProgram() -
Method in class compbio.data.sequence.AlignmentMetadata
+ getRanges() -
+Method in class compbio.data.sequence.Score
+Return Ranges if any Collections.EMPTY_SET otherwise
+ GetResult - Class in compbio.data.msa.jaxws GetResult() -
+Constructor for class compbio.data.msa.jaxws.GetResult
+
getResult(String) -
Method in interface compbio.data.msa.MsaWS
Return the result of the job.
+ GetResultResponse - Class in compbio.data.msa.jaxws GetResultResponse() -
+Constructor for class compbio.data.msa.jaxws.GetResultResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.AlignResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.AnalizeResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.CustomAlignResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.CustomAnalizeResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetAnnotationResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetJobStatusResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetLastTestedResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetLimitResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetLimitsResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetPresetsResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetResultResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.PresetAlignResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.PresetAnalizeResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.TestAllServicesResponse
+
+ getReturn() -
+Method in class compbio.data.msa.jaxws.TestServiceResponse
+
+ getRunnerByJobDirectory(File) -
+Static method in class compbio.ws.client.ServicesUtil
+
getRunnerClassName() -
Method in class compbio.metadata.PresetManager
getRunnerClassName() -
Method in class compbio.metadata.RunnerConfig
- getRunnerOptions() -
-Method in interface compbio.data.msa.MsaWS
+GetRunnerOptions - Class in compbio.data.msa.jaxws GetRunnerOptions() -
+Constructor for class compbio.data.msa.jaxws.GetRunnerOptions
+
+ getRunnerOptions() -
+Method in interface compbio.data.msa.Metadata
Get options supported by a web service
+ GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws GetRunnerOptionsResponse() -
+Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse
+
+ getScoreByMethod(Enum<?>) -
+Method in class compbio.data.sequence.ScoreManager.ScoreHolder
+
+ getScoreByMethod(String) -
+Method in class compbio.data.sequence.ScoreManager.ScoreHolder
+
+ getScores() -
+Method in class compbio.data.sequence.Score
+The column scores for the alignment
getSeqNumber() -
Method in class compbio.metadata.Limit
getSequence() -
Method in class compbio.data.sequence.FastaSequence
Gets the value of sequence
+ getSequenceLenghtActual() -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
getSequenceLenghtActual() -
Method in exception compbio.metadata.LimitExceededException
+ getSequenceLenghtAllowed() -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
getSequenceLenghtAllowed() -
Method in exception compbio.metadata.LimitExceededException
@@ -266,21 +515,66 @@ Method in class compbio.data.sequence.getService(String) -
Static method in enum compbio.ws.client.Services
- getService(Class) -
-Static method in enum compbio.ws.client.Services
+getServiceByJobDirectory(File) -
+Static method in class compbio.ws.client.ServicesUtil
+
+ getServiceByRunner(Class<? extends Executable>) -
+Static method in class compbio.ws.client.ServicesUtil
- getServiceName(String[]) -
+GetServiceCategories - Class in compbio.data.msa.jaxws GetServiceCategories() -
+Constructor for class compbio.data.msa.jaxws.GetServiceCategories
+
+ getServiceCategories() -
+Method in interface compbio.data.msa.RegistryWS
+Gets the list of services per category.
+ GetServiceCategoriesResponse - Class in compbio.data.msa.jaxws GetServiceCategoriesResponse() -
+Constructor for class compbio.data.msa.jaxws.GetServiceCategoriesResponse
+
+ GetServiceDescription - Class in compbio.data.msa.jaxws GetServiceDescription() -
+Constructor for class compbio.data.msa.jaxws.GetServiceDescription
+
+ getServiceDescription(Services) -
+Method in interface compbio.data.msa.RegistryWS
+Gives the description of the service.
+ GetServiceDescriptionResponse - Class in compbio.data.msa.jaxws GetServiceDescriptionResponse() -
+Constructor for class compbio.data.msa.jaxws.GetServiceDescriptionResponse
+
+ getServiceImpl(Services) -
+Static method in class compbio.ws.client.ServicesUtil
+
+ getServiceInfo() -
+Method in enum compbio.ws.client.Services
+
+ getServices() -
+Method in class compbio.data.msa.Category
+
+ getServices(String) -
Static method in class compbio.ws.client.Jws2Client
-Extracts service name from the command line
+
getSize() -
Method in class compbio.data.sequence.Alignment
+ getSMERFSColumnScore(String) -
+Static method in enum compbio.data.sequence.SMERFSConstraints
+
+ GetSupportedServices - Class in compbio.data.msa.jaxws GetSupportedServices() -
+Constructor for class compbio.data.msa.jaxws.GetSupportedServices
+
+ getSupportedServices() -
+Method in interface compbio.data.msa.RegistryWS
+List of services that are functioning on the server.
+ GetSupportedServicesResponse - Class in compbio.data.msa.jaxws GetSupportedServicesResponse() -
+Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse
+
getType() -
Method in class compbio.metadata.ValueConstrain
getValidValue() -
Method in class compbio.metadata.Parameter
+ GLOBPLOT_INFO -
+Static variable in enum compbio.ws.client.Services
+