X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-6.html;h=113b47f40b3057a0970f22b2ff0239f3a8ecbe6c;hb=46419ca632a15de10fda41831d5a738a3313d662;hp=f39621da0adfb25e5755e6cf8e774c87c7c4a137;hpb=6582e82919b0d3697fe5e96f1be6a369f90a2d93;p=jabaws.git diff --git a/website/dm_javadoc/index-files/index-6.html b/website/dm_javadoc/index-files/index-6.html index f39621d..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 - + @@ -85,17 +85,38 @@ 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(String) - -Method in interface compbio.data.msa.Annotation +
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. -
getAnnotation() - -Method in class compbio.data.sequence.AnnotatedSequence +
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
  -
getAnnotations() - -Method in class compbio.data.sequence.MultiAnnotatedSequence +
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 @@ -116,6 +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
  @@ -137,6 +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. @@ -155,36 +197,102 @@ Method in class compbio.data.sequence.getId() - Method in class compbio.data.sequence.FastaSequence
Gets the value of id +
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 - 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
  +
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.Method +
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
  @@ -200,6 +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
  @@ -212,6 +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
  @@ -221,6 +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
  @@ -230,48 +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
  +
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 - 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
  @@ -281,15 +515,66 @@ Method in class compbio.data.sequence.getService(String) - 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 +
  +
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 +
 
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 +