X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-6.html;h=b1fd1a40d61e0eb5f808700c83428458d2edd9b5;hb=7d95ae4c69a42a125d385912a49b31b38ac99e3b;hp=38104adc675bfc31635a1fa3acfbc5193027e311;hpb=14a41b0acd5d808ae1cdd8ecc82c85b4d3329b72;p=jabaws.git diff --git a/website/dm_javadoc/index-files/index-6.html b/website/dm_javadoc/index-files/index-6.html index 38104ad..b1fd1a4 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 +85,35 @@ 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
  -
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 @@ -137,6 +155,24 @@ 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. @@ -155,27 +191,93 @@ 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
  @@ -200,6 +302,15 @@ 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 +323,12 @@ 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 +338,9 @@ 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
  @@ -230,36 +350,132 @@ 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.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 @@ -269,9 +485,15 @@ Method in class compbio.metadata.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
  @@ -281,12 +503,33 @@ 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<Executable<?>>) - +Static method in class compbio.ws.client.ServicesUtil +
  +
getServiceImpl(Services) - +Static method in class compbio.ws.client.ServicesUtil +
  +
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