X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-16.html;h=87f5b0b8f9f8f66a45ed778a9a952d9114914a8e;hb=370eba4341a85f3eed877e9bb4648c73e345faa4;hp=0c6ba55bfcde25c4cc90d31233c2c2478358383c;hpb=6582e82919b0d3697fe5e96f1be6a369f90a2d93;p=jabaws.git
diff --git a/website/dm_javadoc/index-files/index-16.html b/website/dm_javadoc/index-files/index-16.html
index 0c6ba55..87f5b0b 100644
--- a/website/dm_javadoc/index-files/index-16.html
+++ b/website/dm_javadoc/index-files/index-16.html
@@ -2,12 +2,12 @@
-
+
S-Index
-
+
@@ -82,10 +82,48 @@ function windowTitle()
S
-- Score - Class in compbio.data.sequence
-
- Score(Method, List<Float>) -
+
- Score - Class in compbio.data.sequence
- A value class for AACon annotation results storage.
- Score(Enum<?>, ArrayList<Float>) -
Constructor for class compbio.data.sequence.Score
+
- Instantiate the Score
+
- Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) -
+Constructor for class compbio.data.sequence.Score
+
-
+
- Score(Enum<?>, TreeSet<Range>) -
+Constructor for class compbio.data.sequence.Score
+
-
+
- Score(Enum<?>, float[]) -
+Constructor for class compbio.data.sequence.Score
+
-
+
- ScoreManager - Class in compbio.data.sequence
-
- ScoreManager.ScoreHolder - Class in compbio.data.sequence
-
- scores -
+Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
+
-
+
- SequenceAnnotation<T> - Interface in compbio.data.msa
- Interface for tools that results to one or more annotation to sequence(s)
+
+ Single, multiple sequences their groups or alignments can be annotated
- SequenceUtil - Class in compbio.data.sequence
- Utility class for operations on sequences
- SERVICE_NAMESPACE -
+Static variable in interface compbio.data.msa.JABAService
+
-
+
- Services - Enum in compbio.ws.client
- List of web services currently supported by JABAWS version 2
- ServicesUtil - Class in compbio.ws.client
-
- ServicesUtil() -
+Constructor for class compbio.ws.client.ServicesUtil
-
-
- SequenceUtil - Class in compbio.data.sequence
- Utility class for operations on sequences
- Services - Enum in compbio.ws.client
- List of web services currently supported by JABAWS version 2
- setDefaultValue(String) -
+
- setActualNumberofSequences(int) -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
-
+
- setArg0(Services) -
+Method in class compbio.data.msa.jaxws.GetLastTested
+
-
+
- setArg0(Services) -
+Method in class compbio.data.msa.jaxws.GetLastTestedOn
+
-
+
- setArg0(Services) -
+Method in class compbio.data.msa.jaxws.GetServiceDescription
+
-
+
- setArg0(Services) -
+Method in class compbio.data.msa.jaxws.IsOperating
+
-
+
- setArg0(Services) -
+Method in class compbio.data.msa.jaxws.TestService
+
-
+
- setDefaultValue(String) -
Method in class compbio.metadata.Option
- Sets one of the values defined in optionList as default.
- setDefaultValue(String) -
@@ -97,12 +135,60 @@ Method in class compbio.metadata.setDescription(String) -
Method in class compbio.metadata.Preset
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.Align
+
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.Analize
+
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.CustomAlign
+
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.CustomAnalize
+
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.PresetAlign
+
-
+
- setFastaSequences(List<FastaSequence>) -
+Method in class compbio.data.msa.jaxws.PresetAnalize
+
-
- setFurtherDetails(URL) -
Method in class compbio.metadata.Option
-
+
- setJobId(String) -
+Method in class compbio.data.msa.jaxws.CancelJob
+
-
+
- setJobId(String) -
+Method in class compbio.data.msa.jaxws.GetAnnotation
+
-
+
- setJobId(String) -
+Method in class compbio.data.msa.jaxws.GetJobStatus
+
-
+
- setJobId(String) -
+Method in class compbio.data.msa.jaxws.GetResult
+
-
+
- setJobId(String) -
+Method in class compbio.data.msa.jaxws.PullExecStatistics
+
-
- setMax(String) -
Method in class compbio.metadata.ValueConstrain
-
+
- setMessage(String) -
+Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean
+
-
+
- setMessage(String) -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
-
+
- setMessage(String) -
+Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
+
-
+
- setMessage(String) -
+Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
+
-
+
- setMessage(String) -
+Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean
+
-
- setMin(String) -
Method in class compbio.metadata.ValueConstrain
-
@@ -112,6 +198,9 @@ Method in class compbio.metadata.setName(String) -
Method in class compbio.metadata.Preset
-
+
- setNumberOfSequencesAllowed(int) -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
-
- setOptionName(String) -
Method in class compbio.metadata.Parameter
-
@@ -121,6 +210,12 @@ Method in class compbio.metadata.setOptionNames(Set<String>) -
Method in class compbio.metadata.Parameter
-
+
- setOptions(List<Option>) -
+Method in class compbio.data.msa.jaxws.CustomAlign
+
-
+
- setOptions(List<Option>) -
+Method in class compbio.data.msa.jaxws.CustomAnalize
+
-
- setOptions(List<String>) -
Method in class compbio.metadata.Preset
-
@@ -130,24 +225,114 @@ Method in class compbio.metadata.setParameters(List<Parameter<T>>) -
Method in class compbio.metadata.RunnerConfig
- Sets the list of parameters as internal list
+
- setPosition(long) -
+Method in class compbio.data.msa.jaxws.PullExecStatistics
+
-
- setPossibleValues(Set<String>) -
Method in class compbio.metadata.Parameter
-
+
- setPreset(Preset) -
+Method in class compbio.data.msa.jaxws.PresetAlign
+
-
+
- setPreset(Preset) -
+Method in class compbio.data.msa.jaxws.PresetAnalize
+
-
+
- setPresetName(String) -
+Method in class compbio.data.msa.jaxws.GetLimit
+
-
- setPresets(List<Preset<T>>) -
Method in class compbio.metadata.PresetManager
-
- setPrmSeparator(String) -
Method in class compbio.metadata.RunnerConfig
- Sets name value separator character
+
- setRanges(TreeSet<Range>) -
+Method in class compbio.data.sequence.Score
+
-
- setRequired(boolean) -
Method in class compbio.metadata.Option
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.AlignResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.AnalizeResponse
+
-
+
- setReturn(boolean) -
+Method in class compbio.data.msa.jaxws.CancelJobResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.CustomAlignResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.CustomAnalizeResponse
+
-
+
- setReturn(ScoreManager) -
+Method in class compbio.data.msa.jaxws.GetAnnotationResponse
+
-
+
- setReturn(JobStatus) -
+Method in class compbio.data.msa.jaxws.GetJobStatusResponse
+
-
+
- setReturn(Date) -
+Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse
+
-
+
- setReturn(int) -
+Method in class compbio.data.msa.jaxws.GetLastTestedResponse
+
-
+
- setReturn(Limit) -
+Method in class compbio.data.msa.jaxws.GetLimitResponse
+
-
+
- setReturn(LimitsManager) -
+Method in class compbio.data.msa.jaxws.GetLimitsResponse
+
-
+
- setReturn(PresetManager) -
+Method in class compbio.data.msa.jaxws.GetPresetsResponse
+
-
+
- setReturn(Alignment) -
+Method in class compbio.data.msa.jaxws.GetResultResponse
+
-
+
- setReturn(RunnerConfig) -
+Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse
+
-
+
- setReturn(Set<Category>) -
+Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse
+
-
+
- setReturn(Set<Services>) -
+Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse
+
-
+
- setReturn(boolean) -
+Method in class compbio.data.msa.jaxws.IsOperatingResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.PresetAlignResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.PresetAnalizeResponse
+
-
+
- setReturn(ChunkHolder) -
+Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.TestAllServicesResponse
+
-
+
- setReturn(String) -
+Method in class compbio.data.msa.jaxws.TestServiceResponse
+
-
- setRunnerClassName(String) -
Method in class compbio.metadata.PresetManager
-
- setRunnerClassName(String) -
Method in class compbio.metadata.RunnerConfig
- Set the name of a runner class
+
- setSequenceLenghtActual(int) -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
-
+
- setSequenceLenghtAllowed(int) -
+Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
+
-
- setType(ValueConstrain.Type) -
Method in class compbio.metadata.ValueConstrain
-
@@ -160,7 +345,10 @@ Method in interface compbio.metadata.setValue(String) -
Method in class compbio.metadata.Option
-
-
+SINGLE_ENTRY_KEY -
+Static variable in class compbio.data.sequence.ScoreManager
+
+SMERFSConstraints - Enum in compbio.data.sequenceEnumeration defining two constraints for SMERFS columns score calculation.