- Parameter() - Constructor for class compbio.engine.client.CommandBuilder.Parameter
-
- Parameter(String) - Constructor for class compbio.engine.client.CommandBuilder.Parameter
-
- Parameter(String, String) - Constructor for class compbio.engine.client.CommandBuilder.Parameter
-
- Parameter<T> - Class in compbio.metadata
-
A single value containing an option supported by the web service e.g.
- Parameter() - Constructor for class compbio.metadata.Parameter
-
- Parameter(String, String) - Constructor for class compbio.metadata.Parameter
-
- parameterkey - Static variable in class compbio.ws.client.Constraints
-
- parameters - Variable in class compbio.engine.client.RunConfiguration
-
Parameters
- parameters - Variable in class compbio.metadata.RunnerConfig
-
- parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - Method in class compbio.runner.OptionCombinator
-
- parameterToString(List<CommandBuilder.Parameter>) - Method in class compbio.engine.client.CommandBuilder
-
- paramFile - Static variable in class compbio.ws.client.Constraints
-
- paramList - Variable in class compbio.engine.client.CommandBuilder
-
- paramList - Static variable in class compbio.ws.client.Constraints
-
- paramValueUpdater() - Method in class compbio.engine.client.SkeletalExecutable
-
This is a generic method of changing values of the parameters with
properties
This method iterates via commands for an executable finding matches from
the Executable.properties file and replacing values in CommandBuilder
with a combination of value from CommandBuilder to merge path from
properties
- parseIUPredDomains(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
-
# P53_HUMA
Number of globular domains: 2
globular domain 1.
- parseIUPredScores(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
-
- parseRanges(Enum, String) - Static method in class compbio.data.sequence.SequenceUtil
-
Parsing:
# COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343,
350-391, 429-485, 497-506, 539-547
# REM465 355-368
# HOTLOOPS 190-204
- PATH - Static variable in class compbio.engine.client.EnvVariableProcessor
-
Special variable keys Absolute path(s) will be merged with the content of
the system PATH variable
- PathValidator - Class in compbio.engine.client
-
- PathValidator() - Constructor for class compbio.engine.client.PathValidator
-
- pbuilder - Variable in class compbio.engine.local.ExecutableWrapper
-
- ph - Static variable in class compbio.engine.client.ConfExecutable
-
- ph - Static variable in class compbio.engine.client.EngineUtil
-
- ph - Static variable in class compbio.engine.client.SkeletalExecutable
-
- ph - Static variable in class compbio.engine.client.Util
-
- ph - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
-
- ph - Static variable in class compbio.engine.conf.PropertyHelperManager
-
- ph - Static variable in class compbio.engine.Configurator
-
- ph - Static variable in class compbio.runner.msa.Tcoffee
-
- ph - Static variable in class compbio.runner.Util
-
- ph - Static variable in class compbio.stat.servlet.StatisticCollector
-
- ph - Static variable in class compbio.ws.server.MainManager
-
- PipedExecutable<T> - Interface in compbio.engine.client
-
This is a marker interface to indicate that the output of the process must be
captured.
- position - Variable in class compbio.data.msa.jaxws.PullExecStatistics
-
- position - Variable in class compbio.engine.client.CommandBuilder.Parameter
-
- position - Variable in class compbio.metadata.ChunkHolder
-
- possibleValues - Variable in class compbio.metadata.Parameter
-
- preset - Variable in class compbio.data.msa.jaxws.PresetAlign
-
- preset - Variable in class compbio.data.msa.jaxws.PresetAnalize
-
- preset - Variable in class compbio.data.msa.jaxws.PresetFold
-
- preset - Variable in class compbio.metadata.Limit
-
- Preset<T> - Class in compbio.metadata
-
Collection of Options and Parameters with their values
- Preset() - Constructor for class compbio.metadata.Preset
-
- preset - Variable in class compbio.metadata.PresetManager
-
- PresetAlign - Class in compbio.data.msa.jaxws
-
- PresetAlign() - Constructor for class compbio.data.msa.jaxws.PresetAlign
-
- presetAlign(List<FastaSequence>, Preset<T>) - Method in interface compbio.data.msa.MsaWS
-
Align a list of sequences with preset.
- presetAlign(MsaWS<T>, List<Preset<T>>) - Method in class compbio.ws.client.WSTester
-
Calls alignment with preset
- presetAlign(List<FastaSequence>, Preset<ClustalO>) - Method in class compbio.ws.server.ClustalOWS
-
- presetAlign(List<FastaSequence>, Preset<ClustalW>) - Method in class compbio.ws.server.ClustalWS
-
- presetAlign(List<FastaSequence>, Preset<GLprobs>) - Method in class compbio.ws.server.GLprobsWS
-
- presetAlign(List<FastaSequence>, Preset<Mafft>) - Method in class compbio.ws.server.MafftWS
-
- presetAlign(List<FastaSequence>, Preset<MSAprobs>) - Method in class compbio.ws.server.MSAprobsWS
-
- presetAlign(List<FastaSequence>, Preset<Muscle>) - Method in class compbio.ws.server.MuscleWS
-
- presetAlign(List<FastaSequence>, Preset<Probcons>) - Method in class compbio.ws.server.ProbconsWS
-
- presetAlign(List<FastaSequence>, Preset<Tcoffee>) - Method in class compbio.ws.server.TcoffeeWS
-
- PresetAlignResponse - Class in compbio.data.msa.jaxws
-
- PresetAlignResponse() - Constructor for class compbio.data.msa.jaxws.PresetAlignResponse
-
- PresetAnalize - Class in compbio.data.msa.jaxws
-
- PresetAnalize() - Constructor for class compbio.data.msa.jaxws.PresetAnalize
-
- presetAnalize(List<FastaSequence>, Preset<T>) - Method in interface compbio.data.msa.SequenceAnnotation
-
Analyse the sequences according to the preset settings.
- presetAnalize(List<FastaSequence>, Preset<AACon>) - Method in class compbio.ws.server.AAConWS
-
- presetAnalize(List<FastaSequence>, Preset<Disembl>) - Method in class compbio.ws.server.DisemblWS
-
- presetAnalize(List<FastaSequence>, Preset<GlobPlot>) - Method in class compbio.ws.server.GlobPlotWS
-
- presetAnalize(List<FastaSequence>, Preset<IUPred>) - Method in class compbio.ws.server.IUPredWS
-
- presetAnalize(List<FastaSequence>, Preset<RNAalifold>) - Method in class compbio.ws.server.RNAalifoldWS
-
- presetAnalize(List<FastaSequence>, Preset<T>) - Method in class compbio.ws.server.SequenceAnnotationService
-
- PresetAnalizeResponse - Class in compbio.data.msa.jaxws
-
- PresetAnalizeResponse() - Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse
-
- PresetFold - Class in compbio.data.msa.jaxws
-
- PresetFold() - Constructor for class compbio.data.msa.jaxws.PresetFold
-
- PresetFoldResponse - Class in compbio.data.msa.jaxws
-
- PresetFoldResponse() - Constructor for class compbio.data.msa.jaxws.PresetFoldResponse
-
- presetkey - Static variable in class compbio.ws.client.Constraints
-
- presetList - Static variable in class compbio.ws.client.Constraints
-
- PresetManager<T> - Class in compbio.metadata
-
Collection of presets and methods to manipulate them @see
Preset
- PresetManager() - Constructor for class compbio.metadata.PresetManager
-
- presetName - Variable in class compbio.data.msa.jaxws.GetLimit
-
- print() - Static method in class compbio.engine.PulledFileCache
-
- printUsage(int) - Static method in class compbio.ws.client.AAConClient
-
Prints AAConClient usage information to standard out
- printUsage() - Static method in class compbio.ws.client.WSTester
-
Prints usage
- priority - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- prmSeparator - Variable in class compbio.metadata.RunnerConfig
-
- Probcons - Class in compbio.runner.msa
-
- Probcons() - Constructor for class compbio.runner.msa.Probcons
-
- PROBCONS_INFO - Static variable in enum compbio.ws.client.Services
-
- probconsOptions - Static variable in class compbio.ws.server.ProbconsWS
-
- ProbconsWS - Class in compbio.ws.server
-
- ProbconsWS() - Constructor for class compbio.ws.server.ProbconsWS
-
- PROC_ERR_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
-
- PROC_IN_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
-
- PROC_OUT_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
-
- processParameters(List<String>, RunnerConfig<T>) - Static method in class compbio.ws.client.MetadataHelper
-
Converts options supplied via parameters file into Option objects
- program - Variable in class compbio.data.sequence.AlignmentMetadata
-
- Program - Enum in compbio.data.sequence
-
The list of programmes that can produce alignments
- Program() - Constructor for enum compbio.data.sequence.Program
-
- ProgressGetter - Class in compbio.engine
-
- ProgressGetter() - Constructor for class compbio.engine.ProgressGetter
-
- PROP_HELPER - Static variable in class compbio.ws.server.GAUtils
-
- PROP_NAME_VALUE_SEPARATOR - Static variable in class compbio.engine.client.EnvVariableProcessor
-
- PropertyHelperManager - Class in compbio.engine.conf
-
- PropertyHelperManager() - Constructor for class compbio.engine.conf.PropertyHelperManager
-
- protocol - Static variable in class compbio.stat.collector.StatDB
-
- provider - Variable in class compbio.engine.client.ConfExecutable
-
- ps - Static variable in class compbio.data.sequence.RNAStructReader
-
- pseparator - Static variable in class compbio.ws.client.Constraints
-
- PStructP - Static variable in class compbio.data.sequence.RNAStructReader
-
- pull(long) - Method in class compbio.engine.FilePuller
-
- pull(String, long, long, TimeUnit) - Static method in class compbio.engine.ProgressGetter
-
- pull(String, long) - Static method in class compbio.engine.ProgressGetter
-
- PulledFileCache - Class in compbio.engine
-
- PulledFileCache() - Constructor for class compbio.engine.PulledFileCache
-
- PullExecStatistics - Class in compbio.data.msa.jaxws
-
- PullExecStatistics() - Constructor for class compbio.data.msa.jaxws.PullExecStatistics
-
- pullExecStatistics(String, long) - Method in interface compbio.data.msa.JManagement
-
Reads 1kb chunk from the statistics file which is specific to a given web
service from the position.
- pullExecStatistics(String, long) - Method in class compbio.ws.server.AAConWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.ClustalOWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.ClustalWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.GenericMetadataService
-
Assume statistics is not supported
- pullExecStatistics(String, long) - Method in class compbio.ws.server.GLprobsWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.JronnWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.MafftWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.MSAprobsWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.MuscleWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.ProbconsWS
-
- pullExecStatistics(String, long) - Method in class compbio.ws.server.TcoffeeWS
-
- PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
-
- PullExecStatisticsResponse() - Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse
-
- pullFile(String, long) - Static method in class compbio.ws.server.WSUtil
-
- put(FilePuller) - Static method in class compbio.engine.PulledFileCache
-
This method allows duplicates to be added.