-P-Index -

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-P

Pairwise - Class in compbio.pipeline._jpred
Pairwise(List<FastaSequence>) - -Constructor for class compbio.pipeline._jpred.Pairwise -: -
Parameter<T> - Class in compbio.metadata: A single value containing an option supported by the web service e.g.
Parameter(String, String) - -Constructor for class compbio.metadata.Parameter -: -
parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - -Method in class compbio.runner.OptionCombinator -: -
parse(String) - -Static method in class compbio.engine.conf._Key -: Deprecated. -
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 -: -
PipedExecutable<T> - Interface in compbio.engine.client: This is a marker interface to indicate that the output of the process must be - captured.
Preset<T> - Class in compbio.metadata: Collection of Options and Parameters with their values
Preset() - -Constructor for class compbio.metadata.Preset -: -
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(List<FastaSequence>, Preset<T>) - -Method in class compbio.ws.server._MsaService -: -
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<Mafft>) - -Method in class compbio.ws.server.MafftWS -: -
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<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<T>) - -Method in class compbio.ws.server.SequenceAnnotationService -: -
PresetAnalizeResponse - Class in compbio.data.msa.jaxws
PresetAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse -: -
PresetManager<T> - Class in compbio.metadata: Collection of presets and methods to manipulate them @see Preset
PresetManager() - -Constructor for class compbio.metadata.PresetManager -: -
Probcons - Class in compbio.runner.msa
Probcons() - -Constructor for class compbio.runner.msa.Probcons -: -
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_OUT_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -: -
Program - Enum in compbio.data.sequence: The list of programmes that can produce alignments
ProgressGetter - Class in compbio.engine
ProgressGetter() - -Constructor for class compbio.engine.ProgressGetter -: -
PropertyHelperManager - Class in compbio.engine.conf
PropertyHelperManager() - -Constructor for class compbio.engine.conf.PropertyHelperManager -: -
PScore - Class in compbio.pipeline._jpred
PScore() - -Constructor for class compbio.pipeline._jpred.PScore -: -
PSIBlast - Class in compbio.runner._impl
PSIBlast(String) - -Constructor for class compbio.runner._impl.PSIBlast -: -
pull(long) - -Method in class compbio.engine.FilePuller -: -
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._MsaService -: -
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.JronnWS -: -
pullExecStatistics(String, long) - -Method in class compbio.ws.server.MafftWS -: -
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. -