A B C D E F G H I J K L M N O P R S T U V W _

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 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

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<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

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

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

PsiBlast - Class in compbio.runner.psiblast

PsiBlast() - Constructor for class compbio.runner.psiblast.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.MsaWS

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.ClustalWS

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 - Class in compbio.data.msa.jaxws

PullFile() - Constructor for class compbio.data.msa.jaxws.PullFile

pullFile(String, long) - Static method in class compbio.ws.server.WSUtil

PullFileResponse - Class in compbio.data.msa.jaxws

PullFileResponse() - Constructor for class compbio.data.msa.jaxws.PullFileResponse

put(FilePuller) - Static method in class compbio.engine.PulledFileCache

This method allows duplicates to be added.