- name - Variable in class compbio.data.msa.Category
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- name - Variable in class compbio.engine.client.CommandBuilder.Parameter
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- name - Variable in class compbio.metadata.Option
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- name - Variable in class compbio.metadata.Preset
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- nameValueSeparator - Variable in class compbio.engine.client.CommandBuilder
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- ncoreNumber - Variable in class compbio.runner.conservation.AACon
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Number of cores to use, defaults to 1 for local execution or the value of
"jronn.cluster.cpunum" property for cluster execution
- ncoreNumber - Variable in class compbio.runner.disorder.Jronn
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- ncoreNumber - Variable in class compbio.runner.msa.ClustalO
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Number of cores to use, defaults to 1 for local execution or the value of
"tcoffee.cluster.cpunum" property for cluster execution
- ncoreNumber - Variable in class compbio.runner.msa.Tcoffee
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Number of cores to use, defaults to 1 for local execution or the value of
"tcoffee.cluster.cpunum" property for cluster execution
- ncorePrm - Variable in class compbio.runner.conservation.AACon
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- ncorePrm - Variable in class compbio.runner.disorder.Jronn
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- ncorePrm - Static variable in class compbio.runner.msa.ClustalO
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Number of cores parameter name
- ncorePrm - Static variable in class compbio.runner.msa.Tcoffee
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- newCommandBuilder(List<? extends Option<T>>, String) - Static method in class compbio.engine.client.CommandBuilder
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This produces the same result as getCommands method.
- newConfExecutable(RunConfiguration) - Static method in class compbio.engine.client.ConfExecutable
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- newEmptyScore(Enum<?>) - Static method in class compbio.data.sequence.RNAStructReader
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- newFilePuller(String, int) - Static method in class compbio.engine.FilePuller
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- newIncompleteStat(String) - Static method in class compbio.stat.collector.JobStat
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- newInstance(List<String>, List<TreeSet<Score>>) - Static method in class compbio.data.sequence.RNAStructScoreManager
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- newInstance(Map<String, Set<Score>>) - Static method in class compbio.data.sequence.ScoreManager
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- newInstance(Services, String, String, long, long, long, long, boolean, boolean) - Static method in class compbio.stat.collector.JobStat
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- newInstance(Services, String, String, Timestamp, Timestamp, long, long, boolean, boolean) - Static method in class compbio.stat.collector.JobStat
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- newInstanceSingleScore(Map<String, Score>) - Static method in class compbio.data.sequence.ScoreManager
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- newInstanceSingleSequence(Set<Score>) - Static method in class compbio.data.sequence.ScoreManager
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- newLimitExceeded(Limit<?>, List<FastaSequence>) - Static method in exception compbio.metadata.LimitExceededException
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- newLine - Static variable in class compbio.engine.cluster.drmaa.StatisticManager
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- newParameter(String) - Method in class compbio.engine.client.CommandBuilder
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- newProgressPuller(String) - Static method in class compbio.engine.FilePuller
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Progress Puller is designed to read 3 characters from the beginning of
the file, nothing more.
- newSetScore(Enum<?>, List<Float>) - Static method in class compbio.data.sequence.RNAStructReader
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- newStatCollecton(Date, Date) - Static method in class compbio.stat.servlet.util.StatCollection
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- newUnsupportedOutputException() - Method in class compbio.runner.disorder.IUPred
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- next() - Method in class compbio.data.sequence.FastaReader
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Reads the next FastaSequence from the input
- NEXT_ENV_PROPERTY_DELIMITER - Static variable in class compbio.engine.client.EnvVariableProcessor
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- NON_AA - Static variable in class compbio.data.sequence.SequenceUtil
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inversion of AA pattern
- NON_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
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Non nucleotide
- nonoperating - Static variable in class compbio.ws.server.RegistryWS
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- NONWORD - Static variable in class compbio.data.sequence.SequenceUtil
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Non word
- notData - Static variable in class compbio.data.sequence.RNAStructReader
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- NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
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Nucleotides a, t, g, c, u
- NUMBER_FORMAT - Static variable in class compbio.data.sequence.Score
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- numberOfLetters() - Method in class compbio.metadata.Limit
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- numberOfSequencesAllowed - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
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- numberOfSequencesAllowed - Variable in exception compbio.metadata.LimitExceededException
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- numTasks - Variable in class compbio.engine.local.LocalExecutorService
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