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

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initPull() - Method in class compbio.engine.FilePuller

IS_CLUSTER_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator

IS_LOCAL_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator

isAbsolutePath(String) - Static method in class compbio.engine.client.PathValidator

Whether a certain path is absolute or not is operation system dependent!

isAmbiguosProtein(String) - Static method in class compbio.data.sequence.SequenceUtil

Check whether the sequence confirms to amboguous protein sequence

isDefault() - Method in class compbio.metadata.Limit

isExceeded(List<FastaSequence>) - Method in class compbio.metadata.Limit

Checks if the number of sequences or their average length in the dataset exceeds limits the values defined by this Limit

isFileCreated() - Method in class compbio.engine.FilePuller

isMarked(String, JobStatus) - Static method in class compbio.engine.client.Util

isNonAmbNucleotideSequence(String) - Static method in class compbio.data.sequence.SequenceUtil

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char

isNucleotideSequence(FastaSequence) - Static method in class compbio.data.sequence.SequenceUtil

isProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil

isRequired() - Method in class compbio.metadata.Option

Flag that indicated that this option must be specified in the command line for an executable to run

isReturn() - Method in class compbio.data.msa.jaxws.CancelJobResponse

isShutdown() - Method in class compbio.engine.local._TrackingExecutor

isTerminated() - Method in class compbio.engine.local._TrackingExecutor

isValidClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil

isValidDirectory(String) - Static method in class compbio.engine.client.PathValidator

isValidExecutable(String) - Static method in class compbio.engine.client.PathValidator

isValidJobId(String) - Static method in class compbio.engine.client.Util