- id - Variable in class compbio.data.sequence.FastaSequence
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Sequence id
- id - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
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- identify(String) - Static method in class compbio.data.sequence.RNAStructReader
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- identifyLine(String) - Static method in class compbio.data.sequence.RNAStructReader
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- input - Variable in class compbio.data.sequence.FastaReader
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- isAmbiguosProtein(String) - Static method in class compbio.data.sequence.SequenceUtil
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Check whether the sequence confirms to amboguous protein sequence
- isComposite(String) - Method in class compbio.metadata.PresetManager
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- isDefault - Variable in class compbio.metadata.Limit
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- isDefault() - Method in class compbio.metadata.Limit
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- isExceeded(List<FastaSequence>) - Method in class compbio.metadata.Limit
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Checks if the number of sequences or their average length in the dataset
exceeds this limit.
- isNonAmbNucleotideSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
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Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
(!) - B char
- isNucleotideSequence(FastaSequence) - Static method in class compbio.data.sequence.SequenceUtil
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- isNumeric(String) - Method in class compbio.metadata.PresetManager
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- isProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
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- isRequired - Variable in class compbio.metadata.Option
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- isRequired() - Method in class compbio.metadata.Option
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Flag that indicated that this option must be specified in the command
line for an executable to run
- isValidClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
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Please note this method closes the input stream provided as a parameter
- isValidValue(String) - Method in class compbio.metadata.Parameter
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- IUPredResult - Enum in compbio.data.sequence
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- IUPredResult() - Constructor for enum compbio.data.sequence.IUPredResult
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