- centStructP - Static variable in class compbio.data.sequence.RNAStructReader
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- checkValue(String) - Method in class compbio.metadata.ValueConstrain
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Validate that the value is within the constrain boundaries
- chunk - Variable in class compbio.metadata.ChunkHolder
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- ChunkHolder - Class in compbio.metadata
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Represents a chunk of a string data together with the position in a file for
the next read operation.
- ChunkHolder() - Constructor for class compbio.metadata.ChunkHolder
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- ChunkHolder(String, long) - Constructor for class compbio.metadata.ChunkHolder
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- cleanProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
-
Remove all non AA chars from the sequence
- cleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
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Removes all whitespace chars in the sequence string
- close() - Method in class compbio.data.sequence.FastaReader
-
Call this method to close the connection to the input file if you want to
free up the resources.
- closeSilently(Logger, Closeable) - Static method in class compbio.data.sequence.SequenceUtil
-
Closes the Closable and logs the exception if any
- ClustalAlignmentUtil - Class in compbio.data.sequence
-
Tools to read and write clustal formated files
- ClustalAlignmentUtil() - Constructor for class compbio.data.sequence.ClustalAlignmentUtil
-
- compareTo(Range) - Method in class compbio.data.sequence.Range
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- compareTo(Score) - Method in class compbio.data.sequence.Score
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- compbio.data.sequence - package compbio.data.sequence
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A data model for multiple sequence alignment web services and utility methods
that work on the objects of this model.
- compbio.metadata - package compbio.metadata
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A meta-data model for multiple sequence alignment web services
Classes in this package have no dependencies to other sources in the project.
- ConservationMethod - Enum in compbio.data.sequence
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Enumeration listing of all the supported methods.
- ConservationMethod() - Constructor for enum compbio.data.sequence.ConservationMethod
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- containsValue(List<String>, String) - Method in class compbio.metadata.PresetManager
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- containValue(String) - Method in class compbio.metadata.Preset
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- convertToNumber(String[]) - Static method in class compbio.data.sequence.SequenceUtil
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- copyAndValidateRConfig(RunnerConfig<?>) - Method in class compbio.metadata.RunnerConfig
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- countMatchesInSequence(String, String) - Static method in class compbio.data.sequence.FastaSequence
-