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

C

cancelJob(String) - Method in interface compbio.data.msa.JManagement

Stop running the job jobId but leave its output untouched

ChunkHolder - Class in compbio.metadata

Represents a chunk of a string data together with the position in a file for the next read operation.

ChunkHolder(String, long) - Constructor for class compbio.metadata.ChunkHolder

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

Removes all whitespace chars in the sequence string

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

compbio.data.msa - package compbio.data.msa

Web Service interfaces for JAva Bioinformatics Analysis Web Services.

connect(String, Services) - Static method in class compbio.ws.client.Jws2Client

Connects to a web service by the host and the service name

copyAndValidateRConfig(RunnerConfig<?>) - Method in class compbio.metadata.RunnerConfig

countMatchesInSequence(String, String) - Static method in class compbio.data.sequence.FastaSequence

customAlign(List<FastaSequence>, List<Option<T>>) - Method in interface compbio.data.msa.MsaWS

Align a list of sequences with options.

customAnalize(List<FastaSequence>, List<Option<T>>) - Method in interface compbio.data.msa.Annotation

Analyse the sequences according to custom settings defined in options list.