+C-Index +

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+C

CancelJob - Class in compbio.data.msa.jaxws
CancelJob() - +Constructor for class compbio.data.msa.jaxws.CancelJob +: +
cancelJob(String) - +Method in interface compbio.data.msa.JManagement +: Stop running the job jobId but leave its output untouched +
CancelJobResponse - Class in compbio.data.msa.jaxws
CancelJobResponse() - +Constructor for class compbio.data.msa.jaxws.CancelJobResponse +: +
Category - Class in compbio.data.msa: Class that splits Services to categories.
CATEGORY_ALIGNMENT - +Static variable in class compbio.data.msa.Category +: All of the Category names +
CATEGORY_CONSERVATION - +Static variable in class compbio.data.msa.Category +: +
CATEGORY_DISORDER - +Static variable in class compbio.data.msa.Category +: +
checkService(Services) - +Method in class compbio.ws.client.WSTester +: Test JABA web service +
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 +: +
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 +: 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 +
CLUSTAL_INFO - +Static variable in enum compbio.ws.client.Services +: +
CLUSTAL_OMEGA_INFO - +Static variable in enum compbio.ws.client.Services +: +
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 +: +
compareTo(Score) - +Method in class compbio.data.sequence.Score +: +
compbio.data.msa.jaxws - package compbio.data.msa.jaxws
connect() - +Static method in class compbio.ws.client.AAConClient +: Connects to a AACon web service by the host and the service name +
connect(String, Services) - +Static method in class compbio.ws.client.Jws2Client +: Connects to a web service by the host and the service name web service + type +
connectToRegistry(String) - +Static method in class compbio.ws.client.Jws2Client +: Get a connection of JABAWS registry +
ConservationMethod - Enum in compbio.data.sequence: Enumeration listing of all the supported methods.
copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +: +
countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +: +
CustomAlign - Class in compbio.data.msa.jaxws
CustomAlign() - +Constructor for class compbio.data.msa.jaxws.CustomAlign +: +
customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +: Align a list of sequences with options. +
CustomAlignResponse - Class in compbio.data.msa.jaxws
CustomAlignResponse() - +Constructor for class compbio.data.msa.jaxws.CustomAlignResponse +: +
CustomAnalize - Class in compbio.data.msa.jaxws
CustomAnalize() - +Constructor for class compbio.data.msa.jaxws.CustomAnalize +: +
customAnalize(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.SequenceAnnotation +: Analyse the sequences according to custom settings defined in options + list. +
CustomAnalizeResponse - Class in compbio.data.msa.jaxws
CustomAnalizeResponse() - +Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse +: +