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

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

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

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 - package compbio.data.msa

Web Service interfaces for JAva Bioinformatics Analysis Web Services.

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