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

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 - package compbio.data.msa

Web Service interfaces for JAva Bioinformatics Analysis Web Services.

compbio.data.sequence - package compbio.data.sequence

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

A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project.

compbio.ws.client - package compbio.ws.client

A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.

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(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.SequenceAnnotation

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