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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
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