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A
AA
- Static variable in class compbio.data.sequence.
SequenceUtil
Valid Amino acids
AACon
- Class in
compbio.runner.conservation
Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
AACon()
- Constructor for class compbio.runner.conservation.
AACon
AACON_INFO
- Static variable in enum compbio.ws.client.
Services
AAConClient
- Class in
compbio.ws.client
A command line client for AACon web service
AAConWS
- Class in
compbio.ws.server
AAConWS()
- Constructor for class compbio.ws.server.
AAConWS
addOption(Option<T>)
- Method in class compbio.metadata.
RunnerConfig
Adds Option to the internal list of options
addOptionNames(String...)
- Method in class compbio.metadata.
Option
Adds an option to the optionName list
addOptionNames(String...)
- Method in class compbio.metadata.
Parameter
addParameter(Parameter<T>)
- Method in class compbio.metadata.
RunnerConfig
Adds parameter to the internal parameter list
addParameters(List<String>)
- Method in class compbio.engine.client.
ConfExecutable
addParameters(List<String>)
- Method in interface compbio.engine.client.
Executable
Adds parameter to the list of parameters for a native executable
addParameters(List<String>)
- Method in class compbio.engine.client.
SkeletalExecutable
addParameters(List<String>)
- Method in class compbio.runner.msa.
Mafft
Mafft input must always be the last parameter!
addParams(List<String>)
- Method in class compbio.engine.client.
CommandBuilder
addPossibleValues(String...)
- Method in class compbio.metadata.
Parameter
addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>)
- Static method in class compbio.engine.
SubmissionManager
Align
- Class in
compbio.data.msa.jaxws
Align()
- Constructor for class compbio.data.msa.jaxws.
Align
align(List<FastaSequence>)
- Method in interface compbio.data.msa.
MsaWS
Align a list of sequences with default settings.
align(List<FastaSequence>)
- Method in class compbio.ws.server.
ClustalOWS
align(List<FastaSequence>)
- Method in class compbio.ws.server.
ClustalWS
align(List<FastaSequence>)
- Method in class compbio.ws.server.
MafftWS
align(List<FastaSequence>)
- Method in class compbio.ws.server.
MuscleWS
align(List<FastaSequence>)
- Method in class compbio.ws.server.
ProbconsWS
align(List<FastaSequence>)
- Method in class compbio.ws.server.
TcoffeeWS
align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>)
- Static method in class compbio.ws.server.
WSUtil
Alignment
- Class in
compbio.data.sequence
Multiple sequence alignment.
Alignment(List<FastaSequence>, Program, char)
- Constructor for class compbio.data.sequence.
Alignment
Alignment(List<FastaSequence>, AlignmentMetadata)
- Constructor for class compbio.data.sequence.
Alignment
AlignmentMetadata
- Class in
compbio.data.sequence
Alignment metadata e.g.
AlignmentMetadata(Program, char)
- Constructor for class compbio.data.sequence.
AlignmentMetadata
AlignResponse
- Class in
compbio.data.msa.jaxws
AlignResponse()
- Constructor for class compbio.data.msa.jaxws.
AlignResponse
AMBIGUOUS_AA
- Static variable in class compbio.data.sequence.
SequenceUtil
Same as AA pattern but with two additional letters - XU
AMBIGUOUS_NUCLEOTIDE
- Static variable in class compbio.data.sequence.
SequenceUtil
Ambiguous nucleotide
Analize
- Class in
compbio.data.msa.jaxws
Analize()
- Constructor for class compbio.data.msa.jaxws.
Analize
analize(List<FastaSequence>)
- Method in interface compbio.data.msa.
SequenceAnnotation
Analyse the sequences.
analize(List<FastaSequence>)
- Method in class compbio.ws.server.
AAConWS
analize(List<FastaSequence>)
- Method in class compbio.ws.server.
SequenceAnnotationService
analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>)
- Static method in class compbio.ws.server.
WSUtil
AnalizeResponse
- Class in
compbio.data.msa.jaxws
AnalizeResponse()
- Constructor for class compbio.data.msa.jaxws.
AnalizeResponse
AnnualStat
- Class in
compbio.stat.servlet
AnnualStat()
- Constructor for class compbio.stat.servlet.
AnnualStat
Argument
<
T
> - Interface in
compbio.metadata
An unmodifiable view for the options and parameters, with one exception - it allows to set a value
argumentsToCommandString(List<? extends Option<?>>)
- Method in class compbio.runner.
OptionCombinator
argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>)
- Static method in class compbio.runner.
OptionCombinator
asMap()
- Method in class compbio.data.sequence.
ScoreManager
asSet()
- Method in class compbio.data.sequence.
ScoreManager
AsyncExecutor
- Interface in
compbio.engine
An asynchronous executor engine, capable of running, cancelling, obtaining results calculated by a native executable wrapper in Executable interface.
AsyncJobRunner
- Class in
compbio.engine.cluster.drmaa
Single cluster job runner class
AsyncJobRunner()
- Constructor for class compbio.engine.cluster.drmaa.
AsyncJobRunner
AsyncLocalRunner
- Class in
compbio.engine.local
AsyncLocalRunner()
- Constructor for class compbio.engine.local.
AsyncLocalRunner
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