- AA - Static variable in class compbio.data.sequence.SequenceUtil
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Valid Amino acids
- AACon - Class in compbio.runner.conservation
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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
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- AACON_INFO - Static variable in enum compbio.ws.client.Services
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- AAConClient - Class in compbio.ws.client
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A command line client for AACon web service
- AAConClient(String[]) - Constructor for class compbio.ws.client.AAConClient
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Connects to the service and do the job as requested, if something goes
wrong reports or/and prints usage help.
- aaconOptions - Variable in class compbio.ws.server.GenericMetadataService
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- aaconPresets - Variable in class compbio.ws.server.GenericMetadataService
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- AAConWS - Class in compbio.ws.server
-
- AAConWS() - Constructor for class compbio.ws.server.AAConWS
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- abandoned - Variable in class compbio.stat.servlet.util.Totals
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- accept(File) - Static method in class compbio.stat.collector.InputFilter
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Accepts input as valid unless it is a test input
- acct_cpu - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- acct_io - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- acct_iow - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- acct_maxvmem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- acct_mem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- actualNumberofSequences - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
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- actualNumberofSequences - Variable in exception compbio.metadata.LimitExceededException
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- addJob(String, ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.ClusterSession
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- addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig
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Adds Option to the internal list of options
- addOptionNames(String...) - Method in class compbio.metadata.Option
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Adds an option to the optionName list
- addOptionNames(String...) - Method in class compbio.metadata.Parameter
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- 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
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- addParameters(List<String>) - Method in interface compbio.engine.client.Executable
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Adds parameter to the list of parameters for a native executable
- addParameters(List<String>) - Method in class compbio.engine.client.SkeletalExecutable
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- addParameters(List<String>) - Method in class compbio.runner.msa.Mafft
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Mafft input must always be the last parameter!
- addParams(List<String>) - Method in class compbio.engine.client.CommandBuilder
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- addPossibleValues(String...) - Method in class compbio.metadata.Parameter
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- addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - Static method in class compbio.engine.SubmissionManager
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- afterExecute(Runnable, Throwable) - Method in class compbio.engine.local.LocalExecutorService
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- AlifoldLine(String) - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldLine
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- AlifoldResult() - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldResult
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- Align - Class in compbio.data.msa.jaxws
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- Align() - Constructor for class compbio.data.msa.jaxws.Align
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- align(List<FastaSequence>) - Method in interface compbio.data.msa.MsaWS
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Align a list of sequences with default settings.
- align(File, MsaWS<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
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Align sequences from the file using MsaWS
- align(List<FastaSequence>) - Method in class compbio.ws.server.ClustalOWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.ClustalWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.GLprobsWS
-
- align(List<FastaSequence>) - Method in class compbio.ws.server.MafftWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.MSAprobsWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.MuscleWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.ProbconsWS
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- align(List<FastaSequence>) - Method in class compbio.ws.server.TcoffeeWS
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- align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - Static method in class compbio.ws.server.WSUtil
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- alignment - Variable in class compbio.data.msa.jaxws.CustomFold
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- alignment - Variable in class compbio.data.msa.jaxws.Fold
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- alignment - Variable in class compbio.data.msa.jaxws.PresetFold
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- Alignment - Class in compbio.data.sequence
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Multiple sequence alignment.
- Alignment() - Constructor for class compbio.data.sequence.Alignment
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- Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment
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- Alignment(List<FastaSequence>, AlignmentMetadata) - Constructor for class compbio.data.sequence.Alignment
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- AlignmentMetadata - Class in compbio.data.sequence
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Alignment metadata e.g.
- AlignmentMetadata() - Constructor for class compbio.data.sequence.AlignmentMetadata
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- AlignmentMetadata(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata
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- alignmentP - Static variable in class compbio.data.sequence.RNAStructReader
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- AlignResponse - Class in compbio.data.msa.jaxws
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- AlignResponse() - Constructor for class compbio.data.msa.jaxws.AlignResponse
-
- allStat - Variable in class compbio.stat.servlet.util.StatCollection
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- allTested - Static variable in class compbio.ws.server.RegistryWS
-
Indicate whether the services were tested at all
- AMBIGUOUS_AA - Static variable in class compbio.data.sequence.SequenceUtil
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Same as AA pattern but with two additional letters - XU
- AMBIGUOUS_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
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Ambiguous nucleotide
- Analize - Class in compbio.data.msa.jaxws
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- Analize() - Constructor for class compbio.data.msa.jaxws.Analize
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- analize(List<FastaSequence>) - Method in interface compbio.data.msa.SequenceAnnotation
-
Analyse the sequences.
- analize(File, SequenceAnnotation<AAConWS>, Preset<AAConWS>, List<Option<AAConWS>>) - Static method in class compbio.ws.client.AAConClient
-
Calculate conservation for sequences loaded from the file
- analize(List<FastaSequence>, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
-
Calculate conservation for sequences loaded from a FASTA record list structure
- analize(File, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
-
Calculate conservation for sequences loaded from the file
- analize(List<FastaSequence>) - Method in class compbio.ws.server.AAConWS
-
- analize(List<FastaSequence>) - Method in class compbio.ws.server.RNAalifoldWS
-
- 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
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- AnalizeResponse() - Constructor for class compbio.data.msa.jaxws.AnalizeResponse
-
- ANNOTATION - Static variable in class compbio.runner.msa.GLprobs
-
- ANNOTATION - Static variable in class compbio.runner.msa.MSAprobs
-
- ANNOTATION - Static variable in class compbio.runner.msa.Probcons
-
- AnnualStat - Class in compbio.stat.servlet
-
- AnnualStat() - Constructor for class compbio.stat.servlet.AnnualStat
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- anonymizeIP() - Static method in class compbio.ws.server.GAUtils
-
- arg0 - Variable in class compbio.data.msa.jaxws.GetLastTested
-
- arg0 - Variable in class compbio.data.msa.jaxws.GetLastTestedOn
-
- arg0 - Variable in class compbio.data.msa.jaxws.GetServiceDescription
-
- arg0 - Variable in class compbio.data.msa.jaxws.IsOperating
-
- arg0 - Variable in class compbio.data.msa.jaxws.TestService
-
- Argument<T> - Interface in compbio.metadata
-
An unmodifiable view for the options and parameters, with one exception - it
allows to set a value
- arguments - Variable in class compbio.metadata.RunnerConfig
-
- argumentsToCommandString(List<? extends Option<?>>) - Method in class compbio.runner.OptionCombinator
-
- argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - Static method in class compbio.runner.OptionCombinator
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- aSequenceLenghtActual - Variable in exception compbio.metadata.LimitExceededException
-
- aSequenceLenghtAllowed - Variable in exception compbio.metadata.LimitExceededException
-
- asMap() - Method in class compbio.data.sequence.ScoreManager
-
- asSet() - Method in class compbio.data.sequence.ScoreManager
-
- AsyncClusterRunner - Class in compbio.engine.cluster.drmaa
-
Single cluster job runner class
- AsyncClusterRunner() - Constructor for class compbio.engine.cluster.drmaa.AsyncClusterRunner
-
- 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
-
- autoOption - Static variable in class compbio.runner.msa.Mafft
-