- taskDirectory - Variable in class compbio.engine.client.ConfExecutable
-
- taskId - Variable in class compbio.engine.client.RunConfiguration
-
Task ID (is a part of workDirectory but extracting it from there could be
tricky)
- taskId - Variable in class compbio.engine.Job
-
- Tcoffee - Class in compbio.runner.msa
-
- Tcoffee() - Constructor for class compbio.runner.msa.Tcoffee
-
- TCOFFEE_INFO - Static variable in enum compbio.ws.client.Services
-
- tcoffeeOptions - Static variable in class compbio.ws.server.TcoffeeWS
-
- tcoffeePresets - Static variable in class compbio.ws.server.TcoffeeWS
-
- TcoffeeWS - Class in compbio.ws.server
-
- TcoffeeWS() - Constructor for class compbio.ws.server.TcoffeeWS
-
- terminated() - Method in class compbio.engine.local.LocalExecutorService
-
- termSignal() - Method in class compbio.engine.cluster.drmaa.StatisticManager
-
- TestAllServices - Class in compbio.data.msa.jaxws
-
- TestAllServices() - Constructor for class compbio.data.msa.jaxws.TestAllServices
-
- testAllServices() - Method in interface compbio.data.msa.RegistryWS
-
Test all JABAWS services on the server
- testAllServices() - Method in class compbio.ws.server.RegistryWS
-
TODO improve reporting.
- TestAllServicesResponse - Class in compbio.data.msa.jaxws
-
- TestAllServicesResponse() - Constructor for class compbio.data.msa.jaxws.TestAllServicesResponse
-
- testDefaultAlignment(MsaWS<T>, Services) - Method in class compbio.ws.client.WSTester
-
Align using default settings
- testDefaultAnalyse(List<FastaSequence>, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Method in class compbio.ws.client.WSTester
-
- testKey - Static variable in class compbio.ws.client.Constraints
-
- testMetadata(Metadata<T>) - Method in class compbio.ws.client.WSTester
-
- testMsaWS(MsaWS<T>, Services) - Method in class compbio.ws.client.WSTester
-
- testSequenceAnnotationWS(SequenceAnnotation<T>, Services) - Method in class compbio.ws.client.WSTester
-
- TestService - Class in compbio.data.msa.jaxws
-
- TestService() - Constructor for class compbio.data.msa.jaxws.TestService
-
- testService(Services) - Method in interface compbio.data.msa.RegistryWS
-
Test a particular service
- testService(String[]) - Static method in class compbio.ws.client.CmdHelper
-
tests service
- testService(String, Services, PrintWriter) - Static method in class compbio.ws.client.Jws2Client
-
Asks registry to test the service on the host hostname
- testService(Services) - Method in class compbio.ws.server.RegistryWS
-
- TestServiceResponse - Class in compbio.data.msa.jaxws
-
- TestServiceResponse() - Constructor for class compbio.data.msa.jaxws.TestServiceResponse
-
- threadNumPropName - Static variable in class compbio.engine.local.LocalExecutorService
-
- timeOutInHours - Variable in class compbio.stat.collector.ExecutionStatCollector
-
Consider the job that has been working for longer than timeOutInHours
completed, whatever the outcome
- timeToTest() - Method in class compbio.ws.server.RegistryWS
-
- to - Variable in class compbio.data.sequence.Range
-
- toCommand(String) - Method in class compbio.engine.client.CommandBuilder.Parameter
-
- toCommand(String) - Method in class compbio.metadata.Option
-
Convert the option to the command string.
- toCommand(String) - Method in class compbio.metadata.Parameter
-
- toFastaSequence(String) - Static method in class compbio.data.sequence.FastaReader
-
- toList(float[]) - Method in class compbio.data.sequence.Score
-
- toString() - Method in class compbio.data.sequence.Alignment
-
- toString() - Method in class compbio.data.sequence.FastaSequence
-
Same as oneLineFasta
- toString() - Method in class compbio.data.sequence.Range
-
- toString() - Method in class compbio.data.sequence.RNAStructScoreManager
-
- toString() - Method in class compbio.data.sequence.Score
-
- toString() - Method in class compbio.engine.client.CommandBuilder.Parameter
-
- toString() - Method in class compbio.engine.client.CommandBuilder
-
- toString() - Method in class compbio.engine.client.ConfExecutable
-
- toString() - Method in class compbio.engine.client.RunConfiguration
-
- toString() - Method in class compbio.engine.client.SkeletalExecutable
-
- toString() - Method in class compbio.engine.cluster.drmaa.StatisticManager
-
- toString() - Method in class compbio.engine.FilePuller
-
- toString() - Method in class compbio.engine.Job
-
- toString() - Method in class compbio.metadata.ChunkHolder
-
- toString() - Method in class compbio.metadata.Limit
-
- toString() - Method in class compbio.metadata.LimitsManager
-
- toString() - Method in class compbio.metadata.Option
-
- toString() - Method in class compbio.metadata.Parameter
-
- toString() - Method in class compbio.metadata.Preset
-
- toString() - Method in class compbio.metadata.PresetManager
-
- toString() - Method in class compbio.metadata.RunnerConfig
-
- toString() - Method in class compbio.metadata.ValueConstrain
-
- toString() - Method in class compbio.stat.collector.JobStat
-
- toString() - Method in class compbio.stat.collector.StatProcessor
-
- toString() - Method in class compbio.stat.servlet.ServiceTestResult
-
- toString() - Method in class compbio.stat.servlet.util.StatCollection
-
- toString() - Method in class compbio.ws.client.Services.ServiceInfo
-
- toString(Set<Services>) - Static method in enum compbio.ws.client.Services
-
- total - Variable in class compbio.stat.servlet.util.Totals
-
- Totals - Class in compbio.stat.servlet.util
-
- Totals() - Constructor for class compbio.stat.servlet.util.Totals
-
- totalTime - Variable in class compbio.engine.local.LocalExecutorService
-
- TRACKER - Static variable in class compbio.ws.server.GAUtils
-
- TREE_FILE_EXT - Static variable in class compbio.runner.msa.ClustalW
-
- type - Variable in class compbio.engine.local.StreamGobbler
-
- type - Variable in class compbio.metadata.ValueConstrain
-
- Type() - Constructor for enum compbio.metadata.ValueConstrain.Type
-