- id - Variable in class compbio.data.sequence.FastaSequence
-
Sequence id
- id - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
-
- identify(String) - Static method in class compbio.data.sequence.RNAStructReader
-
- identifyLine(String) - Static method in class compbio.data.sequence.RNAStructReader
-
- incomplete - Variable in class compbio.stat.servlet.util.Totals
-
- init() - Static method in class compbio.data.msa.Category
-
- init() - Method in class compbio.engine.FilePuller
-
- init() - Static method in class compbio.engine.local.LocalExecutorService
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.ClustalOWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.ClustalWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.GenericMetadataService
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.GLprobsWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.MafftWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.MSAprobsWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.MuscleWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.ProbconsWS
-
- init() - Method in class compbio.ws.server.RegistryWS
-
- init(List<FastaSequence>) - Method in class compbio.ws.server.TcoffeeWS
-
- initBooleanValue(String) - Static method in class compbio.engine.Configurator
-
- initClusterWorkDirectory() - Static method in class compbio.engine.Configurator
-
- initLocalDirectory() - Static method in class compbio.engine.Configurator
-
- initPull() - Method in class compbio.engine.FilePuller
-
- input - Variable in class compbio.data.sequence.FastaReader
-
- input - Variable in class compbio.engine.client.RunConfiguration
-
Input
- INPUT - Static variable in class compbio.engine.client.SkeletalExecutable
-
- inputFile - Variable in class compbio.engine.client.SkeletalExecutable
-
- InputFilter - Class in compbio.stat.collector
-
- InputFilter() - Constructor for class compbio.stat.collector.InputFilter
-
- inputkey - Static variable in class compbio.ws.client.Constraints
-
- inputSize - Variable in class compbio.stat.collector.JobStat
-
- insertData(Set<JobStat>) - Method in class compbio.stat.collector.StatDB
-
- INSTANCE - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
-
- INSTANCE - Static variable in class compbio.engine.local.LocalExecutorService
-
- io - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- IOHelper - Class in compbio.ws.client
-
- IOHelper() - Constructor for class compbio.ws.client.IOHelper
-
- iow - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- is - Variable in class compbio.engine.local.StreamGobbler
-
- IS_CLUSTER_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator
-
- IS_GA_ENABLED - Static variable in class compbio.ws.server.GAUtils
-
- IS_LOCAL_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator
-
- isAbsolutePath(String) - Static method in class compbio.engine.client.PathValidator
-
Whether a certain path is absolute or not is operation system dependent!
- isAdmin(HttpServletRequest) - Static method in class compbio.stat.servlet.AnnualStat
-
- isAmbiguosProtein(String) - Static method in class compbio.data.sequence.SequenceUtil
-
Check whether the sequence confirms to amboguous protein sequence
- isCancelled() - Method in class compbio.stat.collector.JobDirectory
-
- isCancelled - Variable in class compbio.stat.collector.JobStat
-
- isClusterJob() - Method in class compbio.stat.collector.JobStat
-
- isCollected() - Method in class compbio.stat.collector.JobDirectory
-
- isCollected - Variable in class compbio.stat.collector.JobStat
-
- isCombinedValue(String) - Method in class compbio.engine.client.CommandBuilder
-
- isComposite(String) - Method in class compbio.metadata.PresetManager
-
- isDefault - Variable in class compbio.metadata.Limit
-
- isDefault() - Method in class compbio.metadata.Limit
-
- isErrorSet - Variable in class compbio.engine.client.SkeletalExecutable
-
- isErrorSet() - Method in class compbio.engine.client.SkeletalExecutable
-
- isExceeded(List<FastaSequence>) - Method in class compbio.metadata.Limit
-
Checks if the number of sequences or their average length in the dataset
exceeds this limit.
- isFileCreated() - Method in class compbio.engine.FilePuller
-
- isFirst() - Method in class compbio.engine.client.CommandBuilder.Parameter
-
- isGoogleAnalyticsEnabled() - Static method in class compbio.ws.server.GAUtils
-
- isInputSet - Variable in class compbio.engine.client.SkeletalExecutable
-
- isInputSet() - Method in class compbio.engine.client.SkeletalExecutable
-
- isJavaLibrary(Class<?>) - Static method in class compbio.engine.client.EngineUtil
-
Returns true of executableName.jar.file property has some value in the
Executable.properties file, false otherwise.
- isJavaLibrary(Class<?>) - Static method in class compbio.engine.client.Util
-
Returns true of executableName.jar.file property has some value in the
Executable.properties file, false otherwise.
- isLast() - Method in class compbio.engine.client.CommandBuilder.Parameter
-
- isLocal(String) - Static method in class compbio.engine.Configurator
-
- isMarked(String, JobStatus) - Static method in class compbio.engine.client.EngineUtil
-
- isMarked(String, JobStatus) - Static method in class compbio.engine.client.Util
-
- isNonAmbNucleotideSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
-
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
(!) - B char
- isNucleotideSequence(FastaSequence) - Static method in class compbio.data.sequence.SequenceUtil
-
- isNumeric(String) - Method in class compbio.metadata.PresetManager
-
- IsOperating - Class in compbio.data.msa.jaxws
-
- IsOperating() - Constructor for class compbio.data.msa.jaxws.IsOperating
-
- isOperating(Services) - Method in interface compbio.data.msa.RegistryWS
-
Check whether a particular web service is working on this server
- isOperating(Services) - Method in class compbio.ws.server.RegistryWS
-
- IsOperatingResponse - Class in compbio.data.msa.jaxws
-
- IsOperatingResponse() - Constructor for class compbio.data.msa.jaxws.IsOperatingResponse
-
- isOutputSet - Variable in class compbio.engine.client.SkeletalExecutable
-
- isOutputSet() - Method in class compbio.engine.client.SkeletalExecutable
-
- isParameter(String) - Static method in class compbio.ws.client.MetadataHelper
-
- isProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
-
- isRequired - Variable in class compbio.metadata.Option
-
- isRequired() - Method in class compbio.metadata.Option
-
Flag that indicated that this option must be specified in the command
line for an executable to run
- isReturn() - Method in class compbio.data.msa.jaxws.CancelJobResponse
-
- isReturn() - Method in class compbio.data.msa.jaxws.IsOperatingResponse
-
- isTargetedForLocalExecution(ConfiguredExecutable<?>) - Static method in class compbio.engine.Configurator
-
- isValidClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
-
Please note this method closes the input stream provided as a parameter
- isValidDirectory(String) - Static method in class compbio.engine.client.PathValidator
-
- isValidEnvVariableProperty(String) - Static method in class compbio.engine.client.EnvVariableProcessor
-
- isValidExecutable(String) - Static method in class compbio.engine.client.PathValidator
-
- isValidJobId(String) - Static method in class compbio.engine.client.EngineUtil
-
- isValidJobId(String) - Static method in class compbio.engine.client.Util
-
- isValidValue(String) - Method in class compbio.metadata.Parameter
-
- isWhiteSpaceSeparator() - Method in class compbio.engine.client.CommandBuilder
-
- IUPred - Class in compbio.runner.disorder
-
iupred sequenceFile
Maximum sequence length is 40000 chars.
- IUPred() - Constructor for class compbio.runner.disorder.IUPred
-
- IUPRED_INFO - Static variable in enum compbio.ws.client.Services
-
- iupred_path - Static variable in class compbio.engine.client.EnvVariableProcessor
-
- IUPredResult - Enum in compbio.data.sequence
-
- IUPredResult() - Constructor for enum compbio.data.sequence.IUPredResult
-
- IUPredWS - Class in compbio.ws.server
-
- IUPredWS() - Constructor for class compbio.ws.server.IUPredWS
-