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gapchar
- Static variable in class compbio.data.sequence.
ClustalAlignmentUtil
Dash char to be used as gap char in the alignments
getActualNumberofSequences()
- Method in exception compbio.metadata.
LimitExceededException
getArgument(String)
- Method in class compbio.metadata.
RunnerConfig
Returns the argument by its name if found, NULL otherwise
getArgumentByOptionName(String)
- Method in class compbio.metadata.
RunnerConfig
Returns the argument by option name, NULL if the argument is not found
getArguments(RunnerConfig<T>)
- Method in class compbio.metadata.
Preset
Converts list of options as String to type Option
getArguments()
- Method in class compbio.metadata.
RunnerConfig
getAvgSeqLength()
- Method in class compbio.metadata.
Limit
getAvgSequenceLength(List<FastaSequence>)
- Static method in class compbio.metadata.
Limit
Calculates an average sequence length of the dataset
getChunk()
- Method in class compbio.metadata.
ChunkHolder
getDefaultLimit()
- Method in class compbio.metadata.
LimitsManager
getDefaultValue()
- Method in interface compbio.metadata.
Argument
getDefaultValue()
- Method in class compbio.metadata.
Option
A default value of the option.
getDescription()
- Method in interface compbio.metadata.
Argument
getDescription()
- Method in class compbio.metadata.
Option
A long description of the Option
getDescription()
- Method in class compbio.metadata.
Preset
getFormatedSequence(int)
- Method in class compbio.data.sequence.
FastaSequence
Format sequence per width letter in one string.
getFormattedFasta()
- Method in class compbio.data.sequence.
FastaSequence
getFurtherDetails()
- Method in interface compbio.metadata.
Argument
getFurtherDetails()
- Method in class compbio.metadata.
Option
The URL where further details about the option can be found
getGapchar()
- Method in class compbio.data.sequence.
AlignmentMetadata
getHost(String[])
- Static method in class compbio.ws.client.
Jws2Client
Extracts host name from the command line
getId()
- Method in class compbio.data.sequence.
FastaSequence
Gets the value of id
getLength()
- Method in class compbio.data.sequence.
FastaSequence
getLimitByName(String)
- Method in class compbio.metadata.
LimitsManager
getLimits()
- Method in class compbio.metadata.
LimitsManager
getMax()
- Method in class compbio.metadata.
ValueConstrain
getMetadata()
- Method in class compbio.data.sequence.
Alignment
getMin()
- Method in class compbio.metadata.
ValueConstrain
getName()
- Method in interface compbio.metadata.
Argument
getName()
- Method in class compbio.metadata.
Option
Human readable name of the option
getName()
- Method in class compbio.metadata.
Preset
getNextPosition()
- Method in class compbio.metadata.
ChunkHolder
getNumberOfSequencesAllowed()
- Method in exception compbio.metadata.
LimitExceededException
getOnelineFasta()
- Method in class compbio.data.sequence.
FastaSequence
getOptionName()
- Method in class compbio.metadata.
Parameter
getOptionNames()
- Method in class compbio.metadata.
Option
getOptions()
- Method in class compbio.metadata.
Preset
getOptions()
- Method in class compbio.metadata.
RunnerConfig
getParameters()
- Method in class compbio.metadata.
RunnerConfig
getPossibleValues()
- Method in interface compbio.metadata.
Argument
getPossibleValues()
- Method in class compbio.metadata.
Option
List of possible optionNames
getPossibleValues()
- Method in class compbio.metadata.
Parameter
List is more convenient to work with
getPreset()
- Method in class compbio.metadata.
Limit
getPresetByName(String)
- Method in class compbio.metadata.
PresetManager
getPresets()
- Method in class compbio.metadata.
PresetManager
getPrmSeparator()
- Method in class compbio.metadata.
RunnerConfig
getProgram()
- Method in class compbio.data.sequence.
AlignmentMetadata
getRunnerClassName()
- Method in class compbio.metadata.
PresetManager
getRunnerClassName()
- Method in class compbio.metadata.
RunnerConfig
getSeqNumber()
- Method in class compbio.metadata.
Limit
getSequence()
- Method in class compbio.data.sequence.
FastaSequence
Gets the value of sequence
getSequenceLenghtActual()
- Method in exception compbio.metadata.
LimitExceededException
getSequenceLenghtAllowed()
- Method in exception compbio.metadata.
LimitExceededException
getSequences()
- Method in class compbio.data.sequence.
Alignment
getServiceName(String[])
- Static method in class compbio.ws.client.
Jws2Client
Extracts service name from the command line
getSize()
- Method in class compbio.data.sequence.
Alignment
getType()
- Method in class compbio.metadata.
ValueConstrain
getValidValue()
- Method in class compbio.metadata.
Parameter
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