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R

readAAConResults(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
Read AACon result with no alignment files.
readClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
Read Clustal formatted alignment.
readClustalFile(File) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
 
readFasta(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
Reads fasta sequences from inStream into the list of FastaSequence objects
readJRonn(File) - Static method in class compbio.data.sequence.SequenceUtil
 
readJRonn(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
Reader for JRonn horizontal file format
removeArgument(String) - Method in class compbio.metadata.RunnerConfig
Removes the argument Argument if found.
removeArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
Removes the argument which can be a Parameter or an Option instance by the value in element of the runner configuration descriptor.
ResultNotAvailableException - Exception in compbio.metadata
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.
ResultNotAvailableException(String) - Constructor for exception compbio.metadata.ResultNotAvailableException
 
ResultNotAvailableException(Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
 
ResultNotAvailableException(String, Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
 
RunnerConfig<T> - Class in compbio.metadata
The list of Parameters and Options supported by executable.
RunnerConfig() - Constructor for class compbio.metadata.RunnerConfig
 

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