Uses of Class
compbio.engine.client.SkeletalExecutable

Packages that use SkeletalExecutable

Package	Description
compbio.engine.client
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.runner.structure
compbio.ws.server

Uses of SkeletalExecutable in compbio.engine.client

Methods in compbio.engine.client that return SkeletalExecutable

Modifier and Type	Method and Description
SkeletalExecutable<T>	SkeletalExecutable.setError(java.lang.String errFile)
SkeletalExecutable<T>	SkeletalExecutable.setInput(java.lang.String inFile)
SkeletalExecutable<T>	SkeletalExecutable.setOutput(java.lang.String outFile)

Uses of SkeletalExecutable in compbio.runner.conservation

Subclasses of SkeletalExecutable in compbio.runner.conservation

Modifier and Type	Class and Description
class	AACon Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out

Uses of SkeletalExecutable in compbio.runner.disorder

Subclasses of SkeletalExecutable in compbio.runner.disorder

Modifier and Type	Class and Description
class	Disembl DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' This version of DisEMBL is 1.4 (latest available for download in Feb 2011) capable of outputting raw values The values of the parameters are hard coded in DisEMBL.py script.
class	GlobPlot ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' Hard-coded values are 10 15 74 4 5.
class	IUPred iupred sequenceFile Maximum sequence length is 40000 chars.
class	Jronn Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out

Uses of SkeletalExecutable in compbio.runner.msa

Subclasses of SkeletalExecutable in compbio.runner.msa

Modifier and Type	Class and Description
class	ClustalO
class	ClustalW
class	GLprobs
class	Mafft
class	MSAprobs
class	Muscle
class	Probcons
class	Tcoffee

Uses of SkeletalExecutable in compbio.runner.structure

Subclasses of SkeletalExecutable in compbio.runner.structure

Modifier and Type	Class and Description
class	RNAalifold

Uses of SkeletalExecutable in compbio.ws.server

Fields in compbio.ws.server declared as SkeletalExecutable

Modifier and Type	Field and Description
private SkeletalExecutable<T>	GenericMetadataService.exec

Constructors in compbio.ws.server with parameters of type SkeletalExecutable

Constructor and Description
GenericMetadataService(SkeletalExecutable<T> exec, org.apache.log4j.Logger log)
SequenceAnnotationService(SkeletalExecutable<T> exec, org.apache.log4j.Logger log)