+Uses of Class compbio.engine.client.SkeletalExecutable +

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+Uses of Class
compbio.engine.client.SkeletalExecutable

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+Packages that use SkeletalExecutable
compbio.engine.client
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)

+ +

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+Uses of SkeletalExecutable in compbio.engine.client
+ +

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Methods in compbio.engine.client that return SkeletalExecutable
+ SkeletalExecutable<T> SkeletalExecutable.setError(String errFile) + +
+
+ SkeletalExecutable<T> SkeletalExecutable.setInput(String inFile) + +
+
+ SkeletalExecutable<T> SkeletalExecutable.setOutput(String outFile) + +
+
+ +

Methods in compbio.engine.client that return SkeletalExecutable
+ `SkeletalExecutable<T>`	`SkeletalExecutable.setError(String errFile)` + + +
+ `SkeletalExecutable<T>`	`SkeletalExecutable.setInput(String inFile)` + + +
+ `SkeletalExecutable<T>`	`SkeletalExecutable.setOutput(String outFile)` + + +

+ + + + + +
+Uses of SkeletalExecutable in compbio.runner.conservation
+ +

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Subclasses of SkeletalExecutable in compbio.runner.conservation
+ class AACon + +
+ Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
+ +

Subclasses of SkeletalExecutable in compbio.runner.conservation
+ `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
+ +

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Subclasses of SkeletalExecutable in compbio.runner.disorder
+ 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
+ +

Subclasses of SkeletalExecutable in compbio.runner.disorder
+ `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
+ +

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Subclasses of SkeletalExecutable in compbio.runner.msa
+ class ClustalO + +
+
+ class ClustalW + +
+
+ class Mafft + +
+
+ class Muscle + +
+
+ class Probcons + +
+
+ class Tcoffee + +
+
+ +

Subclasses of SkeletalExecutable in compbio.runner.msa
+ `class`	`ClustalO` + + +
+ `class`	`ClustalW` + + +
+ `class`	`Mafft` + + +
+ `class`	`Muscle` + + +
+ `class`	`Probcons` + + +
+ `class`	`Tcoffee` + + +