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+Uses of Class
compbio.engine.client.CommandBuilder

+
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+Packages that use CommandBuilder
compbio.engine.client  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
+  +

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

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Methods in compbio.engine.client that return CommandBuilder
+ CommandBuilder<?>RunConfiguration.getParameters() + +
+           
+ CommandBuilder<T>ConfiguredExecutable.getParameters() + +
+           
+ CommandBuilder<T>ConfExecutable.getParameters() + +
+           
+ CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) + +
+           
+ CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) + +
+           
+ CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) + +
+           
+static + + + + +
+<T> CommandBuilder<T>
+		CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, + String nameValueSeparator) + +
+          This produces the same result as getCommands method.
+  +

+ + + + + + + + + +
Methods in compbio.engine.client with parameters of type CommandBuilder
+ voidRunConfiguration.setParameters(CommandBuilder<?> parameters) + +
+           
+  +

+ + + + + +
+Uses of CommandBuilder in compbio.runner
+  +

+ + + + + + + + + +
Methods in compbio.runner that return CommandBuilder
+ CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) + +
+          Deprecated.  
+  +

+ + + + + +
+Uses of CommandBuilder in compbio.runner._impl
+  +

+ + + + + + + + + +
Methods in compbio.runner._impl that return CommandBuilder
+ CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) + +
+           
+  +

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

+ + + + + + + + + +
Methods in compbio.runner.conservation that return CommandBuilder
+ CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) + +
+           
+  +

+ + + + + +
+Uses of CommandBuilder in compbio.runner.disorder
+  +

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Methods in compbio.runner.disorder that return CommandBuilder
+ CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) + +
+           
+  +

+ + + + + +
+Uses of CommandBuilder in compbio.runner.msa
+  +

+ + + + + + + + + + + + + +
Methods in compbio.runner.msa that return CommandBuilder
+ CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
+           
+ CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) + +
+           
+  +

+

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