Package org.forester.msa
Class Mafft
- java.lang.Object
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- org.forester.msa.MsaInferrer
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- org.forester.msa.Mafft
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public final class Mafft extends MsaInferrer
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static MsaInferrer
createInstance(java.lang.String path_to_prg)
static java.lang.String
getDefaultParameters()
java.lang.String
getErrorDescription()
int
getExitCode()
Msa
infer(java.io.File path_to_input_seqs, java.util.List<java.lang.String> opts)
Msa
infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
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Methods inherited from class org.forester.msa.MsaInferrer
clone, isInstalled
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Method Detail
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createInstance
public static MsaInferrer createInstance(java.lang.String path_to_prg) throws java.io.IOException
- Throws:
java.io.IOException
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getDefaultParameters
public static java.lang.String getDefaultParameters()
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getErrorDescription
public java.lang.String getErrorDescription()
- Specified by:
getErrorDescription
in classMsaInferrer
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getExitCode
public int getExitCode()
- Specified by:
getExitCode
in classMsaInferrer
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infer
public Msa infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts) throws java.io.IOException, java.lang.InterruptedException
- Specified by:
infer
in classMsaInferrer
- Throws:
java.io.IOException
java.lang.InterruptedException
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infer
public Msa infer(java.io.File path_to_input_seqs, java.util.List<java.lang.String> opts) throws java.io.IOException, java.lang.InterruptedException
- Specified by:
infer
in classMsaInferrer
- Throws:
java.io.IOException
java.lang.InterruptedException
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