Mafft

java.lang.Object

org.forester.msa.MsaInferrer

org.forester.msa.Mafft

public final class Mafft extends MsaInferrer

Method Summary

Modifier and Type

Method

Description

static MsaInferrer

createInstance(String path_to_prg)

static String

getDefaultParameters()

String

getErrorDescription()

int

getExitCode()

Msa

infer(File path_to_input_seqs, List<String> opts)

Msa

infer(List<MolecularSequence> seqs, List<String> opts)

Methods inherited from class org.forester.msa.MsaInferrer
clone, isInstalled

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details
- createInstance
  
  public static MsaInferrer createInstance(String path_to_prg) throws IOException
  
  Throws:
  
  IOException
- getDefaultParameters
  
  public static String getDefaultParameters()
- getErrorDescription
  
  public String getErrorDescription()
  
  Specified by:
  
  getErrorDescription in class MsaInferrer
- getExitCode
  
  public int getExitCode()
  
  Specified by:
  
  getExitCode in class MsaInferrer
- infer
  
  public Msa infer(List<MolecularSequence> seqs, List<String> opts) throws IOException, InterruptedException
  
  Specified by:
  
  infer in class MsaInferrer
  
  Throws:
  
  IOException
  
  InterruptedException
- infer
  
  public Msa infer(File path_to_input_seqs, List<String> opts) throws IOException, InterruptedException
  
  Specified by:
  
  infer in class MsaInferrer
  
  Throws:
  
  IOException
  
  InterruptedException