org.forester.msa
Class Mafft

java.lang.Object
  org.forester.msa.Mafft

All Implemented Interfaces:

MsaInferrer

public final class Mafft
extends java.lang.Object
implements MsaInferrer

Method Summary

java.lang.Object	clone()
static MsaInferrer	createInstance()
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)
static boolean	isInstalled()

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createInstance

public static MsaInferrer createInstance()
                                  throws java.io.IOException

Throws:

java.io.IOException

createInstance

public static MsaInferrer createInstance(java.lang.String path_to_prg)
                                  throws java.io.IOException

Throws:

java.io.IOException

isInstalled

public static boolean isInstalled()

getDefaultParameters

public static java.lang.String getDefaultParameters()

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

getErrorDescription

public java.lang.String getErrorDescription()

Specified by:

getErrorDescription in interface MsaInferrer

getExitCode

public int getExitCode()

Specified by:

getExitCode in interface MsaInferrer

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 interface MsaInferrer

Throws:

java.io.IOException

java.lang.InterruptedException