Package org.biojava.nbio.core.alignment.matrices

Class DefaultAAIndexProvider

java.lang.Object

org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider

All Implemented Interfaces:

AAIndexProvider

public class DefaultAAIndexProvider
extends Object
implements AAIndexProvider

The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor	Description
DefaultAAIndexProvider()

Method Summary

Modifier and Type	Method	Description
InputStream	getInputStreamToAAindexFile()
SubstitutionMatrix<AminoAcidCompound>	getMatrix(String matrixName)	Gets a substitution matrix by its name.

Methods inherited from class java.lang.Object

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

Constructor Details

DefaultAAIndexProvider

public DefaultAAIndexProvider()

Method Details

getMatrix

public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName)

Description copied from interface: AAIndexProvider

Gets a substitution matrix by its name. The matrices are defined in src/main/resources/matrices/AAINDEX.txt

Specified by:

getMatrix in interface AAIndexProvider

Parameters:

matrixName -

Returns:

The @{code}SubstitutionMatrix or null if not exists

getInputStreamToAAindexFile

public InputStream getInputStreamToAAindexFile()