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## jprotein.tree.tools
Class SubstitutionMatrix

    java.lang.Object
      jprotein.tree.tools.SubstitutionMatrix

All Implemented Interfaces:
  java.io.Serializable

    public class SubstitutionMatrix

extends java.lang.Object
implements java.io.Serializable

See Also:
  Serialized Form

Constructor Summary
`SubstitutionMatrix(java.lang.String matrixFile)`

Method Summary
`double` | `getDistance(Residue res1, Residue res2)`
`double` | `getExpectedValue()`

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

Constructor Detail

### SubstitutionMatrix

    public SubstitutionMatrix(java.lang.String matrixFile)

Method Detail

### getDistance

    public double getDistance(Residue res1,
                              Residue res2)

### getExpectedValue

    public double getExpectedValue()

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