org.strbio.mol.lib
Interface AlignmentDependent

All Known Implementing Classes:
ScoreUFSippl90

public interface AlignmentDependent

Interface for scoring functions that are dependent on the rest of the alignment. These cannot be used in Needleman-Wunsch scoring schemes.

Version:
1.0, 1/11/00
Author:
JMC
See Also:
ScoreList, ScoreFunction, ScoreSetup

Method Summary
 void setAlignment(Alignment al)
          This function is called to provide the alignment.
 

Method Detail

setAlignment

void setAlignment(Alignment al)
This function is called to provide the alignment. Calls to the scoring function are evaluated on the basis of this alignment.