charite.christo.interfaces
Interface SequenceAlignerSorting

All Superinterfaces:

SequenceAligner

All Known Implementing Classes:

ClustalW_3D, MultiFromPairAligner, MultipleAlignerAmap, MultipleAlignerClustalW, MultipleAlignerDialignT, MultipleAlignerKalign, MultipleAlignerMuscle, MultipleAlignerT_Coffee

public interface SequenceAlignerSorting
extends SequenceAligner

It can reorder proteins so that similar sequences are in adjacent lines.

Field Summary

Fields inherited from interface charite.christo.interfaces.SequenceAligner

OPTION_USE_SECONDARY_STRUCTURE

Method Summary

int[]

getIndicesOfSequences()

Methods inherited from interface charite.christo.interfaces.SequenceAligner

compute, getAlignedSequences, getMaxNumberOfSequences, getSequences, isLocal, setOptions, setSequences

Method Detail

getIndicesOfSequences

int[] getIndicesOfSequences()