charite.christo.protein
Interface SequenceAlignerSorting

All Superinterfaces:

SequenceAligner

All Known Implementing Classes:

Aligner3D, MultiFromPairAligner, MultipleAlignerAmap, MultipleAlignerClustalW, MultipleAlignerKalign, MultipleAlignerMafft, MultipleAlignerMuscle, MultipleAlignerProbcons2, 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.protein.SequenceAligner

OPTION_CHECK_PERFECT_MATCH, OPTION_NOT_TO_SECURITY_LIST, OPTION_USE_SECONDARY_STRUCTURE, PROPERTY_LOCAL_ALIGNMENT, PROPERTY_ONLY_TWO_SEQUENCES, SCORE_FOR_PERFECT_MATCH

Method Summary

int[]

getIndicesOfSequences()

Methods inherited from interface charite.christo.protein.SequenceAligner

compute, getAlignedSequences, getOptions, getPropertyFlags, getSequences, setOptions, setSequences

Method Detail

getIndicesOfSequences

int[] getIndicesOfSequences()