Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
Modifier and Type | Method and Description |
---|---|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createDelInitial(StrictAlignmentScoreAlgorithm.ScoreEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createInitial()
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createInsInitial(StrictAlignmentScoreAlgorithm.ScoreEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createNewEntry(StrictAlignmentScoreAlgorithm.ScoreEntry delOld,
StrictAlignmentScoreAlgorithm.ScoreEntry insOld,
StrictAlignmentScoreAlgorithm.ScoreEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
Modifier and Type | Method and Description |
---|---|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createDelInitial(StrictAlignmentScoreAlgorithm.ScoreEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createInsInitial(StrictAlignmentScoreAlgorithm.ScoreEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAlignmentScoreAlgorithm.createNewEntry(StrictAlignmentScoreAlgorithm.ScoreEntry delOld,
StrictAlignmentScoreAlgorithm.ScoreEntry insOld,
StrictAlignmentScoreAlgorithm.ScoreEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
Double |
StrictAlignmentScoreAlgorithm.transformToResult(StrictAlignmentScoreAlgorithm.ScoreEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
Copyright (C) 2013-2015 Benjamin Paaßen, Georg Zentgraf, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/