Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ legacy overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

org.xmlcml.legacy
Class DynamicAligner  

java.lang.Object
  org.xmlcml.legacy.DynamicAligner

---

public class DynamicAligner

extends java.lang.Object

dynamic alignment of sequences (in the general sense) based on Kruskal's description - would be better in a different package

---

Field Summary
static int	BY_TYPE           penalty on basis of type (e.g.
(package private)  int	cont
static int	INDIVIDUAL           penalty on basis of score (e.g.
static int	LEFT
(package private)  int[]	len
(package private)  double[][]	matrix
(package private)  double[][]	penalties
(package private)  int[][]	pointers
(package private)  int[][]	seq
static int	UP
static int	UPLEFT

 

Constructor Summary

DynamicAligner()

DynamicAligner(int[][] seq, double[][] penalties)           create a DynamicAligner from a substitution matrix

DynamicAligner(java.lang.String s1, java.lang.String s2, double[][] penalties)

 

Method Summary
void	align(double gap)           this does the alignment; the gap penalty should be given
IntArray[]	extractAlignment()           get the two sequences as gapped arrays of integers (e.g.
(package private)  void	fillMatrices(double gap, int cont)
double	getDistance()           return the distance between the two sequences (i.e.
private static int[][]	getInts(java.lang.String s1, java.lang.String s2)
static void	main(java.lang.String[] args)
void	setPenalties(double[][] penalties)

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

UP

public static final int UP

See Also:

Constant Field Values

---

LEFT

public static final int LEFT

See Also:

Constant Field Values

---

UPLEFT

public static final int UPLEFT

See Also:

Constant Field Values

---

BY_TYPE

public static final int BY_TYPE

penalty on basis of type (e.g. letter or aminoacid)

See Also:

Constant Field Values

---

INDIVIDUAL

public static final int INDIVIDUAL

penalty on basis of score (e.g. string alignment)

See Also:

Constant Field Values

---

seq

int[][] seq

---

len

int[] len

---

penalties

double[][] penalties

---

pointers

int[][] pointers

---

matrix

double[][] matrix

---

cont

int cont

Constructor Detail

DynamicAligner

public DynamicAligner()

---

DynamicAligner

public DynamicAligner(int[][] seq,
                      double[][] penalties)
               throws NonSquareException,
                      java.lang.IllegalArgumentException

create a DynamicAligner from a substitution matrix

---

DynamicAligner

public DynamicAligner(java.lang.String s1,
                      java.lang.String s2,
                      double[][] penalties)
               throws java.lang.Exception

Method Detail

setPenalties

public void setPenalties(double[][] penalties)

---

getInts

private static int[][] getInts(java.lang.String s1,
                               java.lang.String s2)

---

align

public void align(double gap)

this does the alignment; the gap penalty should be given

---

fillMatrices

void fillMatrices(double gap,
                  int cont)

---

getDistance

public double getDistance()

return the distance between the two sequences (i.e. the sum of the PAM elements for each pair + the gaps)

---

extractAlignment

public IntArray[] extractAlignment()

get the two sequences as gapped arrays of integers (e.g. 0,1,2,3,-1,-1,4,-1,5) where the -1 represent gaps and the nonzero numers are serial numbers of the sequences

---

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ legacy overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---