org.metaqtl
Class CMarkerSequence

java.lang.Object
  org.metaqtl.CMarkerSequence

public class CMarkerSequence
extends java.lang.Object

A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse). For example : Set 1 : {a,b,c,d,e} Set 2 : {a,b,e,d,c} Then this two sets have two common sequences {a,b} and {d,e}. Hereafter the term 'Common Marker Sequence' is used as well as for a single commom sequence than for the set of common sequences for a same comparison between two ordered sets.

Field Summary

int[]	css The sizes of the common sequences
boolean[]	frames The frame of the common marker sequences
int[][]	idx1 The indices of the markers on the first chromosome for the common sequences.
int[][]	idx2 The indices of the marker on the second chromosome for the common sequences.
boolean[]	incms
int[][]	mcidx The common marker indices on the chromosomes.
int	ncs The number of common sequences.
int	nmc The number of common marker between chromosomes

Constructor Summary

CMarkerSequence(int[][] mcidx, int nmc)
Initiates a new Common marker sequence from the tow arrays of common marker indices mcidx[0..1][0..nmc-1].

Method Summary

int[]	getCSIdx(int i, int m1)
int[]	getLeftCSMarker(int cs1, int m1x) Returns the indices of the marker at the left of the given one.
int	getMarkerIdx(int i, int cidx, int midx)
int[]	getRightCSMarker(int cs2, int m2x)
boolean	haveSameFrame(int cs1, int cs2)

Methods inherited from class java.lang.Object

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

Field Detail

nmc

public int nmc

The number of common marker between chromosomes

mcidx

public int[][] mcidx

The common marker indices on the chromosomes.

incms

public boolean[] incms

ncs

public int ncs

The number of common sequences.

css

public int[] css

The sizes of the common sequences

frames

public boolean[] frames

The frame of the common marker sequences

idx1

public int[][] idx1

The indices of the markers on the first chromosome for the common sequences.

idx2

public int[][] idx2

The indices of the marker on the second chromosome for the common sequences.

Constructor Detail

CMarkerSequence

public CMarkerSequence(int[][] mcidx,
                       int nmc)

Initiates a new Common marker sequence from the tow arrays of common marker indices mcidx[0..1][0..nmc-1]. This assumes that mcidx has been obtained by using one of the two orderd set as the reference.

Parameters:

mcidx - the two arrays of common marker indices.

nmc - the number of common markers.

Method Detail

getCSIdx

public int[] getCSIdx(int i,
                      int m1)

Parameters:

m1 - the indice of the marker.

Returns:

the indices of both the common sequence which contains the marker and the indice of the marker inside the sequence.

getLeftCSMarker

public int[] getLeftCSMarker(int cs1,
                             int m1x)

Returns the indices of the marker at the left of the given one.

Parameters:

cs1 -

m1x -

Returns:

getRightCSMarker

public int[] getRightCSMarker(int cs2,
                              int m2x)

Parameters:

cs2 -

m2x -

Returns:

getMarkerIdx

public int getMarkerIdx(int i,
                        int cidx,
                        int midx)

Parameters:

i -

cs1 -

m1x -

Returns:

haveSameFrame

public boolean haveSameFrame(int cs1,
                             int cs2)

Parameters:

cs1 -

cs2 -