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java.lang.Objectorg.metaqtl.CMarkerSequence
public class CMarkerSequence
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 | |
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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 | |
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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 | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public int nmc
public int[][] mcidx
public boolean[] incms
public int ncs
public int[] css
public boolean[] frames
public int[][] idx1
public int[][] idx2
Constructor Detail |
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public CMarkerSequence(int[][] mcidx, int nmc)
mcidx[0..1][0..nmc-1]
. This assumes
that mcidx
has been obtained by using
one of the two orderd set as the reference.
mcidx
- the two arrays of common marker indices.nmc
- the number of common markers.Method Detail |
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public int[] getCSIdx(int i, int m1)
m1
- the indice of the marker.
public int[] getLeftCSMarker(int cs1, int m1x)
cs1
- m1x
-
public int[] getRightCSMarker(int cs2, int m2x)
cs2
- m2x
-
public int getMarkerIdx(int i, int cidx, int midx)
i
- cs1
- m1x
-
public boolean haveSameFrame(int cs1, int cs2)
cs1
- cs2
-
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