|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectbaobab.bio.permutation.SignedPermutationBPGraph
baobab.bio.permutation.WeightedSignedPermutationBPGraph
public class WeightedSignedPermutationBPGraph
The WeightedSignedPermutationBPGraph class represents a weighted signed permutation pair and its breakpoint graph (the WeightedSignedPermutationBPGraph class does not deal with hurdles)
Constructor Summary | |
---|---|
WeightedSignedPermutationBPGraph(int[] permutationList,
boolean isLinear,
double[] weights)
Creates a new permutation (assumes the identity permutation as target) |
|
WeightedSignedPermutationBPGraph(int[] permutationList,
double[] weights)
Creates a new linear permutation (assumes the identity permutation as target) |
|
WeightedSignedPermutationBPGraph(int[] originList,
int[] targetList,
boolean isLinear,
double[] originWeights)
Creates a new permutation |
|
WeightedSignedPermutationBPGraph(int[] originList,
int[] targetList,
double[] originWeights)
Creates a new linear permutation |
|
WeightedSignedPermutationBPGraph(java.util.Vector<java.lang.String> origin,
java.util.Vector<java.lang.String> target,
boolean isLinear,
java.util.Vector<java.lang.Double> originWeights)
Creates a new permutation |
Method Summary | |
---|---|
static java.util.Vector<int[]> |
blocksToIntArrays(java.util.Collection blocks)
Transforms the collection of blocks to a collection of arrays of int (with length = 2) |
int |
compareTo(java.lang.Object object)
Compares this block to another block |
double |
getAverageWeightOfInterval(int startPos,
int endPos)
Gets the average weight of an interval of the permutation |
java.util.TreeSet<BPGraphPoint> |
getBreakpoints()
Gets the breakpoint list of this block |
BPGraphCycle |
getCycle(int number)
Gets the list of cycles of this group of cycles |
java.util.SortedSet<BPGraphCycle> |
getCycles()
Gets the list of cycles of this group of cycles |
int |
getNumberOfBreakpoints()
Gets the number of breakpoints |
int |
getNumberOfCycles()
Gets the number of cycles of this group of cycles |
java.util.SortedSet |
getOrientedCycles()
Gets the list of oriented cycles of this group of cycles |
java.util.SortedSet<BPGraphPoint> |
getPoints()
Gets all points which belong to this group of cycles |
SignedPermutationBPGraphReversalFilter |
getReversalFilter()
Gets the reversal filter of this permutation |
java.util.SortedSet<BPGraphCycle> |
getUnorientedCycles()
Gets the list of non-oriented cycles of this group of cycles |
double |
getWeightOf(java.lang.String name)
Gets the weight of the value identified by the given name |
boolean |
isOriented()
Tests whether this cycle group is oriented |
int |
length()
Gets the length of the block (the number of values of the permutation between its start and end points) |
int[] |
toIntArray()
Gets a representation of the block as an array of int, with size 2, representing its start and end positions |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface baobab.bio.permutation.PermutationBPGraph |
---|
getNumberOfCycles |
Constructor Detail |
---|
public WeightedSignedPermutationBPGraph(int[] permutationList, double[] weights)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intpublic WeightedSignedPermutationBPGraph(int[] permutationList, boolean isLinear, double[] weights)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intisLinear
- indicates whether the permutation is linear or circularpublic WeightedSignedPermutationBPGraph(int[] originList, int[] targetList, double[] originWeights)
originList
- the origin list of signed integers (from +/-1 to +/-n), as an array of inttargetList
- the target list of signed integers (from +/-1 to +/-n), as an array of intpublic WeightedSignedPermutationBPGraph(int[] originList, int[] targetList, boolean isLinear, double[] originWeights)
originList
- the origin list of signed integers (from +/-1 to +/-n), as an array of inttargetList
- the target list of signed integers (from +/-1 to +/-n), as an array of intisLinear
- indicates whether the permutation is linear or circularpublic WeightedSignedPermutationBPGraph(java.util.Vector<java.lang.String> origin, java.util.Vector<java.lang.String> target, boolean isLinear, java.util.Vector<java.lang.Double> originWeights)
origin
- the origin list of signed markerstarget
- the target list of signed markersisLinear
- indicates whether the permutation is linear or circularoriginWeights
- the weights of the markers with respect to the origin listMethod Detail |
---|
public double getWeightOf(java.lang.String name)
SignedPermutationBPGraph
getWeightOf
in class SignedPermutationBPGraph
name
- the name of the value
public double getAverageWeightOfInterval(int startPos, int endPos)
SignedPermutationBPGraph
getAverageWeightOfInterval
in class SignedPermutationBPGraph
startPos
- the start of the intervalendPos
- the end of the interval
public SignedPermutationBPGraphReversalFilter getReversalFilter()
SignedPermutationBPGraph
getReversalFilter
in class SignedPermutationBPGraph
public java.util.TreeSet<BPGraphPoint> getBreakpoints()
public int getNumberOfBreakpoints()
public int getNumberOfCycles()
public java.util.SortedSet<BPGraphCycle> getCycles()
public java.util.SortedSet getOrientedCycles()
public boolean isOriented()
public java.util.SortedSet<BPGraphPoint> getPoints()
public BPGraphCycle getCycle(int number)
public java.util.SortedSet<BPGraphCycle> getUnorientedCycles()
public int length()
public int[] toIntArray()
public int compareTo(java.lang.Object object)
compareTo
in interface java.lang.Comparable
object
- the other block
public static java.util.Vector<int[]> blocksToIntArrays(java.util.Collection blocks)
blocks
- a collection of blocks
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |