|
||||||||||
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.ComplexSignedPermutationBPGraph
public class ComplexSignedPermutationBPGraph
The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
Constructor Summary | |
---|---|
ComplexSignedPermutationBPGraph(int[] permutationList)
Creates a new linear permutation (assumes the identity permutation as target) |
|
ComplexSignedPermutationBPGraph(int[] permutationList,
boolean isLinear)
Creates a new permutation (assumes the identity permutation as target) |
|
ComplexSignedPermutationBPGraph(int[] permutationList,
boolean isLinear,
double[] weightList)
Creates a new permutation (assumes the identity permutation as target) |
|
ComplexSignedPermutationBPGraph(int[] permutationList,
double[] weightList)
Creates a new linear permutation (assumes the identity permutation as target) |
|
ComplexSignedPermutationBPGraph(int[] originList,
int[] targetList)
Creates a new linear permutation |
|
ComplexSignedPermutationBPGraph(int[] originList,
int[] targetList,
boolean isLinear)
Creates a new permutation |
|
ComplexSignedPermutationBPGraph(int[] originList,
int[] targetList,
boolean isLinear,
double[] weightList)
Creates a new permutation |
|
ComplexSignedPermutationBPGraph(int[] originList,
int[] targetList,
double[] weightList)
Creates a new linear permutation |
|
ComplexSignedPermutationBPGraph(SignedPermutationBPGraph other)
Creates a complex signed permutation over a simple signed permutation |
|
ComplexSignedPermutationBPGraph(java.util.Vector<java.lang.String> origin,
java.util.Vector<java.lang.String> target,
boolean isLinear,
java.util.Vector<java.lang.Double> weights)
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) |
java.lang.Object |
clone()
|
int |
compareTo(java.lang.Object object)
Compares this block to another block |
java.util.TreeSet<ComplexSignedPermutationBPGraph> |
decompose()
Decompose this graph in its components + adajacencies to replace other components |
boolean |
equals(ComplexSignedPermutationBPGraph perm)
|
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 |
java.lang.String |
getData()
|
int |
getNumberOfAdjacencies()
Gets the number of adjacencies of the permutation |
int |
getNumberOfBreakpoints()
Gets the number of breakpoints |
int |
getNumberOfComponents()
Gets the number of components of the permutation |
int |
getNumberOfCycles()
Gets the number of cycles of this group of cycles |
int |
getNumberOfHurdles()
Gets the number of hurdles of the permutation |
int |
getNumberOfOrientedComponents()
Gets the number of oriented components of the permutation |
int |
getNumberOfSuperHurdles()
Gets the number of super hurdles of the permutation |
int |
getNumberOfUnorientedComponents()
Gets the number of non-oriented components of the permutation |
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 |
int |
getReversalDistance()
Gets the reversal distance of this permutation |
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 |
boolean |
isFortress()
Tests whether this permutation is a fortress |
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) |
SignedPermutationBPGraph |
revert(BPGraphPoint start,
BPGraphPoint end)
Reverts the permutation between the specified points |
SignedPermutationBPGraph |
revert(BPGraphReversalBlock block)
Reverts the specified block of the permutation |
SignedPermutationBPGraph |
revert(int start,
int end)
Reverts the permutation between the specified positions |
SignedPermutationBPGraph |
revertToNewPermutation(BPGraphPoint start,
BPGraphPoint end)
Make a new permutation, by reverting the permutation between the specified positions |
int[] |
toIntArray()
Gets a representation of the block as an array of int, with size 2, representing its start and end positions |
java.lang.String |
toString()
|
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 ComplexSignedPermutationBPGraph(SignedPermutationBPGraph other)
other
- the simple signed permutationpublic ComplexSignedPermutationBPGraph(int[] permutationList)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intpublic ComplexSignedPermutationBPGraph(int[] permutationList, double[] weightList)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intpublic ComplexSignedPermutationBPGraph(int[] permutationList, boolean isLinear)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intisLinear
- indicates whether the permutation is linear or circularpublic ComplexSignedPermutationBPGraph(int[] permutationList, boolean isLinear, double[] weightList)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intisLinear
- indicates whether the permutation is linear or circularpublic ComplexSignedPermutationBPGraph(int[] originList, int[] targetList)
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 ComplexSignedPermutationBPGraph(int[] originList, int[] targetList, double[] weightList)
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 ComplexSignedPermutationBPGraph(int[] originList, int[] targetList, boolean isLinear)
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 ComplexSignedPermutationBPGraph(int[] originList, int[] targetList, boolean isLinear, double[] weightList)
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 ComplexSignedPermutationBPGraph(java.util.Vector<java.lang.String> origin, java.util.Vector<java.lang.String> target, boolean isLinear, java.util.Vector<java.lang.Double> weights)
origin
- the origin list of signed markerstarget
- the target list of signed markersisLinear
- indicates whether the permutation is linear or circularweights
- theMethod Detail |
---|
public int getReversalDistance()
SignedPermutationBPGraph
getReversalDistance
in class SignedPermutationBPGraph
public int getNumberOfComponents()
public int getNumberOfAdjacencies()
public int getNumberOfUnorientedComponents()
public int getNumberOfOrientedComponents()
public int getNumberOfHurdles()
public int getNumberOfSuperHurdles()
public java.util.TreeSet<ComplexSignedPermutationBPGraph> decompose()
public SignedPermutationBPGraph revert(BPGraphReversalBlock block) throws PermutationException
revert
in class SignedPermutationBPGraph
block
- the block to be reverted
PermutationException
public SignedPermutationBPGraph revert(BPGraphPoint start, BPGraphPoint end) throws PermutationException
revert
in class SignedPermutationBPGraph
start
- the beginning of the reversion blockend
- the end of the reversion block
PermutationException
public SignedPermutationBPGraph revert(int start, int end)
revert
in class SignedPermutationBPGraph
start
- the beginning of the reversion blockend
- the end of the reversion block
public SignedPermutationBPGraph revertToNewPermutation(BPGraphPoint start, BPGraphPoint end) throws PermutationException
revertToNewPermutation
in class SignedPermutationBPGraph
start
- the beginning of the reversion blockend
- the end of the reversion block
PermutationException
public boolean isFortress()
public SignedPermutationBPGraphReversalFilter getReversalFilter()
SignedPermutationBPGraph
getReversalFilter
in class SignedPermutationBPGraph
public java.lang.Object clone()
clone
in class SignedPermutationBPGraph
public boolean equals(ComplexSignedPermutationBPGraph perm)
public java.lang.String toString()
toString
in class SignedPermutationBPGraph
public java.lang.String getData()
getData
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 |