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java.lang.Objectbaobab.bio.permutation.SignedPermutation
baobab.bio.permutation.ComplexSignedPermutation
public class ComplexSignedPermutation
The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
Constructor Summary | |
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ComplexSignedPermutation(int[] permutationList)
Creates a new linear permutation (assumes the identity permutation as target) |
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ComplexSignedPermutation(int[] permutationList,
boolean isLinear)
Creates a new permutation (assumes the identity permutation as target) |
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ComplexSignedPermutation(int[] originList,
int[] targetList)
Creates a new linear permutation |
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ComplexSignedPermutation(int[] originList,
int[] targetList,
boolean isLinear)
Creates a new permutation |
Method Summary | |
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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()
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int |
compareTo(java.lang.Object object)
Compares this block to another block |
boolean |
equals(ComplexSignedPermutation perm)
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java.util.SortedSet<Point> |
getBreakpoints()
Gets the breakpoint list of this block |
java.util.SortedSet<Cycle> |
getCycles()
Gets the list of cycles of this group of cycles |
java.lang.String |
getData()
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int |
getNumberOfCycles()
Gets the number of cycles of this group of cycles |
int |
getNumberOfHurdles()
Gets the number of hurdles of the permutation |
int |
getNumberOfSuperHurdles()
Gets the number of super hurdles of the permutation |
java.util.SortedSet |
getOrientedCycles()
Gets the list of oriented cycles of this group of cycles |
java.util.SortedSet<Point> |
getPoints()
Gets all points which belong to this group of cycles |
int |
getReversalDistance()
Gets the reversal distance of this permutation |
SignedPermutationReversalFilter |
getReversalFilter()
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java.util.SortedSet<Cycle> |
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) |
SignedPermutation |
revert(int start,
int end)
Reverts the permutation between the specified positions |
SignedPermutation |
revert(Point start,
Point end)
Reverts the permutation between the specified points |
SignedPermutation |
revert(ReversalBlock block)
Reverts the specified block of the permutation |
SignedPermutation |
revertToNewPermutation(Point start,
Point 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()
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Methods inherited from class baobab.bio.permutation.SignedPermutation |
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equals, getEndPoint, getEndPointIndex, getFormatter, getIntToNamesMap, getLongestNameLength, getMappedPositions, getMappedValueOf, getMappedValues, getMinimalReversalDistance, getNameOf, getPermutation, getPointAt, getPositionOf, getPositionOfMapped, getStartPoint, getValueOf, isAdjacency, isLinear, isRevertedAt, isSorted, revertToNewPermutation, size |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface baobab.bio.permutation.Permutation |
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getNumberOfCycles |
Constructor Detail |
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public ComplexSignedPermutation(int[] permutationList)
permutationList
- the list of signed integers (from +/-1 to +/-n), as an array of intpublic ComplexSignedPermutation(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 ComplexSignedPermutation(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 ComplexSignedPermutation(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 circularMethod Detail |
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public int getReversalDistance()
SignedPermutation
getReversalDistance
in class SignedPermutation
public int getNumberOfHurdles()
public int getNumberOfSuperHurdles()
public SignedPermutation revert(ReversalBlock block) throws PermutationException
revert
in class SignedPermutation
block
- the block to be reverted
PermutationException
public SignedPermutation revert(Point start, Point end) throws PermutationException
revert
in class SignedPermutation
start
- the beginning of the reversion blockend
- the end of the reversion block
PermutationException
public SignedPermutation revert(int start, int end)
revert
in class SignedPermutation
start
- the beginning of the reversion blockend
- the end of the reversion block
public SignedPermutation revertToNewPermutation(Point start, Point end) throws PermutationException
revertToNewPermutation
in class SignedPermutation
start
- the beginning of the reversion blockend
- the end of the reversion block
PermutationException
public boolean isFortress()
public SignedPermutationReversalFilter getReversalFilter()
getReversalFilter
in class SignedPermutation
public java.lang.Object clone()
clone
in class SignedPermutation
public boolean equals(ComplexSignedPermutation perm)
public java.lang.String toString()
toString
in class SignedPermutation
public java.lang.String getData()
getData
in class SignedPermutation
public java.util.SortedSet<Point> getBreakpoints()
public int getNumberOfCycles()
public java.util.SortedSet<Cycle> getCycles()
public java.util.SortedSet getOrientedCycles()
public boolean isOriented()
public java.util.SortedSet<Point> getPoints()
public java.util.SortedSet<Cycle> 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
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