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java.lang.Objectbaobab.bio.permutation.SignedBPGraphComponent
public class SignedBPGraphComponent
The SignedBPGraphComponent class represents a component of signed cycles of the breakpoint graph of a signed permutation pair
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) |
int |
compareTo(java.lang.Object object)
Compares this block to another block |
java.util.TreeSet<BPGraphPoint> |
getBreakpoints()
Gets the breakpoint list of this block |
java.util.SortedSet<SignedBPGraphComponent> |
getCoveredUnorientedComponents()
Gets all unoriented components directly covered by this component |
SignedBPGraphComponent |
getCovererUnorientedComponent()
Gets the direct coverer unoriented component of this component |
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 |
BPGraphPoint |
getFirstPoint()
Gets the start point of this component in the permutation |
BPGraphPoint |
getLastPoint()
Gets the end point of this component in the permutation |
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 |
PermutationBPGraph |
getPermutationBPGraph()
Gets the permutation breakpoint graph to which this element belongs |
java.util.SortedSet<BPGraphPoint> |
getPoints()
Gets all points which belong to this group of cycles |
java.util.SortedSet<BPGraphCycle> |
getUnorientedCycles()
Gets the list of non-oriented cycles of this group of cycles |
boolean |
isAdjacency()
Tests whether this component is an adjacency |
boolean |
isHurdle()
Tests whether this component is a hurdle |
boolean |
isMaxHurdle()
Tests whether this component is the maximum hurdle |
boolean |
isOriented()
Tests whether this cycle group is oriented |
boolean |
isSuperHurdle()
Tests whether this component is a super hurdle |
int |
length()
Gets the length of the block (the number of values of the permutation between its start and end points) |
void |
setSuperHurdle()
Sets this component as super hurdle |
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 java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Method Detail |
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public BPGraphPoint getFirstPoint()
public BPGraphPoint getLastPoint()
public boolean isAdjacency()
public boolean isHurdle()
public boolean isSuperHurdle()
public void setSuperHurdle()
public SignedBPGraphComponent getCovererUnorientedComponent()
public boolean isMaxHurdle()
public java.util.SortedSet<SignedBPGraphComponent> getCoveredUnorientedComponents()
public java.lang.String toString()
toString
in class java.lang.Object
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
public PermutationBPGraph getPermutationBPGraph()
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