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java.lang.Objectbaobab.bio.permutation.BPGraphCycle
public class BPGraphCycle
The BPGraphCycle class represents a cycle of points of a permutation breakpoint graph
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.SortedSet<BPGraphPoint> |
getBreakpoints()
Gets the breakpoint list of this cycle |
BPGraphPoint |
getFirstPoint()
Gets the first point of this cycle in the breakpoint graph |
BPGraphPoint |
getLastPoint()
Gets the last point of this cycle in the breakpoint graph |
int |
getNumber()
Gets the cycle number |
BPGraphCyclePartition |
getPartition(int id)
Gets a partition of this cycle, given its id |
PermutationBPGraph |
getPermutationBPGraph()
Gets the permutation breakpoint graph to which this element belongs |
java.util.SortedSet<BPGraphPoint> |
getPoints()
Gets the points of this cycle sorted in ascendant order |
java.util.Iterator |
getPointsAsCycle()
Gets the points of this cycle ordered as a cycle |
boolean |
isActive()
Tests whether this cycle is active (analyzed) |
boolean |
isAdjacency()
Tests whether this block is an adjacency |
int |
length()
Gets the length of the block (the number of values of the permutation between its start and end points) |
int |
size()
Gets the number of points in this cycle |
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 int getNumber()
public int size()
public java.util.SortedSet<BPGraphPoint> getBreakpoints()
public boolean isActive()
public java.util.Iterator getPointsAsCycle()
public java.util.SortedSet<BPGraphPoint> getPoints()
public BPGraphCyclePartition getPartition(int id)
id
- the partition id
public java.lang.String toString()
toString
in class java.lang.Object
public boolean isAdjacency()
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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