baobab.bio.permutation
Interface PermutationBPGraph

All Known Implementing Classes:
ComplexSignedPermutationBPGraph, SignedPermutationBPGraph, UnsignedPermutationBPGraph, WeightedSignedPermutationBPGraph

public interface PermutationBPGraph

The PermutationBPGraph interface represents a general permutation pair and its breakpoint graph

Author:
Marilia D. V. Braga

Method Summary
 BPGraphPoint getFirstPoint()
          Gets the first point of the permutation breakpoint graph
 PermutationBPGraphFormatter getFormatter()
          Gets this breakpoint graph formatter
 BPGraphPoint getLastPoint()
          Gets the last point of the permutation breakpoint graph
 int getLastPointIndex()
          Gets the index of the last point of the permutation breakpoint graph
 int getLongestNameLength()
          Gets the longest length of a value name in the breakpoint graph
 int getMappedValueAt(int pos)
          Gets the value of the mapped element located at a specified position of the permutation breakpoint graph
 java.lang.String getNameAt(int pos)
          Gets the value of the element located at a specified position of the permutation breakpoint graph
 int getNumberOfCycles()
          Gets the number of cycles of the permutation breakpoint graph
 BPGraphPoint getPointAt(int pos)
          Gets a point at a specific position of the permutation breakpoint graph
 int getPositionOf(int value)
          Gets the position where a specified element of the permutation is located
 int getPositionOf(java.lang.String name)
          Gets the position of the element identified by the given name
 int getPositionOfMapped(int value)
          Gets the position where a specified mapped element of the permutation breakpoint graph is located
 int getValueAt(int pos)
          Gets the value of the element located at a specified position of the permutation breakpoint graph
 boolean isLinear()
          Tests whether the breakpoint graph corresponds to a linear or a circular permutation
 boolean isRevertedAt(int pos)
          Gets the value of the element located at a specified position of the permutation breakpoint graph
 boolean isSorted()
          Tests whether the breakpoint graph represents a sorted permutation
 int size()
          Gets the size (or the number of values) of the breakpoint graph
 

Method Detail

size

int size()
Gets the size (or the number of values) of the breakpoint graph

Returns:
the size of the permutation

getNumberOfCycles

int getNumberOfCycles()
Gets the number of cycles of the permutation breakpoint graph

Returns:
the number of cycles of the breakpoint graph

isSorted

boolean isSorted()
Tests whether the breakpoint graph represents a sorted permutation

Returns:
true / false

getFormatter

PermutationBPGraphFormatter getFormatter()
Gets this breakpoint graph formatter

Returns:
the breakpoint graph formatter

getPointAt

BPGraphPoint getPointAt(int pos)
Gets a point at a specific position of the permutation breakpoint graph

Parameters:
pos - the given position
Returns:
the point at the given position

getMappedValueAt

int getMappedValueAt(int pos)
Gets the value of the mapped element located at a specified position of the permutation breakpoint graph

Parameters:
pos - the specified position
Returns:
the value of the mapped element

getValueAt

int getValueAt(int pos)
Gets the value of the element located at a specified position of the permutation breakpoint graph

Parameters:
pos - the specified position
Returns:
the value of the element

getPositionOf

int getPositionOf(int value)
Gets the position where a specified element of the permutation is located

Parameters:
value - the value of the specified element
Returns:
the position

getPositionOfMapped

int getPositionOfMapped(int value)
Gets the position where a specified mapped element of the permutation breakpoint graph is located

Parameters:
value - the value of the specified mapped element
Returns:
the position

isLinear

boolean isLinear()
Tests whether the breakpoint graph corresponds to a linear or a circular permutation

Returns:
true / false

getNameAt

java.lang.String getNameAt(int pos)
Gets the value of the element located at a specified position of the permutation breakpoint graph

Parameters:
pos - the specified position
Returns:
the value of the element

getPositionOf

int getPositionOf(java.lang.String name)
Gets the position of the element identified by the given name

Parameters:
name - the given name
Returns:
the position of the element

isRevertedAt

boolean isRevertedAt(int pos)
Gets the value of the element located at a specified position of the permutation breakpoint graph

Parameters:
pos - the specified position
Returns:
the value of the element

getLongestNameLength

int getLongestNameLength()
Gets the longest length of a value name in the breakpoint graph

Returns:
the longest length of a value name

getFirstPoint

BPGraphPoint getFirstPoint()
Gets the first point of the permutation breakpoint graph

Returns:
the first point

getLastPointIndex

int getLastPointIndex()
Gets the index of the last point of the permutation breakpoint graph

Returns:
the last point index

getLastPoint

BPGraphPoint getLastPoint()
Gets the last point of the permutation breakpoint graph

Returns:
the last point