mesquite.lib
Class Bits

java.lang.Object
  mesquite.lib.Bits

All Implemented Interfaces:

Listable

public class Bits
extends java.lang.Object
implements Listable

Bits - an object to contain and manage a field of booleans. This was invented before the Java Bitfield was discovered. Perhaps not needed.

Constructor Summary

Bits(int numBits)

Method Summary

static boolean[]	addParts(boolean[] d, int starting, int num) Inserts num (cleared) bits just after bit "starting"
void	addParts(int starting, int num) Inserts num (cleared) bits just after bit "starting"
static boolean[][]	addRows(boolean[][] d, int starting, int num)
boolean	anyBitsOn()
void	clearAllBits()
void	clearBit(int whichBit)
Bits	cloneBits()
void	copyBits(Bits b)
static boolean[]	deleteParts(boolean[] values, int starting, int num)
void	deleteParts(int starting, int num) Removes num bits starting with and incuding bit "starting"
static boolean[][]	deleteRows(boolean[][] d, int starting, int num)
boolean	equals(Bits other)
int	firstBitOn()
java.lang.String	getListOfBitsOn(int offset) returns a string listing the bits on.
java.lang.String	getName()
NameReference	getNameReference()
int	getNumInts()
int	getSize()
boolean	isBitOn(int whichBit)
static boolean	isBitOn(int[] bits, int whichBit)
static void	moveColumns(boolean[][] d, int starting, int num, int justAfter)
void	moveParts(int starting, int num, int justAfter)
static void	moveRows(boolean[][] d, int starting, int num, int justAfter)
int	nextBit(int startBit, boolean on) returns the next bit, starting a startBit, that has the same value as "on"
int	numBitsOn()
int	numBitsOnPlural()
boolean	oneBitOn(MesquiteInteger single) Returns true iff exactly one bit is on.
void	resetSize(int newNumBits)
static boolean[]	reverseBooleanArray(boolean[] d) Reverses the elements of a boolean array
void	setAllBits()
void	setBit(int whichBit)
void	setBit(int[] a, int whichBit)
void	setBit(int whichBit, boolean on)
void	setNameReference(NameReference nr)
static void	swapColumns(boolean[][] d, int first, int second)
void	swapParts(int first, int second)
void	swapValues(int i, int j)
java.lang.String	toString()
static java.lang.String	toString(boolean[] bits)
static java.lang.String	toString(byte s) converts passed int to string, as its bits representation.
static java.lang.String	toString(int s) converts passed int to string, as its bits representation.
static java.lang.String	toString(int[] bits)
static java.lang.String	toString(long s) converts passed long to string, as its bits representation.
static java.lang.String	toString(short s) converts passed int to string, as its bits representation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Bits

public Bits(int numBits)

Method Detail

getSize

public int getSize()

getNumInts

public int getNumInts()

cloneBits

public Bits cloneBits()

copyBits

public void copyBits(Bits b)

setNameReference

public void setNameReference(NameReference nr)

getNameReference

public NameReference getNameReference()

getName

public java.lang.String getName()

Specified by:

getName in interface Listable

resetSize

public void resetSize(int newNumBits)

addParts

public void addParts(int starting,
                     int num)

Inserts num (cleared) bits just after bit "starting"

deleteParts

public void deleteParts(int starting,
                        int num)

Removes num bits starting with and incuding bit "starting"

swapParts

public void swapParts(int first,
                      int second)

moveParts

public void moveParts(int starting,
                      int num,
                      int justAfter)

numBitsOn

public int numBitsOn()

numBitsOnPlural

public int numBitsOnPlural()

clearAllBits

public void clearAllBits()

setAllBits

public void setAllBits()

clearBit

public void clearBit(int whichBit)

setBit

public void setBit(int[] a,
                   int whichBit)

setBit

public void setBit(int whichBit)

setBit

public void setBit(int whichBit,
                   boolean on)

swapValues

public void swapValues(int i,
                       int j)

equals

public boolean equals(Bits other)

isBitOn

public boolean isBitOn(int whichBit)

isBitOn

public static boolean isBitOn(int[] bits,
                              int whichBit)

nextBit

public int nextBit(int startBit,
                   boolean on)

returns the next bit, starting a startBit, that has the same value as "on"

anyBitsOn

public boolean anyBitsOn()

firstBitOn

public int firstBitOn()

oneBitOn

public boolean oneBitOn(MesquiteInteger single)

Returns true iff exactly one bit is on. If one bit is on, it returns in "single" the single bit that is on.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getListOfBitsOn

public java.lang.String getListOfBitsOn(int offset)

returns a string listing the bits on. In the format of NEXUS character, taxa lists (e.g., "1- 3 6 201-455". The offset is what the first element is to be numbered (e.g., 0 or 1)

moveColumns

public static void moveColumns(boolean[][] d,
                               int starting,
                               int num,
                               int justAfter)

swapColumns

public static void swapColumns(boolean[][] d,
                               int first,
                               int second)

moveRows

public static void moveRows(boolean[][] d,
                            int starting,
                            int num,
                            int justAfter)

addRows

public static boolean[][] addRows(boolean[][] d,
                                  int starting,
                                  int num)

deleteRows

public static boolean[][] deleteRows(boolean[][] d,
                                     int starting,
                                     int num)

addParts

public static boolean[] addParts(boolean[] d,
                                 int starting,
                                 int num)

Inserts num (cleared) bits just after bit "starting"

deleteParts

public static boolean[] deleteParts(boolean[] values,
                                    int starting,
                                    int num)

reverseBooleanArray

public static boolean[] reverseBooleanArray(boolean[] d)

Reverses the elements of a boolean array

toString

public static java.lang.String toString(int[] bits)

toString

public static java.lang.String toString(boolean[] bits)

toString

public static java.lang.String toString(byte s)

converts passed int to string, as its bits representation. Used for development/debugging. �

toString

public static java.lang.String toString(short s)

converts passed int to string, as its bits representation. Used for development/debugging. �

toString

public static java.lang.String toString(int s)

converts passed int to string, as its bits representation. Used for development/debugging. �

toString

public static java.lang.String toString(long s)

converts passed long to string, as its bits representation. Used for development/debugging. �