org.jmol.modelset
Class Chain

java.lang.Object
  org.jmol.modelset.Chain

public final class Chain
extends Object

Field Summary

private BitSet	bsSelectedGroups
(package private) char	chainID
(package private) int	groupCount
(package private) Group[]	groups
private boolean	isDna
private boolean	isRna
(package private) Model	model
(package private) ModelSet	modelSet
private int	selectedGroupCount

Constructor Summary

Chain(ModelSet modelSet, Model model, char chainID)

Method Summary

(package private) void	calcSelectedGroupsCount(BitSet bsSelected) prior to coloring by group, we need the chain count per chain that is selected
(package private) void	fixIndices(int atomsDeleted, BitSet bsDeleted)
Atom	getAtom(int index)
char	getChainID()
(package private) Group	getGroup(int groupIndex)
(package private) int	getGroupCount()
(package private) ModelSet	getModelSet()
(package private) int	getSelectedGroupCount()
boolean	isDna()
boolean	isRna()
(package private) int	selectSeqcodeRange(int index0, int seqcodeA, int seqcodeB, BitSet bs)
(package private) void	setAtomBitSet(BitSet bs)
void	setIsDna(boolean TF)
void	setIsRna(boolean TF)
(package private) void	setModelSet(ModelSet modelSet)

Methods inherited from class java.lang.Object

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

Field Detail

modelSet

ModelSet modelSet

model

Model model

chainID

char chainID

groupCount

int groupCount

groups

Group[] groups

selectedGroupCount

private int selectedGroupCount

isDna

private boolean isDna

isRna

private boolean isRna

bsSelectedGroups

private BitSet bsSelectedGroups

Constructor Detail

Chain

Chain(ModelSet modelSet,
      Model model,
      char chainID)

Method Detail

getChainID

public char getChainID()

isDna

public boolean isDna()

isRna

public boolean isRna()

setIsDna

public void setIsDna(boolean TF)

setIsRna

public void setIsRna(boolean TF)

getAtom

public Atom getAtom(int index)

setModelSet

void setModelSet(ModelSet modelSet)

getModelSet

ModelSet getModelSet()

getGroup

Group getGroup(int groupIndex)

getGroupCount

int getGroupCount()

calcSelectedGroupsCount

void calcSelectedGroupsCount(BitSet bsSelected)

prior to coloring by group, we need the chain count per chain that is selected

Parameters:

bsSelected -

selectSeqcodeRange

int selectSeqcodeRange(int index0,
                       int seqcodeA,
                       int seqcodeB,
                       BitSet bs)

getSelectedGroupCount

int getSelectedGroupCount()

fixIndices

void fixIndices(int atomsDeleted,
                BitSet bsDeleted)

setAtomBitSet

void setAtomBitSet(BitSet bs)