org.jmol.modelset
Class Chain

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

public final class Chain
extends java.lang.Object

Field Summary

(package private) java.util.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
(package private) int	selectedGroupCount

Constructor Summary

Chain(ModelSet modelSet, Model model, char chainID)

Method Summary

void	calcSelectedGroupsCount(java.util.BitSet bsSelected) prior to coloring by group, we need the chain count per chain that is selected
void	fixIndices(int atomsDeleted)
Atom	getAtom(int index)
int	getAtomCount()
char	getChainID()
Group	getGroup(int groupIndex)
int	getGroupCount()
ModelSet	getModelSet()
(package private) int	getSelectedGroupCount()
boolean	isDna()
boolean	isRna()
int	selectSeqcodeRange(int index0, int seqcodeA, int seqcodeB, java.util.BitSet bs)
void	setIsDna(boolean TF)
void	setIsRna(boolean TF)
void	setModelSet(ModelSet modelSet)
void	updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected, int nAltLocInModel, byte[] offsets, int firstAtomIndex, int lastAtomIndex)

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

selectedGroupCount

int selectedGroupCount

isDna

private boolean isDna

isRna

private boolean isRna

bsSelectedGroups

java.util.BitSet bsSelectedGroups

groups

Group[] groups

Constructor Detail

Chain

public Chain(ModelSet modelSet,
             Model model,
             char chainID)

Method Detail

setModelSet

public void setModelSet(ModelSet modelSet)

getChainID

public char getChainID()

getModelSet

public ModelSet getModelSet()

isDna

public boolean isDna()

isRna

public boolean isRna()

setIsDna

public void setIsDna(boolean TF)

setIsRna

public void setIsRna(boolean TF)

getGroup

public Group getGroup(int groupIndex)

getGroupCount

public int getGroupCount()

getAtomCount

public int getAtomCount()

getAtom

public Atom getAtom(int index)

calcSelectedGroupsCount

public void calcSelectedGroupsCount(java.util.BitSet bsSelected)

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

Parameters:

bsSelected -

selectSeqcodeRange

public int selectSeqcodeRange(int index0,
                              int seqcodeA,
                              int seqcodeB,
                              java.util.BitSet bs)

getSelectedGroupCount

int getSelectedGroupCount()

updateOffsetsForAlternativeLocations

public final void updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected,
                                                       int nAltLocInModel,
                                                       byte[] offsets,
                                                       int firstAtomIndex,
                                                       int lastAtomIndex)

fixIndices

public void fixIndices(int atomsDeleted)