org.jmol.modelset

Class Chain

public final class Chain extends Object

Field Summary
BitSetbsSelectedGroups
charchainID
intgroupCount
Group[]groups
booleanisDna
booleanisRna
Modelmodel
ModelSetmodelSet
intselectedGroupCount
Constructor Summary
Chain(ModelSet modelSet, Model model, char chainID)
Method Summary
voidcalcSelectedGroupsCount(BitSet bsSelected)
prior to coloring by group, we need the chain count per chain that is selected
voidfixIndices(int atomsDeleted)
AtomgetAtom(int index)
intgetAtomCount()
chargetChainID()
GroupgetGroup(int groupIndex)
intgetGroupCount()
ModelSetgetModelSet()
intgetSelectedGroupCount()
booleanisDna()
booleanisRna()
intselectSeqcodeRange(int index0, int seqcodeA, int seqcodeB, BitSet bs)
voidsetIsDna(boolean TF)
voidsetIsRna(boolean TF)
voidsetModelSet(ModelSet modelSet)
voidupdateOffsetsForAlternativeLocations(BitSet bsSelected, int nAltLocInModel, byte[] offsets, int firstAtomIndex, int lastAtomIndex)

Field Detail

bsSelectedGroups

BitSet bsSelectedGroups

chainID

char chainID

groupCount

int groupCount

groups

Group[] groups

isDna

private boolean isDna

isRna

private boolean isRna

model

Model model

modelSet

ModelSet modelSet

selectedGroupCount

int selectedGroupCount

Constructor Detail

Chain

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

Method Detail

calcSelectedGroupsCount

public void calcSelectedGroupsCount(BitSet bsSelected)
prior to coloring by group, we need the chain count per chain that is selected

Parameters: bsSelected

fixIndices

public void fixIndices(int atomsDeleted)

getAtom

public Atom getAtom(int index)

getAtomCount

public int getAtomCount()

getChainID

public char getChainID()

getGroup

public Group getGroup(int groupIndex)

getGroupCount

public int getGroupCount()

getModelSet

public ModelSet getModelSet()

getSelectedGroupCount

int getSelectedGroupCount()

isDna

public boolean isDna()

isRna

public boolean isRna()

selectSeqcodeRange

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

setIsDna

public void setIsDna(boolean TF)

setIsRna

public void setIsRna(boolean TF)

setModelSet

public void setModelSet(ModelSet modelSet)

updateOffsetsForAlternativeLocations

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