org.jmol.modelset
Class Chain
java.lang.Object
org.jmol.modelset.Chain
public final class Chain
- extends java.lang.Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
Chain
public Chain(ModelSet modelSet,
Model model,
char chainID)
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)