org.jmol.modelset
Class Chain

java.lang.Object
  extended by 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)