org.jmol.modelset
Class Chain

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

public final class Chain
extends java.lang.Object


Field Summary
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
           
private  int selectedGroupCount
           
 
Constructor Summary
Chain(ModelSet modelSet, Model model, char chainID)
           
 
Method Summary
(package private)  void calcSelectedGroupsCount(java.util.BitSet bsSelected)
          prior to coloring by group, we need the chain count per chain that is selected
(package private)  void fixIndices(int atomsDeleted, java.util.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, java.util.BitSet bs)
           
(package private)  void setAtomBitSet(java.util.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 java.util.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(java.util.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,
                       java.util.BitSet bs)

getSelectedGroupCount

int getSelectedGroupCount()

fixIndices

void fixIndices(int atomsDeleted,
                java.util.BitSet bsDeleted)

setAtomBitSet

void setAtomBitSet(java.util.BitSet bs)