Class Pdb2Fasta.MyChain

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Residue>
              meshi.molecularElements.ResidueList
                  meshi.molecularElements.Chain
                      Pdb2Fasta.MyChain

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Residue>, java.util.Collection<Residue>, java.util.List<Residue>, java.util.RandomAccess

Enclosing class:

Pdb2Fasta

private static class Pdb2Fasta.MyChain
extends Chain

Nested Class Summary

Nested classes/interfaces inherited from class meshi.molecularElements.ResidueList

ResidueList.NonDummyFilter

Field Summary

private Residue

previousResidue

Fields inherited from class meshi.molecularElements.Chain

GENERIC_CHAIN_NAME, name, protein

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Pdb2Fasta.MyChain(AtomList atomList, java.lang.String name, MeshiLog log)

Method Summary

(package private) boolean	add(Residue residue, Residue previousResidue, MeshiLog log)
(package private) java.lang.Object[]	getResidue(java.util.Iterator atoms, Atom first)

Methods inherited from class meshi.molecularElements.Chain

assertChain, atoms, filter, firstNonDummyResidue, missingResidues, name, nowhereAtoms, numberOfNonDummyResidues, residue, residueAt, sequence, toString

Methods inherited from class meshi.molecularElements.ResidueList

print, sort

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

previousResidue

private Residue previousResidue

Constructor Detail

Pdb2Fasta.MyChain

public Pdb2Fasta.MyChain(AtomList atomList,
                         java.lang.String name,
                         MeshiLog log)

Method Detail

getResidue

java.lang.Object[] getResidue(java.util.Iterator atoms,
                              Atom first)

add

boolean add(Residue residue,
            Residue previousResidue,
            MeshiLog log)