meshi.sequences
Class AtomAlignment

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<AtomAlignmentColumn>
              meshi.sequences.AtomAlignment

All Implemented Interfaces:

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

public class AtomAlignment
extends java.util.ArrayList<AtomAlignmentColumn>

See Also:

Serialized Form

Nested Class Summary

private static class

AtomAlignment.IsAlignmentColumn

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

AtomAlignment()

AtomAlignment(AtomList atomList0, AtomList atomList1)

AtomAlignment(ResidueAlignment residueAlignment)

AtomAlignment(ResidueAlignment residueAlignment, Filter filter)

Method Summary

Atom	atomAt(int coulumnIndex, int rowIndex)
AtomList	atomList(int row)
boolean	hasGaps() Does the alignemnt include gaps? .
Rms	rms()

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, toString

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

Constructor Detail

AtomAlignment

public AtomAlignment()

AtomAlignment

public AtomAlignment(AtomList atomList0,
                     AtomList atomList1)

AtomAlignment

public AtomAlignment(ResidueAlignment residueAlignment)

AtomAlignment

public AtomAlignment(ResidueAlignment residueAlignment,
                     Filter filter)

Method Detail

rms

public Rms rms()

atomAt

public Atom atomAt(int coulumnIndex,
                   int rowIndex)

atomList

public AtomList atomList(int row)

hasGaps

public boolean hasGaps()

Does the alignemnt include gaps? .