meshi.sequences
Class ResidueAlignment

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<ResidueAlignmentColumn>
              meshi.sequences.ResidueAlignment

All Implemented Interfaces:

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

Direct Known Subclasses:

ResidueAlignmentOfModels

public class ResidueAlignment
extends java.util.ArrayList<ResidueAlignmentColumn>

See Also:

Serialized Form

Field Summary

StringList	comments
private ResidueAlignmentColumn	lastColumn

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ResidueAlignment()
Empty alignment.

ResidueAlignment(Chain chain0, Chain chain1, SequenceList sequenceList)

ResidueAlignment(Chain chain1, java.lang.String name1, Chain chain2, java.lang.String name2)
A trevial alignment of two protein objects which are assumed to be two models of the same protein.

ResidueAlignment(ResidueSequence residueSequence0, ResidueSequence residueSequence1)

ResidueAlignment(SequenceAlignment sequenceAlignment)

Method Summary

boolean	add(ResidueAlignmentColumn column)
ResidueAlignment	filter(Filter filter)
AtomList	getCaList(int row)
ResidueAlignment	insert(ResidueAlignmentColumn column)
java.lang.String	toString()

Methods inherited from class java.util.ArrayList

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

lastColumn

private ResidueAlignmentColumn lastColumn

comments

public final StringList comments

Constructor Detail

ResidueAlignment

public ResidueAlignment()

Empty alignment.

ResidueAlignment

public ResidueAlignment(Chain chain1,
                        java.lang.String name1,
                        Chain chain2,
                        java.lang.String name2)

A trevial alignment of two protein objects which are assumed to be two models of the same protein.

ResidueAlignment

public ResidueAlignment(ResidueSequence residueSequence0,
                        ResidueSequence residueSequence1)

ResidueAlignment

public ResidueAlignment(Chain chain0,
                        Chain chain1,
                        SequenceList sequenceList)

ResidueAlignment

public ResidueAlignment(SequenceAlignment sequenceAlignment)

Method Detail

add

public boolean add(ResidueAlignmentColumn column)

Specified by:

add in interface java.util.Collection<ResidueAlignmentColumn>

Specified by:

add in interface java.util.List<ResidueAlignmentColumn>

Overrides:

add in class java.util.ArrayList<ResidueAlignmentColumn>

insert

public ResidueAlignment insert(ResidueAlignmentColumn column)

getCaList

public AtomList getCaList(int row)

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<ResidueAlignmentColumn>

filter

public ResidueAlignment filter(Filter filter)