meshi.sequences
Class ResidueSequence

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<SequenceAlignmentColumn>
              meshi.sequences.SequenceAlignment
                  meshi.sequences.Sequence
                      meshi.sequences.ResidueSequence

All Implemented Interfaces:

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

public class ResidueSequence
extends Sequence

See Also:

Serialized Form

Nested Class Summary

private static class

ResidueSequence.ResidueSequenceCharFilter

Field Summary

static ResidueSequence.ResidueSequenceCharFilter

residueCharFilter

Fields inherited from class meshi.sequences.Sequence

charFilter, UNKNOWN

Fields inherited from class meshi.sequences.SequenceAlignment

comments

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ResidueSequence()

ResidueSequence(FastaList fastaList)

ResidueSequence(FastaList fastaList, int index)

ResidueSequence(ResidueList residueList, java.lang.String comment)

ResidueSequence(Sequence sequence)

ResidueSequence(java.lang.String comment)

ResidueSequence(java.lang.String sequence, java.lang.String comment)

Method Summary

Methods inherited from class meshi.sequences.Sequence

add, add, cell, charAt, comment, getChar, getCharAsString, getSs, renumber, renumber, startsIn, tail, toString, weirdChar

Methods inherited from class meshi.sequences.SequenceAlignment

getColumn, identityAlignment, isExactMach, isExactMachWithGaps, print, score, setScore

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

residueCharFilter

public static final ResidueSequence.ResidueSequenceCharFilter residueCharFilter

Constructor Detail

ResidueSequence

public ResidueSequence()

ResidueSequence

public ResidueSequence(java.lang.String comment)

ResidueSequence

public ResidueSequence(java.lang.String sequence,
                       java.lang.String comment)

ResidueSequence

public ResidueSequence(Sequence sequence)

ResidueSequence

public ResidueSequence(FastaList fastaList)

ResidueSequence

public ResidueSequence(FastaList fastaList,
                       int index)

ResidueSequence

public ResidueSequence(ResidueList residueList,
                       java.lang.String comment)