meshi.sequences
Class AccesibilitySequence

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

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 AccesibilitySequence
extends Sequence

See Also:

Serialized Form

Nested Class Summary

private static class

AccesibilitySequence.AccesibilitySequenceCharFilter

Field Summary

static AccesibilitySequence.AccesibilitySequenceCharFilter

AccesibilityCharFilter

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

AccesibilitySequence(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

AccesibilityCharFilter

public static final AccesibilitySequence.AccesibilitySequenceCharFilter AccesibilityCharFilter

Constructor Detail

AccesibilitySequence

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