meshi.sequences
Class SecondaryStructureSequence

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

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 SecondaryStructureSequence
extends Sequence

See Also:

Serialized Form

Nested Class Summary

private static class

SecondaryStructureSequence.SecondaryStructureSequenceCharFilter

Field Summary

static SecondaryStructureSequence.SecondaryStructureSequenceCharFilter

secondaryStructureCharFilter

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

SecondaryStructureSequence(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

secondaryStructureCharFilter

public static final SecondaryStructureSequence.SecondaryStructureSequenceCharFilter secondaryStructureCharFilter

Constructor Detail

SecondaryStructureSequence

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