meshi.sequences
Class SequenceAlignment

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

All Implemented Interfaces:

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

Direct Known Subclasses:

PredictionSequenceAlignment, Sequence

public class SequenceAlignment
extends java.util.ArrayList<SequenceAlignmentColumn>

See Also:

Serialized Form

Field Summary

StringList	comments
private java.lang.Double	score

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

SequenceAlignment()

SequenceAlignment(ResidueAlignment residueAlignment)

SequenceAlignment(SequenceList sequenceList)

SequenceAlignment(Sequence sequence1, Sequence sequence2)

Method Summary

AlignmentColumn	getColumn(int row, int number) Fetches a column with a specific cell number in a specific row.
static SequenceAlignment	identityAlignment(Sequence sequence1, Sequence sequence2)
boolean	isExactMach()
boolean	isExactMachWithGaps()
void	print()
double	score()
void	setScore(double score)
java.lang.String	toString()

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

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

score

private java.lang.Double score

comments

public final StringList comments

Constructor Detail

SequenceAlignment

public SequenceAlignment()

SequenceAlignment

public SequenceAlignment(ResidueAlignment residueAlignment)

SequenceAlignment

public SequenceAlignment(Sequence sequence1,
                         Sequence sequence2)

SequenceAlignment

public SequenceAlignment(SequenceList sequenceList)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<SequenceAlignmentColumn>

isExactMach

public boolean isExactMach()

isExactMachWithGaps

public boolean isExactMachWithGaps()

identityAlignment

public static SequenceAlignment identityAlignment(Sequence sequence1,
                                                  Sequence sequence2)

score

public double score()

setScore

public void setScore(double score)

print

public void print()

getColumn

public AlignmentColumn getColumn(int row,
                                 int number)

Fetches a column with a specific cell number in a specific row. This column now is a handle to the corresponding elements of the other proteins.