meshi.sequences
Class Sequence

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

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:

AccesibilitySequence, ResidueSequence, SecondaryStructureSequence

public class Sequence
extends SequenceAlignment

Sequence is a single row alignment.

See Also:

Serialized Form

Nested Class Summary

private static class

Sequence.kolDichfin

Field Summary

SequenceCharFilter	charFilter
static char	UNKNOWN

Fields inherited from class meshi.sequences.SequenceAlignment

comments

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Sequence(Chain chain, java.lang.String comment)

Sequence(SequenceCharFilter charFilter)

Sequence(Sequence source, SequenceCharFilter charFilter)

Sequence(java.lang.String comment)

Sequence(java.lang.String comment, SequenceCharFilter charFilter)

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

Sequence(java.lang.String sequence, java.lang.String comment, SequenceCharFilter charFilter)

Method Summary

boolean	add(SequenceAlignmentCell cell)
boolean	add(SequenceAlignmentColumn column)
SequenceAlignmentCell	cell(int index)
char	charAt(int index)
java.lang.String	comment()
private static java.lang.String	getChainSequence(Chain chain)
char	getChar(int index)
java.lang.String	getCharAsString(int index)
SecondaryStructure	getSs(int index)
Sequence	renumber(Sequence reference)
Sequence	renumber(SequenceAlignment alignment)
int	startsIn()
Sequence	tail()
java.lang.String	toString()
java.lang.Character	weirdChar(java.lang.String sequence)

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

charFilter

public final SequenceCharFilter charFilter

UNKNOWN

public static final char UNKNOWN

See Also:

Constant Field Values

Constructor Detail

Sequence

public Sequence(java.lang.String comment)

Sequence

public Sequence(SequenceCharFilter charFilter)

Sequence

public Sequence(java.lang.String comment,
                SequenceCharFilter charFilter)

Sequence

public Sequence(Chain chain,
                java.lang.String comment)

Sequence

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

Sequence

public Sequence(java.lang.String sequence,
                java.lang.String comment,
                SequenceCharFilter charFilter)

Sequence

public Sequence(Sequence source,
                SequenceCharFilter charFilter)

Method Detail

add

public boolean add(SequenceAlignmentColumn column)

Specified by:

add in interface java.util.Collection<SequenceAlignmentColumn>

Specified by:

add in interface java.util.List<SequenceAlignmentColumn>

Overrides:

add in class java.util.ArrayList<SequenceAlignmentColumn>

weirdChar

public java.lang.Character weirdChar(java.lang.String sequence)

comment

public java.lang.String comment()

startsIn

public int startsIn()

toString

public java.lang.String toString()

Overrides:

toString in class SequenceAlignment

cell

public SequenceAlignmentCell cell(int index)

getChar

public char getChar(int index)

getCharAsString

public java.lang.String getCharAsString(int index)

getSs

public SecondaryStructure getSs(int index)

charAt

public char charAt(int index)

renumber

public Sequence renumber(Sequence reference)

tail

public Sequence tail()

renumber

public Sequence renumber(SequenceAlignment alignment)

add

public boolean add(SequenceAlignmentCell cell)

getChainSequence

private static java.lang.String getChainSequence(Chain chain)