meshi.sequences
Class SequenceAlignmentCell

java.lang.Object
  meshi.sequences.AlignmentCell
      meshi.sequences.SequenceAlignmentCell

All Implemented Interfaces:

Attributable, MeshiAttribute

public class SequenceAlignmentCell
extends AlignmentCell
implements MeshiAttribute

Field Summary

static java.lang.Character	GAP
static char	GAP_CHAR
static java.lang.Character	WILDCARD
static char	WILDCARD_CHAR

Fields inherited from class meshi.sequences.AlignmentCell

comment, number, obj

Fields inherited from interface meshi.util.MeshiAttribute

BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE

Constructor Summary

SequenceAlignmentCell()

SequenceAlignmentCell(char c, int number)

SequenceAlignmentCell(int number)

Method Summary

boolean	equals(java.lang.Object obj)
boolean	gap()
MeshiAttribute	getAttribute()
char	getChar()
java.lang.String	getCharAsString()
int	key()
java.lang.String	toString()
boolean	wildcard()
static boolean	wildcardOrGap(SequenceAlignmentCell cell)
static boolean	wildcardOrGap(SequenceAlignmentColumn column)

Methods inherited from class meshi.sequences.AlignmentCell

addAttribute, column, getAttribute, number, object

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

GAP_CHAR

public static final char GAP_CHAR

See Also:

Constant Field Values

GAP

public static final java.lang.Character GAP

WILDCARD_CHAR

public static final char WILDCARD_CHAR

See Also:

Constant Field Values

WILDCARD

public static final java.lang.Character WILDCARD

Constructor Detail

SequenceAlignmentCell

public SequenceAlignmentCell(char c,
                             int number)

SequenceAlignmentCell

public SequenceAlignmentCell(int number)

SequenceAlignmentCell

public SequenceAlignmentCell()

Method Detail

getChar

public char getChar()

getCharAsString

public java.lang.String getCharAsString()

gap

public boolean gap()

Specified by:

gap in class AlignmentCell

wildcard

public boolean wildcard()

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

wildcardOrGap

public static boolean wildcardOrGap(SequenceAlignmentCell cell)

wildcardOrGap

public static boolean wildcardOrGap(SequenceAlignmentColumn column)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAttribute

public MeshiAttribute getAttribute()

key

public int key()

Specified by:

key in interface MeshiAttribute