meshi.sequences
Class SequenceAlignmentColumn

java.lang.Object
  meshi.sequences.AlignmentColumn
      meshi.sequences.SequenceAlignmentColumn

All Implemented Interfaces:

MeshiAttribute

public class SequenceAlignmentColumn
extends AlignmentColumn
implements MeshiAttribute

Field Summary

Fields inherited from class meshi.sequences.AlignmentColumn

cells

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

SequenceAlignmentColumn(char char0, int number0, char char1, int number1)

SequenceAlignmentColumn(int numberOfRows)

SequenceAlignmentColumn(ResidueAlignmentColumn residueAlignmentColumn)

SequenceAlignmentColumn(SequenceAlignmentCell cell)

SequenceAlignmentColumn(SequenceAlignmentCell cell0, SequenceAlignmentCell cell1)

Method Summary

void	add(int index, char char1, int position)
private static SequenceAlignmentCell	createCell(char char1, int number1)
char	getChar(int index)
boolean	isExactMach()
boolean	isExactMachWithGaps()
int	key()

Methods inherited from class meshi.sequences.AlignmentColumn

add, allGaps, cell, cell0, cell1, hasGap, size, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceAlignmentColumn

public SequenceAlignmentColumn(ResidueAlignmentColumn residueAlignmentColumn)

SequenceAlignmentColumn

public SequenceAlignmentColumn(int numberOfRows)

SequenceAlignmentColumn

public SequenceAlignmentColumn(SequenceAlignmentCell cell)

SequenceAlignmentColumn

public SequenceAlignmentColumn(SequenceAlignmentCell cell0,
                               SequenceAlignmentCell cell1)

SequenceAlignmentColumn

public SequenceAlignmentColumn(char char0,
                               int number0,
                               char char1,
                               int number1)

Method Detail

add

public void add(int index,
                char char1,
                int position)

createCell

private static SequenceAlignmentCell createCell(char char1,
                                                int number1)

getChar

public char getChar(int index)

isExactMachWithGaps

public boolean isExactMachWithGaps()

isExactMach

public boolean isExactMach()

key

public int key()

Specified by:

key in interface MeshiAttribute