meshi.sequences
Class AlignmentColumn

java.lang.Object
  meshi.sequences.AlignmentColumn

Direct Known Subclasses:

AtomAlignmentColumn, ResidueAlignmentColumn, SequenceAlignmentColumn

public class AlignmentColumn
extends java.lang.Object

A container for an ordered set of coresponding protein elements. Each of the elements comes form a different protein.

Field Summary

protected AlignmentCell[]

cells

Constructor Summary

	AlignmentColumn(AlignmentCell cell0, AlignmentCell cell1)
protected	AlignmentColumn(int numberOfRows) Utility constructor for the sub-classes.

Method Summary

void	add(int index, AlignmentCell cell)
boolean	allGaps()
AlignmentCell	cell(int index)
AlignmentCell	cell0()
AlignmentCell	cell1()
boolean	hasGap()
int	size()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

cells

protected AlignmentCell[] cells

Constructor Detail

AlignmentColumn

protected AlignmentColumn(int numberOfRows)

Utility constructor for the sub-classes.

AlignmentColumn

public AlignmentColumn(AlignmentCell cell0,
                       AlignmentCell cell1)

Method Detail

add

public void add(int index,
                AlignmentCell cell)

cell0

public AlignmentCell cell0()

cell1

public AlignmentCell cell1()

cell

public AlignmentCell cell(int index)

hasGap

public boolean hasGap()

allGaps

public boolean allGaps()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

size

public int size()