org.peace_tools.data
Class ESTEntry

java.lang.Object
  org.peace_tools.data.ESTEntry

public class ESTEntry
extends java.lang.Object

A class that represents a single EST entry in PreAlignmentModel. This class is a pure data class that is used to encapsulate the information pertaining to the position of an EST node as used by the PreAlignmentModel class. This class is used to encapsulate information that is needed to represent the relative position of an EST in an alignment model. This class encapsulates the following information:

• The data about the actual EST itself. This information is useful when rendering EST entries in a given view.
• The cluster number to which this EST belongs.
• The column from where this EST is to be rendered on screen.

Field Summary

(package private) int	alignmentMetric The alignment metric generated by a given EST analyzer indicating some of the alignment relationship between this node and its parent node.
private int	clusterID The ID of the cluster to which the EST Entry belongs.
private int	colPos The starting column position for this entry.
private EST	est The EST node for this ESTEntry.

Constructor Summary

protected

ESTEntry(EST est, int clusterID, int colPos) Constructor to create an object.

Method Summary

int	getClusterID() Returns the ID of the cluster to which this entry belongs.
int	getColumn() Obtain the starting column position where this entry is to be placed.
EST	getEST() Returns the actual EST object set for this node.

Methods inherited from class java.lang.Object

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

Field Detail

est

private final EST est

The EST node for this ESTEntry. This value is set in the constructor and is never changed during the life-time of this object.

clusterID

private final int clusterID

The ID of the cluster to which the EST Entry belongs. This information is set in the constructor and is never changed during the life time of this class.

colPos

private final int colPos

The starting column position for this entry. This value is set when this object is created.

alignmentMetric

int alignmentMetric

The alignment metric generated by a given EST analyzer indicating some of the alignment relationship between this node and its parent node.

Constructor Detail

ESTEntry

protected ESTEntry(EST est,
                   int clusterID,
                   int colPos)

Constructor to create an object. This constructor provides a convenient mechanism to create and initialize an ESTEntry object with necessary information. This constructor is primarily used by the PreAlignmentModel class.

Parameters:

est - The actual EST object for which this entry is being created.

clusterID - The ID of the cluster to which the given EST entry belongs.

colPos - The zero-based column position from where the EST is to be rendered. This column position indicates the position of the left-most nucleotide in the EST.

See Also:

OverlapModel

Method Detail

getEST

public EST getEST()

Returns the actual EST object set for this node. This method returns the actual EST entry associated with this entry when it was instantiated.

Returns:

The actual EST object set for this entry.

getClusterID

public int getClusterID()

Returns the ID of the cluster to which this entry belongs. This method returns the cluster ID value set for this entry when it was instantiated.

Returns:

The ID of the cluster to which this entry belongs.

getColumn

public int getColumn()

Obtain the starting column position where this entry is to be placed.

Returns:

The starting column position for this entry. This value indicates the position of the left-most nucleotide in this EST.