taskspaces.rna
Class DatabaseEntry

java.lang.Object
  |
  +--taskspaces.rna.DatabaseEntry

All Implemented Interfaces:

java.io.Serializable

public class DatabaseEntry

extends java.lang.Object

implements java.io.Serializable

DatabaseEntry represents a lab-isolated set of motifs, structures and constraints. The class instantiated by a parser for XML data representing the entries.

Version:

1.00 2 January 2003

Author:

Rob Markel

See Also:

Serialized Form

Field Summary

(package private) java.lang.String[]	basePairs Holds the valid base pairs.
(package private) float[]	composition Holds the current percentage composition of bases.
(package private) java.util.ArrayList	constraints Holds integer arrays representing pairing rules for this entry.
(package private) boolean	gu Indicates whether to allow GU or UG pairs.
(package private) java.lang.String[]	modules Holds the entry sequence modules.
(package private) java.lang.String	name Holds the name of the entry.
(package private) float[]	pairProbs Holds the probabilities for each base pair being selected based on the current composition.
(package private) java.lang.String[]	structures Holds the entry sequence structures.

Constructor Summary

DatabaseEntry(java.lang.String name, java.lang.String[] modules, java.lang.String[] structures, java.util.ArrayList constraints)

Method Summary

java.lang.String[]	generateModules() Modifies modules to match the entry's set of pairing constraints.
java.util.ArrayList	getConstraints() Returns this entry's constraints.
java.lang.String[]	getModules() Returns this entry's sequence modules.
java.lang.String	getName() Returns this entry's name.
private char[]	getPair() Returns a pair of bases using the probabilities in the pairProbs array set by the initializeArrays method.
java.lang.String[]	getStructures() Returns this entry's sequence structures.
private void	initializeArrays() Initializes the pairProbs probabilities array with the probabilities of each base pair being selected based on the percentages in the composition array.
void	setComposition(float[] f, boolean b) Sets the composition for this entry.

Methods inherited from class java.lang.Object

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

Field Detail

name

java.lang.String name

Holds the name of the entry.

modules

java.lang.String[] modules

Holds the entry sequence modules.

structures

java.lang.String[] structures

Holds the entry sequence structures.

basePairs

java.lang.String[] basePairs

Holds the valid base pairs.

pairProbs

float[] pairProbs

Holds the probabilities for each base pair being selected based on the current composition.

composition

float[] composition

Holds the current percentage composition of bases.

gu

boolean gu

Indicates whether to allow GU or UG pairs.

constraints

java.util.ArrayList constraints

Holds integer arrays representing pairing rules for this entry.

Constructor Detail

DatabaseEntry

public DatabaseEntry(java.lang.String name,
                     java.lang.String[] modules,
                     java.lang.String[] structures,
                     java.util.ArrayList constraints)

Method Detail

setComposition

public void setComposition(float[] f,
                           boolean b)

Sets the composition for this entry.

Parameters:

f - holds percent values for the composition.

b - true if allow GU, false to disallow.

generateModules

public java.lang.String[] generateModules()

Modifies modules to match the entry's set of pairing constraints.

Returns:

the modified modules.

getConstraints

public java.util.ArrayList getConstraints()

Returns this entry's constraints.

Returns:

the constriants.

getModules

public java.lang.String[] getModules()

Returns this entry's sequence modules.

Returns:

the sequence modules.

getStructures

public java.lang.String[] getStructures()

Returns this entry's sequence structures.

Returns:

the sequence structures.

getName

public java.lang.String getName()

Returns this entry's name.

Returns:

the entry name.

initializeArrays

private void initializeArrays()

Initializes the pairProbs probabilities array with the probabilities of each base pair being selected based on the percentages in the composition array.

Returns:

void.

getPair

private char[] getPair()

Returns a pair of bases using the probabilities in the pairProbs array set by the initializeArrays method.

Returns:

the base pair.