org.pistoiaalliance.helm.HELMSimilarityLibrary

Class PathGenerator

java.lang.Object

org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

public class PathGenerator
extends Object

PathGenerator class takes a moleculeGraph and finds all path from each monomer (vertex) up to a maximal length (searchDepth). Paths are found by depth first search.

Author:

bueltel

Field Summary

Fields

Modifier and Type	Field and Description
static Set<String>	totalNaturalPaths
static Set<String>	totalPaths

Constructor Summary

Constructors

Constructor and Description
PathGenerator()

Method Summary

Modifier and Type	Method and Description
static void	checkAndStorePath(String newOrigPath, List<String> listNewOrigPath, String newNatPath, List<String> listNewNatPath) Checks if path already exists as palindrome, stores valide paths depending on lexicographical order.
void	clearPaths()
void	findPaths(Graph moleculeGraph) Calls depthFirstSearch for every monomer (vertex).
Set<String>	getNaturalPaths()
String	getNaturalPeptide(String monomerUnit) Gets the natural analog of a peptide monomer.
String	getNaturalRNA(String monomerUnit) Gets the natural analog of a RNA monomer.
Set<String>	getPaths()

Methods inherited from class java.lang.Object

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

Field Detail

totalPaths

public static Set<String> totalPaths

totalNaturalPaths

public static Set<String> totalNaturalPaths

Constructor Detail

PathGenerator

public PathGenerator()

Method Detail

findPaths

public void findPaths(Graph moleculeGraph)
               throws NaturalAnalogException

Calls depthFirstSearch for every monomer (vertex).

Parameters:

moleculeGraph - The moleculeGraph of a HELM notation

Throws:

NaturalAnalogException - if natural analog of a modified monomer cannot be found

checkAndStorePath

public static void checkAndStorePath(String newOrigPath,
                                     List<String> listNewOrigPath,
                                     String newNatPath,
                                     List<String> listNewNatPath)

Checks if path already exists as palindrome, stores valide paths depending on lexicographical order.

Parameters:

newOrigPath - original path to be checked

listNewOrigPath - list of original path to be checked

newNatPath - natural path to be checked

listNewNatPath - list of natural path to be checked

getNaturalPeptide

public String getNaturalPeptide(String monomerUnit)

Gets the natural analog of a peptide monomer. If no natural analog is found, the original monomer is returned.

Parameters:

monomerUnit - The modified monomer that the natural analog is looked for

Returns:

natural analog string

getNaturalRNA

public String getNaturalRNA(String monomerUnit)

Gets the natural analog of a RNA monomer. If no natural analog is found, the original monomer is returned.

Parameters:

monomerUnit - The modified monomer that the natural analog is looked for

Returns:

natural analog string

getPaths

public Set<String> getPaths()

getNaturalPaths

public Set<String> getNaturalPaths()

clearPaths

public void clearPaths()