vn.edu.tlu.hatrang.autoRWRMTN.internal.model

Class Common

java.lang.Object

vn.edu.tlu.hatrang.autoRWRMTN.internal.model.Common

public class Common
extends Object

Author:

Administrator

Field Summary

Fields

Modifier and Type	Field and Description
static ArrayList<ArrayList<Double>>	AllFPFs
static ArrayList<ArrayList<Double>>	AllPrecisions
static ArrayList<ArrayList<Double>>	AllTPFs
static Map<String,Map<String,Double>>	Disease2miRNA2WeightMapMap
static String	DiseaseFileName
static ArrayList<Interaction>	DiseaseInteractionArray
static Set<String>	DiseasekNodeSet
static ArrayList<String>	DiseaseNodeArray
static String	DiseaseTerm
static Evaluation	Eval
static ArrayList<Interaction>	Gene2MimNetwork
static Map<String,String>	ID2NameMap
static Map<String,ArrayList<NodeInteraction>>	IncomingNodeTable
static boolean	isWeighted
static ArrayList<Interaction>	Mim2GeneNetwork
static Map<String,Map<String,Double>>	miRNA2Gene2WeightMapMap
static String	NetworkFileName
static ArrayList<Interaction>	NetworkInteractionArray
static Set<String>	NetworkMIMSet
static ArrayList<String>	NetworkNodeArray
static Set<String>	NetworkNodeSet
static int	numOfEvidence
static ArrayList<Interaction>	OriginalNetwork
static ArrayList<String>	OriginalNetworkNode
static ArrayList<Interaction>	OriginalPhenotypeNetwork
static ArrayList<String>	OriginalPhenotypeNetworkNode
static Map<String,PMInfo>	PMID_info
static String	RankMethod

Constructor Summary

Constructors

Constructor and Description
Common()

Method Summary

Modifier and Type	Method and Description
static void	applyNetworkVisualStyle(org.cytoscape.model.CyNetwork network, org.cytoscape.view.model.CyNetworkView view, String vsNetworkName, org.cytoscape.view.vizmap.VisualMappingManager vmm, org.cytoscape.view.vizmap.VisualStyleFactory visualStyleFactory, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryP, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryD, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryC)
static Map<String,ArrayList<NodeInteraction>>	calculateIncomingNeighbors(ArrayList<Interaction> Network)
static Map<String,ArrayList<NodeInteraction>>	calculateOutgoingNeighbors(ArrayList<Interaction> Network)
static org.cytoscape.view.vizmap.VisualStyle	createNetworkVisualStyle(org.cytoscape.model.CyNetwork network, String vsNetworkName, org.cytoscape.view.vizmap.VisualStyleFactory visualStyleFactory, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryP, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryD, org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryC)
static ArrayList<Integer>	evaluateByRWRMDA(Set<String> AssociatedmiRNASet, Map<String,ArrayList<NodeInteraction>> IncomingNodeTable, double gamma)
static Map<Integer,String>	evaluateByRWRMTN(Map<String,Double> NodeScore, Set<String> AssociatedmiRNASet, Map<String,Map<String,Double>> miRNA2GeneMap, Map<String,ArrayList<NodeInteraction>> IncomingNodeTable, double alpha, double gamma, ArrayList<String> arrUserMiRNA)
static void	evaluatePerformance(int MaxRank, ArrayList<Integer> HoldoutRanks)
static <T,E> T	getKeyByValue(Map<T,E> map, E value)
static <T,E> Set<T>	getKeysByValue(Map<T,E> map, E value)
static org.cytoscape.model.CyNetwork	getNetworkByName(org.cytoscape.model.CyNetworkManager cyNetworkManager, String name)
static PMInfo	getPMIDinfo(String id)
static Set<String>	getPubMedIDFromPubMedSearch(String term, Map<String,PMInfo> map)
static org.cytoscape.view.vizmap.VisualStyle	getVisualStyleByName(String styleName, org.cytoscape.view.vizmap.VisualMappingManager vmm)
static Map<String,Set<String>>	loadEntity2Elements(String Entity2ElementFile)
static double	normL2(Map<String,Double> vector0, Map<String,Double> vector1)
static void	preprocessInteractionList(ArrayList<Interaction> Interactions, String By)
static void	quickSortInteraction(ArrayList<Interaction> A, int lower, int upper)
static void	quickSortNodeInDescScore(ArrayList<Node> A, int lower, int upper)
static Map<String,Integer>	rankByRWR(Map<String,ArrayList<NodeInteraction>> IncomingNodeTable, double gamma, Map<String,Double> Priors, Map<String,Double> NodeScore)
static PMInfo	readJsonStream(InputStream in)
static PMInfo	readStream(InputStream in)
static ArrayList<Integer>	searchUsingBinaryInteraction(String searchterm, ArrayList<Interaction> List)
static int	searchUsingBinaryInteractionDetail(String key, ArrayList<Interaction> a, int lo, int hi)
static void	sortQuickInteractionListInAsc(ArrayList<Interaction> Interactions)
static void	sortQuickNodeListInDescScore(ArrayList<Node> Nodes)

Methods inherited from class java.lang.Object

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

Field Detail

RankMethod

public static String RankMethod

NetworkFileName

public static String NetworkFileName

DiseaseFileName

public static String DiseaseFileName

miRNA2Gene2WeightMapMap

public static Map<String,Map<String,Double>> miRNA2Gene2WeightMapMap

Disease2miRNA2WeightMapMap

public static Map<String,Map<String,Double>> Disease2miRNA2WeightMapMap

ID2NameMap

public static Map<String,String> ID2NameMap

PMID_info

public static Map<String,PMInfo> PMID_info

NetworkNodeArray

public static ArrayList<String> NetworkNodeArray

NetworkNodeSet

public static Set<String> NetworkNodeSet

IncomingNodeTable

public static Map<String,ArrayList<NodeInteraction>> IncomingNodeTable

NetworkInteractionArray

public static ArrayList<Interaction> NetworkInteractionArray

DiseaseNodeArray

public static ArrayList<String> DiseaseNodeArray

DiseasekNodeSet

public static Set<String> DiseasekNodeSet

DiseaseInteractionArray

public static ArrayList<Interaction> DiseaseInteractionArray

DiseaseTerm

public static String DiseaseTerm

AllTPFs

public static ArrayList<ArrayList<Double>> AllTPFs

AllPrecisions

public static ArrayList<ArrayList<Double>> AllPrecisions

AllFPFs

public static ArrayList<ArrayList<Double>> AllFPFs

Eval

public static Evaluation Eval

isWeighted

public static boolean isWeighted

OriginalNetworkNode

public static ArrayList<String> OriginalNetworkNode

OriginalPhenotypeNetworkNode

public static ArrayList<String> OriginalPhenotypeNetworkNode

OriginalNetwork

public static ArrayList<Interaction> OriginalNetwork

OriginalPhenotypeNetwork

public static ArrayList<Interaction> OriginalPhenotypeNetwork

NetworkMIMSet

public static Set<String> NetworkMIMSet

Mim2GeneNetwork

public static ArrayList<Interaction> Mim2GeneNetwork

Gene2MimNetwork

public static ArrayList<Interaction> Gene2MimNetwork

numOfEvidence

public static int numOfEvidence

Constructor Detail

Common

public Common()

Method Detail

evaluatePerformance

public static void evaluatePerformance(int MaxRank,
                                       ArrayList<Integer> HoldoutRanks)

getNetworkByName

public static org.cytoscape.model.CyNetwork getNetworkByName(org.cytoscape.model.CyNetworkManager cyNetworkManager,
                                                             String name)

getKeysByValue

public static <T,E> Set<T> getKeysByValue(Map<T,E> map,
                                          E value)

getKeyByValue

public static <T,E> T getKeyByValue(Map<T,E> map,
                                    E value)

rankByRWR

public static Map<String,Integer> rankByRWR(Map<String,ArrayList<NodeInteraction>> IncomingNodeTable,
                                            double gamma,
                                            Map<String,Double> Priors,
                                            Map<String,Double> NodeScore)

evaluateByRWRMDA

public static ArrayList<Integer> evaluateByRWRMDA(Set<String> AssociatedmiRNASet,
                                                  Map<String,ArrayList<NodeInteraction>> IncomingNodeTable,
                                                  double gamma)

evaluateByRWRMTN

public static Map<Integer,String> evaluateByRWRMTN(Map<String,Double> NodeScore,
                                                   Set<String> AssociatedmiRNASet,
                                                   Map<String,Map<String,Double>> miRNA2GeneMap,
                                                   Map<String,ArrayList<NodeInteraction>> IncomingNodeTable,
                                                   double alpha,
                                                   double gamma,
                                                   ArrayList<String> arrUserMiRNA)

normL2

public static double normL2(Map<String,Double> vector0,
                            Map<String,Double> vector1)

loadEntity2Elements

public static Map<String,Set<String>> loadEntity2Elements(String Entity2ElementFile)
                                                   throws Exception

Throws:

Exception

preprocessInteractionList

public static void preprocessInteractionList(ArrayList<Interaction> Interactions,
                                             String By)

sortQuickInteractionListInAsc

public static void sortQuickInteractionListInAsc(ArrayList<Interaction> Interactions)

quickSortInteraction

public static void quickSortInteraction(ArrayList<Interaction> A,
                                        int lower,
                                        int upper)

searchUsingBinaryInteraction

public static ArrayList<Integer> searchUsingBinaryInteraction(String searchterm,
                                                              ArrayList<Interaction> List)

searchUsingBinaryInteractionDetail

public static int searchUsingBinaryInteractionDetail(String key,
                                                     ArrayList<Interaction> a,
                                                     int lo,
                                                     int hi)

sortQuickNodeListInDescScore

public static void sortQuickNodeListInDescScore(ArrayList<Node> Nodes)

quickSortNodeInDescScore

public static void quickSortNodeInDescScore(ArrayList<Node> A,
                                            int lower,
                                            int upper)

calculateOutgoingNeighbors

public static Map<String,ArrayList<NodeInteraction>> calculateOutgoingNeighbors(ArrayList<Interaction> Network)

calculateIncomingNeighbors

public static Map<String,ArrayList<NodeInteraction>> calculateIncomingNeighbors(ArrayList<Interaction> Network)

getVisualStyleByName

public static org.cytoscape.view.vizmap.VisualStyle getVisualStyleByName(String styleName,
                                                                         org.cytoscape.view.vizmap.VisualMappingManager vmm)

applyNetworkVisualStyle

public static void applyNetworkVisualStyle(org.cytoscape.model.CyNetwork network,
                                           org.cytoscape.view.model.CyNetworkView view,
                                           String vsNetworkName,
                                           org.cytoscape.view.vizmap.VisualMappingManager vmm,
                                           org.cytoscape.view.vizmap.VisualStyleFactory visualStyleFactory,
                                           org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryP,
                                           org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryD,
                                           org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryC)

createNetworkVisualStyle

public static org.cytoscape.view.vizmap.VisualStyle createNetworkVisualStyle(org.cytoscape.model.CyNetwork network,
                                                                             String vsNetworkName,
                                                                             org.cytoscape.view.vizmap.VisualStyleFactory visualStyleFactory,
                                                                             org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryP,
                                                                             org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryD,
                                                                             org.cytoscape.view.vizmap.VisualMappingFunctionFactory vmfFactoryC)

getPubMedIDFromPubMedSearch

public static Set<String> getPubMedIDFromPubMedSearch(String term,
                                                      Map<String,PMInfo> map)

getPMIDinfo

public static PMInfo getPMIDinfo(String id)

readStream

public static PMInfo readStream(InputStream in)

readJsonStream

public static PMInfo readJsonStream(InputStream in)
                             throws UnsupportedEncodingException

Throws:

UnsupportedEncodingException