public class SubnetworkProperties
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
ADD_FIRST_NEIGHBOURS |
boolean |
addOnlyConnectingNeighbours |
float |
averageSizeOfRandomBiggestComponent |
java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> |
complexMap |
static int |
CONNECT_BY_SHORTEST_PATHS |
java.util.HashMap<java.lang.Integer,java.util.Vector<Node>> |
degreeDistribution |
java.util.Vector<java.lang.Integer> |
degrees |
int[][] |
distributionOfConnectedComponentSizes |
java.util.Vector<Node> |
listOfNodesInitial |
int |
modeOfSubNetworkConstruction |
Graph |
network |
int[][] |
networkDistanceMatrix |
java.lang.String |
path |
java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> |
proteinComplexMap |
java.util.Vector<Graph> |
sampling |
float[] |
significanceOfConnectedComponents |
static int |
SIMPLY_CONNECT |
static int |
SIMPLY_CONNECT_WITH_COMPLEX_NODES |
static int |
SIMPLY_CONNECT_WITH_SECOND_ORDER_CONNECTIONS |
Graph |
subnetwork |
java.util.HashMap<java.lang.String,java.lang.Integer> |
SubnetworkComplexProfile |
double[][] |
subnetworkDistanceMatrix |
Constructor and Description |
---|
SubnetworkProperties() |
Modifier and Type | Method and Description |
---|---|
void |
addComplexesToNetworkAsClicks() |
void |
addComplexesToNetworksAsNodes() |
void |
addComplexNodes() |
static void |
addComplexNodes(Graph subgraph,
Graph network) |
void |
addFirstNeighbours() |
static void |
addFirstNeighbours(Graph subgraph,
Graph network,
boolean onlyConnecting) |
static void |
assignEdgeWeightsByConnectivity(Graph graph,
boolean directedVersion) |
static double |
calcAveragePairwiseDistance(double[][] distMat) |
static void |
calcDegreeDistribution(Graph network,
java.util.HashMap<java.lang.Integer,java.util.Vector<Node>> degreeDistribution,
java.util.Vector<java.lang.Integer> degrees,
boolean printDistribution) |
static int[][] |
calcDistributionOfConnectedComponentSizes(Graph graph) |
static double[] |
calcNodeBetweenness(Graph graph,
java.util.Vector<java.lang.String> selected,
boolean directed,
boolean assignAttribute) |
static void |
calcPercolationThreshold(Graph graph) |
static java.lang.String |
calcSignificanceVsNumberOfGenes(Graph network,
java.util.Vector<java.lang.String> rankedListOfProteins,
int numberOfPermutations,
int[] nga) |
void |
calcSubnetworkComplexProfile() |
void |
connectByShortestPaths() |
static double[][] |
connectByShortestPaths(Graph subgraph,
Graph network) |
static double[][] |
extractDistanceSubMatrix(int[][] fullMat,
java.util.Vector<java.lang.Integer> listOfIndices) |
java.util.Vector<java.lang.Integer> |
generateSample(java.util.Vector<java.lang.Integer> listOfIndices,
boolean conserveDegrees,
java.util.Vector<java.lang.String> complexes,
java.util.Vector<java.lang.Integer> fixedIndices) |
void |
generateSampling(int numberOfSamples) |
void |
generateSamplingConserveDegreeDistribution(int numberOfSamples) |
float[] |
getAverageConnectivities() |
static float |
getAverageConnectivity(Graph gr) |
static java.util.Vector<Node> |
getNeighbours(Graph network,
Node n) |
static float |
getPValue(float val,
float[] samplings,
boolean toBeSmaller) |
float[] |
getSamplingSizes() |
void |
loadNetwork(java.lang.String fn) |
static void |
main(java.lang.String[] args) |
void |
makeCompactnessTest(java.lang.String distMatrixFile,
java.util.Vector<java.lang.Integer> listOfIndices,
int numOfSamples,
boolean conserveDegrees,
java.lang.String fileNameForComplexProfile,
int thresholdForComplexProfile,
java.util.Vector<java.lang.String> fixedNodes) |
void |
makeCompactnessTest(java.lang.String distMatrixFile,
java.util.Vector<java.lang.Integer> listOfIndices,
int numOfSamples,
boolean conserveDegrees,
java.util.Vector<java.lang.String> fixedNodes) |
void |
makeComplexProfile(java.lang.String fn) |
java.lang.String |
makeTestOfConnectivity(int numOfSamples,
boolean conserveDegrees,
java.lang.String fileNameForComplexProfile,
int thresholdForComplexProfile,
java.util.Vector<java.lang.String> fixedNodes) |
static Graph |
MergeGraphs(java.util.Vector<Graph> graphs) |
static void |
printMassif(float[] f) |
void |
produceConnectionsSecondOrder(Graph graph,
java.lang.String distMatrixFile) |
void |
produceConnectionsSecondOrderFromDistMatrix(Graph graph) |
void |
readComplexes(java.lang.String fn,
int complexMaximumSize) |
java.util.Vector<java.lang.String> |
readComplexProfile(java.lang.String fileNameForComplexProfile,
int thresholdForComplexProfile) |
void |
removeDoubleEdges() |
static void |
removeSelfInteractions(Graph gr) |
static void |
saveDistanceMatrix(double[][] distMat,
java.lang.String fn,
boolean roundDistance) |
void |
saveSampling() |
static Graph |
selectNodesFromList(Graph graph,
java.util.Vector<java.lang.String> list) |
void |
selectNodesFromList(java.util.Vector<java.lang.String> list) |
public Graph network
public java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> complexMap
public java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> proteinComplexMap
public java.util.HashMap<java.lang.String,java.lang.Integer> SubnetworkComplexProfile
public java.util.HashMap<java.lang.Integer,java.util.Vector<Node>> degreeDistribution
public java.util.Vector<java.lang.Integer> degrees
public java.util.Vector<Node> listOfNodesInitial
public Graph subnetwork
public java.util.Vector<Graph> sampling
public double[][] subnetworkDistanceMatrix
public int[][] networkDistanceMatrix
public boolean addOnlyConnectingNeighbours
public java.lang.String path
public int[][] distributionOfConnectedComponentSizes
public float[] significanceOfConnectedComponents
public float averageSizeOfRandomBiggestComponent
public static int SIMPLY_CONNECT
public static int SIMPLY_CONNECT_WITH_COMPLEX_NODES
public static int SIMPLY_CONNECT_WITH_SECOND_ORDER_CONNECTIONS
public static int ADD_FIRST_NEIGHBOURS
public static int CONNECT_BY_SHORTEST_PATHS
public int modeOfSubNetworkConstruction
public static void main(java.lang.String[] args)
args
- public void loadNetwork(java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public static void removeSelfInteractions(Graph gr)
public static void calcDegreeDistribution(Graph network, java.util.HashMap<java.lang.Integer,java.util.Vector<Node>> degreeDistribution, java.util.Vector<java.lang.Integer> degrees, boolean printDistribution)
public void selectNodesFromList(java.util.Vector<java.lang.String> list)
public static Graph selectNodesFromList(Graph graph, java.util.Vector<java.lang.String> list)
public void generateSampling(int numberOfSamples)
public void saveSampling() throws java.lang.Exception
java.lang.Exception
public void generateSamplingConserveDegreeDistribution(int numberOfSamples)
public static float getPValue(float val, float[] samplings, boolean toBeSmaller)
public static float getAverageConnectivity(Graph gr)
public float[] getAverageConnectivities()
public float[] getSamplingSizes()
public static void printMassif(float[] f)
public static void addFirstNeighbours(Graph subgraph, Graph network, boolean onlyConnecting)
public void addFirstNeighbours()
public void addComplexNodes()
public static double[][] connectByShortestPaths(Graph subgraph, Graph network)
public static double[] calcNodeBetweenness(Graph graph, java.util.Vector<java.lang.String> selected, boolean directed, boolean assignAttribute)
public void connectByShortestPaths()
public static void saveDistanceMatrix(double[][] distMat, java.lang.String fn, boolean roundDistance) throws java.lang.Exception
java.lang.Exception
public static void assignEdgeWeightsByConnectivity(Graph graph, boolean directedVersion)
public void makeCompactnessTest(java.lang.String distMatrixFile, java.util.Vector<java.lang.Integer> listOfIndices, int numOfSamples, boolean conserveDegrees, java.util.Vector<java.lang.String> fixedNodes) throws java.lang.Exception
java.lang.Exception
public void makeCompactnessTest(java.lang.String distMatrixFile, java.util.Vector<java.lang.Integer> listOfIndices, int numOfSamples, boolean conserveDegrees, java.lang.String fileNameForComplexProfile, int thresholdForComplexProfile, java.util.Vector<java.lang.String> fixedNodes) throws java.lang.Exception
java.lang.Exception
public java.lang.String makeTestOfConnectivity(int numOfSamples, boolean conserveDegrees, java.lang.String fileNameForComplexProfile, int thresholdForComplexProfile, java.util.Vector<java.lang.String> fixedNodes) throws java.lang.Exception
java.lang.Exception
public java.util.Vector<java.lang.String> readComplexProfile(java.lang.String fileNameForComplexProfile, int thresholdForComplexProfile) throws java.lang.Exception
java.lang.Exception
public java.util.Vector<java.lang.Integer> generateSample(java.util.Vector<java.lang.Integer> listOfIndices, boolean conserveDegrees, java.util.Vector<java.lang.String> complexes, java.util.Vector<java.lang.Integer> fixedIndices)
public static double[][] extractDistanceSubMatrix(int[][] fullMat, java.util.Vector<java.lang.Integer> listOfIndices)
public static double calcAveragePairwiseDistance(double[][] distMat)
public static int[][] calcDistributionOfConnectedComponentSizes(Graph graph)
public void readComplexes(java.lang.String fn, int complexMaximumSize)
public void addComplexesToNetworkAsClicks()
public void addComplexesToNetworksAsNodes()
public void removeDoubleEdges()
public void makeComplexProfile(java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public void produceConnectionsSecondOrder(Graph graph, java.lang.String distMatrixFile)
public void produceConnectionsSecondOrderFromDistMatrix(Graph graph)
public static java.lang.String calcSignificanceVsNumberOfGenes(Graph network, java.util.Vector<java.lang.String> rankedListOfProteins, int numberOfPermutations, int[] nga) throws java.lang.Exception
java.lang.Exception
public void calcSubnetworkComplexProfile()
public static void calcPercolationThreshold(Graph graph)