public class DataPathConsistencyAnalyzer
extends java.lang.Object
Modifier and Type | Class and Description |
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class |
DataPathConsistencyAnalyzer.optCutSetData
Simple data structure to store optimal intervention sets data
|
Modifier and Type | Field and Description |
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java.lang.String |
activityAttribute |
static int |
ALL_PATHS |
java.util.HashSet<Node> |
allNodes
all individual nodes from elementary paths (target nodes excepted)
|
java.util.Vector<Node> |
AllNodesWithActivities |
boolean |
checkedForConsistency |
static float |
defaultActivityThreshold |
java.util.HashSet<Node> |
elemNodes
set of unique nodes from elementary paths
|
java.util.ArrayList<Path> |
elemPaths
elementary paths, set of paths sinking to target nodes
|
java.util.Vector<java.util.Vector<java.util.Vector<Path>>> |
EnrichedNodePaths |
java.util.Vector<Node> |
EnrichedNodes |
Graph |
graph |
long |
maxSetNb
Maximum set number cutoff value
|
int |
maxSetSize
Maximum set size cutoff value.
|
static java.lang.String |
newline
System independent newline character
|
java.util.HashMap<java.lang.String,java.lang.String> |
nodeID2attribute
Node Id to attribute value map
|
java.util.HashMap<Node,java.lang.Integer> |
nodeInconsistencies |
int |
numberOfPermutations |
static int |
OCS_BERGE
Ocsana search option: Berge's algorithm
|
static int |
OCS_PARTIAL
Ocsana search option: partial search
|
static int |
OCS_SEED
Ocsana search option: seed based search
|
int |
ocsSearch
Ocsana search option by default
|
java.util.HashMap<java.lang.String,java.lang.Double> |
omegaScoreMap
Omega score per elementary node = OCSANA Score
|
java.util.ArrayList<OmegaScoreData> |
omegaScores
Ocsana Omega scores
|
java.lang.StringBuffer |
optCutSetReport
Report for the optimal intervention set search
|
java.util.ArrayList<java.util.ArrayList<Node>> |
optIntSets
List of optimal intervention sets as node objects.
|
int[][] |
pathMatrix
Elementary paths matrix
|
int |
pathMatrixNbCol
Path matrix number of rows and columns
|
int |
pathMatrixNbRow
Path matrix number of rows and columns
|
java.util.ArrayList<java.lang.String> |
pathMatrixNodeList
Elementary paths matrix node names list
|
java.util.Vector<Node> |
pathwayNodes |
static int |
PERMUTE_NODE_ACTIVITIES |
java.util.HashMap<java.lang.String,java.lang.Double> |
piquantAbsSetScoreMap |
boolean |
restrictBerge
Flag for restricting Berge's algorithm search
|
float[] |
SA_activities |
float[] |
SA_observedPathScores |
float[] |
SA_observedTargetScores |
float[][] |
SA_pathScoresRandomDistribution |
float[][] |
SA_targetScoreRandomDistribution |
int |
searchPathMode |
double |
searchRadius |
static int |
SHORTEST_PATHS |
java.util.ArrayList<Node> |
sideNodes
List of nodes to be considered for scoring side effects
|
java.util.HashMap<java.lang.String,java.lang.Double> |
sideScoreMap |
java.util.HashMap<java.lang.String,Graph> |
sourceGraphs
Ocsana list of "source" graphs
|
java.util.ArrayList<Node> |
sourceNodes
List of source nodes
|
static int |
SUBOPTIMAL_SHORTEST_PATHS |
java.util.ArrayList<Node> |
targetNodes
List of target nodes
|
boolean |
testSignificance |
int |
testSignificanceMode |
boolean |
useAllnodesAttributes |
boolean |
useMaxSetSize
Flag for using maximum set size
|
boolean |
useSignAlgebra |
Constructor and Description |
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DataPathConsistencyAnalyzer() |
Modifier and Type | Method and Description |
---|---|
float[][] |
calcAllToAllInfluences() |
float |
calcAveragePathLength(java.util.Vector<Path> vpaths) |
long |
calcCombinations(int n,
int k)
Calculate the number of combinations of k size for a set of n elements.
|
float |
calcNodeInfluence(float nodeActivity,
java.util.Vector<Path> vpaths) |
float |
calcNodeInfluence(Node n,
java.util.Vector<Path> vpaths,
boolean verbose) |
float |
calcPathInfluence(Path p) |
void |
calcPathProperties(Path p) |
float |
calcPathwayInfluence(java.util.Vector<java.util.Vector<Path>> vvpaths) |
float[] |
calcPValues(float[] scores,
float[][] distributions) |
float |
calcRandomPathwayInfluence(java.util.Vector<java.util.Vector<Path>> vvpaths,
float[] activities) |
float |
calcSpecialPValue(float[] scores,
float[][] distributions) |
int |
checkEdgeInfluence()
Convert every edge with no influence attribute to "activation".
|
void |
fillPathMatrix(java.util.ArrayList<Path> p)
Fill a matrix of integers with elementary paths data.
|
void |
findPaths() |
java.lang.String |
generatePathActivitiesReport() |
java.lang.String |
generateReport() |
float[] |
getActivityDistribution() |
float |
getNodeActivity(Node n) |
void |
getPathConsistencyAndSummaryActivity(Path p) |
void |
getPathConsistencyAndSummaryActivity(Path p,
float[] randomNodeActivities) |
void |
getPathwayNodes() |
java.util.Vector<Node> |
getSystematicallyInconsistentNodes() |
void |
initializeSignificanceAnalysis() |
void |
loadGraph(java.lang.String file) |
Graph |
makePathNetwork(java.util.Vector<Path> listOfPath) |
boolean |
ocsanaScore()
Determine paths for optimal combinations sets analysis and calculate the scores
for elementary nodes.
|
void |
ocsanaSearch()
Performs optimal intervention set search.
|
void |
print(java.lang.String line,
java.lang.StringBuffer sb) |
java.lang.String |
printAllToAllInfluenceTable(float[][] inf) |
void |
printPaths(java.util.ArrayList<Path> p)
Print out elementary path matrix data.
|
void |
printSignificanceAnalysisReport() |
void |
saveOptCutSetData(java.io.File file)
save optimal intervention set list to a text file.
|
void |
significanceAnalysis(int mode,
int _numberOfPermutations) |
void |
significanceAnalysisDoPermutation(int k) |
java.util.Vector<Path> |
sortPathsByActivities() |
java.util.Vector<Path> |
sortPathsByActivities(float[] randomNodeActivities) |
public Graph graph
public java.util.Vector<Node> pathwayNodes
public boolean testSignificance
public int testSignificanceMode
public int numberOfPermutations
public float[] SA_activities
public float[] SA_observedTargetScores
public float[][] SA_targetScoreRandomDistribution
public float[] SA_observedPathScores
public float[][] SA_pathScoresRandomDistribution
public int searchPathMode
public static int SHORTEST_PATHS
public static int SUBOPTIMAL_SHORTEST_PATHS
public static int ALL_PATHS
public double searchRadius
public static int PERMUTE_NODE_ACTIVITIES
public static int OCS_BERGE
public static int OCS_PARTIAL
public static int OCS_SEED
public int ocsSearch
public java.util.Vector<java.util.Vector<java.util.Vector<Path>>> EnrichedNodePaths
public java.util.Vector<Node> EnrichedNodes
public java.util.Vector<Node> AllNodesWithActivities
public static float defaultActivityThreshold
public java.lang.String activityAttribute
public boolean checkedForConsistency
public boolean useSignAlgebra
public boolean useAllnodesAttributes
public java.util.HashMap<Node,java.lang.Integer> nodeInconsistencies
public java.util.ArrayList<java.util.ArrayList<Node>> optIntSets
public java.util.HashMap<java.lang.String,Graph> sourceGraphs
public static java.lang.String newline
public java.util.ArrayList<Node> sourceNodes
public java.util.ArrayList<Node> targetNodes
public java.util.ArrayList<Node> sideNodes
public java.util.HashSet<Node> elemNodes
public java.util.ArrayList<Path> elemPaths
public java.util.HashSet<Node> allNodes
public java.util.HashMap<java.lang.String,java.lang.Double> omegaScoreMap
public java.util.HashMap<java.lang.String,java.lang.Double> piquantAbsSetScoreMap
public java.util.HashMap<java.lang.String,java.lang.Double> sideScoreMap
public java.util.ArrayList<OmegaScoreData> omegaScores
public java.lang.StringBuffer optCutSetReport
public long maxSetNb
public int maxSetSize
public boolean useMaxSetSize
public boolean restrictBerge
public java.util.HashMap<java.lang.String,java.lang.String> nodeID2attribute
public int[][] pathMatrix
public java.util.ArrayList<java.lang.String> pathMatrixNodeList
public int pathMatrixNbRow
public int pathMatrixNbCol
public void loadGraph(java.lang.String file) throws java.lang.Exception
java.lang.Exception
public void getPathwayNodes()
public void calcPathProperties(Path p)
public float[] calcPValues(float[] scores, float[][] distributions)
public float calcSpecialPValue(float[] scores, float[][] distributions)
public void findPaths()
public float calcPathInfluence(Path p)
public float calcAveragePathLength(java.util.Vector<Path> vpaths)
public float calcNodeInfluence(Node n, java.util.Vector<Path> vpaths, boolean verbose)
public float calcNodeInfluence(float nodeActivity, java.util.Vector<Path> vpaths)
public float calcPathwayInfluence(java.util.Vector<java.util.Vector<Path>> vvpaths)
public float calcRandomPathwayInfluence(java.util.Vector<java.util.Vector<Path>> vvpaths, float[] activities)
public float getNodeActivity(Node n)
public float[] getActivityDistribution()
public java.lang.String generateReport()
public void print(java.lang.String line, java.lang.StringBuffer sb)
public java.util.Vector<Path> sortPathsByActivities()
public java.util.Vector<Path> sortPathsByActivities(float[] randomNodeActivities)
public void getPathConsistencyAndSummaryActivity(Path p)
public void getPathConsistencyAndSummaryActivity(Path p, float[] randomNodeActivities)
public java.lang.String generatePathActivitiesReport()
public void initializeSignificanceAnalysis()
public void significanceAnalysisDoPermutation(int k)
public void printSignificanceAnalysisReport()
public void significanceAnalysis(int mode, int _numberOfPermutations)
public float[][] calcAllToAllInfluences()
public java.lang.String printAllToAllInfluenceTable(float[][] inf)
public java.util.Vector<Node> getSystematicallyInconsistentNodes()
public boolean ocsanaScore()
public void ocsanaSearch()
public void saveOptCutSetData(java.io.File file)
file
- public long calcCombinations(int n, int k)
n
- the total number of elementsk
- the size of the subsetpublic int checkEdgeInfluence()
public void printPaths(java.util.ArrayList<Path> p)
p
- elementary paths listpublic void fillPathMatrix(java.util.ArrayList<Path> p)
p
- elementary paths list