A B C D E F G H I L M N P R S T U

A

AboutWindow - Class in fr.umlv.gramofone.ui
 
AboutWindow() - Constructor for class fr.umlv.gramofone.ui.AboutWindow
 
add(Edge) - Method in class fr.umlv.gramofone.graphs.Edges
add an edge add (u,v) and (v,u)
ApplyMyVisualStyle(CyNetworkView) - Static method in class fr.umlv.gramofone.ui.MyVisualStyle
 

B

BatchLaunch - Class in fr.umlv.gramofone.batch
 
BatchLaunch() - Constructor for class fr.umlv.gramofone.batch.BatchLaunch
 
bfs(int) - Method in class fr.umlv.gramofone.graphs.GraphSearchs
 

C

clear() - Method in class fr.umlv.gramofone.graphs.Edges
delete all existing edges
closePanel() - Static method in class fr.umlv.gramofone.ui.StartPanel
 
compareTo(SubGraphResult) - Method in class fr.umlv.gramofone.graphs.SubGraphResult
used to sort the results
components(MyGraph) - Static method in class fr.umlv.gramofone.graphs.Tools
Return a hashmap with the connected component of the graph
componentsIte() - Method in class fr.umlv.gramofone.graphs.GraphSearchs
Get all connected components of the graph (by iterative depth first search)
computeNeighbours(List<CyNode>) - Method in class fr.umlv.gramofone.graphs.MyGraph
Return a list with CyNode wich are connected to nodes in the list nodes
computePatternProteinWithoutHomologs(Set<String>) - Method in class fr.umlv.gramofone.proteins.Homologies
Return the set of pattern proteins without homologous proteins in the network
Constraints - Class in fr.umlv.gramofone.pb
Class which create the constraints for the java pseudoboolean solver SAT4J Constraints are writen into a file, the solver as to read the file next
Constraints() - Constructor for class fr.umlv.gramofone.pb.Constraints
 
contains(Edge) - Method in class fr.umlv.gramofone.graphs.Edges
return true if the edge e exists in the grpah

D

DefinedPatterns - Class in fr.umlv.gramofone.graphs
Class managing all predefined patterns, loaded from text files
DefinedPatterns() - Constructor for class fr.umlv.gramofone.graphs.DefinedPatterns
Constructor.
DefinedPatterns(String) - Constructor for class fr.umlv.gramofone.graphs.DefinedPatterns
load a specific text file with patterns
DELETION_KEY - Static variable in class fr.umlv.gramofone.graphs.SubGraphResult
 
deserialize() - Static method in class fr.umlv.gramofone.commons.Parameters
Deserialization of the parameters (loading)
discardCurrentSolution() - Method in class fr.umlv.gramofone.pb.PseudoAllSolutionDecorator
 
dotty(MyGraph) - Static method in class fr.umlv.gramofone.graphs.Tools
launch dotty and print the graph

E

Edge - Class in fr.umlv.gramofone.graphs
 
Edge(int, int, float) - Constructor for class fr.umlv.gramofone.graphs.Edge
Build a new undirected Edge {u,v}, with a weight
Edges - Class in fr.umlv.gramofone.graphs
Manage all edges of a graph
Edges() - Constructor for class fr.umlv.gramofone.graphs.Edges
 
equals(Object) - Method in class fr.umlv.gramofone.graphs.Edge
 
Example - Class in fr.umlv.gramofone.pb
 
Example() - Constructor for class fr.umlv.gramofone.pb.Example
 

F

fetchBatch(List<String>, String, GMTask, String) - Static method in class fr.umlv.gramofone.proteins.MyWSDbFetchClient
Take a list of proteins, and return a file with the fastas sequence of these proteins
fr.umlv.gramofone.batch - package fr.umlv.gramofone.batch
 
fr.umlv.gramofone.commons - package fr.umlv.gramofone.commons
 
fr.umlv.gramofone.graphs - package fr.umlv.gramofone.graphs
 
fr.umlv.gramofone.pb - package fr.umlv.gramofone.pb
 
fr.umlv.gramofone.proteins - package fr.umlv.gramofone.proteins
 
fr.umlv.gramofone.ui - package fr.umlv.gramofone.ui
 

G

getAverageTime() - Method in class fr.umlv.gramofone.batch.MyStats
 
getAverageTimeJustPB() - Method in class fr.umlv.gramofone.batch.MyStats
 
getAverageTimeWithoutBlast() - Method in class fr.umlv.gramofone.batch.MyStats
 
getColor(String) - Method in class fr.umlv.gramofone.graphs.MyPattern
Return the color associated to the protein id in the motif
getColorfulSize() - Method in class fr.umlv.gramofone.graphs.MyPattern
Return the number of different colors in the motif
getColors(int) - Method in class fr.umlv.gramofone.graphs.MyGraph
Get the colors associated to this node
getColors() - Method in class fr.umlv.gramofone.graphs.MyPattern
Return a set with the different colors used in the motif
getConnectedComponent() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get the list of connected components
getConstraints(MyGraph) - Method in class fr.umlv.gramofone.pb.Constraints
took a graph, and return a file.
getDelPenalty() - Method in class fr.umlv.gramofone.commons.Parameters
get the cost of a deletion
getEdgeObject() - Method in class fr.umlv.gramofone.graphs.MyGraph
 
getEdges() - Method in class fr.umlv.gramofone.graphs.Edges
Get all edges of a graph
getEdges() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get a set with edges of the MyGraph
getFastaFileDirectory() - Method in class fr.umlv.gramofone.commons.Parameters
get the directory for fasta files
getHomeGramoDirectory() - Method in class fr.umlv.gramofone.commons.Parameters
 
getHomologieThreshold() - Method in class fr.umlv.gramofone.commons.Parameters
get the homology threshold value for blast
getId() - Method in class fr.umlv.gramofone.graphs.Edge
 
getId(char, int, int) - Method in class fr.umlv.gramofone.pb.Constraints
give the correct number of variable given the variable
getImage() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
get an image with the good number of nodes but no the correct placement
getInformations(int) - Method in class fr.umlv.gramofone.graphs.SubGraphResult
Text informations writen in the result panel
getInsPenalty() - Method in class fr.umlv.gramofone.commons.Parameters
get the cost of an insertion
getInstance() - Static method in class fr.umlv.gramofone.commons.Parameters
get the singleton instance of parameters
getInstance() - Static method in class fr.umlv.gramofone.ui.StartPanel
 
getJPanel() - Method in class fr.umlv.gramofone.ui.MainPanel
 
getJPanel() - Method in class fr.umlv.gramofone.ui.ResultsPanel
 
getLogEValue() - Method in class fr.umlv.gramofone.commons.Parameters
get the value of log(eValue) when eValue is 0
getName() - Method in class fr.umlv.gramofone.graphs.MyPattern
return the name of the motif
getNDel() - Method in class fr.umlv.gramofone.commons.Parameters
Get the number of allowed deletions
getNdel() - Method in class fr.umlv.gramofone.graphs.MyGraph
Return the number of deletions allowed (updated after the apriori deletions)
getNeighbors(int) - Method in class fr.umlv.gramofone.graphs.MyGraph
Get the neighbors of the node v in the MyGraph
getNetwork() - Method in class fr.umlv.gramofone.graphs.MyGraph
get the cynetwork of the MyGraph
getNetwork() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
get the result cynetwork
getNetworkFastaFile() - Method in class fr.umlv.gramofone.commons.Parameters
return the potential path to the fasta file for the network
getNetworkWithNeighbor() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
get the cynetwork of the result with 1 neigbhourg
getNIns() - Method in class fr.umlv.gramofone.commons.Parameters
Get the number of allowed insertions
getNins() - Method in class fr.umlv.gramofone.graphs.MyGraph
Return the number of insertions allowed
getNodes() - Method in class fr.umlv.gramofone.graphs.MyGraph
Return the list of nodes id in the graph
getNodesOfThisColors(int) - Method in class fr.umlv.gramofone.graphs.MyGraph
return a set with all nodes with the color color
getNodesWithoutColors() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get a set of nodes without colors in the MyGraph after the coloring
getOccurence(int) - Method in class fr.umlv.gramofone.graphs.MyPattern
Return the occurences of the protein id in the motif
getOriginalNetwork() - Method in class fr.umlv.gramofone.graphs.MyGraph
 
getPathBlast() - Method in class fr.umlv.gramofone.commons.Parameters
get the path of the blast bin directory
getPattern(String, String) - Method in class fr.umlv.gramofone.graphs.DefinedPatterns
get the list of proteins for this specie and this pattern
getPattern() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get the motif
getPattern() - Method in class fr.umlv.gramofone.graphs.MyPattern
Get all the proteins in the pattern
getPatternColorful() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get only different colors of the pattern
getPatternFastaFile() - Method in class fr.umlv.gramofone.commons.Parameters
return the potential path to the fasta file for the pattern
getPatterns(String) - Method in class fr.umlv.gramofone.graphs.DefinedPatterns
Return the patterns for a given specie
getPatterns() - Method in class fr.umlv.gramofone.graphs.DefinedPatterns
Return all the patterns for all the species
getPatternText() - Method in class fr.umlv.gramofone.graphs.MyPattern
Return a String representing the pattern
getPluginName() - Method in class fr.umlv.gramofone.commons.Parameters
get the plugin name
getPreviouslyDeletedProteins() - Method in class fr.umlv.gramofone.graphs.MyGraph
Get the set of proteins deleted before the computation (if there got no homologous in the network)
getProteinsFromColor(int) - Method in class fr.umlv.gramofone.graphs.MyPattern
Get the protein who got this color
getResult2Pattern() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
get the result match between pattern and this result
getResults() - Method in class fr.umlv.gramofone.ui.GMTask
get the list of results found by the solver
getScore() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
get the score of this result
getSize() - Method in class fr.umlv.gramofone.graphs.MyGraph
Return the number of nodes in the MyGraph
getSpecies() - Method in class fr.umlv.gramofone.graphs.DefinedPatterns
return names of files
getStartTime() - Method in class fr.umlv.gramofone.ui.GMTask
 
getTimeOut() - Method in class fr.umlv.gramofone.commons.Parameters
get the timeout in seconds for the LPB solver
getTitle() - Method in class fr.umlv.gramofone.ui.GMTask
 
getTmpDirectory() - Method in class fr.umlv.gramofone.commons.Parameters
 
getTotalMotifSize() - Method in class fr.umlv.gramofone.graphs.MyPattern
return the size of the motif (with repetitions)
getU() - Method in class fr.umlv.gramofone.graphs.Edge
 
getV() - Method in class fr.umlv.gramofone.graphs.Edge
 
getVersion() - Method in class fr.umlv.gramofone.commons.Parameters
return the version of the plugin
getWeight() - Method in class fr.umlv.gramofone.graphs.Edge
 
GMTask - Class in fr.umlv.gramofone.ui
Cytoscape task for the plugin
GMTask(CyNetwork, MyPattern) - Constructor for class fr.umlv.gramofone.ui.GMTask
 
GraphSearchs - Class in fr.umlv.gramofone.graphs
Some class searchs (bfs, dfs) on graphs
GraphSearchs(MyGraph) - Constructor for class fr.umlv.gramofone.graphs.GraphSearchs
 

H

h(String, String) - Method in class fr.umlv.gramofone.proteins.Homologies
get the hhomologie between the network node n and the query node q
halt() - Method in class fr.umlv.gramofone.ui.GMTask
 
hashCode() - Method in class fr.umlv.gramofone.graphs.Edge
 
Homologies - Class in fr.umlv.gramofone.proteins
Manage homologies of proteins
Homologies(CyNetwork, MyPattern, GMTask) - Constructor for class fr.umlv.gramofone.proteins.Homologies
Compute homologies between proteins Retrieve fasta from internet if no fasta file given

I

IDEDGE - Static variable in class fr.umlv.gramofone.graphs.MyGraph
 
INSERTION_VALUE - Static variable in class fr.umlv.gramofone.graphs.SubGraphResult
 
interrupt(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
put the interrupt signal
isChooseFastaAsPattern() - Method in class fr.umlv.gramofone.commons.Parameters
if the pattern is determined by the fasta file or not
isChooseNetworkFastaFile() - Method in class fr.umlv.gramofone.commons.Parameters
if there is a path for the fasta file for the network or not
isChoosePatternFastaFile() - Method in class fr.umlv.gramofone.commons.Parameters
if there is a path for the fasta file for the pattern or not
isConnected() - Method in class fr.umlv.gramofone.graphs.GraphSearchs
Return true if the graph is connected (use a depth first search)
isConnected(MyGraph) - Static method in class fr.umlv.gramofone.graphs.Tools
Return true if the graph is connected
isInterrupted() - Method in class fr.umlv.gramofone.commons.Parameters
check if plugin has to be interrupted
isModeBatch() - Method in class fr.umlv.gramofone.commons.Parameters
check if the plugin is in mode batch or not
isMultiSetHomologsPattern() - Method in class fr.umlv.gramofone.commons.Parameters
check if the pattern is as a multiset (same color for homologous proteins)
isOnlyFirstSolution() - Method in class fr.umlv.gramofone.commons.Parameters
check if only the first solution as to be returned

L

LaunchAction - Class in fr.umlv.gramofone.ui
 
LaunchAction(MyPattern) - Constructor for class fr.umlv.gramofone.ui.LaunchAction
Launch the plugin with the LPB solver
LaunchPseudoBoolean - Class in fr.umlv.gramofone.pb
Class to launch the pseudo boolean solver
LaunchPseudoBoolean() - Constructor for class fr.umlv.gramofone.pb.LaunchPseudoBoolean
 
loadedNetworks - Static variable in class fr.umlv.gramofone.ui.LaunchAction
Launch action of the plugin

M

main(String[]) - Static method in class fr.umlv.gramofone.batch.BatchLaunch
 
main(String[]) - Static method in class fr.umlv.gramofone.pb.Example
 
Main - Class in fr.umlv.gramofone.ui
Main class.
Main() - Constructor for class fr.umlv.gramofone.ui.Main
CytoscapePlugin call this default constructor
MainPanel - Class in fr.umlv.gramofone.ui
Main panel of the cytoplugin (inputs)
MainPanel() - Constructor for class fr.umlv.gramofone.ui.MainPanel
 
model2SubGraph(int[], Number, Constraints) - Method in class fr.umlv.gramofone.graphs.MyGraph
From the result of the pseudoBoolean resolution, extract the corresponding subgraph in Cytoscape
multiH(String, Set<String>) - Method in class fr.umlv.gramofone.proteins.Homologies
Homologie for multiset
MyGraph - Class in fr.umlv.gramofone.graphs
Manage the network (and the connected component of a graph are considered as MyGraphs too)
MyGraph(int, int, MyPattern, int, int) - Constructor for class fr.umlv.gramofone.graphs.MyGraph
Create a new random network with n nodes and m edges.
MyGraph(CyNetwork, MyPattern, Homologies, int, int, GMTask) - Constructor for class fr.umlv.gramofone.graphs.MyGraph
Create a new MyGraph to manage the cytoscape network
MyPattern - Class in fr.umlv.gramofone.graphs
Manage a motif
MyPattern(MyPattern) - Constructor for class fr.umlv.gramofone.graphs.MyPattern
Build a motif from a motif (copy)
MyPattern() - Constructor for class fr.umlv.gramofone.graphs.MyPattern
 
MyPattern(List<String>) - Constructor for class fr.umlv.gramofone.graphs.MyPattern
Build a pattern from a list of proteins (the name of the pattern wil be NONAMEPATTERN)
MyPattern(String, List<String>) - Constructor for class fr.umlv.gramofone.graphs.MyPattern
Build a pattern from a list of proteins with a given name for this pattern
MyPattern(String) - Constructor for class fr.umlv.gramofone.graphs.MyPattern
Initialize a pattern from a FASTA file !
MyStats - Class in fr.umlv.gramofone.batch
 
MyStats() - Constructor for class fr.umlv.gramofone.batch.MyStats
 
MyVisualStyle - Class in fr.umlv.gramofone.ui
Visual style (all nodes in black, highlight solution nodes in yellow
MyVisualStyle() - Constructor for class fr.umlv.gramofone.ui.MyVisualStyle
 
MyWSDbFetchClient - Class in fr.umlv.gramofone.proteins
Class to get fasta files from internet
MyWSDbFetchClient() - Constructor for class fr.umlv.gramofone.proteins.MyWSDbFetchClient
 

N

neighbors(int) - Method in class fr.umlv.gramofone.graphs.Edges
get all the neighbors of a node u
NONAMEPATTERN - Static variable in class fr.umlv.gramofone.graphs.MyPattern
 

P

Parameters - Class in fr.umlv.gramofone.commons
Singleton to manage with parameters of the programms (nb insertions, ..)
parseFastaFile(String) - Static method in class fr.umlv.gramofone.graphs.MyPattern
Return a list of proteins in a Fasta file
perform(MyGraph, GMTask) - Method in class fr.umlv.gramofone.pb.LaunchPseudoBoolean
Launch the LPB solver on the graph g with the cytoscape task Return the list of solution founded
performOnlyFirstSolution(MyGraph, GMTask) - Method in class fr.umlv.gramofone.pb.LaunchPseudoBoolean
Launch the LPB solver on the graph g with the cytoscape task Return THE unique solution founded (quicker but maybe not the best one)
printErrorMessageAndInterrupt(String) - Static method in class fr.umlv.gramofone.graphs.Tools
Print an cytoscape error message and interrupt the program
PseudoAllSolutionDecorator - Class in fr.umlv.gramofone.pb
 
PseudoAllSolutionDecorator(IPBSolver) - Constructor for class fr.umlv.gramofone.pb.PseudoAllSolutionDecorator
 

R

removeProteins(Set<String>) - Method in class fr.umlv.gramofone.graphs.MyPattern
Remove a set of proteins in the motif (used in apriori deletions)
ResultsPanel - Class in fr.umlv.gramofone.ui
Right panel, ouput panel, results
ResultsPanel(ArrayList<SubGraphResult>, CyNetwork) - Constructor for class fr.umlv.gramofone.ui.ResultsPanel
 
run() - Method in class fr.umlv.gramofone.ui.GMTask
 

S

serialize() - Method in class fr.umlv.gramofone.commons.Parameters
Serialization of the parameters
setChooseNetworkFastaFile(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set if there is a path for the fasta file for the network or not
setChoosePatternFastaFile(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set if there is a path for the fasta file for the pattern or not
setDefault() - Method in class fr.umlv.gramofone.commons.Parameters
set default values for options
setDelPenalty(int) - Method in class fr.umlv.gramofone.commons.Parameters
set the cost of a deletion
setFastaAsPattern(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set if the pattern is determined by the fasta file or not
setHomologieThreshold(double) - Method in class fr.umlv.gramofone.commons.Parameters
set the homology threshold value for blast
setInsPenalty(int) - Method in class fr.umlv.gramofone.commons.Parameters
set the cost of an insertion
setLogEValue(double) - Method in class fr.umlv.gramofone.commons.Parameters
set the value of log(eValue) when eValue is 0
setModeBatch(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set the mode batch
setMultiSetHomologsPattern(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set the pattern as multiset (same color for homologous proteins)
setNDel(int) - Method in class fr.umlv.gramofone.commons.Parameters
set the number of allowed deletions
setNetworkFastaFile(String) - Method in class fr.umlv.gramofone.commons.Parameters
set the path of fasta file for the network
setNIns(int) - Method in class fr.umlv.gramofone.commons.Parameters
set the number of allowed insertions
setOnlyFirstSolution(boolean) - Method in class fr.umlv.gramofone.commons.Parameters
set the only first solution or not
setPathBlast(String) - Method in class fr.umlv.gramofone.commons.Parameters
set the path of the blast bin directory
setPatternFastaFile(String) - Method in class fr.umlv.gramofone.commons.Parameters
set the path of fasta file for the pattern
setStartTime() - Method in class fr.umlv.gramofone.ui.GMTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.umlv.gramofone.ui.GMTask
 
setTimeOut(int) - Method in class fr.umlv.gramofone.commons.Parameters
set the timeout in seconds for the LPB solver
showView() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
show the network result
showViewNeighbor() - Method in class fr.umlv.gramofone.graphs.SubGraphResult
Show the network with 1 neighbourg, and select the nodes in the result
spanningTree(MyGraph) - Static method in class fr.umlv.gramofone.graphs.Tools
Return a spanning tree of the graph
StartPanel - Class in fr.umlv.gramofone.ui
Singleton, starts the plugin
SubGraphResult - Class in fr.umlv.gramofone.graphs
Manage a subgraph representing a solution
SubGraphResult(List<CyNode>, List<CyEdge>, List<Integer>, Number, MyGraph, int[], Constraints) - Constructor for class fr.umlv.gramofone.graphs.SubGraphResult
Create a solution from this list of nodes and edges.

T

toMultiSet(Homologies) - Method in class fr.umlv.gramofone.graphs.MyPattern
Convert the original pattern set as a multiset : proteins in the pattern which are homologs now use the same color
Tools - Class in fr.umlv.gramofone.graphs
Some tools on graph
Tools() - Constructor for class fr.umlv.gramofone.graphs.Tools
 
toString() - Method in class fr.umlv.gramofone.batch.MyStats
 
toString() - Method in class fr.umlv.gramofone.graphs.Edge
 
toString() - Method in class fr.umlv.gramofone.graphs.Edges
 
toString() - Method in class fr.umlv.gramofone.graphs.MyGraph
 

U

update(long, long, long) - Method in class fr.umlv.gramofone.batch.MyStats
 
updatePercent(float) - Method in class fr.umlv.gramofone.ui.GMTask
 
updateStatus(int) - Method in class fr.umlv.gramofone.ui.GMTask
update the taskStatus with the number of current results found
updateStatusText(String) - Method in class fr.umlv.gramofone.ui.GMTask
 

A B C D E F G H I L M N P R S T U