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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
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