def buildNetwork(self):
net = GRNetwork(self.nodes);
c = np.random.random(len(self.nodes));
self.buildPaStore();
for index in range(len(self.nodes)):
ntempDist = self.buildPaDistribution(index);
pachoice = mysample(ntempDist, c[index], self.paStore[index]);
net.initializeParent(self.nodes[index], pachoice);
return net;
def buildNetwork(self):
net = GRNetwork(self.nodes)
c = np.random.random(len(self.nodes))
self.buildPaStore()
for index in range(len(self.nodes)):
ntempDist = self.buildPaDistribution(index)
pachoice = mysample(ntempDist, c[index], self.paStore[index])
net.initializeParent(self.nodes[index], pachoice)
return net
def buildNetwork2(gdict, paDict, logWeightMap):
net = GRNetwork( list(gdict.values()) );
for k,v in gdict.items():
allPaSets = paDict[k];
dist1 = [];
for paSet in allPaSets:
hkey = buildHKey(v,paSet);
dist1.append(logWeightMap[hkey]);
dist2 = np.array(dist1);
distribution = dist2/np.sum(dist2);
initPa = mysample(distribution, np.random.random() , allPaSets);
net.initializeParent(v, initPa);
return net;
def buildNetwork(gdict,paDict, weightMap ):
net = GRNetwork( list(gdict.values()) );
for k,v in gdict.items():
allPaSets = paDict[k];
distribution = [];
for paSet in allPaSets:
speciesId = v.getSpeciesId();
gid = v.getGeneId();
pasId = ':'.join([pa.getGeneId() for pa in paSet]);
distribution.append(weightMap[buildKey(speciesId, gid, pasId)]);
initPa = mysample(distribution, np.random.random() , allPaSets);
net.initializeParent(v, initPa);
return net;
def buildNetwork2(gdict, paDict, logWeightMap):
net = GRNetwork(list(gdict.values()))
for k, v in gdict.items():
allPaSets = paDict[k]
dist1 = []
for paSet in allPaSets:
hkey = buildHKey(v, paSet)
dist1.append(logWeightMap[hkey])
dist2 = np.array(dist1)
distribution = dist2 / np.sum(dist2)
initPa = mysample(distribution, np.random.random(), allPaSets)
net.initializeParent(v, initPa)
return net
def buildNetwork(gdict, paDict, weightMap):
net = GRNetwork(list(gdict.values()))
for k, v in gdict.items():
allPaSets = paDict[k]
distribution = []
for paSet in allPaSets:
speciesId = v.getSpeciesId()
gid = v.getGeneId()
pasId = ':'.join([pa.getGeneId() for pa in paSet])
distribution.append(weightMap[buildKey(speciesId, gid, pasId)])
initPa = mysample(distribution, np.random.random(), allPaSets)
net.initializeParent(v, initPa)
return net
