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A
absorbEvent()
(in
ConstrainedHistory
)
addEdgeEstimate()
(in
cnavg.avg.balanced
)
addStartCap()
(in
CNV
)
absorbEvent()
(in
EuclidianHistory
)
addEdgeEstimate()
(in
cnavg.cactus.balanced
)
adjacencies()
(in
cnavg.historySampling.cycleCover
)
absorbEvent()
(in
CactusHistory
)
addEdgePrecision()
(in
cnavg.avg.balanced
)
adjacencyIndex()
(in
Edge
)
absorbEvent()
(in
History
)
addEdgePrecision()
(in
cnavg.cactus.balanced
)
adjacencyIndex()
(in
cnavg.flows.unitFlows
)
absorbEvent()
(in
OverlapHistory
)
addEdgeToOverlapTable()
(in
cnavg.history.overlap
)
adjacencyIndex()
(in
cnavg.history.overlap
)
absorbEvent()
(in
ScheduledHistory
)
addElement()
(in
PartialOrderSet
)
adjacencyOverlaps()
(in
OverlapHistory
)
add()
(in
CNVSlice
)
addEvents()
(in
cnavg.historySampling.sampleModuleCycles
)
adjacencyString()
(in
NodeFlow
)
add_node()
(in
cnavg.historySampling.cycleCover
)
addEventToOverlapTable()
(in
cnavg.history.overlap
)
alternates()
(in
Cycle
)
addAncestry()
(in
ScheduledHistory
)
addFinishCap()
(in
CNV
)
areUnitFlows()
(in
cnavg.flows.unitFlows
)
addBreakend()
(in
BreakendGraph
)
addLiftedEdge()
(in
Graph
)
argmax()
(in
cnavg.clock.EM
)
addChain()
(in
Mapping
)
addMissingCNV()
(in
cnavg.preprocess.bambam
)
arguments()
(in
cnavg.preprocess.discrepancies
)
addChainEstimate()
(in
cnavg.cactus.balanced
)
addMissingCNVs()
(in
cnavg.preprocess.bambam
)
assignCap()
(in
BreakendGraph
)
addChainPrecision()
(in
cnavg.cactus.balanced
)
addModuleSegment()
(in
Module
)
assignCaps()
(in
BreakendGraph
)
addConstraint()
(in
LPProblem
)
addNetEnd()
(in
Module
)
assignSNV()
(in
cnavg.clock.timeEvents
)
addConstraint()
(in
PartialOrderSet
)
addNewHistory()
(in
cnavg.historySampling.sampleGraphCycles
)
assignSNVs()
(in
cnavg.clock.timeEvents
)
addConstraint()
(in
LPProblem
)
addNode()
(in
Graph
)
attachNode()
(in
Breakend
)
addDescent()
(in
ScheduledHistory
)
addNodeEdgesEstimates()
(in
cnavg.avg.balanced
)
avg
(in
cnavg
)
addEdge()
(in
Mapping
)
addNodeEdgesPrecisions()
(in
cnavg.avg.balanced
)
avg()
(in
BreakendGraph
)
addEdge()
(in
NodeFlow
)
addSegment()
(in
Mapping
)
avg()
(in
WeightedHistory
)
addEdge()
(in
Mapping
)
addSegmentEstimate()
(in
cnavg.avg.balanced
)
addEdge()
(in
Mapping
)
addSegmentPrecision()
(in
cnavg.avg.balanced
)
B
balanced
(in
cnavg.avg
)
Block
(in
cnavg.cactus.block
)
breakendGraph
(in
cnavg.preprocess
)
balanced
(in
cnavg.cactus
)
blocksAreFullyNormalized()
(in
NormalizedCactus
)
BreakendGraph
(in
cnavg.preprocess.breakendGraph
)
balanced()
(in
Graph
)
bondIndices()
(in
EuclidianHistory
)
breakEvenOverlap()
(in
cnavg.flows.unitFlows
)
balanced()
(in
Module
)
BRANCHPROB
(in
cnavg.simulator.simulator
)
breakEvenOverlaps()
(in
cnavg.flows.unitFlows
)
balanced()
(in
NodeFlow
)
braneyText()
(in
Cycle
)
breakEvenOverlaps_Event()
(in
cnavg.flows.unitFlows
)
BalancedAVG
(in
cnavg.avg.balanced
)
braneyText()
(in
Edge
)
bridges()
(in
Cactus
)
BalancedCactus
(in
cnavg.cactus.balanced
)
braneyText()
(in
Event
)
BUFFER_LENGTH
(in
cnavg.preprocess.bambam
)
bambam
(in
cnavg.preprocess
)
braneyText()
(in
History
)
buildGraph()
(in
cnavg.cactusTree.cactusTree
)
basics
(in
cnavg
)
breakend
(in
cnavg.preprocess
)
block
(in
cnavg.cactus
)
Breakend
(in
cnavg.preprocess.breakend
)
C
cactus
(in
cnavg
)
cnvNodeWeight()
(in
CNVSlice
)
copy()
(in
Cactus
)
Cactus
(in
cnavg.cactus.graph
)
CNVSlice
(in
cnavg.clock.cnvTree
)
copy()
(in
OrientedCactus
)
CactusHistory
(in
cnavg.history.history
)
CNVSliceTree
(in
cnavg.clock.cnvTree
)
copy()
(in
EuclidianHistory
)
cactusHistoryOverlapTable()
(in
cnavg.clock.timeEvents
)
cnvTree
(in
cnavg.clock
)
copy()
(in
CactusHistory
)
cactusSampling
(in
cnavg
)
CNVTree
(in
cnavg.clock.cnvTree
)
copy()
(in
History
)
cactusTree
(in
cnavg
)
components
(in
cnavg.cactus.threeWay
)
copy()
(in
OverlapHistory
)
cactusTree
(in
cnavg.cactusTree
)
compute()
(in
cnavg.cactus.threeWay.components
)
copy()
(in
ScheduledHistory
)
cbs
(in
cnavg.preprocess
)
computeAllelicVariance()
(in
cnavg.preprocess.bambam
)
copyAdjacencyOverlaps()
(in
cnavg.history.overlap
)
cbs
(in
cnavg.preprocess.cbs
)
computeBasicNets()
(in
Cactus
)
copyCatResolution()
(in
cnavg.avg.balanced
)
chain
(in
cnavg.cactus
)
computeBlocks()
(in
Cactus
)
copynumber()
(in
Block
)
Chain
(in
cnavg.cactus.chain
)
computeChains()
(in
Cactus
)
correctIncongruities()
(in
BalancedAVG
)
chainIsFullyNormalized()
(in
NormalizedCactus
)
computeCopyNumberChange()
(in
cnavg.clock.cnvTree
)
correctIncongruities()
(in
cnavg.cactus.balanced
)
chainIsPloidyDetermined()
(in
NormalizedCactus
)
computeEvenDistances()
(in
cnavg.historySampling.cycleCover
)
correctIncongruity()
(in
BalancedAVG
)
chainIsUnnormalized()
(in
NormalizedCactus
)
computeGroups()
(in
Cactus
)
correctIncongruity()
(in
cnavg.cactus.balanced
)
chainMean()
(in
NormalizedCactus
)
computeHistorySlices()
(in
CNVTree
)
correctInsufficientEdges()
(in
cnavg.cactus.balanced
)
chainsAreFullyNormalized()
(in
NormalizedCactus
)
computeJointProbs()
(in
cnavg.clock.EM
)
correctSchedulingError()
(in
ConstrainedHistory
)
chainsArePloidyDetermined()
(in
NormalizedCactus
)
computeJointProbs_Phase()
(in
cnavg.clock.EM
)
correctSchedulingErrors()
(in
ConstrainedHistory
)
chainSpans()
(in
Cactus
)
computeJointProbs_SNV()
(in
cnavg.clock.EM
)
cost()
(in
History
)
chainsStr()
(in
Mapping
)
computeLikelihoods()
(in
cnavg.clock.timeEvents
)
countComponents()
(in
ConstrainedHistory
)
chainStr()
(in
Mapping
)
computeLikelihoods_Block()
(in
cnavg.clock.timeEvents
)
countComponents_Node()
(in
ConstrainedHistory
)
chainTreeString()
(in
OrientedCactus
)
computeNetBlocks()
(in
Cactus
)
countForks()
(in
ScheduledHistory
)
changedCNVs()
(in
cnavg.historySampling.sampleGraphCycles
)
computeNetChains()
(in
OrientedCactus
)
coverageStats()
(in
Graph
)
changeEventsInHistory()
(in
cnavg.historySampling.sampleModuleCycles
)
computeNets()
(in
Cactus
)
coverageStats()
(in
NodeFlow
)
changeLiftedEdge()
(in
Graph
)
computeNodeAdjacencies()
(in
cnavg.historySampling.cycleCover
)
createAdjacency()
(in
Graph
)
changeModuleSegment()
(in
Module
)
computeNodeOffsets()
(in
cnavg.cactus.balanced
)
createBlockTrees()
(in
cnavg.clock.timeEvents
)
changeSegment()
(in
Graph
)
computeNormalizationFactors()
(in
cnavg.clock.EM
)
createBlockTrees_Block()
(in
cnavg.clock.timeEvents
)
childDesperateInsertionPoints()
(in
ConstrainedHistory
)
computeNormalizationFactors_Phase()
(in
cnavg.clock.EM
)
createMate()
(in
Breakend
)
childErrors()
(in
ConstrainedHistory
)
computeNormalizationFactors_SNV()
(in
cnavg.clock.EM
)
createModuleSegment()
(in
Module
)
childInsertionPoints()
(in
ConstrainedHistory
)
computeOddDistances()
(in
cnavg.historySampling.cycleCover
)
createNewHistory()
(in
cnavg.historySampling.sampleModuleCycles
)
chiSquare()
(in
cnavg.clock.EM
)
computeOffsets()
(in
cnavg.cactus.balanced
)
createNode()
(in
Graph
)
chiSquareTest()
(in
cnavg.clock.EM
)
computePosteriors()
(in
cnavg.clock.EM
)
createPartner()
(in
Breakend
)
chooseNet()
(in
cnavg.historySampling.sampleGraphCycles
)
conditionedLikelihoods()
(in
CNVTree
)
createSegment()
(in
Graph
)
chooseNewHistory()
(in
cnavg.historySampling.sampleGraphCycles
)
connectionNames()
(in
cnavg.cactus.threeWay.components
)
crossProduct()
(in
cnavg.clock.cnvTree
)
chooseNextNode()
(in
cnavg.historySampling.cycleCover
)
connections()
(in
Cactus
)
cumulativeImpactChanges_CNVNode()
(in
CNVTree
)
chromosomeNames
(in
cnavg.preprocess.cbs.cbs
)
connectNode()
(in
Breakend
)
cumulativeImpactChanges_SliceTree()
(in
CNVTree
)
chroms
(in
cnavg.cactusTree.cactusTree
)
consolidate()
(in
BreakendGraph
)
cutpoints()
(in
NormalizedCactus
)
clock
(in
cnavg
)
consolidateEmptyBreakend()
(in
Breakend
)
cutpoints2()
(in
NormalizedCactus
)
close()
(in
Module
)
constrained
(in
cnavg.history
)
cycle
(in
cnavg.flows
)
closePseudoTelomere()
(in
cnavg.historySampling.cycleCover
)
ConstrainedHistory
(in
cnavg.history.constrained
)
Cycle
(in
cnavg.flows.cycle
)
closePseudoTelomeres()
(in
cnavg.historySampling.cycleCover
)
convertThreeWayResultLine()
(in
Cactus
)
cycleAdjacencyIndexes()
(in
cnavg.flows.unitFlows
)
cnavg
convertThreeWayResults()
(in
Cactus
)
cycleCover
(in
cnavg.historySampling
)
cnv
(in
cnavg.preprocess
)
coords
(in
cnavg.basics
)
cycleSelfOverlaps()
(in
cnavg.flows.unitFlows
)
CNV
(in
cnavg.preprocess.cnv
)
copy()
(in
Graph
)
CNVNode
(in
cnavg.clock.cnvTree
)
copy()
(in
Module
)
D
dchisq
(in
cnavg.clock.EM
)
descentTreeString_Node()
(in
ScheduledHistory
)
doesNotContainNodes()
(in
Edge
)
debug
(in
cnavg.history
)
desperateInsertionPoints()
(in
ConstrainedHistory
)
doesNotContainNodes()
(in
Event
)
DEBUG
(in
cnavg.history.debug
)
destructiveOverlap()
(in
cnavg.flows.unitFlows
)
dot()
(in
Group
)
defaultLikelihoods()
(in
CNVTree
)
destructiveOverlaps()
(in
cnavg.flows.unitFlows
)
dot()
(in
Net
)
defaultLikelihoods_Event()
(in
CNVTree
)
detectHairpin()
(in
cnavg.flows.unitFlows
)
dot()
(in
Cycle
)
defaultLikelihoods_SNV()
(in
CNVTree
)
detectRedundancy()
(in
cnavg.flows.unitFlows
)
dot()
(in
Edge
)
Deletion
(in
cnavg.simulator.simulator
)
dijkstra()
(in
cnavg.historySampling.cycleCover
)
dot()
(in
Event
)
density()
(in
OverlapHistory
)
DIRECT_CUT
(in
cnavg.historySampling.sampleGraphCycles
)
dot()
(in
CactusHistory
)
depth_chain()
(in
OrientedCactus
)
discrepancies
(in
cnavg.preprocess
)
dot()
(in
History
)
depth_net()
(in
OrientedCactus
)
discrepancies()
(in
cnavg.preprocess.discrepancies
)
dot()
(in
History
)
descentTreeString()
(in
ScheduledHistory
)
discrepancies_CNV()
(in
cnavg.preprocess.discrepancies
)
dpois
(in
cnavg.clock.cnvTree
)
descentTreeString_Branch()
(in
ScheduledHistory
)
do()
(in
cnavg.cactusTree.cactusTree
)
Duplication
(in
cnavg.simulator.simulator
)
descentTreeString_Event()
(in
ScheduledHistory
)
doesNotContainNodes()
(in
Cycle
)
E
edge
(in
cnavg.flows
)
EM_eventParameters_SNV()
(in
cnavg.clock.EM
)
EuclidianHistory
(in
cnavg.history.euclidian
)
Edge
(in
cnavg.flows.edge
)
EM_sliceTree()
(in
cnavg.clock.EM
)
Event
(in
cnavg.flows.flows
)
edge()
(in
Graph
)
EM_sliceTree_Block()
(in
cnavg.clock.EM
)
eventLengths()
(in
History
)
EDGE_FACTOR
(in
cnavg.avg.balanced
)
EM_sliceTree_likelihood()
(in
cnavg.clock.EM
)
eventString()
(in
CNVTree
)
EDGE_FACTOR
(in
cnavg.cactus.balanced
)
EM_sliceTree_Phase()
(in
cnavg.clock.EM
)
eventVector()
(in
EuclidianHistory
)
edgeConstraint()
(in
cnavg.avg.balanced
)
EM_sliceTree_prior()
(in
cnavg.clock.EM
)
expandComponent()
(in
ConstrainedHistory
)
edgeConstraint()
(in
cnavg.cactus.balanced
)
EM_sliceTree_SliceTreeOption()
(in
cnavg.clock.EM
)
expandComponent()
(in
cnavg.history.constrained
)
edgeOffset()
(in
cnavg.cactus.balanced
)
EM_sliceTree_SNV()
(in
cnavg.clock.EM
)
expandGroup()
(in
Cactus
)
edges()
(in
Graph
)
embalm()
(in
EuclidianHistory
)
expandSliceTreeOptions_Phase()
(in
cnavg.clock.EM
)
edgesStr()
(in
Mapping
)
embalm()
(in
OverlapHistory
)
expandSliceTreeOptions_SliceTree()
(in
cnavg.clock.EM
)
edgesStr()
(in
Mapping
)
embalmDeadHistories()
(in
CactusHistory
)
expandSliceTreeOptions_Solution()
(in
cnavg.clock.EM
)
edgeStr()
(in
Mapping
)
EMIterations()
(in
cnavg.clock.EM
)
expectedCoverages()
(in
CNVTree
)
edgeStr()
(in
Mapping
)
EMStep()
(in
cnavg.clock.EM
)
expectedImpact()
(in
CNVTree
)
EM
(in
cnavg.clock
)
enumerate()
(in
cnavg.avg.gabp.gabp
)
expectedRatio()
(in
CNVTree
)
EM()
(in
cnavg.clock.EM
)
enumerate()
(in
History
)
extendCycle()
(in
cnavg.historySampling.cycleCover
)
EM2()
(in
cnavg.clock.EM
)
enumerateNets()
(in
cnavg.historySampling.sampleGraphCycles
)
extractCycle()
(in
cnavg.historySampling.cycleCover
)
EM_eventParameters()
(in
cnavg.clock.EM
)
errorCost()
(in
ConstrainedHistory
)
extractGraphModules()
(in
cnavg.avg.module
)
EM_eventParameters_Block()
(in
cnavg.clock.EM
)
errorCost_Net()
(in
ConstrainedHistory
)
extractPseudoTelomereCycle()
(in
cnavg.historySampling.cycleCover
)
EM_eventParameters_Phase()
(in
cnavg.clock.EM
)
euclidian
(in
cnavg.history
)
extractSliceTrees()
(in
CNVSlice
)
F
falseVector()
(in
Mapping
)
fixHairpin()
(in
cnavg.flows.unitFlows
)
flows
(in
cnavg.flows
)
filteredSNV()
(in
cnavg.clock.timeEvents
)
flattened
(in
cnavg.history
)
forceOrder()
(in
ScheduledHistory
)
filterOutGermlineBreakends()
(in
cnavg.preprocess.bambam
)
FlattenedHistory
forks()
(in
ScheduledHistory
)
find()
(in
cnavg.avg.gabp.gabp
)
flow()
(in
NodeFlow
)
FUDGE_FACTOR
(in
cnavg.avg.balanced
)
findRootNet()
(in
Cactus
)
flows
(in
cnavg
)
FUDGE_FACTOR
(in
cnavg.cactus.balanced
)
G
gabp
(in
cnavg.avg
)
getCNVs()
(in
History
)
getStartOfReverseRepeat()
(in
cnavg.flows.unitFlows
)
gabp
(in
cnavg.avg.gabp
)
getEdge()
(in
Mapping
)
graph
(in
cnavg.avg
)
generateSliceTreeOptions()
(in
cnavg.clock.EM
)
getEdge()
(in
Mapping
)
Graph
generateSliceTreeOptions_Block()
(in
cnavg.clock.EM
)
getEdge()
(in
Mapping
)
graph
(in
cnavg.cactus
)
generateSliceTreeOptions_Block2()
(in
cnavg.clock.EM
)
getEndOfDirectRepeat()
(in
cnavg.flows.unitFlows
)
graphError()
(in
BalancedAVG
)
getAlleleFrequencies_File()
(in
cnavg.preprocess.bambam
)
getEndOfRepeat()
(in
cnavg.historySampling.sampleModuleCycles
)
graphError()
(in
BalancedCactus
)
getAlleleFrequencies_Line()
(in
cnavg.preprocess.bambam
)
getEndOfReverseRepeat()
(in
cnavg.flows.unitFlows
)
graphError()
(in
cnavg.cactus.balanced
)
getAncestors()
(in
ScheduledHistory
)
getEvenOverlapIndex()
(in
cnavg.flows.unitFlows
)
group
(in
cnavg.cactus
)
getBond()
(in
Mapping
)
getEvenOverlapIndices()
(in
cnavg.flows.unitFlows
)
Group
(in
cnavg.cactus.group
)
getChain()
(in
Mapping
)
getNextNode()
(in
cnavg.historySampling.cycleCover
)
groupPairs()
(in
Cactus
)
getChildren()
(in
cnavg.clock.cnvTree
)
getSegment()
(in
Mapping
)
groupPairs2()
(in
Cactus
)
getCNVs()
(in
Cycle
)
getSliceTreeChildren()
(in
CNVTree
)
groupPairs3()
(in
Cactus
)
getCNVs()
(in
Edge
)
getStartOfDirectRepeat()
(in
cnavg.flows.unitFlows
)
groupString()
(in
cnavg.cactus.threeWay.components
)
getCNVs()
(in
Event
)
getStartOfRepeat()
(in
cnavg.historySampling.sampleModuleCycles
)
H
hairpinLength()
(in
cnavg.flows.unitFlows
)
history
(in
cnavg.history
)
HistoryBranch
(in
cnavg.simulator.simulator
)
highFlowHistory()
(in
cnavg.historySampling.cycleCover
)
History
(in
cnavg.history.history
)
historySampling
(in
cnavg
)
history
(in
cnavg
)
History
(in
cnavg.simulator.simulator
)
I
IDEAL_JOB_RUNTIME
(in
cnavg.cactusTree.cactusTree
)
initialHistory()
(in
cnavg.historySampling.cycleCover
)
inRegion()
(in
NodeFlow
)
Identity
(in
cnavg.simulator.simulator
)
initialize()
(in
ScheduledHistory
)
insertionPoints()
(in
ConstrainedHistory
)
imposeSegmentFlow()
(in
BreakendGraph
)
initialNodeEstimates()
(in
cnavg.avg.balanced
)
Inversion
(in
cnavg.simulator.simulator
)
imposeSegmentFlows()
(in
BreakendGraph
)
initialNodeEstimates()
(in
cnavg.cactus.balanced
)
isClosed()
(in
Cycle
)
incorporateCNVs()
(in
BreakendGraph
)
initialNodePrecisions()
(in
cnavg.avg.balanced
)
isConnected()
(in
Cycle
)
InitialBranch
(in
cnavg.simulator.simulator
)
initialNodePrecisions()
(in
cnavg.cactus.balanced
)
isFullyNormalized()
(in
NormalizedCactus
)
initialChainsEstimates()
(in
cnavg.cactus.balanced
)
initialNodesEstimates()
(in
cnavg.cactus.balanced
)
isHairpinIndex()
(in
cnavg.flows.unitFlows
)
initialChainsPrecisions()
(in
cnavg.cactus.balanced
)
initialNodesPrecisions()
(in
cnavg.cactus.balanced
)
isUnitFlow()
(in
cnavg.flows.unitFlows
)
initialEstimates()
(in
cnavg.avg.balanced
)
initialPrecisions()
(in
cnavg.avg.balanced
)
isUntouchable()
(in
History
)
initialEstimates()
(in
cnavg.cactus.balanced
)
initialPrecisions()
(in
cnavg.cactus.balanced
)
L
length()
(in
Region
)
length()
(in
History
)
load_c_gl()
(in
cnavg.avg.gabp.gabp
)
length()
(in
Block
)
lengths()
(in
Chain
)
LPProblem
(in
cnavg.avg.balanced
)
length()
(in
Chain
)
liftedEdgeString()
(in
NodeFlow
)
LPProblem
(in
cnavg.cactus.balanced
)
length()
(in
Event
)
likelihoodArray()
(in
CNVTree
)
length()
(in
CactusHistory
)
likelihoods()
(in
CNVTree
)
M
main()
(in
cnavg.avg.balanced
)
main()
(in
cnavg.preprocess.segmentCNVs
)
medianLength()
(in
History
)
main()
(in
cnavg.avg.gabp.gabp
)
main()
(in
cnavg.preprocess.vcf
)
MEM2G
(in
cnavg.cactusTree.cactusTree
)
main()
(in
cnavg.avg.module
)
main()
(in
cnavg.simulator.simulator
)
MEM4G
(in
cnavg.cactusTree.cactusTree
)
main()
(in
cnavg.cactus.balanced
)
Mapping
(in
cnavg.avg.balanced
)
mergeCycles()
(in
cnavg.historySampling.sampleModuleCycles
)
main()
(in
cnavg.cactus.graph
)
Mapping
(in
cnavg.cactus.balanced
)
MIN_CYCLE_FLOW
(in
cnavg.historySampling.cycleCover
)
main()
(in
cnavg.cactus.oriented
)
Mapping
(in
cnavg.history.euclidian
)
MIN_FLOW
(in
cnavg.historySampling.cycleCover
)
main()
(in
cnavg.cactus.threeWay.components
)
MAX_NOISE
(in
cnavg.avg.balanced
)
MIN_NOISE
(in
cnavg.avg.balanced
)
main()
(in
cnavg.cactusSampling.sampling
)
MAX_NOISE
(in
cnavg.cactus.balanced
)
MIN_NOISE
(in
cnavg.cactus.balanced
)
main()
(in
cnavg.cactusTree.cactusTree
)
maxBranches()
(in
OrientedCactus
)
MIN_PROB
(in
cnavg.clock.EM
)
main()
(in
cnavg.clock.EM
)
maxDepth()
(in
OrientedCactus
)
minDist()
(in
cnavg.historySampling.cycleCover
)
main()
(in
cnavg.clock.cnvTree
)
maxDepth_Chain()
(in
OrientedCactus
)
MINHISTORY
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.clock.timeEvents
)
maxDepth_Net()
(in
OrientedCactus
)
minimumEdge()
(in
cnavg.historySampling.cycleCover
)
main()
(in
cnavg.flows.unitFlows
)
MAXITERATIONS
(in
cnavg.clock.EM
)
minimumRearrangementCost()
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.history.euclidian
)
maxLength()
(in
CactusHistory
)
modifyCactusHistory()
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.history.scheduled
)
maxLength()
(in
History
)
modifyCactusHistory_Chain()
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.historySampling.cycleCover
)
MCTest()
(in
cnavg.historySampling.sampleGraphCycles
)
modifyCactusHistory_Initiate()
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.historySampling.sampleGraphCycles
)
mean()
(in
cnavg.clock.EM
)
modifyCactusHistory_Net()
(in
cnavg.historySampling.sampleGraphCycles
)
main()
(in
cnavg.historySampling.sampleModuleCycles
)
meanChainCoverage()
(in
cnavg.cactus.balanced
)
module
(in
cnavg.avg
)
main()
(in
cnavg.preprocess.bambam
)
meanOffset()
(in
cnavg.cactus.balanced
)
Module
(in
cnavg.avg.module
)
main()
(in
cnavg.preprocess.breakendGraph
)
meanTotalChainCoverage()
(in
cnavg.cactus.balanced
)
MyParser
(in
cnavg.cactusTree.cactusTree
)
main()
(in
cnavg.preprocess.cbs.cbs
)
median()
(in
cnavg.history.history
)
main()
(in
cnavg.preprocess.discrepancies
)
medianLength()
(in
CactusHistory
)
N
negativeNeighbourhood()
(in
cnavg.historySampling.cycleCover
)
nextNode_block()
(in
Chain
)
NodeFlow
(in
cnavg.avg.nodeFlow
)
net
(in
cnavg.cactus
)
nextNodes()
(in
cnavg.historySampling.cycleCover
)
nodeFlow()
(in
Module
)
Net
(in
cnavg.cactus.net
)
node
(in
cnavg.avg
)
nodeNet()
(in
Cactus
)
netConnections()
(in
Cactus
)
Node
(in
cnavg.avg.node
)
nodePairAdjacency()
(in
cnavg.historySampling.cycleCover
)
netHistoryCosts()
(in
CactusHistory
)
nodeAdjacencies()
(in
cnavg.historySampling.cycleCover
)
nodePairSegment()
(in
cnavg.historySampling.cycleCover
)
netModulePairs()
(in
cnavg.avg.module
)
nodeAdjacenciesTable
(in
cnavg.historySampling.cycleCover
)
nodes()
(in
Graph
)
netSpans()
(in
OrientedCactus
)
nodeBalanced()
(in
Module
)
nodes()
(in
Chain
)
netStats()
(in
Cactus
)
nodeChain()
(in
Cactus
)
nodes()
(in
Net
)
netStats()
(in
OrientedCactus
)
nodeConstraint()
(in
cnavg.avg.balanced
)
nodes()
(in
CNVSliceTree
)
netStats_net()
(in
OrientedCactus
)
nodeConstraint()
(in
cnavg.cactus.balanced
)
nodes()
(in
Cycle
)
netTreeString()
(in
OrientedCactus
)
nodeCount()
(in
Group
)
nodes()
(in
Edge
)
newHistorySlice()
(in
cnavg.clock.cnvTree
)
nodeCutpoints()
(in
NormalizedCactus
)
NON_STUB_COEFF
(in
cnavg.history.overlap
)
newHistorySlice_Node()
(in
cnavg.clock.cnvTree
)
nodeCutpoints2()
(in
NormalizedCactus
)
normalize()
(in
NormalizedCactus
)
newHistorySlices()
(in
cnavg.clock.cnvTree
)
nodeDistances()
(in
cnavg.historySampling.cycleCover
)
normalized()
(in
cnavg.clock.EM
)
newick()
(in
cnavg.clock.timeEvents
)
nodeError()
(in
BalancedAVG
)
NormalizedCactus
(in
cnavg.cactusSampling.sampling
)
newick()
(in
ScheduledHistory
)
nodeError()
(in
BalancedCactus
)
normalizeJointProbs()
(in
cnavg.clock.EM
)
newick_node()
(in
ScheduledHistory
)
nodeError()
(in
cnavg.cactus.balanced
)
normalizeJointProbs_Phase()
(in
cnavg.clock.EM
)
newick_remainderLeaf()
(in
ScheduledHistory
)
nodeErrors()
(in
BalancedAVG
)
normalizeJointProbs_SNV()
(in
cnavg.clock.EM
)
newickFork()
(in
cnavg.clock.timeEvents
)
nodeErrors()
(in
BalancedCactus
)
nullVector()
(in
Mapping
)
newickLeaf()
(in
cnavg.clock.timeEvents
)
nodeErrors()
(in
cnavg.cactus.balanced
)
newicks()
(in
cnavg.clock.timeEvents
)
nodeFlow
(in
cnavg.avg
)
O
offsetAncestral()
(in
cnavg.cactus.balanced
)
orientationChar()
(in
cnavg.basics.coords
)
overlap
(in
cnavg.history
)
offsetNovel()
(in
cnavg.cactus.balanced
)
oriented
(in
cnavg.cactus
)
Overlap
(in
cnavg.history.overlap
)
Operation
(in
cnavg.simulator.simulator
)
OrientedCactus
(in
cnavg.cactus.oriented
)
overlap()
(in
OverlapHistory
)
oppositeNeighbourhood()
(in
cnavg.historySampling.cycleCover
)
OrientedPosition
(in
cnavg.basics.coords
)
OverlapHistory
(in
cnavg.history.overlap
)
optimalSolutions()
(in
cnavg.historySampling.sampleGraphCycles
)
OrientedRegion
(in
cnavg.basics.coords
)
overlapMatrix()
(in
EuclidianHistory
)
ordered
(in
cnavg.history
)
originalVector()
(in
EuclidianHistory
)
overlappingGermlineSomatic()
(in
cnavg.preprocess.bambam
)
OrderedHistory
originators()
(in
CNVSliceTree
)
overlaps()
(in
OverlapHistory
)
organizeByEvents()
(in
cnavg.clock.cnvTree
)
otherNode()
(in
Block
)
orient()
(in
OrientedCactus
)
outAdjacencyOverlaps()
(in
cnavg.history.overlap
)
P
PARAMETER
(in
cnavg.clock.cnvTree
)
ploidy()
(in
NodeFlow
)
prepareGraphChainsMapping()
(in
cnavg.cactus.balanced
)
parse()
(in
cnavg.preprocess.bambam
)
ploidy()
(in
Block
)
prepareGraphMapping()
(in
cnavg.avg.balanced
)
parse()
(in
cnavg.preprocess.vcf
)
ploidy()
(in
CNV
)
prepareGraphMapping()
(in
cnavg.cactus.balanced
)
parse3WayOutput()
(in
cnavg.cactus.threeWay.components
)
pop()
(in
PartialOrderSet
)
prepareGraphNodesMapping()
(in
cnavg.cactus.balanced
)
parse3WayOutputLine()
(in
cnavg.cactus.threeWay.components
)
pop()
(in
EuclidianHistory
)
prepareGraphProblem()
(in
cnavg.avg.balanced
)
parseBBFile()
(in
cnavg.preprocess.bambam
)
pop()
(in
CactusHistory
)
prepareGraphProblem()
(in
cnavg.cactus.balanced
)
parseBBLine()
(in
cnavg.preprocess.bambam
)
pop()
(in
History
)
PrepareIndex
(in
cnavg.cactusTree.cactusTree
)
parseBreaksFile()
(in
cnavg.preprocess.bambam
)
pop()
(in
OverlapHistory
)
prepareNodeMapping()
(in
cnavg.avg.balanced
)
parseBreaksLine()
(in
cnavg.preprocess.bambam
)
pop()
(in
ScheduledHistory
)
prepareNodeMapping()
(in
cnavg.cactus.balanced
)
parseBreaksLineNew()
(in
cnavg.preprocess.bambam
)
popEvent()
(in
ScheduledHistory
)
prepareNodeProblem()
(in
cnavg.avg.balanced
)
parseChromLengths()
(in
cnavg.preprocess.bambam
)
popHistory()
(in
CactusHistory
)
prepareNodeProblem()
(in
cnavg.cactus.balanced
)
parseCNVData()
(in
cnavg.preprocess.bambam
)
popHistory()
(in
ScheduledHistory
)
preprocess
(in
cnavg
)
parseCNVLine()
(in
cnavg.preprocess.bambam
)
Position
(in
cnavg.basics.coords
)
printCNVs()
(in
Graph
)
partialOrderSet
(in
cnavg.basics
)
position()
(in
OrientedRegion
)
printCNVs()
(in
NodeFlow
)
PartialOrderSet
(in
cnavg.basics.partialOrderSet
)
positiveNeighbourhood()
(in
cnavg.historySampling.cycleCover
)
printMajority()
(in
Graph
)
partner()
(in
Graph
)
precision()
(in
cnavg.avg.balanced
)
printMajority()
(in
NodeFlow
)
phaseCNVs()
(in
cnavg.preprocess.bambam
)
precision()
(in
cnavg.cactus.balanced
)
printMinority()
(in
Graph
)
phasedBlockEvents()
(in
cnavg.clock.timeEvents
)
PrepareBAMBAMGraph
(in
cnavg.cactusTree.cactusTree
)
printMinority()
(in
NodeFlow
)
phasedBlockIndex()
(in
cnavg.clock.timeEvents
)
PrepareBreakendGraph
(in
cnavg.cactusTree.cactusTree
)
Process
(in
cnavg.cactusTree.cactusTree
)
phasedNeighbourhood()
(in
cnavg.historySampling.cycleCover
)
PrepareCactusCoverageGraphs
(in
cnavg.cactusTree.cactusTree
)
propagateChainOrientation()
(in
OrientedCactus
)
pickOutCycle()
(in
cnavg.historySampling.cycleCover
)
PrepareCBSGraph
(in
cnavg.cactusTree.cactusTree
)
propagateInitialHistory_Chain()
(in
cnavg.historySampling.cycleCover
)
pickOutCycles()
(in
cnavg.historySampling.cycleCover
)
prepareChainMapping()
(in
cnavg.cactus.balanced
)
propagateInitialHistory_Net()
(in
cnavg.historySampling.cycleCover
)
pinchChain()
(in
NormalizedCactus
)
PrepareCycleGraph
(in
cnavg.cactusTree.cactusTree
)
propagateNetOrientation()
(in
OrientedCactus
)
pinchUnnormalizedChain()
(in
NormalizedCactus
)
prepareEdgeMapping()
(in
cnavg.avg.balanced
)
PLOIDY
(in
cnavg.history.debug
)
prepareEdgeMapping()
(in
cnavg.cactus.balanced
)
R
randomChoice()
(in
cnavg.cactusSampling.sampling
)
Reduce
(in
cnavg.cactusTree.cactusTree
)
rootDesperateInsertionPoints()
(in
ConstrainedHistory
)
RandomHistory
(in
cnavg.simulator.simulator
)
Region
(in
cnavg.basics.coords
)
rootErrors()
(in
ConstrainedHistory
)
RandomWeightedHistory
(in
cnavg.simulator.simulator
)
remove()
(in
CNVSlice
)
rootify()
(in
ScheduledHistory
)
RATIO_CUTOFF
(in
cnavg.history.debug
)
removeChainedBlocks()
(in
Cactus
)
rootInsertionPoints()
(in
ConstrainedHistory
)
readDouble()
(in
cnavg.avg.gabp.gabp
)
removeConstraint()
(in
PartialOrderSet
)
ROUNDING_ERROR
(in
cnavg.history.euclidian
)
readInt()
(in
cnavg.avg.gabp.gabp
)
removeEdgeFlow()
(in
Module
)
ROUNDING_ERROR
(in
cnavg.historySampling.sampleModuleCycles
)
READLENGTH
(in
cnavg.preprocess.bambam
)
removeEdgeFromOverlapTable()
(in
cnavg.history.overlap
)
run()
(in
PrepareBAMBAMGraph
)
readVCFFile()
(in
cnavg.clock.timeEvents
)
removeEventCycleFromOverlapTable()
(in
cnavg.history.overlap
)
run()
(in
PrepareBreakendGraph
)
readVCFRecord()
(in
cnavg.clock.timeEvents
)
removeEventHairpins()
(in
cnavg.flows.unitFlows
)
run()
(in
PrepareCBSGraph
)
readVector()
(in
cnavg.avg.gabp.gabp
)
removeEventsHairpins()
(in
cnavg.flows.unitFlows
)
run()
(in
PrepareCactusCoverageGraphs
)
realValue()
(in
cnavg.historySampling.cycleCover
)
removeGermlineBreakends()
(in
cnavg.preprocess.bambam
)
run()
(in
PrepareCycleGraph
)
rearrangementCost()
(in
ConstrainedHistory
)
removeLowRatioEvents()
(in
CactusHistory
)
run()
(in
PrepareIndex
)
rearrangementCost()
(in
CactusHistory
)
removeLowRatioEvents()
(in
History
)
run()
(in
Process
)
rearrangementCost_Net()
(in
ConstrainedHistory
)
removeNonChromosomalBreakpoints()
(in
cnavg.preprocess.bambam
)
run()
(in
Reduce
)
rearrangementCosts()
(in
cnavg.historySampling.sampleGraphCycles
)
rescheduleRandomEvent()
(in
cnavg.historySampling.sampleModuleCycles
)
run()
(in
SampleCycles
)
redistanceNode()
(in
cnavg.historySampling.cycleCover
)
reverse()
(in
Cycle
)
run()
(in
SetupPhase
)
redoComponents_Edge()
(in
cnavg.history.constrained
)
reverse()
(in
Edge
)
run()
(in
cnavg.preprocess.cbs.cbs
)
redoComponents_Node()
(in
cnavg.history.constrained
)
reverseHash()
(in
cnavg.cactus.oriented
)
runGaBP()
(in
cnavg.avg.gabp.gabp
)
S
sample()
(in
cnavg.historySampling.sampleGraphCycles
)
segregatingLikelihood()
(in
CNVTree
)
snvLikelihoods()
(in
CNVTree
)
SampleCycles
(in
cnavg.cactusTree.cactusTree
)
segregatingLikelihoodArray()
(in
CNVTree
)
sortedCycleAdjacencyIndexes()
(in
cnavg.flows.unitFlows
)
sampleGraphCycles
(in
cnavg.historySampling
)
selectForRegion()
(in
CactusHistory
)
spacify()
(in
ScheduledHistory
)
sampleModuleCycles
(in
cnavg.historySampling
)
selectForRegion()
(in
History
)
span()
(in
Chain
)
sampling
(in
cnavg.cactusSampling
)
selfAdjacencyOverlaps()
(in
cnavg.history.overlap
)
span()
(in
Net
)
save_c_gl()
(in
cnavg.avg.gabp.gabp
)
setEdge()
(in
NodeFlow
)
splitByChroms()
(in
cnavg.preprocess.bambam
)
scheduled
(in
cnavg.history
)
setLiftedEdge()
(in
Graph
)
splitCycles()
(in
cnavg.historySampling.sampleModuleCycles
)
ScheduledHistory
(in
cnavg.history.scheduled
)
setRatio()
(in
Cycle
)
splitDirectRedundancy()
(in
cnavg.flows.unitFlows
)
scheduleEvent()
(in
ConstrainedHistory
)
setRatio()
(in
Event
)
splitEventsRedundancies()
(in
cnavg.flows.unitFlows
)
schedulingErrors()
(in
ConstrainedHistory
)
SetupPhase
(in
cnavg.cactusTree.cactusTree
)
splitPhases()
(in
cnavg.preprocess.bambam
)
searchBreakend()
(in
BreakendGraph
)
shadow()
(in
CNVNode
)
splitRedundancies_Event()
(in
cnavg.flows.unitFlows
)
seedHistory()
(in
cnavg.historySampling.cycleCover
)
shortString()
(in
Node
)
splitRedundancy()
(in
cnavg.flows.unitFlows
)
SEG_FACTOR
(in
cnavg.avg.balanced
)
shortString()
(in
Edge
)
splitReverseRedundancy()
(in
cnavg.flows.unitFlows
)
SEG_FACTOR
(in
cnavg.cactus.balanced
)
signedEdges()
(in
cnavg.historySampling.cycleCover
)
square()
(in
cnavg.avg.balanced
)
segment()
(in
Graph
)
signf()
(in
cnavg.historySampling.cycleCover
)
square()
(in
cnavg.cactus.balanced
)
segmentCNVs
(in
cnavg.preprocess
)
simplifyEventCycles()
(in
cnavg.flows.unitFlows
)
square()
(in
cnavg.history.overlap
)
segmentCNVs()
(in
cnavg.preprocess.segmentCNVs
)
simplifyStubsAndTrivials()
(in
Cycle
)
startAt()
(in
Cycle
)
segmentLength()
(in
Graph
)
simplifyStubsAndTrivials()
(in
Event
)
startAtEdge()
(in
Cycle
)
segmentLength()
(in
NodeFlow
)
simplifyStubsAndTrivials()
(in
CactusHistory
)
stats()
(in
Net
)
segmentLengths()
(in
cnavg.cactus.balanced
)
simplifyStubsAndTrivials()
(in
History
)
stats()
(in
OrientedCactus
)
segmentNodeString()
(in
Module
)
simulator
(in
cnavg
)
stats()
(in
CactusHistory
)
segmentNodeStrings()
(in
Module
)
simulator
(in
cnavg.simulator
)
stats()
(in
ScheduledHistory
)
segmentOffset()
(in
cnavg.cactus.balanced
)
sliceLikelihoods()
(in
CNVTree
)
stop_EM()
(in
cnavg.clock.EM
)
segmentsStr()
(in
Mapping
)
sliceTreeLikelihoods()
(in
CNVTree
)
StubNode
(in
cnavg.avg.node
)
segmentStr()
(in
Mapping
)
sliceTreePrior()
(in
cnavg.clock.EM
)
swapIn()
(in
ScheduledHistory
)
segmentString()
(in
NodeFlow
)
slideIn()
(in
ScheduledHistory
)
swapOut()
(in
ScheduledHistory
)
segmentStrings()
(in
Module
)
slideIn_Event()
(in
ScheduledHistory
)
swapUnder()
(in
ScheduledHistory
)
segmentValue()
(in
NodeFlow
)
SNV
(in
cnavg.clock.timeEvents
)
T
telomericGroups()
(in
Cactus
)
timeEvents
(in
cnavg.clock
)
TOLERANCE
(in
cnavg.clock.EM
)
TEMPERATURE
(in
cnavg.historySampling.sampleGraphCycles
)
timeEvents()
(in
cnavg.clock.timeEvents
)
totalImpact()
(in
CNVTree
)
Test()
(in
NormalizedCactus
)
TIMER_END
(in
cnavg.historySampling.sampleGraphCycles
)
totalImpact_Node()
(in
CNVTree
)
test_main()
(in
cnavg.basics.partialOrderSet
)
TIMER_LENGTH
(in
cnavg.historySampling.sampleGraphCycles
)
treeString()
(in
OrientedCactus
)
testSegment()
(in
NormalizedCactus
)
TOL
(in
cnavg.avg.balanced
)
tTest()
(in
cnavg.preprocess.bambam
)
threeWay
(in
cnavg.cactus
)
TOL
(in
cnavg.cactus.balanced
)
twin()
(in
Graph
)
U
undoComponent_Node()
(in
cnavg.history.constrained
)
updateChainPloidy()
(in
cnavg.cactus.balanced
)
updateLikelihoods()
(in
cnavg.clock.cnvTree
)
undoComponents_Edge()
(in
cnavg.history.constrained
)
updateCNVs()
(in
CactusHistory
)
updateNetChains_Block()
(in
OrientedCactus
)
unitFlows
(in
cnavg.flows
)
updateComponents()
(in
cnavg.history.constrained
)
updateNetChains_Chain()
(in
OrientedCactus
)
unnormalizedChain()
(in
NormalizedCactus
)
updateEdge()
(in
BalancedAVG
)
updateNetChains_Node()
(in
OrientedCactus
)
unnormalizedChains()
(in
NormalizedCactus
)
updateEdge()
(in
cnavg.cactus.balanced
)
updateNetGroupGroupMapping()
(in
Cactus
)
update()
(in
Chain
)
updateGraph()
(in
BalancedAVG
)
updateNetGroupMapping()
(in
Cactus
)
update()
(in
CactusHistory
)
updateGraph()
(in
cnavg.cactus.balanced
)
updateNetMapping()
(in
Cactus
)
updateBlock()
(in
cnavg.cactus.balanced
)
updateGraphChains()
(in
cnavg.cactus.balanced
)
updateNode()
(in
BalancedAVG
)
updateChain()
(in
cnavg.cactus.balanced
)
updateGraphNodes()
(in
cnavg.cactus.balanced
)
updateNode()
(in
cnavg.cactus.balanced
)
V
validate()
(in
BalancedAVG
)
validate()
(in
EuclidianHistory
)
validateNode()
(in
Graph
)
validate()
(in
Graph
)
validate()
(in
CactusHistory
)
validateNodeAdjacency()
(in
Graph
)
validate()
(in
Region
)
validate()
(in
History
)
validateNodeEdge()
(in
Graph
)
validate()
(in
PartialOrderSet
)
validate()
(in
OverlapHistory
)
validateNodeEdges()
(in
Graph
)
validate()
(in
Block
)
validate()
(in
ScheduledHistory
)
validateNodeSegment()
(in
Graph
)
validate()
(in
Chain
)
validate()
(in
Breakend
)
validateTree()
(in
ScheduledHistory
)
validate()
(in
Cactus
)
validate()
(in
BreakendGraph
)
variance()
(in
cnavg.avg.balanced
)
validate()
(in
Group
)
validate()
(in
CNV
)
variance()
(in
cnavg.cactus.balanced
)
validate()
(in
Net
)
validateEvent()
(in
ScheduledHistory
)
vcf
(in
cnavg.preprocess
)
validate()
(in
Cycle
)
validateHistory()
(in
ScheduledHistory
)
vector()
(in
Mapping
)
validate()
(in
Event
)
validateNode()
(in
BalancedAVG
)
virginBirth()
(in
cnavg.clock.cnvTree
)
W
weightedChainOffset()
(in
cnavg.cactus.balanced
)
weightedSegmentOffsets2()
(in
cnavg.cactus.balanced
)
writeDouble()
(in
cnavg.avg.gabp.gabp
)
weightedChoice()
(in
cnavg.historySampling.sampleGraphCycles
)
weightedSegmentOffsets3()
(in
cnavg.cactus.balanced
)
writeInt()
(in
cnavg.avg.gabp.gabp
)
WeightedHistory
(in
cnavg.simulator.simulator
)
write3WayGroupInput()
(in
cnavg.cactus.threeWay.components
)
writeVector()
(in
cnavg.avg.gabp.gabp
)
weightedSegmentOffsets()
(in
cnavg.cactus.balanced
)
write3WayInput()
(in
cnavg.cactus.threeWay.components
)
_
__add__()
(in
Net
)
__init__()
(in
CNVSliceTree
)
__package__
(in
cnavg.flows.edge
)
__add__()
(in
Cycle
)
__init__()
(in
CNVTree
)
__package__
(in
cnavg.flows.flows
)
__cmp__()
(in
Node
)
__init__()
(in
SNV
)
__package__
(in
cnavg.flows.unitFlows
)
__cmp__()
(in
NodeFlow
)
__init__()
(in
Cycle
)
__package__
(in
cnavg.history
)
__cmp__()
(in
OrientedRegion
)
__init__()
(in
Edge
)
__package__
(in
cnavg.history.constrained
)
__cmp__()
(in
Region
)
__init__()
(in
Event
)
__package__
(in
cnavg.history.debug
)
__cmp__()
(in
Block
)
__init__()
(in
EuclidianHistory
)
__package__
(in
cnavg.history.euclidian
)
__copy__()
(in
Graph
)
__init__()
(in
Mapping
)
__package__
(in
cnavg.history.flattened
)
__copy__()
(in
Module
)
__init__()
(in
FlattenedHistory
)
__package__
(in
cnavg.history.history
)
__copy__()
(in
NodeFlow
)
__init__()
(in
CactusHistory
)
__package__
(in
cnavg.history.ordered
)
__copy__()
(in
PartialOrderSet
)
__init__()
(in
History
)
__package__
(in
cnavg.history.overlap
)
__copy__()
(in
Cycle
)
__init__()
(in
OrderedHistory
)
__package__
(in
cnavg.history.scheduled
)
__copy__()
(in
Event
)
__init__()
(in
Overlap
)
__package__
(in
cnavg.historySampling
)
__copy__()
(in
ConstrainedHistory
)
__init__()
(in
OverlapHistory
)
__package__
(in
cnavg.historySampling.cycleCover
)
__copy__()
(in
EuclidianHistory
)
__init__()
(in
ScheduledHistory
)
__package__
(in
cnavg.historySampling.sampleGraphCycles
)
__copy__()
(in
FlattenedHistory
)
__init__()
(in
Breakend
)
__package__
(in
cnavg.historySampling.sampleModuleCycles
)
__copy__()
(in
CactusHistory
)
__init__()
(in
CNV
)
__package__
(in
cnavg.preprocess
)
__copy__()
(in
History
)
__init__()
(in
Deletion
)
__package__
(in
cnavg.preprocess.bambam
)
__copy__()
(in
OverlapHistory
)
__init__()
(in
Duplication
)
__package__
(in
cnavg.preprocess.breakend
)
__copy__()
(in
ScheduledHistory
)
__init__()
(in
History
)
__package__
(in
cnavg.preprocess.breakendGraph
)
__eq__()
(in
CNVSlice
)
__init__()
(in
HistoryBranch
)
__package__
(in
cnavg.preprocess.cbs
)
__hash__()
(in
Module
)
__init__()
(in
Identity
)
__package__
(in
cnavg.preprocess.cbs.cbs
)
__hash__()
(in
Node
)
__init__()
(in
InitialBranch
)
__package__
(in
cnavg.preprocess.cnv
)
__hash__()
(in
Chain
)
__init__()
(in
Inversion
)
__package__
(in
cnavg.preprocess.discrepancies
)
__hash__()
(in
CNVSlice
)
__init__()
(in
Operation
)
__package__
(in
cnavg.preprocess.segmentCNVs
)
__hash__()
(in
CNVSliceTree
)
__init__()
(in
RandomHistory
)
__package__
(in
cnavg.preprocess.vcf
)
__hash__()
(in
Cycle
)
__init__()
(in
RandomWeightedHistory
)
__package__
(in
cnavg.simulator
)
__init__()
(in
BalancedAVG
)
__init__()
(in
WeightedHistory
)
__package__
(in
cnavg.simulator.simulator
)
__init__()
(in
LPProblem
)
__iter__()
(in
Group
)
__str__()
(in
LPProblem
)
__init__()
(in
Mapping
)
__or__()
(in
CNVSliceTree
)
__str__()
(in
Mapping
)
__init__()
(in
Graph
)
__package__
(in
cnavg
)
__str__()
(in
Graph
)
__init__()
(in
Module
)
__package__
(in
cnavg.avg
)
__str__()
(in
Module
)
__init__()
(in
Node
)
__package__
(in
cnavg.avg.balanced
)
__str__()
(in
Node
)
__init__()
(in
StubNode
)
__package__
(in
cnavg.avg.gabp
)
__str__()
(in
NodeFlow
)
__init__()
(in
NodeFlow
)
__package__
(in
cnavg.avg.gabp.gabp
)
__str__()
(in
OrientedRegion
)
__init__()
(in
OrientedPosition
)
__package__
(in
cnavg.avg.graph
)
__str__()
(in
Region
)
__init__()
(in
OrientedRegion
)
__package__
(in
cnavg.avg.module
)
__str__()
(in
LPProblem
)
__init__()
(in
Position
)
__package__
(in
cnavg.avg.node
)
__str__()
(in
Mapping
)
__init__()
(in
Region
)
__package__
(in
cnavg.avg.nodeFlow
)
__str__()
(in
Block
)
__init__()
(in
PartialOrderSet
)
__package__
(in
cnavg.basics
)
__str__()
(in
Chain
)
__init__()
(in
BalancedCactus
)
__package__
(in
cnavg.basics.coords
)
__str__()
(in
Cactus
)
__init__()
(in
LPProblem
)
__package__
(in
cnavg.basics.partialOrderSet
)
__str__()
(in
Group
)
__init__()
(in
Mapping
)
__package__
(in
cnavg.cactus
)
__str__()
(in
Net
)
__init__()
(in
Block
)
__package__
(in
cnavg.cactus.balanced
)
__str__()
(in
OrientedCactus
)
__init__()
(in
Cactus
)
__package__
(in
cnavg.cactus.block
)
__str__()
(in
CNVNode
)
__init__()
(in
Group
)
__package__
(in
cnavg.cactus.chain
)
__str__()
(in
CNVTree
)
__init__()
(in
Net
)
__package__
(in
cnavg.cactus.graph
)
__str__()
(in
SNV
)
__init__()
(in
OrientedCactus
)
__package__
(in
cnavg.cactus.group
)
__str__()
(in
Cycle
)
__init__()
(in
NormalizedCactus
)
__package__
(in
cnavg.cactus.net
)
__str__()
(in
Edge
)
__init__()
(in
MyParser
)
__package__
(in
cnavg.cactus.oriented
)
__str__()
(in
Event
)
__init__()
(in
PrepareBAMBAMGraph
)
__package__
(in
cnavg.cactus.threeWay
)
__str__()
(in
Mapping
)
__init__()
(in
PrepareBreakendGraph
)
__package__
(in
cnavg.cactus.threeWay.components
)
__str__()
(in
CactusHistory
)
__init__()
(in
PrepareCBSGraph
)
__package__
(in
cnavg.cactusSampling
)
__str__()
(in
History
)
__init__()
(in
PrepareCactusCoverageGraphs
)
__package__
(in
cnavg.cactusSampling.sampling
)
__str__()
(in
Overlap
)
__init__()
(in
PrepareCycleGraph
)
__package__
(in
cnavg.cactusTree
)
__str__()
(in
OverlapHistory
)
__init__()
(in
PrepareIndex
)
__package__
(in
cnavg.cactusTree.cactusTree
)
__str__()
(in
ScheduledHistory
)
__init__()
(in
Process
)
__package__
(in
cnavg.clock.EM
)
__str__()
(in
Breakend
)
__init__()
(in
Reduce
)
__package__
(in
cnavg.clock
)
__str__()
(in
BreakendGraph
)
__init__()
(in
SampleCycles
)
__package__
(in
cnavg.clock.cnvTree
)
__str__()
(in
CNV
)
__init__()
(in
SetupPhase
)
__package__
(in
cnavg.clock.timeEvents
)
__str__()
(in
History
)
__init__()
(in
CNVNode
)
__package__
(in
cnavg.flows
)
__str__()
(in
HistoryBranch
)
__init__()
(in
CNVSlice
)
__package__
(in
cnavg.flows.cycle
)
__sub__()
(in
Node
)
Home
Trees
Indices
Help
Generated by Epydoc 3.0.1 on Tue Mar 12 12:56:34 2013
http://epydoc.sourceforge.net


Good day Sir, I am Mike Morgan Tsvangirai, A 19 year Son of Mr.Morgan Tsvangirai Jr the opposition leader to President Robert Mugabe of Zimbabwe. Following his ugly land reform exercise, taking over of white farmers land and redistributing it to the Blacks that set the country on the brinks of collapse and the call by international nations including the United Nation for his resignation, my father is a strong party against the decision of President Robert Mugabe. President Robert Mugabe is treating to kill my father in order to reduce opposition because of his decision. Because of President Mugabe's death treat to my father, my father was able to move us out of Zimbabwe to Democratic republic of Congo for safety and further Education. President Robert Mugabe's government has set up secret camps across the country in which thousands of youths are taught how to torture and kill. You can read more concerning President Roberts Mugube bad manner at; http://news.bbc.co.uk/1/hi/world/africa/3493958.stm Before my father’s Death, he further told me that he left the sum of $10,500,000.00 United States Dollars for myself and the family in a payment Finance House in London if anything happens to him, base on the fact that we must use the fund for investment as long as we provide the person who will invest on this fund before the Finance house can release the fund. I will like you to know that I have all the certificate of deposit, which my father gave me concerning the fund. And I have contacted you to present you as the investor. Do get back to me with your full contact information so that I will give you more information on this project.Please contact me on my private email<EMAIL_ADDRESS>Thanks, Mike Morgan (On behalf of the family)


Class WebDriver
- Defined in: WebDriver.js
| Constructor Attributes | Constructor Name and Description |
|---|---|
Method Summary
Class Detail
Field Detail
Method Detail
-
<private> <inner> _errorByCode(code, msg)Throw error by error code.
- Parameters:
- {Number} code
- Error code.
- {String} msg Optional
- Text to omit default error message.
- Throws:
- {AbstractError}
-
<private> <inner> {Object} _get(path)GET request to webdriver on given path.
- Parameters:
- {String} path
- Returns:
- {Object}
- See:
- WebDriver#_request
-
<private> <inner> {Object} _post(path, data)POST request to webdriver on given path.
- Parameters:
- {String} path
- {Object} data Optional
- POST data.
- Returns:
- {Object}
- See:
- WebDriver#_request
-
<private> <inner> {Object} _request(path, method, data)Make a request to webdriver with given params
- Parameters:
- {String} path Optional
- webdriver path (method) to call.
- {String} method Optional
- HTTP method for request (e.g. GET, POST, PUT, ...).
- {String} data Optional
- Data for POST payload
- Returns:
- {Object} Request result.
-
<private> <inner> {WebDriver} _sleep(seconds)Do not do anything for some time.
Some functions are need this to do interval checks for element appearing or disappearing.
- Parameters:
- {Number} seconds
- Time to wait.
- Returns:
- {WebDriver}
-
{WebDriver} acceptAlert()Accepts the currently displayed alert dialog.
Usually, this is equivalent to clicking on the 'OK' button in the dialog.
- Returns:
- {WebDriver}
-
back()Navigate backwards in the browser history, if possible.
-
{WebDriver} buttonDown(button)Click and hold the left mouse button (at the coordinates set by the last moveto command).
Note that the next mouse-related command that should follow is buttonup . Any other mouse command (such as click or another call to buttondown) will yield undefined behaviour.
- Parameters:
- {Number} button
- Which button, enum: {LEFT = 0, MIDDLE = 1 , RIGHT = 2}. Defaults to the left mouse button if not specified.
- Returns:
- {WebDriver}
-
{WebDriver} buttonUp(button)Releases the mouse button previously held (where the mouse is currently at).
Must be called once for every buttondown command issued. See the note in click and buttondown about implications of out-of-order commands.
- Parameters:
- {Number} button
- Which button, enum: {LEFT = 0, MIDDLE = 1 , RIGHT = 2}. Defaults to the left mouse button if not specified.
- Returns:
- {WebDriver}
-
{WebDriver} clear(element)Clear a TEXTAREA or text INPUT element's value.
- Parameters:
- {WebElement} element
- Returns:
- {WebDriver}
-
{WebDriver} click(button)Click any mouse button (at the coordinates set by the last moveto command).
Note that calling this command after calling buttondown and before calling button up (or any out-of-order interactions sequence) will yield undefined behaviour).
- Parameters:
- {Number} button
- Which button, enum: {LEFT = 0, MIDDLE = 1 , RIGHT = 2}. Defaults to the left mouse button if not specified.
- Returns:
- {WebDriver}
-
{WebDriver} clickElement(element)Click on an element.
- Parameters:
- {WebElement} element
- Returns:
- {WebDriver}
-
cookie(name, value, path, domain, secure, expiry)Method for more simple way to add cookie.
- Parameters:
- {String} name
- The name of the cookie.
- {String} value
- The cookie value.
- {String} path Optional
- The cookie path.
- {String} domain Optional
- The domain the cookie is visible to.
- {Boolean} secure Optional
- Whether the cookie is a secure cookie.
- {Number} expiry Optional
- Count of hours from now when the cookie expires.
-
{WebDriver} deleteCookie(name)Delete cookie with given name.
- Parameters:
- {String} name
- Returns:
- {WebDriver}
-
{WebDriver} deleteCookies()Delete all cookies visible to the current page.
- Returns:
- {WebDriver}
-
{WebDriver} dismissAlert()Dismisses the currently displayed alert dialog.
For confirm() and prompt() dialogs, this is equivalent to clicking the 'Cancel' button. For alert() dialogs, this is equivalent to clicking the 'OK' button.
- Returns:
- {WebDriver}
-
{WebDriver} doubleClick()Double-clicks at the current mouse coordinates (set by moveto).
- Returns:
- {WebDriver}
-
{WebDriver} execute(script, args)Inject a snippet of JavaScript into the page for execution in the context of the currently selected frame.
The executed script is assumed to be synchronous and the result of evaluating the script is returned to the client.
The script argument defines the script to execute in the form of a function body. The value returned by that function will be returned to the client. The function will be invoked with the provided args array and the values may be accessed via the arguments object in the order specified.
Arguments may be any JSON-primitive, array, or JSON object. JSON objects that define a {WebElement} reference will be converted to the corresponding DOM element. Likewise, any WebElements in the script result will be returned to the client as {WebElement} JSON objects.
- Parameters:
- {String} script
- The script to execute.
- {Object} args
- The script arguments.
- Returns:
- {WebDriver} The script result.
-
{WebDriver} executeAsync(script, args)Inject a snippet of JavaScript into the page for execution in the context of the currently selected frame.
The executed script is assumed to be asynchronous and must signal that is done by invoking the provided callback, which is always provided as the final argument to the function. The value to this callback will be returned to the client.
Asynchronous script commands may not span page loads. If an unload event is fired while waiting for a script result, an error should be returned to the client.
The script argument defines the script to execute in teh form of a function body. The function will be invoked with the provided args array and the values may be accessed via the arguments object in the order specified. The final argument will always be a callback function that must be invoked to signal that the script has finished.
Arguments may be any JSON-primitive, array, or JSON object. JSON objects that define a {WebElement} reference will be converted to the corresponding DOM element. Likewise, any WebElements in the script result will be returned to the client as {WebElement} JSON objects.
- Parameters:
- {String} script
- The script to execute.
- {Object} args
- The script arguments.
- Returns:
- {WebDriver} The script result.
-
forward()Navigate forwards in the browser history, if possible.
-
get(url)Navigate to a new URL.
- Parameters:
- url
- {String} The URL to navigate to.
-
{String} getAlertText()Gets the text of the currently displayed JavaScript alert(), confirm(), or prompt() dialog.
- Returns:
- {String}
-
{String|null} getAlertTextOrNull()The same as WebDriver.getAlertText(), but returns null if there is no alert dialog.
- Returns:
- {String|null}
-
{String} getAttribute(element, name)Get the value of an element's attribute.
- Parameters:
- {WebElement} element
- {String} name
- Returns:
- {String}
-
{Object} getCapabilities()Retrieve the capabilities of the specified session.
- Returns:
- {Object}
-
{Cookie[]} getCookies()Retrieve all cookies visible to the current page.
- Returns:
- {Cookie[]} A list of cookies.
-
{String} getCssProperty(element, propertyName)Query the value of an element's computed CSS property.
The CSS property to query should be specified using the CSS property name, not the JavaScript property name (e.g. background-color instead of backgroundColor).
- Parameters:
- {WebElement} element
- {String} propertyName
- Returns:
- {String}
-
{String} getCurrentUrl()Retrieve the URL of the current page.
- Returns:
- {String}
-
{WebElement} getElement(using, value)Search for an element on the page, starting from the identified element.
The located element will be returned as a WebElement object.
The table below lists the locator strategies that each server should support. Each locator must return the first matching element located in the DOM.
- class name — Returns an element whose class name contains the search value; compound class names are not permitted
- css selector — Returns an element matching a CSS selector
- id — Returns an element whose ID attribute matches the search value
- name — Returns an element whose NAME attribute matches the search value
- link text — Returns an anchor element whose visible text matches the search value
- partial link text — Returns an anchor element whose visible text partially matches the search value
- tag name — Returns an element whose tag name matches the search value
- xpath — Returns an element matching an XPath expression. The provided XPath expression must be applied to the server "as is"; if the expression is not relative to the element root, the server should not modify it. Consequently, an XPath query may return elements not contained in the root element's subtree
- Parameters:
- {String} using
- The locator strategy to use.
- {String} value
- The search target.
- Returns:
- {WebElement} Located element.
-
{WebElement|null} getElementOrNull(using, value)Get WebElement if query was success full. Otherwise will return null.
It handles only NoSuchElement error. Any other errors will be re-thrown.
- Parameters:
- {String} using
- See WebDriver.getElement() for details.
- {String} value
- Value for query.
- Returns:
- {WebElement|null}
-
{WebElement[]} getElements(using, value)Search for multiple elements on the page, starting from the identified element.
- Parameters:
- {String} using
- The locator strategy to use.
- {String} value
- The search target.
- Returns:
- {WebElement[]} Located elements.
- See:
- WebDriver#getElement
-
{width|height} getElementSize(element)Determine an element's size in pixels.
- Parameters:
- {WebElement} element
- Returns:
- {width|height}
-
{String} getElementTagName(element)Query for an element's tag name.
- Parameters:
- {WebElement} element
- Returns:
- {String} The element's tag name, as a lowercase string.
-
{WebDriver} getElementText(element)Returns the visible text for the element.
- Parameters:
- {WebElement} element
- Returns:
- {WebDriver}
-
{Object} getLocation(element)Determine an element's location on the page. The point (0, 0) refers to the upper-left corner of the page.
- Parameters:
- {WebElement} element
- Returns:
- {Object} The X and Y coordinates for the element on the page.
-
{Object} getLocationInView(element)Determine an element's location on the screen once it has been scrolled into view.
Note: This is considered an internal command and should only be used to determine an element's location for correctly generating native events.
- Parameters:
- {WebElement} element
- Returns:
- {Object} The X and Y coordinates for the element on the page.
-
{String} getSource()Get the current page source.
- Returns:
- {String} The current page source.
-
{String} getTitle()Get the current page title.
- Returns:
- {String} The current page title.
-
{String} getWindowHandle()Retrieve the current window handle.
- Returns:
- {String} The current window handle.
-
{string[]} getWindowHandles()Retrieve the list of all window handles available to the session.
- Returns:
- {string[]} A list of window handles.
-
{Boolean} hasElement(using, value)Returns true if element exists. Otherwise returns false.
- Parameters:
- {String} using
- See WebDriver.getElement() for details.
- {String} value
- Value for query.
- Returns:
- {Boolean}
-
{Object} init(desiredCapabilities, requiredCapabilities)Create a new session and remembers sessionId for future calls.
The server should attempt to create a session that most closely matches the desired and required capabilities.
Required capabilities have higher priority than desired capabilities and must be set for the session to be created.
- Parameters:
- {Object} desiredCapabilities
- {Object} requiredCapabilities
- Returns:
- {Object} Session capabilities and sessionId.
-
{boolean} isAlertOpened()Returns true if there is alert window.
- Returns:
- {boolean}
-
{Boolean} isDisplayed(element)Determine if an element is currently displayed.
- Parameters:
- {WebElement} element
- Returns:
- {Boolean}
-
{Boolean} isEnabled(element)Determine if an element is currently enabled.
- Parameters:
- {WebElement} element
- Returns:
- {Boolean}
-
{Boolean} isSelected(element)Determine if an OPTION element, or an INPUT element of type checkbox or radiobutton is currently selected.
- Parameters:
- {WebElement} element
- Returns:
- {Boolean}
-
{Boolean} isTextPresent(text)Check if given text present in page source.
- Parameters:
- {String} text
- Text to search.
- Returns:
- {Boolean}
-
{WebDriver} keys(value)Send a sequence of key strokes to the active element.
This command is similar to the WebDriver.type command in every aspect except the implicit termination: The modifiers are not released at the end of the call. Rather, the state of the modifier keys is kept between calls, so mouse interactions can be performed while modifier keys are depressed.
- Parameters:
- {String} value
- Returns:
- {WebDriver}
-
{WebDriver} moveTo(el, offsetX, offsetY)Move the mouse by an offset of the specificed element. If no element is specified, the move is relative to the current mouse cursor. If an element is provided but no offset, the mouse will be moved to the center of the element. If the element is not visible, it will be scrolled into view.
- Parameters:
- {WebElement|null} el
- {Number|null} offsetX
- {Number|null} offsetY
- Returns:
- {WebDriver}
-
refresh()Refresh the current page.
-
{WebDriver} setCookie(cookie)Set a cookie.
- Parameters:
- {Cookie} cookie
- Returns:
- {WebDriver}
-
setImplicitTimeout(seconds)Set the amount of time the driver should wait when searching for elements.
When searching for a single element, the driver should poll the page until an element is found or the timeout expires, whichever occurs first. When searching for multiple elements, the driver should poll the page until at least one element is found or the timeout expires, at which point it should return an empty list.
If this command is never sent, the driver should default to an implicit wait of 0ms.
- Parameters:
- {Number} seconds
- The amount of time to wait. This value has a lower bound of 0.
-
setPageLoadTimeout(seconds)Set the amount of time the driver should wait when loading a page.
- Parameters:
- {Number} seconds
- The amount of time to wait. This value has a lower bound of 0.
-
{WebDriver} setPromptValue(value)Sends keystrokes to a JavaScript prompt() dialog.
- Parameters:
- {String} value
- Returns:
- {WebDriver}
-
setScriptTimeout(seconds)Set the amount of time, in milliseconds, that asynchronous scripts executed by /session/:sessionId/execute_async are permitted to run before they are aborted and a {Timeout} error is returned to the client.
- Parameters:
- {Number} seconds
- The amount of time, that time-limited commands are permitted to run.
-
{WebDriver} stop()Delete the session.
- Returns:
- {WebDriver}
-
{WebDriver} submitElement(element)Submit a FORM element.
The submit command may also be applied to any element that is a descendant of a FORM element.
- Parameters:
- {WebElement} element
- Returns:
- {WebDriver}
-
{String} takeScreenshot()Take a screenshot of the current page.
- Returns:
- {String} The screenshot as a base64 encoded PNG.
-
{WebDriver} type(element, value)Send a sequence of key strokes to an element.
The server must process the key sequence as follows:
- - Each key that appears on the keyboard without requiring modifiers are sent as a keydown followed by a key up.
- - If the server does not support native events and must simulate key strokes with JavaScript, it must generate keydown, keypress, and keyup events, in that order. The keypress event should only be fired when the corresponding key is for a printable character;
- - If a key requires a modifier key (e.g. "!" on a standard US keyboard), the sequence is: modifier down, key down, key up, modifier up, where key is the ideal unmodified key value (using the previous example, a "1");
- - Modifier keys (Ctrl, Shift, Alt, and Command/Meta) are assumed to be "sticky"; each modifier should be held down (e.g. only a keydown event) until either the modifier is encountered again in the sequence, or the NULL (U+E000) key is encountered;
- - Each key sequence is terminated with an implicit NULL key. Subsequently, all depressed modifier keys must be released (with corresponding keyup events) at the end of the sequence.
- Parameters:
- {WebElement} element
- {String} value
- Returns:
- {WebDriver}
-
{String} waitForAlert(timeout, interval)Waits for alert dialog appear and returns it's text.
- Parameters:
- {Number} timeout Optional
- Timeout in seconds.
- {Number} interval Optional
- Interval in seconds.
- Returns:
- {String}
-
{Boolean} waitForCondition(conditionFn, thisArg, timeout, interval)Polls specified function.
- Parameters:
- conditionFn
- Function to poll. It should return true or false.
- thisArg
- {Number} timeout Optional
- Timeout in seconds. Defaults to 15 s.
- {Number} interval Optional
- Interval in seconds. Defaults to 0.5 s.
- Returns:
- {Boolean}
-
{WebElement} waitForElement(using, value, timeout, interval)Wait for element and return it when it appears.
- Parameters:
- {String} using
- See WebDriver.getElement() for details.
- {String} value
- Value for query.
- {Number} timeout Optional
- Timeout in seconds.
- {Number} interval Optional
- Interval in seconds.
- Returns:
- {WebElement}
-
waitForElementDisappear(using, value, timeout, interval)Wait for element will be not present on a page.
- Parameters:
- {String} using
- See WebDriver.getElement() for details.
- {String} value
- Value for query.
- {Number} timeout Optional
- Timeout in seconds.
- {Number} interval Optional
- Interval in seconds.
-
waitForNoAlert(timeout, interval)Waits for alert dialog not appear.
- Parameters:
- {Number} timeout Optional
- Timeout in seconds.
- {Number} interval Optional
- Interval in seconds.


Sagar Kuvar
I'm Sagar Kuvar from Navi Mumbai, Maharashtra, India. I was an Software Developer Intern at Nomura Holdings and Finished my Masters of Technology from Indian Institute of Information Technology Pune.
I have spent years studying and applying knowledge of Java,Android,HTML,PHP,Js,Python,Jenkins,Ansible,Docker,Flask/Django and also have done various courses on ML,Data Science etc.
Right now I am Actively looking for a Full Time experience in any Investment Bankings or Product Based Companies
A representation of my proficiency in each skill
Some stats related to my experience and projects.
Designed with ♥ by Sagar Kuvar
© 2019 Sagar Kuvar. All rights reserved.


Smuggler Cove Island Resort
Contact Information
Please email us at<EMAIL_ADDRESS>Smuggler Cove, Pacific Ocean


PI DA Iacobas
Specific Aim 1:
To determine the Gene Commanding Height (GCH) hierarchy in standard prostate, lung, thyroid and blood human cancer cell lines. We will use Next Gen RNA sequencing (Illumina NextSeq 550) and/or (Agilent 4x44k human gene expression) microarray platform, both available at our PVAMU Computational Systems Biology Center – Personalized Genomics Laboratory to profile cancer cell lines purchased from authorized vendors. We will use our Genomic Fabric Paradigm as well as the standard experimental protocol and data processing algorithms established and validated in hundreds of genomic experiments performed in previous IacobasLabs from Albert Einstein College of Medicine and New York Medical College.
Specific Aim 2:
To reprogram cancer cell lines using CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing, lentiviral transfection or siRNA. We will design custom CRISPR clones of the selected GMRs, order them to a specialized company (https://www.sigmaaldrich.com, http://www.crisprtx.com, https://www.editasmedicine.com/crispr) and reprogram the cancer cell lines studied at SA1. As alternatives to CRISPR we can use lentiviral transfection or siRNA for which we have experience.
Specific Aim 3:
To evaluate the effect of CRISPR-GMR reprograming in the survival of the treated cancer cells. The viability of cancer cells (the growth rate and the death rate) will be assessed before and after the treatment.


Registrations to buy Tokyo Games tickets exceed 8 million
More than 8 million residents of Japan have registered to buy tickets for the Tokyo Olympics and Paralympics next summer, the games organizing committee said Monday.
Registration of a “Tokyo 2020 ID” is necessary before buying tickets and 50,000 people had already completed the process when a summary of ticket prices was released in July last year.
Around 3.22 million tickets were sold during the first phase of the Olympics ticket lottery in May that saw heavy traffic disrupt the official ticketing website. An additional 350,000 were sold in August during a window open to those unsuccessful in the initial draw.
The second phase of the lottery began for residents of Japan on Nov. 13, with over 1 million tickets available for nearly all the events including the opening and closing ceremonies.
Applications can be made on the official ticketing website until 11:59 a.m. on Tuesday and the results of the lottery will be announced on Dec. 18. Winners will have until Jan. 10 to complete their purchases.
The second phase of the Paralympics ticket lottery will start in January.
From next spring, tickets will be sold on a first-come, first-served basis on the official ticketing website as well as over the counter in ticketing booths to be set up in Tokyo.
Final ticket sales are expected to surpass 9 million, including overseas sales through designated resellers and distributors.
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CONFIGURE OPENBOX
configure three most important configuration files of Openbox: menu.xml, rc.xml and autostart.
OVERVIEW:
What we will do to have a Openbox Windows manager:
- Step 1: Install the core packages.
- Step 2: Configure Openbox
1. Install the core packages:
Here is the command to install them:
sudo apt-get install xorg openbox suckless-tools terminator lxpanel thunar lightdm wicd firefox geany
From previous chapter, you have known what are these core packages and what they will contribute to your system.
After they have been installed, you will have a bare frame of a operating system with Xorg as the prerequisite of GUI and video driver, Lightdm as the login manager, Openbox as the windows manager, Thunar as the file manager, Lxpanel as taskbar, Wicd as the network manager, Terminator as the the terminal emulator, Geany as the text editor, Firefox as the web browser.
From this frame, we will develop them into a fully functional OS.
2. Configure Openbox:
After Step 1, reboot your system and login for the first time. If a grayish screen are there greeting you (with mouse point). Your Openbox system is ready for further configuration.
There are somethings that I should tell you about our upcoming system.  There will be no such thing in our system. The job of creating icon on your desktop is called “managing desktop” and it is the service of a File Manager.
In my opinion, the feature is redundant and unnecessary with Openbox. With its right clicking menu and shortcut keys, you will feel the superior of these methods is far over finding an icon on your desktop to click.
- Right-click menu: By right clicking your mouse, there is a menu of applications. Click to any app to call it. But at the moment, you only can call Terminator (the terminal entry) or Firefox browser (the Web browser entry).
- Shortcut keys: Pressing the Windows key (the key that have “Microsoft Icon” on it) and the key T: Windows + T, the Terminator terminal should be started. The shortcut key will improve your productivity after you have familiar with it. Openbox let you choose shortcut keys freely. In later part of this chapter I will show you how to create your own shortcut keys.
 You will learn how to make your Openbox system looks decent in some later chapters. In Linux world, some of us really do not care much about the look. I have seen some minimalists using only tiling window manager with just wallpaper on the screen (They even go as far as not using any mouse at all).
At the moment our Ubuntu Openbox has no taskbar, no wallpaper, no volume control, no terminal emulation, no file manager, no power manager, no network manager… A fully functional operation system will also not worry its user about some basic automating tasks such as: shutdown/restart, system monitor, etc. Our system is lacking all of that! 😀
From now on we will add more features to our Openbox:
2.1. Open this guide on Firefox browser:
The reason for telling you to install Firefox at the very beginning is for you to read this guide while installing your system (and also saving you some time by copying/ pasting commands directly from my website). Right-click, then choose “Web Browser” to start Firefox browser, go to UbuntuOpenbox.com/lessons/lessons.html.
2.2. Creating the seed configuration files:
The configuration of Openbox is defined within three files: rc.xml, menu.xml, autostart.
At default, after you have installed Openbox, there are no configuration files for normal user, and your Openbox is using the global configuration files stored at /etc/xdg/openbox. We will use these file as the seed for our further configuration.
Type below command as normal to copy global files over home folder:
cp -R /etc/xdg/openbox ~/.config/
Now if we go to the directory ~/.config/openbox by:
cd ~/.config/openbox
and see what are in it by:
ls -lh
These are the seed files for our Openbox configuration.
showing ls output of the folder
2.3. Configure Openbox:
We will configure the above seed files one by one:
menu.xml:
We have some programs for auto generating right click menu, but I always find the auto generated menu too messy. I like to manually manage it.
We will use my current configuration here: https://pastebin.com/5Cixsqpa. Then replace the current content of menu.xml with mine:
geany ~/.config/openbox/menu.xml
then Save
autostart
Any programs or commands in Openbox need to be instructed specifically if you want them to auto-run at the startup. You can also set timing to start those programs chronologically. Fortunately, the job is fairly easy. All you need to do is put a line of command in the autostart file.
For instance, the command to start lxpanel:
(sleep 3s && lxpanel) &
The command mean: delay 3 second before starting lxpanel.
We are also using mine autostart file. Here is its link: https://pastebin.com/EmY8gx9c.
geany ~/.config/openbox/autostart
rc.xml
This file helds the configuration for all the shotrcut-keys and define how an application will appear on the screen. How to modifying the file is really easy. Below is the typical entry:
<keybind key="W-t">
<action name="Execute">
<startupnotify>
<enabled>true</enabled>
<name>Terminal</name>
</startupnotify>
<command>terminator</command>
</action>
</keybind>
Just change the combination keys “W-t” and the command “terminator” respectively and you will have a new shortcut-key.
Somethings you need to be noted:
- The capital W: the Windows key which have this icon:
- The capital A: the Alt key
- The capital S: the Shift key
- The capital C: the Control key
Go to my rc.xml file here: https://pastebin.com/ajfTFaay. Copy the content and replace the current content of rc.xml file. Mind you, the content is really long!
To open the rc.xml file with Geany:
geany ~/.config/openbox/rc.xml
Restart your computer for all the change to take effect.
3. Using Obmenu to edit menu:
Although edit the menu.xml text file directly is easy, you can also use a program called Obmenu to edit the file using GUI.
To install:
sudo apt-get install obmenu
To call it:
obmenu


Overview
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paint(Graphics)
- Method in class ch.epfl.lis.gnwgui.
GraphSignature
Paint method
paint(Graphics)
- Method in class ch.epfl.lis.gnwgui.
HyperText
Paint
paint(Graphics)
- Method in class ch.epfl.lis.gnwgui.windows.
WaitingSnake
Paint function used to draw the road and the snake.
paintComponent(Graphics)
- Method in class ch.epfl.lis.gnwgui.idesktop.
IElement
paintComponent(Graphics)
- Method in class ch.epfl.lis.gnwgui.windows.
Header
This method paints the content of the header.
parse(String[])
- Static method in class ch.epfl.lis.gnwgui.
GnwGui
This function defines which are the command line arguments that can be specified.
personalGnwSettingsExist()
- Method in class ch.epfl.lis.gnw.
GnwSettings
personalGnwSettingsPath()
- Method in class ch.epfl.lis.gnw.
GnwSettings
Perturbation
- Class in
ch.epfl.lis.gnw
Class offers functionalities to apply perturbations to a gene network.
Perturbation(GeneNetwork)
- Constructor for class ch.epfl.lis.gnw.
Perturbation
Constructor
PerturbationDual
- Class in
ch.epfl.lis.gnw
PerturbationDual(GeneNetwork)
- Constructor for class ch.epfl.lis.gnw.
PerturbationDual
Constructor
PerturbationMultifactorial
- Class in
ch.epfl.lis.gnw
PerturbationSingleGene
- Class in
ch.epfl.lis.gnw
PerturbationSingleGene(GeneNetwork)
- Constructor for class ch.epfl.lis.gnw.
PerturbationSingleGene
Constructor
perturbBasalActivation(double)
- Method in class ch.epfl.lis.gnw.
Gene
Perturb the basal activation with this value (subclass defines what exactly that means)
perturbBasalActivation(double)
- Method in class ch.epfl.lis.gnw.
HillGene
Perturb the basal activation with this value (subclass defines what exactly that means)
png
- Static variable in class ch.epfl.lis.gnwgui.filefilters.
FilterImageAll
printAll(String)
- Method in class ch.epfl.lis.gnw.
SteadyStateExperiment
Print the mRNA data, append the given string to the filenames (e.g.
printAll(String)
- Method in class ch.epfl.lis.gnw.
TimeSeriesExperiment
Print all the trajectories to a single file, the initial conditions are printed to a separate file.
printArray(double[])
- Static method in class ch.epfl.lis.gnw.
GnwSettings
printGraph()
- Method in class ch.epfl.lis.gnwgui.
NetworkGraph.MyGraphViewerController
Print the graph into 3 different format modifiable through the controller: EPS, PNG and JPEG
printHelp()
- Method in class ch.epfl.lis.gnwgui.
GnwConsoleWindow
Print the help.
printMRNA(String)
- Method in class ch.epfl.lis.gnw.
SteadyStateExperiment
Print the mRNA data, append the given string to the filenames (e.g.
printMsg(String)
- Method in class ch.epfl.lis.gnwgui.
GnwConsoleWindow
Use this function to print something inside the console.
printOpeningInfo(GenericElement)
- Static method in class ch.epfl.lis.gnwgui.
IONetwork
printPerturbations(String)
- Method in class ch.epfl.lis.gnw.
Perturbation
Print the perturbations to a file
printPerturbations(String)
- Method in class ch.epfl.lis.gnw.
PerturbationDual
Print the perturbations to a file
printProteins(String)
- Method in class ch.epfl.lis.gnw.
SteadyStateExperiment
Print the protein data, append the given string to the filenames (e.g.
printSettingsContent(String)
- Method in class ch.epfl.lis.gnwgui.
GnwGui
Use this function to print the settings content
printSteadyStates(String, DoubleMatrix1D)
- Method in class ch.epfl.lis.gnw.
SteadyStateExperiment
Print the given steady-state vector (data).
printSteadyStates(String, DoubleMatrix2D)
- Method in class ch.epfl.lis.gnw.
SteadyStateExperiment
Print the perturbation experiments (data).
printVersionAction(JComponent)
- Method in class ch.epfl.lis.gnwgui.
GnwConsoleWindow
Shortcut to print the version of the software
printVersions()
- Method in class ch.epfl.lis.gnwgui.
GnwConsoleWindow
Print the version of the software.
process()
- Method in class ch.epfl.lis.gnwgui.idesktop.
HighlightableImage
Process the "highlightable" image.
processVerticesLabelSearch()
- Method in class ch.epfl.lis.gnwgui.
NetworkGraph.MyGraphViewerController
Called when the field of the search box is updated.
publish(LogRecord)
- Method in class ch.epfl.lis.gnwgui.
GnwConsoleHandler
This is the overridden publish method of the abstract super class Handler.
Overview
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W


WITNESS LIST
Higher Education
April 13, 2011 7:30 AM
Registering, but not testifying:
For:
Baylor, Don Senior Policy Analyst (Center for Public Policy Priorities), Austin, TX
Dimitry, Lauren (Texans Care for Children), Austin, TX
Sabo, Jason Senior Vice President (United Ways of Texas), Austin, TX
Widrow, Woody Executive Director (RAISE Texas), Austin, TX
On:
Blackmore, Lynn Associate Commissioner (Health & Human Services Commission),
Austin, TX
Deiters, Kevin Director (Comptroller of Public Accounts), Austin, TX
North, Vicky Assistant General Counsel (Texas Comptroller of Public Accounts), Austin,
TX
FOR:
Hayes, Tracey Interim Field Director (ACLU of Texas), Austin, TX
Miller, Kathy Executive Director (Texas Freedom Network), Austin, TX
AGAINST:
Saenz, Jonathan Director of Legislative Affairs (Liberty Institute), Austin, TX
Registering, but not testifying:
For:
Banks, Yannis (Texas NAACP), Austin, TX
De Lozanne, Arturo (Self), Austin, TX
Fisher, Kevin Scot (Self), Highland Village, TX
Gregg, Brock Government Relations Director (ATPE), Austin, TX
Quinzi, Patty Legislative Counsel (Texas-American Federation of Teachers), Austin, TX
Against:
Gerstenschlager, MerryLynn Vice President (Texas Eagle Forum), Weatherford, TX
On:
Zamora, Emilio (Self), Austin, TX
ON:
Zimmerman, Bruce Chief Executive Officer and Chief Investment Officer (The University
of Texas Investment Management Company-UTIMCO), Austin, TX
FOR:
Barnett, Charles J. President / Chief Executive Officer Seton Family of Hospitals (Seton
and Greater Austin Chamber of Commerce), Austin, TX
ON:
Shine, Kenneth I. Executive Vice Chancellor for Health Affairs (The University of Texas
System), Austin, TX
1
WITNESS LIST
Higher Education
April 13, 2011 7:30 AM
Registering, but not testifying:
For:
Rollins, Michael President (Austin Chamber of Commerce), Austin, TX
Walkerpeach, Cindy R. Director, Biosciences, Austin Technology Incubator (ATI), Austin,
TX
Wilson, Stacy Director Government Affairs (Central Health & Community Care), Austin,
TX
Yanas, Chris Director, Government Relations (Teaching Hospitals of Texas), Austin, TX
Registering, but not testifying:
For:
Yancy, Justin Executive Director (Governor's Business Council), Austin, TX
On:
Alvarado, Cassandre Assistant Dean, The University of Texas at Austin (The University of
Texas at Austin), Austin, TX
FOR:
Gardner, John Madison Student (The University of Texas at Austin), Austin, TX
Registering, but not testifying:
For:
Yancy, Justin Executive Director (Governor's Business Council), Austin, TX
ON:
Weaver, Dan Assistant Commissioner (Higher Education Coordinating Board), Austin, TX
Registering, but not testifying:
For:
Banks, Yannis (Texas NAACP), Austin, TX
McDonald, Carol President (Independent Colleges and Universities of Texas, Inc.), Austin,
TX
On:
Deithloff, Tim (Vinson and Elkins LLP), Austin, TX
FOR:
Alvarez, Joe W. Student (Texas A&M Kingsville), Kingsville, TX
Cowan, Matthew Board Member (Texas A&I Alumni Association (on behalf of Manuel
Saenz)), TX
Flores, Brianna (Texas A&I Alumni Association), Austin, TX
Garza, Jacinto President/CEO L&G Engineering (Texas A&I Alumni Member),
Harlingen, TX
Garza, Tony Retired Educator (also providing written testimony) (Texas A&I Alumni
Association), Falfurrias, TX
Jaimes, Iona (also providing written testimony) (Texas A&I Alumni Association), Austin,
2
WITNESS LIST
Higher Education
April 13, 2011 7:30 AM
TX
Mata, Jorge Student (Current Student Body of Texas A&M Kingsville), Harlingen, TX
Saenz Jr., Manuel (also providing written testimony) (Texas A&I Alumni), Edinburg, TX
Watson, Dick (also providing written testimony) (Texas A&I Alumni), Franklin, TX
AGAINST:
Bingham, Thomas Alumni-Texas A&M Kingsville (also providing written testimony)
(Self), Kingsville, TX
Fugate, Sam Mayor of Kingsville, TX (Self), Kingsville, TX
Guerrero, Dolores Dean of New Honors College at Texas A&M University Kingsville
(Self), TX
Hees, Harold Alumni (Self), Aransas Pass, TX
James Jr., Paul C. Engineering Student (also providing written testimony) (Self),
Kingsville, TX
Joubert, Rene Executive Vice President (Caldwell Companies), Houston, TX
Scarborough, Rian Vice President of Student Government Association (Texas A&M
University at Kingsville), Kingsville, TX
Womack, Brad Texas A&M University at Kingsville Alumni (also providing written
testimony) (Self), Kingsville, TX
ON:
Tallant, Steven President (Texas A&M University Kingsville), Kingsville, TX
Registering, but not testifying:
For:
Cowan, Laura (Self), Houston, TX
Gallaga, Ricardo (Self), Harlingen, TX
Garza, Dora (Texas A&I Alumni Association), Falfurrias, TX
Jaimes, Lupe C. Retired Educator (Texas A&I Alumni), Austin, TX
Against:
Brown, Kirby Vice President Public Policy (Texas Wildlife Association), San Antonio, TX
Messbarger, Dick Executive Director (Kingsville Economic Development Council),
Kingsville, TX
Providing written testimony:
On:
Stephens, Ralph Executive Director Support Services (Texas A&M
University-Kingsville), Kingsville, TX
Registering, but not testifying:
For:
McDonald, Carol L. President (Independent Colleges and Universities of Texas, Inc.),
Austin, TX
On:
Deithloff, Tim (Vinson and Elkins LLP), Austin, TX
Weaver, Dan Assistant Commissioner (Higher Education Coordinating Board), Austin, TX
3


Kogi poll: 16 candidates accept results, congratulate Bello
by The Eagle OnlineSixteen of the candidates that participated in the November 16 governorship election in Kogi have accepted the results of the election as announced by the Independent National Electoral Commission.
Addressing a news conference in Lokoja on Monday shortly after the announcement of the election results, the coalition of 16 candidates led by Dr Sani Teidi, the candidate of the Young Democratic Party urged losers to work with the winner for accelerated development of the state.
He said: “We congratulate His Excellency, Alhaji Yahaya Bello for the overwhelming victory at the poll and all those who participated in the election.
“We appeal to the winner to be magnanimous in victory and prepare to mend fences for an all-inclusive governance.
“We are also appealing to all Kogi stakeholders to accept the winner for participatory governance,” Teidi said.
The candidates condemned the call for cancellation of the election by civil society groups, saying that they did not consider the enormity of waste and loss of lives that may occur in the course of re-running the election.
“All aggrieved political parties should play the game by the rule. Kogi is our state, and the only panacea for development is peace,” he said.
Some of the parties include: Green Party of Nigeria, Accord Party, Young Democratic Party, Justice Must Prevail Party, Peoples Party of Nigeria, Africa Action Alliance and National Conscience Party among others.
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I would like to start by saying I picked this photo for my profile because this is how I felt completing this homework. I just don't quite get what I am doing, and it was incredibly frustraing trying to complete this assigment. In case you are wondering, when I asked my husband to take this photo I asked him if it looked like I was holding the Louvre. Obviously, he missed by a tinny bit and this how I am turning in this assigment.
My Name is Renata Wattier and I was born and raised in Brazil. I moved to United States in 2000 to attend Union College in Lincoln, NE. In 2005 I started working at State Farm in Lincoln, NE, and because of my job with State Farm I moved to Arizona in 2013. I am married to Jeff but you can call him Jeffy Pooh. I enjoy playing and watching sports, I used to play Roller Derby when I lived in Nebraska and had the opportunity to travel all over the country because of Roller Derby. If you have never attend a Roller Derby Bout and you enjoy watching full contact sports, you should give Roller Derby a try.
Jeff and I enjoy traveling and we go to one big overseas trip every year, we just came back from Brazil the Saturday before the boot camp started and we are planning a trip to Greece next year. We are also planning a trip to Germany during Oktoberfest in a couple of years. I am not quite sure what is more difficult, trying to find things to write about myself or compleing the assigment. If you are curious to learn a little more about me just ask!


A collection of pure CSS3 lightweight animations that can be applied to links, sections, buttons and much more. Available in SCSS, CSS and LESS.


You are given a phone book that consists of people's names and their phone number. After that you will be given some person's name as query. For each query, print the phone number of that person.
Input Format
The first line will have an integer $n$ denoting the number of entries in the phone book. Each entry consists of two lines: a name and the corresponding phone number.
After these, there will be some queries. Each query will contain a person's name. Read the queries until end-of-file.
Constraints:
A person's name consists of only lower-case English letters and it may be in the format 'first-name last-name' or in the format 'first-name'. Each phone number has exactly 8 digits without any leading zeros.
$1 \le n \le 100000$
$1 \le Query \le 100000$
Output Format
For each case, print "Not found" if the person has no entry in the phone book. Otherwise, print the person's name and phone number. See sample output for the exact format.
To make the problem easier, we provided a portion of the code in the editor. You can either complete that code or write completely on your own.
Sample Input
3
uncle sam
99912222
tom
11122222
harry
12299933
uncle sam
uncle tom
harry
Sample Output
uncle sam=99912222
Not found
harry=12299933


Stuff To Know
HTML5, CSS3, SASS, jQuery, introductory Java Script, Github, responsive web design, Adobe Creative Suite to include Photoshop and Illustrator, sketching, wire-framing, prototyping, user testing, Invision
I recently graduated from The Iron Yard Academy studying UI Design and Front End Development. There I was fully immersed in web design and development. This program goes way beyond technical skills and taught me to think like a UI designer and developer. It's intense, fast-paced and comprehensive. The process taught me HOW to learn so that I can remain highly valuable for the rest of my career. It placed a great emphasis on the design process using tools such as Illustrator and Photoshop for wireframes and mockups and then HTML, CSS, and SASS as well as some Java Script, jQuery and PHP for implementation. I also used programs such as Invision to create and test prototypes.
Bachelor of Science in Secondary Education
This particular year I decided to pull my son out of school and homeschool him in order to travel Europe while my husband was deployed. I was thankful for the opportunity that my son had to experience different cultures and environments.
It was an awesome adventure, and a very unique and special time for my son and I.
We were able to visit France, Luxembourg, Belgium, Germany, and the Republic of Georgia.
It was definitely an amazing experience and an adventure that my son and I will never forget!
When I had my son, I decided to stay home to spend quality time with him until he was in school. During this time I was actively involved in community and church volunteer work as well as focusing on my child’s early development.


School of Computing - Macquarie University
Master Program -Internship (COMP8851/COMP8860)
For Students:
- Students MUST fill the Expression of Interest Form here:
- MQ 2023 Calendar
- To be able to shortlist for an internship, you must be in your last semester. Moreover, we highly recommend you have a 75+ WAM.
- If your Program Leader approves your case, you can also be able to do internship in your 3rd semester (2-year program) of your study plan.
- To be able to enroll for the internship, there should be a company supporting your internship. We also highly recommend you also try to find a company yourself.
- You are not allowed to enroll for the internship unless a company approves your internship. It means, if you are enrolled in COMP8860/COMP885 without following the above-mentioned process, your enrolment will become invalid.
- You will be able to enroll for a part-time or full-time internship.
- Part-time Internship (20 cp): you should enroll in COMP8851 unit
- full-time Internship (40 cp): you should enroll in COMP8851+COMP8860 units
- Important Notice:
- You cannot enroll in COMP8860 by itself. This unit can be only combined with COMP8851 (in one semester) to form a Full-time Internship.
- If you are an employee of a company, then you cannot do internship in the ame company.
Such students should do Internal Project instead.
- Students should undertake a relevant project/internship that is consistent with their chosen major/specialisation.
- Internship is a unit and the start and end date *MUST* be from Week 1 to Week 13 of that semester.
- Midterm/Final Report Template Form to be completed and submitted by the students during week 6 (midterm) and week 12 (final).
- Internship Weekly Report Template.
- Internship Proposal
- You have questions regarding Internal Project? Please contact<EMAIL_ADDRESS>For Companies:
- Companies should register their projects here:
- Certificates of Currency/Insurance, Macquarie University
- Template-MQ-Internship Form to be Signed by the Company, before starting the internship.
- Internship Marking Criteria Form to be filled by the Company, at the end of the internship.
- These internships are unpaid and part of the master's program.
- Part-time Internship (20 cp): This internship is equal to 2 units and the student can work 2.5 days a week for 13 weeks in a company (from week 1 to week 13).
- Full-time Internship (40 cp): This internship is equal to 4 units and the student can work 5 days a week for 13 weeks in a company (from week 1 to week 13).
- Please notice that, if you are sponsoring more than 1 student, the internship proposal (project tile and description) should NOT be the same for those students. Students may work on the same high-level projects, but their project titles, description, and tasks should differ.
S1-2023 Internship Workshop:
- We will organize an internship workshop on Friday 14 July 2023 (from 9am to 10am) for the students who plan to do an internship in s2-2023.
- To attend the workshop, students MUST fill the Expression of Interest (EOI) Form (See Above).
- The workhop will be online, ZOOM ID:
CLICK HERE
- Internship Wokshop Recording: Click HERE
- Notice:
- Internship will start from Week 1 and will conclude on Week 13.
- During Week 1, you will finalize your internship with the compnay and submit the Internship Proposal on iLearn.
How to Enroll in the Internship Unit?
We will invite several companies (who have been supporting our internship program) to the workshop.
During the workshop, the companies will present their projects, and if you are interested in the company/project, then:
- Students should submit the EoI form. Then, student details will be shared with the companies.
- You will have access to the list of Available projects on this page "Under for Students" Section. Please notice that, you can also find other companies yourself.
- Please contact the company supervisor (email can be found in the available projects), and share your CV and transcript with the company.
- Company may organize an interview with you. After the interview with the company, you should prepare the Internship Proposal (Download the Proposal Template HERE)
- The Company should complete the "MQ Internship Form" and email it to the PACE Officer of the Internship unit at<EMAIL_ADDRESS>The company should CC the student in this email, and the email subject of the email should be "Internship Unit - COMP8851 - School of Computing".
- Kristy will be in touch with the company supervisor to finalize the internship
- After these steps, if the internship convener approves your proposal and eligibility, then you will be able to enroll in the unit.
- Notice: The Company and The student *MUST* use their official email address.
Notice:
- There have been major changes introduced to Comp8851 (now called Major Projects). It effectively combines the Internal Project (ITEC810/COMP8871) as well as the Internship unit (COMP8851). This means that the students who plan to the Internal Project OR Internship should take the COMP8851unit. In the first week of the unit, the students can choose between the Internal Project OR Internship. To be able to choose an internship, you will need to be (1) in your last semester; (2) have 75+ WAM; and (3) have a company sponsoring your internship.
- Who can do full-time Internship? In particular, if you have COMP8860 available as an option to enroll in, then you should be able to do the full-time internship.
Contact: Prof. Amin Beheshti


I would like you to answer the following questions in a short answer format using Markdown.
For questions that ask for a list, use the appropriate Markdown syntax to create either ordered or unordered lists.
Use bold and italic text for emphasis in your responses.
I have found Jekyll the most useful so far.
Jekyll provides many different shells of websites that I could use/modify to make my own. I've tried making websites several times, but I always got stuck on design. This would allow me to be able to produce something visually appealing without giving up halfway through.
I'm not sure any of these could be compared in levels of difficult.
Because they've all been so different. They all have had their own struggles, and once you factor out knowing other things that help you learn the next thing, they're really all equally difficult.
I'd like to learn more about Pandoc because it seems like something I've been needing, but I still don't fully understand it.
When you are finished with the questions in file:


See below for information regarding unresolved alarms and their cause
Total Alarms: {{ total_alarms }}
Alarm Severity Breakdown:
{% for k, v in alarm_breakdown.items %}{{k}} : {{v}}
{%endfor%}Device: {{k}}
AlarmID: {{id}}
{%for key, val in content.items%}{{key}} : {{val}}
{%endfor%}


perl585delta - what is new for perl v5.8.5
This document describes differences between the 5.8.4 release and the 5.8.5
release.
There are no changes incompatible with 5.8.4.
Perl's regular expression engine now contains support for matching on the
intersection of two Unicode character classes. You can also now refer to
user-defined character classes from within other user defined character
classes.
- Carp improved to work nicely with Safe. Carp's message reporting should
now be anomaly free - it will always print out line number
information.
- CGI upgraded to version 3.05
- charnames now avoids clobbering $_
- Digest upgraded to version 1.08
- Encode upgraded to version 2.01
- FileCache upgraded to version 1.04
- libnet upgraded to version 1.19
- Pod::Parser upgraded to version 1.28
- Pod::Perldoc upgraded to version 3.13
- Pod::LaTeX upgraded to version 0.57
- Safe now works properly with Carp
- Scalar-List-Utils upgraded to version 1.14
- Shell's documentation has been re-written, and its historical partial
auto-quoting of command arguments can now be disabled.
- Test upgraded to version 1.25
- Test::Harness upgraded to version 2.42
- Time::Local upgraded to version 1.10
- Unicode::Collate upgraded to version 0.40
- Unicode::Normalize upgraded to version 0.30
The debugger can now emulate stepping backwards, by restarting and rerunning all
bar the last command from a saved command history.
h2ph is now able to understand a very limited set of C inline functions
-- basically, the inline functions that look like CPP macros. This has been
introduced to deal with some of the headers of the newest versions of the
glibc. The standard warning still applies; to quote h2ph's
documentation, you may need to dicker with the files produced.
Perl 5.8.5 should build cleanly from source on LynxOS.
- •
- Perl -V has several improvements
- correctly outputs local patch names that contain embedded code snippets or
other characters that used to confuse it.
- arguments to -V that look like regexps will give multiple lines of
output.
- a trailing colon suppresses the linefeed and ';' terminator, allowing
embedding of queries into shell commands.
- a leading colon removes the 'name=' part of the response, allowing mapping
to any name.
- •
- When perl fails to find the specified script, it now outputs a second line
suggesting that the user use the "-S"
flag:
$ perl5.8.5 missing.pl
Can't open perl script "missing.pl": No such file or directory.
Use -S to search $PATH for it.
The Unicode character class files used by the regular expression engine are now
built at build time from the supplied Unicode consortium data files, instead
of being shipped prebuilt. This makes the compressed Perl source tarball about
200K smaller. A side effect is that the layout of files inside lib/unicore has
changed.
The regression test t/uni/class.t is now performing considerably more
tests, and can take several minutes to run even on a fast machine.
This release is known not to build on Windows 95.
If you find what you think is a bug, you might check the articles recently
posted to the comp.lang.perl.misc newsgroup and the perl bug database at
http://bugs.perl.org. There may also be information at http://www.perl.org,
the Perl Home Page.
If you believe you have an unreported bug, please run the
perlbug program included with your release. Be sure to trim your bug
down to a tiny but sufficient test case. Your bug report, along with the
output of "perl -V", will be sent off to
<EMAIL_ADDRESS>to be analysed by the Perl porting team. You can browse and
search the Perl 5 bugs at http://bugs.perl.org/
The Changes file for exhaustive details on what changed.
The INSTALL file for how to build Perl.
The README file for general stuff.
The Artistic and Copying files for copyright
information.


Attaching Quality Assessment Reports to Integrity Manager Issues
DIScover allows you to attach QARs to Integrity Manager issues, enabling you to refine your software development process when it comes to proposing changes to source code.
For example, after the development work for a new feature submitted in Integrity Manager is completed, you can perform a quality assessment on the source code containing the feature, then attach the generated QAR (an HTML file) to the related issue for further review and analysis at a code review meeting.
Important: You can only view or print QAR attachments from the Integrity Manager command line interface.
Related Topics


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Animal Trading Cards
Cardinal
Fun Facts
- when a female cardinal sings from the nest it usually means she's telling the male she needs more food
- The Northern Cardinal is the state bird of seven states Illinois, Indiana, Kentucky, North Carolina, Ohio, Virginia and West Virginia
- The male Northern Cardinal is perhaps responsible for getting more people to open up a field guide than any other bird
Fox
Fun Facts
- A group of foxes is called a skulk or leash
- Foxes have whiskers on their legs and face, which help them to navigate
- Grey foxes can retract their claws like cats do
ClownFish
Fun Facts
- Clownfish live up to 10 years in the wild but on average up to 6 - 8 years
- The largest clownfish can reach 18 cm (7.1 in), and the smallest 10 cm (3.9 in)
- Clownfish species include yellow, orange, reddish and blackish varieties with most covered in patches or bars of white color


Class is concerned with doing more than one thing and therefore has many dependencies.
What To Do
If the class is doing too much, it should be refactored into a set of smaller classes. Each class should have a
clearly defined responsibility and therefore a smaller set of dependencies.


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Dog Name Generator!
1. From which movie is the quote "We're not gonna fall for a banana in the tailpipe!"?
Heathers
Beverly Hills Cop
Fast Times at Ridgemont High
Breakfast Club