def minimumCrossingOrdering(refAdjList, queryAdjList):
#get connected components cluster
connectedRefs = graphUtil.findConnectedComps(refAdjList, queryAdjList)
#use connected comps to decide the initial order
refNodes, queryNodes = getOrderedLists(connectedRefs, refAdjList,\
queryAdjList)
#print 'refNodes b4 cross min: ', refNodes
#print 'queryNodes b4 cross min: ', queryNodes
#apply barycenter heuristices alternately on ref then query until their
#position remains same in order
positionChanged = True
counter = 0
#initialize query Rank Dict
queryRankDict = {}
#initialize ref Rank Dict
refRankDict = {}
#strikes to maintain atleast one more trial on failure
strikeCount = 0
while strikeCount < 2:
positionChanged = False
if counter%2 == 0:
#choose ref nodes to play around
queryRankDict = prepareRankDict(queryNodes, queryRankDict)
refNodes, positionChanged = applyBarycenterHeuristics(refNodes,\
refAdjList,\
queryRankDict)
else:
#choose query nodes to play around
refRankDict = prepareRankDict(refNodes, refRankDict)
queryNodes, positionChanged = applyBarycenterHeuristics(queryNodes,\
queryAdjList,\
refRankDict)
if not positionChanged:
strikeCount += 1
elif positionChanged:
strikeCount = 0
counter += 1
return refNodes, queryNodes
def plotCrossMinimizedOrdering(scaffMap):
#try to plot before removing 1-1 or 1-many mappings
refAdjacencyList, queryAdjacencyList = prepareAdjacencyLists(scaffMap)
#refList = refAdjacencyList.keys()
#refList.sort()
#queryList = queryAdjacencyList.keys()
#queryList.sort()
#scaffMapPlotter.plotFromLists(refList,\
# queryList,\
# refAdjacencyList)
#remove contained in itself one-to-many mapping before
#reordering
removeOneToManyMapping(refAdjacencyList, queryAdjacencyList)
removeOneToManyMapping(queryAdjacencyList, refAdjacencyList)
#refList = refAdjacencyList.keys()
#refList.sort()
#queryList = queryAdjacencyList.keys()
#queryList.sort()
#print refList, queryList
#scaffMapPlotter.plotFromLists(refList,\
# queryList,\
# refAdjacencyList)
#get connected clusters
connectedRefComps = graphUtil.findConnectedComps(refAdjacencyList,\
queryAdjacencyList)
#order these clusters and minimize intersection b/w them
orderedClusters = map(getOrderedClusterWNumIntersection,\
[(comp, refAdjacencyList, queryAdjacencyList)\
for comp in connectedRefComps])
totalIntersections = 0
intersectingClusters = []
nonIntersectingClusters = []
#from ordered clusters separate clusters with intersections
for orderedCluster in orderedClusters:
numIntersect = orderedCluster[2]
totalIntersections += numIntersect
if numIntersect != 0:
intersectingClusters.append(orderedCluster)
else:
nonIntersectingClusters.append(orderedCluster)
print 'total intersections: ', totalIntersections
"""
print 'refOrderList: ', refOrderList, '\n'
print 'queryOrderList: ', queryOrderList, '\n'
print 'refAdjacencyList: ', refAdjacencyList, '\n'
print 'queryAdjacencyList: ', queryAdjacencyList, '\n'
"""
"""displayMatchingRegion(scaffMap, refOrderList, refAdjacencyList,\
queryOrderList, queryAdjacencyList,\
False)"""
#plot only these interesectiong refs cluster in the order,
#as reported after cross-minimization
#print refOrderList, queryOrderList
#scaffMapPlotter.plotFromLists(refOrderList, queryOrderList,\
# refAdjacencyList, 0, False)
#plot non intersecting clusters
#as reported after cross-minimization
#scaffMapPlotter.plotFromLists(refNotIntersOrderList, queryNotIntersOrderList,\
# refAdjacencyList, 0, False)
#write the ordered graph intersect file
with open('orderedScaffs.gexf', 'w') as graphFile:
xmlGraphStr = GEXFWriter.getGexfXMLStringFromCluster(refAdjacencyList,\
intersectingClusters)
graphFile.write(xmlGraphStr)
#write the ordered graph non-intersect file
with open('orderedScaffsNonInters.gexf', 'w') as graphFile:
xmlGraphStr = GEXFWriter.getGexfXMLStringFromCluster(refAdjacencyList,\
nonIntersectingClusters)
graphFile.write(xmlGraphStr)