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Checks if one interval contains any overlap with another interval.

Keyword arguments:
t1 -- First tuple.
t2 -- Second tuple.

Returns:
Returns -1 if i1 is before i2; 1 if i1 is after i2; and 0 if there is any overlap.

        def overlap(t1, t2):
    """Checks if one interval contains any overlap with another interval.

    Keyword arguments:
    t1 -- First tuple.
    t2 -- Second tuple.

    Returns:
    Returns -1 if i1 is before i2; 1 if i1 is after i2; and 0 if there is any overlap.
    """
    if(t1[1] <= t2[0]): return -1 # interval1 is before interval2
    if(t2[1] <= t1[0]): return 1 # interval1 is after interval2
    return 0 # interval1 overlaps interval2
        


src/c/a/cadnano2-HEAD/views/sliceview/emptyhelixitem.py   cadnano2(Download)
                            l0, h0 = strand0.idxs()
                            l1, h1 = strand1.idxs()
                            oLow, oHigh = util.overlap(l0, h0, l1, h1)
                            try:
                                lList = filter(lambda x:x>oLow and x<oHigh, part.getPreXoversLow(strandType, p0))

src/c/a/cadnano2-HEAD/model/strand.py   cadnano2(Download)
 
        # get the ovelap
        lowIdx, highIdx = util.overlap(sLowIdx, sHighIdx, cLowIdx, cHighIdx)
 
        # only get the characters we're using, while we're at it, make it the

src/m/o/MotifAnalysisPackage-0.0.1/motifStatistics/genome.py   MotifAnalysisPackage(Download)
            didBreak = False
            while(counter < len(assocDict[chrName])):
                check = util.overlap(coord,assocDict[chrName][counter])
                if(check == 0): # Contain overlap
                    didBreak = True
                else: geneCoord = [assocDict[chrName][counter][0],assocDict[chrName][counter][1]+promoterLength]
 
                check = util.overlap(coord,geneCoord) # Check overlap between coordinate and gene+promoter
 
                if(check == 0): # If contain overlap, then check if the coordinate also contains overlap with the next gene
                        if(assocDict[chrName][counter+1][4] == "+"): geneCoordNext = [assocDict[chrName][counter+1][0]-promoterLength,assocDict[chrName][counter+1][1]]
                        else: geneCoordNext = [assocDict[chrName][counter+1][0],assocDict[chrName][counter+1][1]+promoterLength]
                        checkNext = util.overlap(coord,geneCoordNext) # Verify overlap between coordinate and next gene
                        if(checkNext == 0): genesList.append(assocDict[chrName][counter+1][2]+"_PROX") # If there is an overlap then add this gene to association list
                    #else: # If this is the last gene (there is no 'next') then dont verify overlap
                    genesList = [] # List of overlapping genes
                    maxGeneCoord = [geneCoord[0]-threshDist,geneCoord[1]+threshDist]
                    maxCheck = util.overlap(coord,maxGeneCoord)
                    if(maxCheck == 0): genesList.append(assocDict[chrName][counter][2]+"_DIST") # If it overlapped then put current gene in overlap list
 
                        else: geneCoordPrev = [assocDict[chrName][counter-1][0],assocDict[chrName][counter-1][1]+promoterLength]
                        maxGeneCoordPrev = [geneCoordPrev[0]-threshDist,geneCoordPrev[1]+threshDist]
                        maxCheckPrev = util.overlap(coord,maxGeneCoordPrev)
                        if(maxCheckPrev == 0): genesList.append(assocDict[chrName][counter-1][2]+"_DIST") # If it overlapped then put previous gene in overlap list
 

src/m/o/MotifAnalysisPackage-0.0.1/motifStatistics/motif.py   MotifAnalysisPackage(Download)
                while(counter[factorName] < len(allMpbsDict[factorName][chrName])):
                    currMpbs = allMpbsDict[factorName][chrName][counter[factorName]]
                    check = util.overlap(coord,currMpbs)
                    if(check == 0): # Contain overlap
                        flagMotifs[factorName] = True