gistfile1.py

class ScannedReadDatabase(object):
    """
    Maintain a collection of reads and provide for database (index, search)
    operations on them.

    @param landmarkFinderClasses: A C{list} of landmark classes.
    @param trigPointFinderClasses: A C{list} of trig point classes.
    """
    def __init__(self, landmarkFinderClasses, trigPointFinderClasses):
        self.landmarkFinderClasses = landmarkFinderClasses
        self.trigPointFinderClasses = trigPointFinderClasses
        self.reads = []

    def makeSearchDictionary(self):
        """
        """
        d = defaultdict(set)

        landmarkFinders = []
        for landmarkFinderClass in self.landmarkFinderClasses:
            landmarkFinders.append(landmarkFinderClass().find)

        trigPointFinders = []
        for trigPointFinderClass in self.trigPointFinderClasses:
            trigPointFinders.append(trigPointFinderClass().find)

        for read in self.reads:
            scannedRead = ScannedRead(read)

            for landmarkFinder in landmarkFinders:
                for landmark in landmarkFinder(read):
                    scannedRead.landmarks.append(landmark)

            for trigFinder in trigFinders:
                for trigPoint in trigFinder(read):
                    scannedRead.trigPoints.append(trigPoint)

            for landmark, trigPoint in read.getPairs():
                key = '%s:%s:%s' % (landmark.hashkey(), trigPoint.hashkey(),
                                    landmark.offset - trigPoint.offset)
                d[key].add(read.id)

        return d