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src/s/e/seal-0.4.0-rc2/seal/lib/mr/filter_link.py   seal(Download)
# along with Seal.  If not, see <http://www.gnu.org/licenses/>.
 
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
 
class FilterLink(HitProcessorChainLink):

src/s/e/seal-0.4.0-rc2/seal/lib/mr/emit_sam_link.py   seal(Download)
 
 
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.io.sam_formatter import SamFormatter
 
class EmitSamLink(HitProcessorChainLink):

src/s/e/seal-0.4.0-rc2/seal/seqal/mapper.py   seal(Download)
import seal.lib.io.protobuf_mapping as protobuf_mapping
import seal.lib.mr.utils as utils
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.emit_sam_link import EmitSamLink
from seal.lib.mr.filter_link import FilterLink
class MarkDuplicatesEmitter(HitProcessorChainLink):
    def __init__(self, context, event_monitor, next_link = None):
        super(type(self), self).__init__(next_link)
        self.ctx = context
        self.event_monitor = event_monitor

src/s/e/seal-0.4.0-rc2/seal/seqal/reducer.py   seal(Download)
import seal.lib.io.protobuf_mapping as protobuf_mapping
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.emit_sam_link import EmitSamLink
import seal.lib.deprecation_utils as deprecation_utils

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_hit_processor_chain_link.py   seal(Download)
 
import unittest
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
 
class TestHitProcessorChainLink(unittest.TestCase):
    def setUp(self):
        self.h1 = HitProcessorChainLink()
        self.h2 = HitProcessorChainLink()
    def test_constructor(self):
        h = HitProcessorChainLink(self.h1)
        self.assertEqual(self.h1, h.next_link)
 
    def test_set_next(self):

src/s/e/seal-0.4.0-rc2/tests/seal/seqal/test_mark_duplicates_emitter.py   seal(Download)
 
import seal.lib.io.protobuf_mapping as proto
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.seqal.mapper import MarkDuplicatesEmitter
    class Receiver(HitProcessorChainLink):
        def __init__(self, *args):
            super(type(self), self).__init__(*args)
            self.received = None
 

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_filter_link.py   seal(Download)
import unittest
 
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.filter_link import FilterLink
from seal.lib.aligner.mapping import SimpleMapping
    class Receiver(HitProcessorChainLink):
        def __init__(self, *args):
            super(type(self), self).__init__(*args)
            self.received = None
 
    def test_constructor_link(self):
        h = FilterLink(self.monitor)
        self.assertTrue(h.next_link is None)
        other = HitProcessorChainLink()
        h = FilterLink(self.monitor, other)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/mr/test_emit_sam_link.py   seal(Download)
 
from seal.lib.mr.emit_sam_link import EmitSamLink
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.mr.hadoop_event_monitor import HadoopEventMonitor
from seal.lib.mr.test_utils import map_context, SavingLogger
    def test_constructor_link(self):
        h = EmitSamLink(self.map_ctx, self.monitor)
        self.assertTrue(h.next_link is None)
        other = HitProcessorChainLink()
        h = EmitSamLink(self.map_ctx, self.monitor, other)