# Path: seal/lib/mr/hit_processor_chain_link.py
# class HitProcessorChainLink(object):
#     def __init__(self, next_link = None):
#         self.next_link = next_link
# 
#     def set_next(self, link):
#         self.next_link = link
#         return link
# 
#     def process(self, original, aligned_pair):
#         """
#         Identity action.  Passes to the next link, if any.
#         """
#         if self.next_link:
#             self.next_link.process(original, aligned_pair)


from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.io.sam_formatter import SamFormatter
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Seal is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Seal.  If not, see <http://www.gnu.org/licenses/>.



class EmitSamLink(HitProcessorChainLink):
    def __init__(self, context, event_monitor, next_link = None):
        super(EmitSamLink, self).__init__(next_link)
        self.ctx = context
        self.output_formatter = SamFormatter(strip_pe_tag=True)
        self.event_monitor = event_monitor

    def process(self, original, pair):
        for hit in pair:
            if hit:
                k, v = self.output_formatter.format(hit).split("\t", 1)
                self.ctx.emit(str(k), str(v))
                self.event_monitor.count("emitted sam records", 1)

        super(EmitSamLink, self).process(original, pair) # forward pair to next element in chain


# Path: seal/lib/mr/hit_processor_chain_link.py
# class HitProcessorChainLink(object):
#     def __init__(self, next_link = None):
#         self.next_link = next_link
# 
#     def set_next(self, link):
#         self.next_link = link
#         return link
# 
#     def process(self, original, aligned_pair):
#         """
#         Identity action.  Passes to the next link, if any.
#         """
#         if self.next_link:
#             self.next_link.process(original, aligned_pair)


# Path: seal/lib/mr/emit_sam_link.py
from seal.lib.mr.hit_processor_chain_link import HitProcessorChainLink
from seal.lib.io.sam_formatter import SamFormatter

# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Seal is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Seal.  If not, see <http://www.gnu.org/licenses/>.



class EmitSamLink(HitProcessorChainLink):
    def __init__(self, context, event_monitor, next_link = None):
        super(EmitSamLink, self).__init__(next_link)
        self.ctx = context
        self.output_formatter = SamFormatter(strip_pe_tag=True)
        self.event_monitor = event_monitor

    def process(self, original, pair):
        for hit in pair:
            if hit:
                k, v = self.output_formatter.format(hit).split("\t", 1)
                self.ctx.emit(str(k), str(v))
                self.event_monitor.count("emitted sam records", 1)

        super(EmitSamLink, self).process(original, pair) # forward pair to next element in chain


class RapiEmitSamLink(HitProcessorChainLink):