#cython: language_level=3

from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View
from obitools3.dms.view import RollbackException
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column, Column_line
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
from obitools3.apps.optiongroups import addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.align._qsassemble import QSolexaReverseAssemble
from obitools3.align._qsrassemble import QSolexaRightReverseAssemble
from obitools3.align._solexapairend import buildConsensus, buildJoinedSequence
from obitools3.dms.obiseq cimport Nuc_Seq_Stored


__title__="Aligns paired-ended reads"


def addOptions(parser):

    addMinimalOutputOption(parser)
 
    group = parser.add_argument_group('obi alignpairedend specific options')
 
    group.add_argument('-f', '--forward-reads',
                     action="store", dest="alignpairedend:forward",
                     metavar="<FILENAME>",
                     default=None,
                     type=str,
                     help="URI to the forward reads")

    group.add_argument('-r', '--reverse-reads',
                     action="store", dest="alignpairedend:reverse",
                     metavar="<FILENAME>",
                     default=None,
                     type=str,
                     help="URI to the reverse reads")

# TODO
#    group.add_argument('--index-file',
#                     action="store", dest="alignpairedend:index",
#                     metavar="<FILENAME>",
#                     default=None,
#                     type=str,
#                     help="URI to the index reads")

    group.add_argument('--score-min',
                     action="store", dest="alignpairedend:smin",
                     metavar="#.###",
                     default=None,
                     type=float,
                     help="Minimum score for keeping alignments")


la = QSolexaReverseAssemble()
ra = QSolexaRightReverseAssemble()
def buildAlignment(Nuc_Seq_Stored direct, Nuc_Seq_Stored reverse):
    
    if len(direct)==0 or len(reverse)==0:
        return None
    
    la.seqA = direct
    la.seqB = reverse
    
    ali=la()
    ali.direction='left'

    ra.seqA = direct
    ra.seqB = reverse

    rali=ra()
    rali.direction='right'
     
    if ali.score < rali.score:
        ali = rali
    
    return ali


def alignmentIterator(View_NUC_SEQS forward, View_NUC_SEQS reverse):    
    for i in range(len(forward)):
        ali = buildAlignment(forward[i], reverse[i])
        if ali is None:
            continue
        yield ali


def run(config):
        
    DMS.obi_atexit()
    
    logger("info", "obi alignpairedend")
    
    # Open the input
    finput = open_uri(config["alignpairedend"]["forward"])
    if finput is None:
        raise Exception("Could not open forward reads")
    forward = finput[1]
    rinput = open_uri(config["alignpairedend"]["reverse"])
    if rinput is None:
        raise Exception("Could not open reverse reads")
    reverse = rinput[1]

    if len(forward) != len(reverse):
        raise Exception("Error: the number of forward and reverse reads are different")
    
    if "index" in config["alignpairedend"]:    # TODO
        index = open_uri(config["alignpairedend"]["index"])
    else:
        index = None
    
    # Open the output
    output = open_uri(config['obi']['outputURI'],
                      input=False,
                      newviewtype=View_NUC_SEQS)
    if output is None:
        raise Exception("Could not create output view")

    view = output[1]
    Column.new_column(view, b"QUALITY", OBI_QUAL)   #TODO output URI quality option

    if 'smin' in config['alignpairedend']:
        config['alignpairedend']['sminL'] = config['alignpairedend']['smin']
        config['alignpairedend']['sminR'] = config['alignpairedend']['smin']
        sminL = config['alignpairedend']['sminL']
        sminR = config['alignpairedend']['sminR']
    else:
        sminL = 0
        sminR = 0

    # Initialize the progress bar
    pb = ProgressBar(len(forward), config, seconde=5)
    
    ba = alignmentIterator(forward, reverse)
            
    i = 0
    for ali in ba:
        
        pb(i)
        
        consensus = view[i]
        
        if sminL > 0:
            if ((ali.direction=='left' and ali.score > sminL)
                or (ali.score > sminR)):
                buildConsensus(ali, consensus)
            else:
                buildJoinedSequence(ali, reverse[i], consensus)
                
            consensus[b"sminL"] = sminL
            consensus[b"sminR"] = sminR
        else:
            buildConsensus(ali, consensus)

# TODO            
#        if "index" in config['alignpairedend'] and config['alignpairedend']['index'] is not None:
#            idx = str(config['alignpairedend']['index'].next())
#            consensus[b"illumina_index"] = idx
    
        i+=1
    
    finput[0].close()
    rinput[0].close()
    output[0].close()