#!/usr/bin/python3

from Bio.Blast import NCBIXML
import time, datetime


class BlastResult:
    def __init__(self):
        self.all_found_querys = set()
        self.all_found_accessions = set()
        self.all_found_pairs = {}
        self.all_hps_per_hit = {}
        self.all_hsp_per_sbjct = {}
        self.all_sbjcts = set()
        #self.records = []

class BlastRecord: #TODO is wel nodig voor hps's visualiseren / of deprecated
    def __init__(self, query_name, query_length):
        self.name = query_name
        self.length = query_length
        self.hits = []

class BlastHit:
    def __init__(self, accession, title, length):
        self.accession = accession
        self.title = title
        self.length = length
        self.hsps = []

class BlastHsp:
    def __init__(self, hsp_id, acc_id, expect, identities, query, match, subject, score):
        self.hsp_id = hsp_id
        self.acc_id = acc_id
        self.expect = float(expect)
        self.identities = identities
        self.query = query
        self.match = match
        self.subject = subject
        self.score = float(score)

""" origineel
class BlastHandle:

    @staticmethod
    def obj_to_dict(obj):
        return obj.__dict__

    @staticmethod
    def parse_blast_outfile(outfile="outfile.xml") -> BlastResult:
        hsp_id = 1;
        acc_id = 1;
        blast_result_object = BlastResult()
        with open(outfile) as file:
            records = NCBIXML.parse(file)
            for record in records:
                blast_result_object.all_found_querys.add(record.query)
                for hit in record.alignments:
                    all_hsp_per_hit = []
                    if record.query != hit.title[hit.title.find(" ") + 1:]:  # filter results where query == subject
                        evalue = 1
                        blast_hit = BlastHit(hit.accession,
                                             hit.title,
                                             hit.length)
                        blast_result_object.all_found_accessions.add(hit.title)
                        for hsp in hit.hsps:
                            blast_hsp = BlastHsp(hsp_id,
                                                 acc_id,
                                                 float(hsp.expect),
                                                 hsp.identities,
                                                 hsp.query,
                                                 hsp.match,
                                                 hsp.sbjct,
                                                 float(hsp.score))
                            if hsp.expect < evalue:
                                #data structuur: key als basis naam query + naam hit.
                                #in principe de basis voor opbouw van tabel key=row+header, value=cel
                                blast_result_object.all_found_pairs[record.query + "-" + hit.title] = [blast_hsp, blast_hit]
                                evalue = hsp.expect
                            all_hsp_per_hit.append(BlastHandle.obj_to_dict(blast_hsp))
                            hsp_id += 1
                    blast_result_object.all_hps_per_hit[acc_id] = all_hsp_per_hit
                    acc_id += 1
        return blast_result_object
"""
class BlastHandle:

    @staticmethod
    def obj_to_dict(obj):
        return obj.__dict__

    @staticmethod
    def parse_blast_outfile(outfile="testdata/GCF_000313135.1_Acastellanii.strNEFF_v1_genomic.xml") -> BlastResult:
        hsp_id = 1;
        acc_id = 1;
        blast_result_object = BlastResult()
        with open(outfile) as file:
            records = NCBIXML.parse(file)
            for record in records:
                blast_result_object.all_found_querys.add(record.query)
                for hit in record.alignments:
                    all_hsp_per_hit = []
                    if record.query != hit.title[hit.title.find(" ") + 1:]:  # filter results where query == subject
                        evalue = 1
                        blast_hit = BlastHit(hit.accession,
                                             hit.title,
                                             hit.length)
                        blast_result_object.all_found_accessions.add(hit.title)
                        for hsp in hit.hsps:
                            blast_hsp = BlastHsp(hsp_id,
                                                 acc_id,
                                                 float(hsp.expect),
                                                 hsp.identities,
                                                 hsp.query,
                                                 hsp.match,
                                                 hsp.sbjct,
                                                 float(hsp.score))

                            #extra logic
                            blast_result_object.all_sbjcts.add(blast_hsp.subject)
                            h = hash(record.query+"-"+hit.title+"-"+blast_hsp.subject)
                            blast_result_object.all_hsp_per_sbjct[h] = blast_hsp
                            #end extra logic

                            """
                            if hsp.expect < evalue:
                                #data structuur: key als basis naam query + naam hit.
                                #in principe de basis voor opbouw van tabel key=row+header, value=cel
                                blast_result_object.all_found_pairs[record.query + "-" + hit.title] = [blast_hsp, blast_hit]
                                evalue = hsp.expect
                            all_hsp_per_hit.append(BlastHandle.obj_to_dict(blast_hsp))
                            """
                            hsp_id += 1
                    #blast_result_object.all_hps_per_hit[acc_id] = all_hsp_per_hit
                    acc_id += 1
        return blast_result_object


print("start")
print(datetime.datetime.now())
start = time.time()

test = BlastHandle.parse_blast_outfile()

stop = time.time()

print("done reading: " + str(int(stop - start)) + " - seconden")

print("lengte querys: "+ str(len(test.all_found_querys)))
print("lengte subjects: "+ str(len(test.all_found_accessions)))
print("lengte unieke hsps: "+ str(len(test.all_sbjcts)))

for row in test.all_sbjcts:
    for column in test.all_sbjcts:
        x = 1


stop2 = time.time()

print("done creating table: " + str(int(stop2 - stop)) + " - seconden")