def reportSorted(self, sortedSignatureIDs):
filteredSignatures = (
Signature.readSignatures(self.filteredLocation)) # The output.
# REPORT SORTED SIGNATURES
outputFile = open(self.sortedLocation, 'w')
for ID in sortedSignatureIDs:
if ID in filteredSignatures:
signature = filteredSignatures[ID]
# -- Score Signature -- #
if ID in self.overallScore:
signature.score = self.overallScore[ID]
else:
signature.score = 0.0
if ID in self.inclusionScore:
signature.inscore = self.inclusionScore[ID]
else:
signature.inscore = 0.0
if ID in self.exclusionScore:
signature.exscore = self.exclusionScore[ID]
else:
signature.exscore = 0.0
Signature.writeSignature(signature, outputFile)
outputFile.close()
def is_valid(self):
total_in = 0
total_out = 0
message = self.__gather()
# Self.inputs -> List[Tuples(addr, amount)]
for addr, amount, index in self.inputs:
found = False
for s in self.sigs:
if Signature.verify(message, s, addr):
found = True
if not found:
return False
if amount < 0:
return False
total_in = total_out + amount
for addr in self.reqd:
found = False
for s in self.sigs:
if Signature.verify(message, s, addr):
found = True
if not found:
return False
for addr, amount in self.outputs:
if amount < 0:
return False
total_out = total_out + amount
'''
# Remove as Miners best interest to have transactions where outputs > inputs.
# Miners will be performing these checks.
if total_out > total_in:
return False
'''
return True
def get_similar_signs(smallsign, bigsign, diffPercentage=12, minSimilarity=75):
start = timer()
curs.execute("SELECT datestamp,smallsign,bigsign FROM people")
data = curs.fetchall()
nbSmallCorres = 0
nbBigCorres = 0
similarSmallSign = []
similarBigSign = []
for row in data:
if sign.compare_signs(smallsign, convertItem(row[1]),
diffPercentage)[1] >= minSimilarity:
nbSmallCorres += 1
similarSmallSign.append((row[0], row[1]))
if sign.compare_signs(bigsign, convertItem(row[2]),
diffPercentage)[1] >= minSimilarity:
nbBigCorres += 1
similarBigSign.append((row[0], row[2]))
print("{} similar small sign in DB // {} similare big sign in DB".format(
nbSmallCorres, nbBigCorres))
#print("getSimilarSign: " + str(timer() - start))
return similarSmallSign, similarBigSign
def reportSorted(self, sortedSignatureIDs):
filteredSignatures = (
Signature.readSignatures(self.filteredLocation)) # The output.
# REPORT SORTED SIGNATURES
outputFile = open(self.sortedLocation, 'w')
for ID in sortedSignatureIDs:
if ID in filteredSignatures:
signature = filteredSignatures[ID]
# -- Score Signature -- #
if ID in self.overallScore:
signature.score = self.overallScore[ID]
else:
signature.score = 0.0
if ID in self.inclusionScore:
signature.inscore = self.inclusionScore[ID]
else:
signature.inscore = 0.0
if ID in self.exclusionScore:
signature.exscore = self.exclusionScore[ID]
else:
signature.exscore = 0.0
Signature.writeSignature(signature, outputFile)
outputFile.close()
def post():
message = request.form.get('message')
author = request.form.get('author')
if not message or not author:
flash("You must fill in both a message and an author")
else:
signature = Signature(message=message, author=author)
signature.store()
flash("Signature stored")
return redirect(url_for('display'))
def consolidateSignatures(
signatureLocations, seedSize, outputDirectoryLocation):
# --- Compile Signatures --- #
compiledSignatures = {}
compileSignatures(compiledSignatures, signatureLocations)
# -- Sort Signatures -- #
sortedSignatures = Signature.sortSignatures(compiledSignatures)
# -- Write Signatures -- #
compiledSignatureLocation = os.path.join(
outputDirectoryLocation, COMPILED_SIGNATURES)
compiledSignatureFile = open(compiledSignatureLocation, 'w')
Signature.writeSignatures(sortedSignatures, compiledSignatureFile)
compiledSignatureFile.close()
# --- Build and Query Database --- #
databaseLocation = os.path.join(
outputDirectoryLocation, COMPILED_DATABASE)
queryLocation = os.path.join(
outputDirectoryLocation, COMPILED_DATABASE_QUERY)
Database.createDatabaseJob(compiledSignatureLocation, databaseLocation)
Database.queryDatabase(
databaseLocation, compiledSignatureLocation,
queryLocation, 0.50, seedSize)
# --- Produce Signatures --- #
outputLocation = os.path.join(
outputDirectoryLocation, CONSOLIDATED_SIGNATURES)
outputFile = open(outputLocation, 'w')
queryFile = open(queryLocation, 'r')
produceSignatures(sortedSignatures, queryFile, outputFile)
outputFile.close()
queryFile.close()
# --- Clean Output --- #
filelist = [f for f in os.listdir(outputDirectoryLocation)
if f.startswith(COMPILED_DATABASE)]
for f in filelist:
os.remove(os.path.join(outputDirectoryLocation, f))
os.remove(os.path.join(outputDirectoryLocation, COMPILED_SIGNATURES))
print "\n==== Exiting ====\n"
def consolidateSignatures(
signatureLocations, seedSize, outputDirectoryLocation):
# --- Compile Signatures --- #
compiledSignatures = {}
compileSignatures(compiledSignatures, signatureLocations)
# -- Sort Signatures -- #
sortedSignatures = Signature.sortSignatures(compiledSignatures)
# -- Write Signatures -- #
compiledSignatureLocation = os.path.join(
outputDirectoryLocation, COMPILED_SIGNATURES)
compiledSignatureFile = open(compiledSignatureLocation, 'w')
Signature.writeSignatures(sortedSignatures, compiledSignatureFile)
compiledSignatureFile.close()
# --- Build and Query Database --- #
databaseLocation = os.path.join(
outputDirectoryLocation, COMPILED_DATABASE)
queryLocation = os.path.join(
outputDirectoryLocation, COMPILED_DATABASE_QUERY)
Database.createDatabaseJob(compiledSignatureLocation, databaseLocation)
Database.queryDatabase(
databaseLocation, compiledSignatureLocation,
queryLocation, 0.50, seedSize)
# --- Produce Signatures --- #
outputLocation = os.path.join(
outputDirectoryLocation, CONSOLIDATED_SIGNATURES)
outputFile = open(outputLocation, 'w')
queryFile = open(queryLocation, 'r')
produceSignatures(sortedSignatures, queryFile, outputFile)
outputFile.close()
queryFile.close()
# --- Clean Output --- #
filelist = [f for f in os.listdir(outputDirectoryLocation)
if f.startswith(COMPILED_DATABASE)]
for f in filelist:
os.remove(os.path.join(outputDirectoryLocation, f))
os.remove(os.path.join(outputDirectoryLocation, COMPILED_SIGNATURES))
def sign(self, z):
k = self.deterministic_k(z)
r = (k*G).x.num
k_inv = pow(k, N-2, N)
s = (z + r*self.secret) * k_inv % N
if s > N/2:
s = N - s
return Signature(r, s)
def get_tests(config={}):
tests = []
import Cipher; tests += Cipher.get_tests(config=config)
import Hash; tests += Hash.get_tests(config=config)
import Protocol; tests += Protocol.get_tests(config=config)
import PublicKey; tests += PublicKey.get_tests(config=config)
import Random; tests += Random.get_tests(config=config)
import Util; tests += Util.get_tests(config=config)
import Signature; tests += Signature.get_tests(config=config)
return tests
def startWallet():
global tWS
# Load public and private keys
Wallet.my_private, Wallet.my_public = Signature.loadKeys(
("private.key", "public.key"))
# Start WalletServer
tWS = threading.Thread(target=Wallet.walletServer, args=((my_ip, 5006), ))
tWS.start()
return True
def produceSignatures(sortedSignatures, blastOutputFile, destination):
hits = {} # [SIGNATURE ID] -> [(SIGNATURE ID) LIST] // (alignments)
outputSignatures = {} # Collection of already-output signatures.
# Build a list of all query hits.
# This creates a dictionary mapping signatures that align to each other.
# [SIGNATURE ID] -> [(SIGNATURE ID) LIST]
for line in blastOutputFile:
hit = Database.Hit(line)
# We only keep the hit if the ratio of the signature-to-alignment
# length is sufficiently long.
if (float(hit.alignmentLength) / float(hit.length) < float(0.50)):
continue
# Append the signature ID to the existing list of IDs.
if hit.ID in hits:
hits[hit.ID].append(hit.reference)
# Create a new list of signature IDs associated with specific
# signature ID.
else:
hits[hit.ID] = [hit.reference]
# Write the signatures to output, while maintaining a dictionary of
# signatures that were previously written to output. This attempts to
# avoid writing signatures appear to be duplicates or appear to overlap
# significantly.
for signature in sortedSignatures:
# Is the signature close to anything already written to output?
if(all((ID not in outputSignatures) for ID in hits[signature.ID])):
# The signature appears to be sufficiently unique.
# Write the signature to output and update outputed signatures.
outputSignatures[signature.ID] = signature
Signature.writeSignature(signature, destination)
def produceSignatures(sortedSignatures, blastOutputFile, destination):
hits = {} # [SIGNATURE ID] -> [(SIGNATURE ID) LIST] // (alignments)
outputSignatures = {} # Collection of already-output signatures.
# Build a list of all query hits.
# This creates a dictionary mapping signatures that align to each other.
# [SIGNATURE ID] -> [(SIGNATURE ID) LIST]
for line in blastOutputFile:
hit = Database.Hit(line)
# We only keep the hit if the ratio of the signature-to-alignment
# length is sufficiently long.
if (float(hit.alignmentLength) / float(hit.length) < float(0.50)):
continue
# Append the signature ID to the existing list of IDs.
if hit.ID in hits:
hits[hit.ID].append(hit.reference)
# Create a new list of signature IDs associated with specific
# signature ID.
else:
hits[hit.ID] = [hit.reference]
# Write the signatures to output, while maintaining a dictionary of
# signatures that were previously written to output. This attempts to
# avoid writing signatures appear to be duplicates or appear to overlap
# significantly.
for signature in sortedSignatures:
# Is the signature close to anything already written to output?
if(all((ID not in outputSignatures) for ID in hits[signature.ID])):
# The signature appears to be sufficiently unique.
# Write the signature to output and update outputed signatures.
outputSignatures[signature.ID] = signature
Signature.writeSignature(signature, destination)
def reportFilteredCandidates(self):
outputFile = open(self.filteredLocation, 'w') # The output.
candidateSignatures = Signature.readSignatures(
self.candidatesLocation) # The input.
dictionary = self.exclusionOverallDictionary # Overall dictionary.
for ID in candidateSignatures:
signature = candidateSignatures[ID]
if ID in dictionary:
hit = dictionary[ID]
if (float(hit.alignmentLength) / float(signature.length) <
float(self.filterLength)):
Signature.writeSignature(signature, outputFile)
else:
Signature.writeSignature(signature, outputFile)
outputFile.close()
def createJsonLog(signlist):
data = []
cpt = 1
for s in signList:
data.append({'id': cpt, 'sign': []})
signat = sign.createSign(s, 100)
for val in signat:
data[-1]['sign'].append(val.tolist())
cpt = cpt + 1
filename = "session_" + time.strftime("%d-%m-%Y") + '-' + time.strftime(
"%H-%M-%S") + ".txt"
with open('Log/' + filename, 'w') as outfile:
json.dump(data, outfile)
def reportFilteredCandidates(self):
outputFile = open(self.filteredLocation, 'w') # The output.
candidateSignatures = Signature.readSignatures(
self.candidatesLocation) # The input.
dictionary = self.exclusionOverallDictionary # Overall dictionary.
for ID in candidateSignatures:
signature = candidateSignatures[ID]
if ID in dictionary:
hit = dictionary[ID]
if (float(hit.alignmentLength) / float(signature.length) <
float(self.filterLength)):
Signature.writeSignature(signature, outputFile)
else:
Signature.writeSignature(signature, outputFile)
outputFile.close()
def compileSignatures(compiledSignatures, signatureLocations):
fileID = 0
# -- Read Files -- #
for location in signatureLocations:
signatures = Signature.readSignatures(location)
for signatureID in signatures:
compileID = str(fileID) + "." + signatureID
compiledSignatures[compileID] = signatures[signatureID]
compiledSignatures[compileID].ID = compileID
fileID += 1
return compiledSignatures
def startMiner():
global tMS, tNF
# Load public_key
try:
my_pu = Signature.loadPublic("public.key")
except:
print("No public.key, need to generate?")
pass
# Start nonceFinder
# Start minerServer
tMS = threading.Thread(target=Miner.minerServer, args=((my_ip, 5005), ))
tNF = threading.Thread(target=Miner.nonceFinder, args=(wallets, my_pu))
tMS.start()
tNF.start()
return True
def compileSignatures(compiledSignatures, signatureLocations):
fileID = 0
# -- Read Files -- #
for location in signatureLocations:
signatures = Signature.readSignatures(location)
for signatureID in signatures:
compileID = str(fileID) + "." + signatureID
compiledSignatures[compileID] = signatures[signatureID]
compiledSignatures[compileID].ID = compileID
fileID += 1
return compiledSignatures
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= # Custom functions #-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= print "Test creating default signature" a = Signature() print "a is ", a.data print "-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=" print "Test setting default signatures with new data." x = Signature() print "x is ", x.data x.data = [0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0] print "now, x is ", x.data y = Signature() print "y is ", y.data y.data = [0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0] print "now, y is ", y.data print "-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=" print "Testing signature.weigh()" print "x is", x.data,"and x.weigh() is", x.weigh() print "y is", y.data,"and y.weigh() is", y.weigh() print "-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-="
# -*-coding=utf-8
import json
import requests
from Signature import *
import sys
sys.path.append('..')
import log
import logging
log.initLogging('/data/rx/log')
sign = Signature('2', '123', '5321e33f2819487e99a6d52f92dc7cd7',
str(int(time.time())))
token = sign.create_token_base64()
decode = sign.decode_base64(token)
contentType = 'application/x-www-form-urlencoded' # form数据封装到http body中，然后发送到server name=test&gender=male&[email protected]
header = {'Content-Type': contentType, 'Authorization': 'Bearer %s' % token}
def delete_yidian_ad(feedyidianId):
boby = {
"biz": 2,
"ownerId": 1000001603,
"adId": feedyidianId,
}
try:
url = 'http://183.131.22.111/v1/ad/delete'
resp = requests.post(url, data=boby, headers=header)
resp.close()
if resp.status_code != 200:
logging.error('delete_yidian_ad_fail')
logging.info('delete_yidian_ad_code:' + str(resp.status_code))
logging.info(resp.content)
##
def saveTxList(the_list, filename):
fp = open(filename, "wb")
pickle.dump(the_list, fp)
fp.close
return True
if __name__ == "__main__":
import threading
import time
import Signature
my_pr, my_pu = Signature.loadKeys("private.key", "public_key")
# args need to be passed as a TUPLE, in t1
t1 = threading.Thread(target=minerServer, args=(('localhost', 5005),))
t2 = threading.Thread(target=nonceFinder, args=(wallets, my_pu))
server = SocketUtils.newServerConnect('localhost', 5006)
t1.start()
t2.start()
pr1, pu1 = Signature.generate_keys()
pr2, pu2 = Signature.generate_keys()
pr3, pu3 = Signature.generate_keys()
Tx1 = Transaction.Tx()
# -*-coding=utf-8
import json
import requests
from Signature import *
import sys
sys.path.append('..')
import log
import logging
# log.initLogging('/data/rx/log')
sign = Signature('19', '1113', '9798384b2ccb4f2aa372520758b5b8f8',str(int(time.time())))
token = sign.create_token_base64()
decode = sign.decode_base64(token)
contentType = 'application/x-www-form-urlencoded' # form数据封装到http body中，然后发送到server name=test&gender=male&[email protected]
header = {
'Content-Type': contentType,
'Authorization': 'Bearer %s' % token
}
boby = {
"biz":2,
"name":"自动化内部广告",
"specId":2,
"adType":12,
"brandName":"自动化内部广告",
"copywriter":"aaa",
"tags":"自动化内部广告",
"targetUrl":"http://www.baidu.com",
'materialUrls':'["http://www.vivibride.cn/uploads/allimg/130306/16-130306161552619.jpg"]',
"price":1000,
"billingType":2,
"ownerId":137,
#SecondMiner
import threading
import Miner
import Signature
import time
my_ip = 'localhost'
wallets = [(my_ip, 5005), (my_ip, 5006)]
my_pr, my_pu = Signature.loadKeys("private.key", "public_key")
# args need to be passed as a TUPLE, in t1
t1 = threading.Thread(target=Miner.minerServer, args=(('localhost', 5007),))
t2 = threading.Thread(target=Miner.nonceFinder, args=(wallets, my_pu))
t1.start()
t2.start()
time.sleep(20)
Miner.StopAll()
t1.join()
t2.join()
print(ord(TxBlock.findLongestBlockchain(Miner.head_blocks).previousBlock.previousBlock.nonce[0]))
print(ord(TxBlock.findLongestBlockchain(Miner.head_blocks).previousBlock.nonce[0]))
print(ord(TxBlock.findLongestBlockchain(Miner.head_blocks).nonce[0]))
###
###
def sendBlock(ip_addr, blk):
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.connect((ip_addr, TCP_PORT))
data = pickle.dumps(blk)
s.send(data)
s.close()
return False
if __name__ == "__main__":
pr1, pu1 = Signature.generate_keys()
pr2, pu2 = Signature.generate_keys()
pr3, pu3 = Signature.generate_keys()
Tx1 = Transaction.Tx()
Tx1.add_input(pu1, 2.3)
Tx1.add_output(pu2, 1.0)
Tx1.add_output(pu3, 1.1)
Tx1.sign(pr1)
Tx2 = Transaction.Tx()
Tx2.add_input(pu3, 2.3)
Tx2.add_input(pu2, 1.0)
Tx2.add_output(pu1, 3.1)
Tx2.sign(pr2)
Tx2.sign(pr3)
import WechatLogin import Portrait import Signature import GetLocation import Gender WechatLogin.weChatLogin() Portrait.getPortrait() Signature.getSignature() GetLocation.getLocation() Gender.getGender()
def loadKeys(pr_file, pu_file):
return Signature.loadPrivate(pr_file), Signature.loadPublic(pu_file)
reprstr = reprstr + "REQD:\n"
for r in self.reqd:
reprstr = reprstr + str(r) + "\n"
reprstr = reprstr + "SIGS:\n"
for s in self.sigs:
reprstr = reprstr + str(s) + "\n"
reprstr = reprstr + "END\n"
return reprstr
# Testing
if __name__ == "__main__":
pr1, pul1 = Signature.generate_keys()
pr2, pul2 = Signature.generate_keys()
pr3, pul3 = Signature.generate_keys()
pr4, pul4 = Signature.generate_keys()
# Correct Transactions
#Single Transaction between 2 Parties
Tx1 = Tx()
Tx1.add_input(pul1, 1)
Tx1.add_output(pul2, 1)
Tx1.sign(pr1)
#Multiple Transaction between 3 Parties
Tx2 = Tx()
Tx2.add_input(pul1, 2)
Tx2.add_output(pul2, 1)
Tx2.add_output(pul3, 1)
def sign(self, private):
message = self.__gather()
newSig = Signature.sign(message, private)
self.sigs.append(newSig)
def display():
page = paginate(Signature.all(), 5, request.args.get('start'))
return render_template('display.html', page=page)
type=bool,
default=False,
help="if true, will save detected sign on DB")
args = vars(ap.parse_args())
feed = args["feed_db"]
b = False
hasTarget = False
signList = []
if IsDbEmpty():
feed = True
else:
targetSign = get_sign_from_db(3, 1)
targetPattern = sign.create_pattern_from_sign(targetSign)
hasTarget = True
"""
User Interface
Show the sign and its pattern
"""
createSignPreview(targetSign)
createSignPreview(targetPattern, "Pattern")
# if the video argument is None, then we are reading from webcam
if args.get("video", None) is None:
camera = cv.VideoCapture(0)
time.sleep(0.25)
# otherwise, we are reading from a video file
else:
def extract(references, k, inmers, exmers, size, gap, outputFile):
# references
if references is None or len(references) < 1:
raise RuntimeError("There are no references.")
# 1 <= kmerSize
if k < 1:
raise RuntimeError("The k-mer size is out of range.")
# inclusion k-mers
if inmers is None or len(inmers) < 1:
raise RuntimeError("There are no inclusion k-mers.")
# exclusion k-mers
if exmers is None:
raise RuntimeError("There are no exclusion k-mers.")
# 1 <= size
if size < 1:
raise RuntimeError("The signature size is out of range.")
# 1 <= gap
if gap < 1:
raise RuntimeError("The gap size is out of range.")
# output
if outputFile is None:
raise RuntimeError("The output location is not specified.")
regions = []
# iterate all references
for key in references:
# next reference
ref = references[key]
# initialize positions
start = -1
end = -1
# every kmer in reference
for i in range(len(ref.strip()) - k + 1):
# k-mer and reverse complement
kmer = ref[i:i + k]
reverse = reverseComplement(kmer)
# kmer is in exclusion sufficiently -- break chain
if kmer in exmers or reverse in exmers:
# close the region if started:
if (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
# end the region regardless:
start = -1
end = -1
# k-mer is in inclusion sufficiently -- build chain
# (else -- don't both break and build)
elif kmer in inmers or reverse in inmers:
# new chain
if start < 0 and end < 0:
start = i + k - 1
end = i + 1
# hit with something else started
if start >= 0 and end >= 0:
# gap within size? -- yes
if (i - (end + 1)) <= gap:
end = i + 1
# gap within size? -- no
else:
if (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
start = i + k - 1
end = i + 1
if start >= 0 and end > 0 and (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
for i in range(len(regions)):
signature = Signature.Signature(
i, 0.0, 0.0, 0.0, regions[i].sequence,
regions[i].reference, regions[i].position)
Signature.writeSignature(signature, outputFile)
import SocketUtils
import Transaction
import TxBlock
import pickle
import Signature
break_now = False
head_blocks = [None]
wallets = [('localhost', 5006)]
miners = [('localhost', 5005)]
#miners = [('localhost', 5005), ('localhost', 5007)]
#Transaction Index
tx_index = {}
my_private, my_public = Signature.generate_keys()
def StopAll():
break_now = True
##
def walletServer(my_addr):
global head_blocks
global tx_index
# Load head_blocks
try:
# Save Wallet blocks to different file to Miner: AllBlocks.dat.
# Otherwise dangerous to read at the same time if you were writing to the same file.
def extract(references, k, inmers, exmers, size, gap, outputFile):
# references
if references is None or len(references) < 1:
raise RuntimeError("There are no references.")
# 1 <= kmerSize
if k < 1:
raise RuntimeError("The k-mer size is out of range.")
# inclusion k-mers
if inmers is None or len(inmers) < 1:
raise RuntimeError("There are no inclusion k-mers.")
# exclusion k-mers
if exmers is None:
raise RuntimeError("There are no exclusion k-mers.")
# 1 <= size
if size < 1:
raise RuntimeError("The signature size is out of range.")
# 1 <= gap
if gap < 1:
raise RuntimeError("The gap size is out of range.")
# output
if outputFile is None:
raise RuntimeError("The output location is not specified.")
regions = []
# iterate all references
for key in references:
# next reference
ref = references[key]
# initialize positions
start = -1
end = -1
# every kmer in reference
for i in range(len(ref.strip()) - k + 1):
# k-mer and reverse complement
kmer = ref[i:i + k]
reverse = reverseComplement(kmer)
# kmer is in exclusion sufficiently -- break chain
if kmer in exmers or reverse in exmers:
# close the region if started:
if (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
# end the region regardless:
start = -1
end = -1
# k-mer is in inclusion sufficiently -- build chain
# (else -- don't both break and build)
elif kmer in inmers or reverse in inmers:
# new chain
if start < 0 and end < 0:
start = i + k - 1
end = i + 1
# hit with something else started
if start >= 0 and end >= 0:
# gap within size? -- yes
if (i - (end + 1)) <= gap:
end = i + 1
# gap within size? -- no
else:
if (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
start = i + k - 1
end = i + 1
if start >= 0 and end > 0 and (end - start) >= size:
region = Region(ref[start:end], key, start)
regions.append(region)
for i in range(len(regions)):
signature = Signature.Signature(
i, 0.0, 0.0, 0.0, regions[i].sequence,
regions[i].reference, regions[i].position)
Signature.writeSignature(signature, outputFile)
