def get_Hao(seq_x: SequenceData, seq_y: SequenceData, k: int, result: Result, r: int = None) -> None:
if k < 2:
return
ktuple_1 = seq_x.get_ktuple(k)
total_1 = seq_x.get_total(k)
markov_1 = seq_x.get_markov(k, k - 2)
ktuple_2 = seq_y.get_ktuple(k)
total_2 = seq_y.get_total(k)
markov_2 = seq_y.get_markov(k, k - 2)
res = Dissimilarity._get_Hao(ktuple_1, ktuple_2, total_1, total_2, markov_1, markov_2)
key = 'Hao_k{}'.format(k)
result.add(key, seq_x.id, seq_y.id, res)
def get_D2S(seq_x: SequenceData, seq_y: SequenceData, k: int, result: Result, r_list: List[int]) -> None:
for r in r_list:
if k < r or k < 3:
continue
ktuple_1 = seq_x.get_ktuple(k)
total_1 = seq_x.get_total(k)
markov_1 = seq_x.get_markov(k, r)
ktuple_2 = seq_y.get_ktuple(k)
total_2 = seq_y.get_total(k)
markov_2 = seq_y.get_markov(k, r)
res = Dissimilarity._get_D2S(ktuple_1, ktuple_2, total_1, total_2, markov_1, markov_2)
key = 'D2S_k{}_M{}'.format(k, r)
result.add(key, seq_x.id, seq_y.id, res)
def __init__(self, parent, ID):
wx.Panel.__init__(self, parent, ID)
Registry.add("CONTACT", self)
Result.addListener(self)
self.grid = ContactGrid(self, -1)
gridBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Contact List"), wx.HORIZONTAL)
gridBox.Add(self.grid, 1, wx.GROW|wx.ALIGN_CENTER|wx.ALL, 3)
self.physicalAddress = Address(self, "HOME_PHYSICAL", Colors.HOME)
self.postalAddress = Address(self, "HOME_POSTAL", Colors.HOME)
self.workPhysicalAddress = Address(self, "WORK_PHYSICAL", Colors.WORK)
self.workPostalAdress = Address(self, "WORK_POSTAL", Colors.WORK)
# register the widgets for later access
self.addWidgets = {"HOME_PHYSICAL": self.physicalAddress,
"HOME_POSTAL": self.postalAddress,
"WORK_PHYSICAL": self.workPhysicalAddress,
"WORK_POSTAL": self.workPostalAdress}
agrid = wx.GridSizer(1, 2, 3, 3)
agrid.AddMany([(self.physicalAddress, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3),
(self.workPhysicalAddress, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3),
(self.postalAddress, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3),
(self.workPostalAdress, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)])
#agrid.AddGrowableRow(0, 1)
#agrid.AddGrowableRow(1, 1)
#agrid.SetFlexibleDirection(wx.HORIZONTAL|wx.VERTICAL)
# save
saveBtn = wx.Button(self, wx.ID_SAVE)
self.Bind(wx.EVT_BUTTON, self.__saveData, saveBtn)
# new
newBtn = wx.Button(self, wx.ID_NEW)
self.Bind(wx.EVT_BUTTON, self.new, newBtn)
btnBox = wx.BoxSizer(wx.HORIZONTAL)
btnBox.Add(newBtn, 0, wx.ALIGN_CENTER|wx.ALL, 3)
btnBox.Add(saveBtn, 0, wx.ALIGN_CENTER|wx.ALL, 3)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(gridBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
sizer.Add(agrid, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
sizer.Add(btnBox, 0, wx.ALIGN_CENTER|wx.ALL, 3)
self.SetSizer(sizer)
def deleteEntry(self, evt):
""" delete selected entry"""
from Dialogs.ConfirmationDialog import ConfirmationDialog
i = self.normalResult.GetSelection()
data = Result.getResult()[i]
file_number = data["file_number"]
msg = "Delete %(surname)s, %(first_names)s Folder %(file_number)d from database ?" % data
dlg = ConfirmationDialog(self, msg=msg)
if dlg.ShowModal() == wx.ID_OK:
CONN.deleteEntry(file_number)
self.__searchDB()
Result.notify(self.normalResult.GetSelection())
def search(self, data):
"""search database """
self.lastSearchData = data
query = """
select * from patient.patient where """
filenoquery = "file_number=%(folderno)s" % data
surnamequery = "surname ~* '%(surname)s'" % data
firstnamequery = "first_names ~* '%(name)s'" % data
bdatequery = "birth_date ~* '%(bdate)s'" % data
post = """
order by surname desc
limit 50
"""
qlist = []
if data["folderno"]:
qlist.append(filenoquery)
if data["surname"]:
qlist.append(surnamequery)
if data["name"]:
qlist.append(firstnamequery)
if data["bdate"]:
qlist.append(bdatequery)
if len(qlist) > 1:
mq = " and ".join(qlist)
elif len(qlist) != 0:
mq = qlist[0]
else:
BARWRITER.write("No Matches Found")
return []
q = query + mq + post
cursor = self.conn.cursor()
cursor.execute(q)
# set the rusult
Result.setResult(cursor.dictfetchall())
BARWRITER.write("Save Completed at %s" % time.ctime())
def __init__(self,
k_list: List[int],
seq_file_list: List[str],
dissimilirary_list: List[str],
save_dir: str,
markov_list: List[int] = None):
self._k_list = k_list
self._seq_list = [
SequenceData(seq_file_list[i], i)
for i in range(len(seq_file_list))
]
self._dissimilarity = [
self._DIC_FUNC[name] for name in dissimilirary_list
]
self._markov_list = markov_list
self._dissimilarity_names = dissimilirary_list
self._result = Result(len(seq_file_list))
self._save_dir = save_dir
def __init__(self, parent, ID):
wx.Panel.__init__(self, parent, ID)
Registry.add("VISITS", self)
Result.addListener(self)
self.visits = {}
self.file_number = None
self.selected = None
# visit list
self.visitListCtrl = wx.ListBox(self, -1, size=(100, -1))
self.Bind(wx.EVT_LISTBOX, self.dateSelected, self.visitListCtrl)
visitBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Visit List"), wx.HORIZONTAL)
visitBox.Add(self.visitListCtrl, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# note
self.note = wx.TextCtrl(self, -1, "", style=wx.TE_MULTILINE)
# self.Bind(wx.EVT_CHAR, self.OnKeyDown, self.note)
wx.EVT_CHAR(self.note, self.OnKeyDown)
self.noteLabel = wx.StaticBox(self, -1, "Visit Note")
noteBox = wx.StaticBoxSizer(self.noteLabel, wx.HORIZONTAL)
noteBox.Add(self.note, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
topBox = wx.BoxSizer(wx.HORIZONTAL)
topBox.Add(visitBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
topBox.Add(noteBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# save
saveBtn = wx.Button(self, wx.ID_SAVE)
self.Bind(wx.EVT_BUTTON, self.__saveData, saveBtn)
newBtn = wx.Button(self, wx.ID_NEW)
self.Bind(wx.EVT_BUTTON, self.__new, newBtn)
btnBox = wx.BoxSizer(wx.HORIZONTAL)
btnBox.Add(newBtn, 0, wx.ALIGN_CENTER|wx.ALL, 3)
btnBox.Add(saveBtn, 0, wx.ALIGN_CENTER|wx.ALL, 3)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(topBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
sizer.Add(btnBox, 0, wx.ALIGN_CENTER|wx.ALL, 3)
self.SetSizer(sizer)
def presentResult(self):
"""format and present the result"""
res = Result.getResult()
formatlist = []
for d in res:
formatlist.append("%(surname)s, %(first_names)s" % d)
self.normalResult.Clear()
self.normalResult.InsertItems(formatlist, 0)
if Result.currentIndex:
self.normalResult.SetSelection(Result.currentIndex)
def get_Ma(seq_x: SequenceData, seq_y: SequenceData, k: int, result: Result, r: int = None) -> None:
ktuple_1 = seq_x.get_ktuple(k)
ktuple_2 = seq_y.get_ktuple(k)
res = Dissimilarity._get_Ma(ktuple_1, ktuple_2, seq_x.get_total(k), seq_y.get_total(k))
key = 'Ma_k{}'.format(k)
result.add(key, seq_x.id, seq_y.id, res)
def __init__(self, parent, ID):
wx.Panel.__init__(self, parent, ID)
Registry.add("BIO", self)
Result.addListener(self)
modefont = wx.Font(16, wx.NORMAL , wx.BOLD, wx.NORMAL, False)
self.modeLabel = wx.StaticText(self, -1, editstr, size=(600, -1))
self.modeLabel.SetFont(modefont)
# folder number
bigfont = wx.Font(22, wx.MODERN , wx.BOLD, wx.NORMAL, False)
self.folderNumber = wx.TextCtrl(self, -1, "", size=(130, -1))
self.folderNumber.SetBackgroundColour(Colors.LIGHTBLUE)
self.folderNumber.SetFont(bigfont)
folderBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Folder Number"), wx.HORIZONTAL)
folderBox.Add(self.folderNumber, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# name
self.name = wx.TextCtrl(self, -1, "", size=(350, -1))
self.name.SetFont(bigfont)
self.name.SetBackgroundColour(Colors.PURPLE)
nameBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "First Names"), wx.HORIZONTAL)
nameBox.Add(self.name, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# surname
self.surname = wx.TextCtrl(self, -1, "", size=(250, -1))
self.surname.SetFont(bigfont)
self.surname.SetBackgroundColour(Colors.PURPLE)
surnameBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Surname"), wx.HORIZONTAL)
surnameBox.Add(self.surname, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# callname
self.callname = wx.TextCtrl(self, -1, "", size=(120, -1))
callnameBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Name"), wx.HORIZONTAL)
callnameBox.Add(self.callname, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# add the names to the top ass well, they are written in large font
topBox = wx.BoxSizer(wx.HORIZONTAL)
topBox.Add(folderBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
topBox.Add(nameBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
topBox.Add(surnameBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# names
# mainnameBox = wx.BoxSizer(wx.HORIZONTAL)
# mainnameBox.Add(callnameBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# mainnameBox.Add(nameBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# mainnameBox.Add(surnameBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# birthdate
#self.birthdate = wx.DatePickerCtrl(self, size=(120,-1),
# style=wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
self.birthdate = wx.TextCtrl(self, -1, "", size=(120, -1))
birthdayBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Birth Date"), wx.HORIZONTAL)
birthdayBox.Add(self.birthdate, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# gender
self.gender = wx.Choice(self, -1, choices=["Male", "Female", "Undefined"], size=(120, -1))
genderBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Gender"), wx.HORIZONTAL)
genderBox.Add(self.gender, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# marital status
self.marital_status = wx.Choice(self, -1, choices=["Single", "Married", "Divorced", "Widowed"], size=(120, -1))
maritalBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Marital Status"), wx.HORIZONTAL)
maritalBox.Add(self.marital_status, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
bgBox = wx.BoxSizer(wx.HORIZONTAL)
bgBox.Add(birthdayBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
bgBox.Add(genderBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
bgBox.Add(maritalBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# ID
self.ID = wx.TextCtrl(self, -1, "", size=(200, -1))
IDBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "National ID"), wx.HORIZONTAL)
IDBox.Add(self.ID, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# nationality
self.nationality = wx.TextCtrl(self, -1, "")
nationalBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Nationality"), wx.HORIZONTAL)
nationalBox.Add(self.nationality, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# language
self.language = wx.TextCtrl(self, -1, "", size=(200, -1))
languageBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Language"), wx.HORIZONTAL)
languageBox.Add(self.language, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# race
self.race = wx.TextCtrl(self, -1, "", size=(200, -1))
raceBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Ethnicity"), wx.HORIZONTAL)
raceBox.Add(self.race, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# id
allidBox = wx.BoxSizer(wx.HORIZONTAL)
allidBox.Add(IDBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
allidBox.Add(nationalBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
allidBox.Add(languageBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
allidBox.Add(raceBox, 0, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# occupation
self.occupation = wx.TextCtrl(self, -1, "", size=(300, -1))
occupationBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Occupation"), wx.HORIZONTAL)
occupationBox.Add(self.occupation, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# employer
self.employer = wx.TextCtrl(self, -1, "", size=(300, -1))
employerBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Employer"), wx.HORIZONTAL)
employerBox.Add(self.employer, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
workBox = wx.BoxSizer(wx.HORIZONTAL)
workBox.Add(occupationBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
workBox.Add(employerBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# dependants
self.dependants = wx.TextCtrl(self, -1, "", style=wx.TE_MULTILINE)
self.dependants.SetBackgroundColour(Colors.INFOCOL)
dependantBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Dependants, Only spouse and Children under 18"), wx.HORIZONTAL)
dependantBox.Add(self.dependants, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# note
self.note = wx.TextCtrl(self, -1, "", style=wx.TE_MULTILINE)
self.note.SetBackgroundColour(Colors.INFOCOL)
noteBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Additional Notes"), wx.HORIZONTAL)
noteBox.Add(self.note, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
depnoteBox = wx.BoxSizer(wx.HORIZONTAL)
depnoteBox.Add(dependantBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
depnoteBox.Add(noteBox, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# synopsis
self.synopsis = wx.TextCtrl(self, -1, "", style=wx.TE_MULTILINE)
synopsisBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Synopsis"), wx.HORIZONTAL)
synopsisBox.Add(self.synopsis, 1, wx.ALIGN_CENTER|wx.GROW|wx.ALL, 3)
# save
saveBtn = wx.Button(self, wx.ID_SAVE)
self.Bind(wx.EVT_BUTTON, self.__saveData, saveBtn)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.modeLabel, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(topBox, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(callnameBox, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(bgBox, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(allidBox, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(workBox, 0, wx.ALIGN_LEFT|wx.ALL, 3)
sizer.Add(depnoteBox, 2, wx.ALIGN_LEFT|wx.GROW|wx.ALL, 3)
sizer.Add(synopsisBox, 1, wx.ALIGN_LEFT|wx.GROW|wx.ALL, 3)
sizer.Add(saveBtn, 0, wx.ALIGN_CENTER|wx.ALL, 3)
self.SetSizer(sizer)
self.widgetList = [
self.folderNumber,
self.surname,
self.name,
self.birthdate,
#self.gender,
self.ID,
self.nationality,
self.note,
self.callname,
self.language,
self.occupation,
self.synopsis,
self.dependants,
self.race,
self.employer
]
class Core:
_DIC_FUNC = {
'd2': Dissimilarity.get_D2,
'Ch': Dissimilarity.get_Ch,
'Eu': Dissimilarity.get_Eu,
'Ma': Dissimilarity.get_Ma,
'd2S': Dissimilarity.get_D2S,
'd2Star': Dissimilarity.get_D2Star,
'Hao': Dissimilarity.get_Hao
}
def __init__(self,
k_list: List[int],
seq_file_list: List[str],
dissimilirary_list: List[str],
save_dir: str,
markov_list: List[int] = None):
self._k_list = k_list
self._seq_list = [
SequenceData(seq_file_list[i], i)
for i in range(len(seq_file_list))
]
self._dissimilarity = [
self._DIC_FUNC[name] for name in dissimilirary_list
]
self._markov_list = markov_list
self._dissimilarity_names = dissimilirary_list
self._result = Result(len(seq_file_list))
self._save_dir = save_dir
def n_to_n(self):
names = [seq.name for seq in self._seq_list]
for i in tqdm(range(len(self._seq_list) - 1)): # type: int
self.one_to_n(self._seq_list[i], self._seq_list[i + 1:])
self._seq_list[i] = None
self._result.save_to_file(self._save_dir, names)
def one_to_n(self, one: SequenceData, others: List[SequenceData]):
for seq in others:
Core._one_to_one(one, seq, self._k_list, self._dissimilarity,
self._result, self._markov_list)
@staticmethod
def _one_to_one(seq_x: SequenceData, seq_y: SequenceData,
k_list: List[int], func_list: List[Callable],
result: Result, markov_list: List[int]):
for k in k_list:
[func(seq_x, seq_y, k, result, markov_list) for func in func_list]
def _clear(self, k: int, r: int = None):
if 'd2S' in self._dissimilarity_names or 'd2Star' in self._dissimilarity_names:
if k in self._markov_list:
return
if 'Hao' in self._dissimilarity_names:
k -= 3
for seq in self._seq_list:
seq.clear(k)
@staticmethod
def star(k_list: List[int],
seq_dir: str,
dissimilirary_list: List[str],
save_dir: str,
markov_list: List[int] = None):
dirs = Core.recurrence_load(seq_dir)
for dir_ in dirs:
name = os.path.split(dir_)[-1]
print('{} start.................'.format(name))
seq_file_list = Core.get_file_path(dir_)
save = os.path.join(save_dir, name)
os.makedirs(save) if not os.path.exists(save) else None
Core(k_list, seq_file_list, dissimilirary_list, save,
markov_list).n_to_n()
@staticmethod
def recurrence_load(dir_path: str):
dirs = []
def _rec_load(path: str):
tmps = os.listdir(path)
p = os.path.join(path, tmps[0])
if os.path.isfile(p):
dirs.append(path)
elif os.path.isdir(p):
[_rec_load(os.path.join(path, sub_path)) for sub_path in tmps]
else:
return
_rec_load(dir_path)
return dirs
@staticmethod
def get_file_path(dir_path: str) -> List[str]:
tmps = os.listdir(dir_path)
return [os.path.join(dir_path, sub_path) for sub_path in tmps]
def __resultSelected(self, evt):
"""user selected a result"""
Result.notify(evt.GetInt())
