def __init__(self, parent, title):
super(ChildFrame, self).__init__(parent,
title='Admix',
size=(300, 325))
#pan = wx.Panel(self,wx.ID_ANY)
self.currentDirectory = os.getcwd()
self.InitUI()
self.Centre()
self._DH = DataHolder
self._FI = FileImporter()
pub.subscribe(self.GetPanel, "GetPanelAdmix")
def __init__(self, parent, title):
super(PCAFrame,
self).__init__(parent,
title='Pca',
size=(400, 400),
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
#pan = wx.Panel(self,wx.ID_ANY)
self.currentDirectory = os.getcwd()
self.InitUI()
self.Centre()
#creates File Importer for now
self._FI = FileImporter()
self._DH = DataHolder
pub.subscribe(self.GetPanel, "GetPanelPca")
def setUp(self):
self.FI = FileImporter()
admixData = self.getAdmixData('../Data/small.Q.4')
famData = self.getFamData('../Data/small.fam')
pheData = self.getPhenoData('../Data/small.phe')
self.graph = AdmixGraph.AdmixGraph(admixData,
famData,
None,
"graph",
phenoData=pheData)
self.graph.groupColIndex = 2
def __init__(self, *args, **kwargs):
super(windowClass, self).__init__(*args, **kwargs)
self.Size = (3000, 4500)
self._panel = self.basicGUI()
self.AdmixPath = AdmixPath = ''
#find data holder
self._DH = DataHolder
#create a fileimporter to hold graphs
self._FI = FileImporter()
self.Graphs = {}
#the main graph is listening so that it can get file importers PCA and ADMIX main
pub.subscribe(self.mylistener, "panelListener")
#create a list of ids
self._cid = []
#create a notebook to store graphs
self.plotter = PlotNotebook(self._panel)
currentGraphName = ""
self.currentDirectory = os.getcwd()
self.sb = self.CreateStatusBar()
self.sb.SetStatusText("Genesis2.o")
def test_TestGetFileData(self):
fi = FileImporter()
_var =fi.GetFileData('..\\Data\\comm-SYMCL.pca.evec')
self.assertIsNotNone(_var)
_var =fi.GetFileData(None)
self.assertIsNone(_var)
_var =fi.GetFileData('')
self.assertIsNone(_var)
_var =fi.GetFileData('..\\Data\\Empty.txt')
self.assertIsNone(_var)
class windowClass(wx.Frame):
""" Creates the main interface for the program."""
def __init__(self, *args, **kwargs):
super(windowClass, self).__init__(*args, **kwargs)
self.Size = (3000, 4500)
self._panel = self.basicGUI()
self.AdmixPath = AdmixPath = ''
#find data holder
self._DH = DataHolder
#create a fileimporter to hold graphs
self._FI = FileImporter()
self.Graphs = {}
#the main graph is listening so that it can get file importers PCA and ADMIX main
pub.subscribe(self.mylistener, "panelListener")
#create a list of ids
self._cid = []
#create a notebook to store graphs
self.plotter = PlotNotebook(self._panel)
currentGraphName = ""
self.currentDirectory = os.getcwd()
self.sb = self.CreateStatusBar()
self.sb.SetStatusText("Genesis2.o")
def returnPanel(self):
""" Returns the panel for the main UI frame. """
return self._panel
def basicGUI(self):
"""Initialises GUI for the main frame. """
panel = wx.Panel(self)
menuBar = wx.MenuBar()
#Declare new buttons
fileButton = wx.Menu()
graphButton = wx.Menu()
helpButton = wx.Menu()
#File Button options
Save_Item = fileButton.Append(wx.ID_ANY, 'Save Project',
'status msg...')
Load_Item = fileButton.Append(wx.ID_ANY, 'Load Project',
'status msg...')
Export_Item = fileButton.Append(wx.ID_ANY, 'Export image',
'status msg...')
Exit_Item = fileButton.Append(wx.ID_ANY, 'Exit', 'status msg...')
self.Bind(wx.EVT_TOOL, self.SaveEvent, Save_Item)
self.Bind(wx.EVT_TOOL, self.LoadEvent, Load_Item)
self.Bind(wx.EVT_TOOL, self.ExportEvent, Export_Item)
self.Bind(wx.EVT_TOOL, self.QuitEvent, Exit_Item)
#Toolbars
importItem = wx.Menu()
Import_Admix = importItem.Append(wx.ID_ANY, 'New Admixture Graph')
Import_PCA = importItem.Append(wx.ID_ANY, 'New PCA Graph')
self.Bind(wx.EVT_TOOL, self.PCAEvent, Import_PCA)
self.Bind(wx.EVT_TOOL, self.AdmixEvent, Import_Admix)
fileButton.Append(wx.ID_ANY, 'New Graph', importItem)
self.Makebar()
#Graph Button options
Data_Options_Item = graphButton.Append(
wx.ID_ANY, 'Data options',
'status msg...') #Append new items to buttons
Appearance_Options_Item = graphButton.Append(wx.ID_ANY,
'Appearence options',
'status msg...')
Delete_Annotations_Item = graphButton.Append(wx.ID_ANY,
'Delete Annotations',
'status msg...')
self.Bind(wx.EVT_TOOL, self.AppearenceEvent, Appearance_Options_Item)
self.Bind(wx.EVT_TOOL, self.DataOptionsEvent, Data_Options_Item)
self.Bind(wx.EVT_TOOL, self.DelAnnotationsEvent,
Delete_Annotations_Item)
#Help Button options
Help_Item = helpButton.Append(wx.ID_EXIT, 'Help', 'status msg...')
About_Item = helpButton.Append(wx.ID_EXIT, 'About', 'status msg...')
#Add buttons to menubar
menuBar.Append(fileButton, 'File')
menuBar.Append(graphButton, 'Graph')
menuBar.Append(helpButton, 'Help')
self.SetMenuBar(menuBar)
#self.Bind(wx.EVT_MENU, self.QuitEvent, exitItem)
self.SetTitle('Genesis')
self.Show(True)
return panel
def Makebar(self):
"""Initialises tool bar at the top of the GUI """
toolBar = self.CreateToolBar()
#toolBar.SetBackgroundColour((0xff,0xcc,0xcc))
#Declare all toolbar buttons
InputAdmixButton = toolBar.AddTool(wx.ID_ANY,
'Quite',
wx.Bitmap('../images/admix.bmp'),
shortHelp='Admix')
self.Bind(wx.EVT_ENTER_WINDOW, self.OnMouseEnter, InputAdmixButton)
#InputAdmixButton.Bind(wx.EVT_ENTER_WINDOW, self.OnMouseEnter)
InputPCAButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/pca.bmp'),
shortHelp='PCA')
toolBar.AddSeparator()
SaveButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/save.bmp'),
shortHelp='Save')
OpenFilesButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/open.bmp'),
shortHelp='Open Files')
toolBar.AddSeparator()
DataOptionsButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/dataOp.bmp'),
shortHelp='Data Options')
AppearenceButton = toolBar.AddTool(
wx.ID_ANY,
'Import',
wx.Bitmap('../images/appearanceOp.bmp'),
shortHelp='Appearence')
RefreshButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/refresh.bmp'),
shortHelp='Refresh')
ShowHideButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/hiddenInd.bmp'),
shortHelp='Show/Hide Individual')
SearchIndividualButton = toolBar.AddTool(
wx.ID_ANY,
'Import',
wx.Bitmap('../images/search.bmp'),
shortHelp='Search for Individual')
SearchHiddenIndividualButton = toolBar.AddTool(
wx.ID_ANY,
'Import',
wx.Bitmap('../images/hiddenInd.bmp'),
shortHelp='Search Hidden Individual')
toolBar.AddSeparator()
DrawLineButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/drawLine.bmp'),
shortHelp='Draw Line')
DrawArrowButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/drawArrow.bmp'),
shortHelp='Draw Arrow')
toolBar.AddSeparator()
ExportButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/Export.bmp'),
shortHelp='Export')
CloseProjectButton = toolBar.AddTool(
wx.ID_ANY,
'Import',
wx.Bitmap('../images/closeProject.bmp'),
shortHelp='Close Project')
UndoButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/Undo.bmp'),
shortHelp='Undo')
RedoButton = toolBar.AddTool(wx.ID_ANY,
'Import',
wx.Bitmap('../images/redo.bmp'),
shortHelp='Redo')
toolBar.Realize()
#Bind functions to buttons
self.Bind(wx.EVT_TOOL, self.AdmixEvent, InputAdmixButton)
self.Bind(wx.EVT_TOOL, self.PCAEvent, InputPCAButton)
self.Bind(wx.EVT_TOOL, self.SaveEvent, SaveButton)
self.Bind(wx.EVT_TOOL, self.LoadEvent, OpenFilesButton)
self.Bind(wx.EVT_TOOL, self.DataOptionsEvent, DataOptionsButton)
self.Bind(wx.EVT_TOOL, self.AppearenceEvent, AppearenceButton)
self.Bind(wx.EVT_TOOL, self.RefreshEvent, RefreshButton)
self.Bind(wx.EVT_TOOL, self.ShowHideEvent, ShowHideButton)
self.Bind(wx.EVT_TOOL, self.SearchIndividualEvent,
SearchIndividualButton)
self.Bind(wx.EVT_TOOL, self.SearchHiddenIndividualEvent,
SearchHiddenIndividualButton)
self.Bind(wx.EVT_TOOL, self.DrawLineEvent, DrawLineButton)
self.Bind(wx.EVT_TOOL, self.DrawArrowEvent, DrawArrowButton)
self.Bind(wx.EVT_TOOL, self.ExportEvent, ExportButton)
self.Bind(wx.EVT_TOOL, self.QuitEvent, CloseProjectButton)
self.Bind(wx.EVT_TOOL, self.UndoEvent, UndoButton)
self.Bind(wx.EVT_TOOL, self.RedoEvent, RedoButton)
#All button and label functions
def DelAnnotationsEvent(self, e):
"""Delete annotations from program """
#Not currently implemented
pass
def OnMouseEnter(self, e):
""" Shows a description of the icons function."""
self.Statusbar.SetStatusText("TRIGGERED")
e.Skip()
def AdmixEvent(self, e):
"""Runs admix creator GUI. """
self.child = AdmixFrame(self, title='Admix')
self.child.Show()
self.child.SetFocus()
pub.sendMessage('GetPanelAdmix', message=self.plotter)
def PCAEvent(self, e):
"""Runs the pca creator GUI. """
self.child = PCAFrame(self, title='PCA')
self.child.Show()
pub.sendMessage('GetPanelPca', message=self.plotter)
def SaveEvent(self, e):
"""Saves the current graph. """
graph = DataHolder.Graphs[windowClass.currentGraphName]
defName = ""
#determines graph type
if (type(graph) is Admix):
wildcard = admixSaveWildcard
defName = windowClass.currentGraphName + ".gaf"
elif (type(graph) is PCA):
wildcard = pcaSaveWildcard
defName = windowClass.currentGraphName + ".gpf"
dlg = wx.FileDialog(self,
message="Select a save locations",
defaultDir=self.currentDirectory,
defaultFile=defName,
wildcard=wildcard,
style=wx.FD_SAVE | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
filePath = dlg.GetPath()
baseName = ntpath.basename(filePath) #get base name
#update dictionary key for graph and figure
graph.setName(baseName, windowClass.currentGraphName)
#Set notebook as none so it can be pickled
graph.setNotebook(None)
GraphSaver.saveGraph(graph, filePath)
nb = self.plotter.getNoteBook()
#reset notebook
graph.setNotebook(self.plotter)
pageIndex = nb.GetSelection()
nb.SetPageText(pageIndex, baseName)
windowClass.currentGraphName = baseName
dlg.Destroy()
def OpenFileEvent(self, e):
""" Opens extra files GUI."""
wx.MessageBox('Open file')
def DataOptionsEvent(self, e):
"""Opens data options GUI"""
self.child = AdmixDataFrame(self, title='Graph Options')
self.child.Show()
def AppearenceEvent(self, e):
"""Opens up the relevant customization options GUI. """
graph = self._DH.Graphs.get(windowClass.currentGraphName)
#Checks graph type and chooses relevant window to display
if (isinstance(graph, PCA)):
self.child = PcaCustom(self, windowClass.currentGraphName,
self.plotter.nb.GetCurrentPage(),
self.plotter.nb,
self.plotter.nb.GetSelection())
self.child.Show()
elif (isinstance(graph, Admix)):
self.child = admixMM(self, graph, self.plotter, self.plotter.nb)
self.child.Show()
def RefreshEvent(self, e):
""" Opens refresh GUI."""
wx.MessageBox('Refresh file')
def ShowHideEvent(self, e):
""" Opens Show hiders GUI."""
wx.MessageBox('Hide file')
def SearchIndividualEvent(self, e):
""" Opens search individual GUI."""
wx.MessageBox('Search Individual file')
def SearchHiddenIndividualEvent(self, e):
""" Opens search hidden individuals GUI."""
wx.MessageBox('Search Hidden Individual file')
def DrawLineEvent(self, e):
"""Turns on ability to draw a line. """
An.Annotate(self._DH.Figures)
def DrawArrowEvent(self, e):
""" Turns on ability to draw an arrow."""
An.AnnotateArrow(self._DH.Figures)
def ExportEvent(self, e):
"""Ooens export GUI. """
wx.MessageBox('Export file')
self.child = EXFrame(self, title='Export as')
self.child.Show()
def QuitEvent(self, e):
"""Exits the program."""
wx.MessageBox('Exit')
self.Destroy()
def UndoEvent(self, e):
"""Will undo previous action. """
wx.MessageBox('Undo')
def RedoEvent(self, e):
"""Will redo previous undo action. """
wx.MessageBox('Redo')
def LoadEvent(self, e):
""" Load graph object into the scene."""
#Creates a dialog to locate previous projects
dlg = wx.FileDialog(self,
message="Select a Genesis graph file",
defaultDir=self.currentDirectory,
defaultFile="",
wildcard=loadWildcard,
style=wx.FD_OPEN | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
filePath = dlg.GetPath()
graph = GraphSaver.loadGraph(filePath)
nb = self.plotter
graph.setNotebook(nb)
if type(graph) is Admix:
phenoCol = graph.getPhenoColumn()
graph.plotGraph(False, phenoCol=phenoCol)
elif type(graph) is PCA:
graph.PlotPca(
False
) #False indicates this graph is not being plotted the first time
self._DH.Graphs.update({graph.getName(): graph})
def mylistener(self, message, arg2=None):
"""Gets file managers returned from graphing frames. """
_temp = message.GetManagers()
for i in range(0, len(_temp)):
self._FI.AddFileManager(_temp[i])
self._FI.PrintFileManagers()
class PCAFrame(wx.Frame):
'''This is the main PCA frame.'''
def __init__(self, parent, title):
super(PCAFrame,
self).__init__(parent,
title='Pca',
size=(400, 400),
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
#pan = wx.Panel(self,wx.ID_ANY)
self.currentDirectory = os.getcwd()
self.InitUI()
self.Centre()
#creates File Importer for now
self._FI = FileImporter()
self._DH = DataHolder
pub.subscribe(self.GetPanel, "GetPanelPca")
def InitUI(self):
'''Initialise user interface.'''
panel = wx.Panel(self, wx.ID_ANY)
self.Columns = []
self.m_textCtrl1 = wx.TextCtrl(panel, wx.ID_ANY, wx.EmptyString,
wx.DefaultPosition, wx.DefaultSize, 0)
self.comboPCA1 = wx.ComboBox(panel, choices=self.Columns)
self.comboPCA1.Bind(wx.EVT_COMBOBOX, self.OnCombo)
self.comboPCA2 = wx.ComboBox(panel, choices=self.Columns)
self.comboPCA2.Bind(wx.EVT_COMBOBOX, self.OnCombo)
self.comboPCA3 = wx.ComboBox(panel, choices=self.Columns)
self.comboPCA3.Bind(wx.EVT_COMBOBOX, self.OnCombo)
self.comboPhe = wx.ComboBox(panel, choices=self.Columns)
self.comboPhe.Bind(wx.EVT_COMBOBOX, self.OnCombo)
self.comboPCA1.Hide()
self.comboPCA2.Hide()
self.comboPCA3.Hide()
self.comboPhe.Hide()
self.ColumnLabel = wx.StaticText(panel, label="Select PCAs")
self.ColumnLabel.Hide()
self.PheLabel = wx.StaticText(panel,
label="Which Column is the phenotype")
self.PheLabel.Hide()
self.m_textCtrl1.Value = "Name"
vbox = wx.BoxSizer(wx.VERTICAL)
fgsTop = wx.FlexGridSizer(2, 2, 15, 15)
fgs = wx.FlexGridSizer(8, 1, 15, 15)
fgsBotPhe = wx.FlexGridSizer(1, 2, 15, 15)
fgsBot = wx.FlexGridSizer(1, 2, 15, 50)
fgsBotRight = wx.FlexGridSizer(1, 2, 15, 15)
OpenFileBtn = wx.Button(panel, wx.ID_ANY, label='Import Data File')
OpenFileBtn.parameterVal = 'Data'
OpenPheBtn = wx.Button(panel, wx.ID_ANY, label='Import Phe File')
OpenPheBtn.parameterVal = 'Phe'
AcceptBtn = wx.Button(panel, wx.ID_ANY, label='Accept')
ExitBtn = wx.Button(panel, wx.ID_EXIT, label='Exit')
OpenFileBtn.Bind(wx.EVT_BUTTON, self.onOpenFile)
OpenPheBtn.Bind(wx.EVT_BUTTON, self.onOpenFile)
AcceptBtn.Bind(wx.EVT_BUTTON, self.onAcceptFile)
ExitBtn.Bind(wx.EVT_BUTTON, self.Quit)
self.tc1 = wx.TextCtrl(panel)
self.tc3 = wx.TextCtrl(panel)
fgsTop.AddMany([(OpenFileBtn), (self.tc1, 1, wx.EXPAND),
(OpenPheBtn, 1, wx.EXPAND), (self.tc3, 1, wx.EXPAND)])
fgsBotPhe.AddMany([(self.PheLabel, 1, wx.EXPAND),
(self.comboPhe, 1, wx.EXPAND)])
fgsBot.AddMany([(AcceptBtn), (ExitBtn)])
fgs.AddMany([(self.m_textCtrl1, 1, wx.EXPAND), (fgsTop, 1, wx.EXPAND),
(self.ColumnLabel, 1, wx.EXPAND),
(self.comboPCA1, 1, wx.EXPAND),
(self.comboPCA2, 1, wx.EXPAND),
(self.comboPCA3, 1, wx.EXPAND), (fgsBotPhe, 1, wx.EXPAND),
(fgsBot, 1, wx.EXPAND)])
fgsBotPhe.AddGrowableCol(1, 2)
fgsTop.AddGrowableCol(1, 2)
fgs.AddGrowableCol(0, 1)
vbox.Add(fgs, proportion=2, flag=wx.ALL | wx.EXPAND, border=15)
panel.SetSizer(vbox)
def AppearFrame(self, event):
'''Calls appearence frame.'''
self.child = AppFrame(self, title='Appearance')
self.child.Show()
def Quit(self, event):
'''Exits frame'''
self.Destroy()
pub.sendMessage('panelListener', message=self._FI)
def OnCombo(self, event):
'''Gets values from combobox.'''
print(self.comboPhe.GetValue())
def onAcceptFile(self, event):
'''Takes in file using file dialog.'''
#splitting the coloumn names up to get the numbers
name = self.m_textCtrl1.Value
pheCol = self.comboPhe.Value.split(' ')
Col1 = self.comboPCA1.Value.split(' ')
Col2 = self.comboPCA2.Value.split(' ')
Col3 = self.comboPCA3.Value.split(' ')
#creates graph dependant on if there is phen data
try:
if (self.tc3.Value != ""):
self._FI.CreatePca(self._FI, self.tc1.Value, self.tc3.Value,
name, int(Col1[1]), int(Col2[1]),
int(pheCol[1]), self._panel)
else:
self._FI.CreatePca(self._FI, self.tc1.Value, None, name,
int(Col1[1]), int(Col2[1]), 3, self._panel)
except IndexError:
print("Index Error")
plt.show()
def onOpenFile(self, event):
'''Gets file path for use.'''
self.button = event.GetEventObject()
if self.button.parameterVal == 'Data':
wildcard = pcaWildcard
if self.button.parameterVal == 'Phe':
wildcard = pheWildcard
dlg = wx.FileDialog(self,
message="Choose a file",
defaultDir=self.currentDirectory,
defaultFile="",
wildcard=wildcard,
style=wx.FD_OPEN | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
self.DataFilePath = dlg.GetPath()
print('You chose the following file:')
print(self.DataFilePath)
if self.button.parameterVal == 'Data':
if (VC.CheckPcaValid(self.DataFilePath)):
self.tc1.SetValue(self.DataFilePath)
else:
dlg = wx.MessageDialog(None, "Invalid Admix File", "ERROR",
wx.OK | wx.ICON_ERROR)
dlg.ShowsModal()
if self.button.parameterVal == 'Phe':
if (VC.CheckPhenValid(self.DataFilePath)):
self.tc3.SetValue(self.DataFilePath)
else:
dlg = wx.MessageDialog(None, "Invalid Phe File", "ERROR",
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
print(self.button.parameterVal)
#CountsColumns
self.CountColumns(self.button)
dlg.Destroy()
#counts coloumns in the file
def CountColumns(self, val):
'''Counts number of columns in input file.'''
self.Columns.clear()
with open(self.DataFilePath) as myFile:
reader = csv.reader(myFile, delimiter=' ', skipinitialspace=True)
first_row = next(reader)
num_cols = len(first_row)
for index in range(0, num_cols):
self.Columns.insert(index, 'Column ' + str(index + 1))
if self.button.parameterVal == 'Data':
self.comboPCA1.Clear()
self.comboPCA1.AppendItems(self.Columns)
self.comboPCA1.Value = self.Columns[0]
self.comboPCA2.Clear()
self.comboPCA2.AppendItems(self.Columns)
self.comboPCA2.Value = self.Columns[1]
self.comboPCA3.Clear()
self.comboPCA3.AppendItems(self.Columns)
self.comboPCA1.Show()
self.comboPCA2.Show()
self.comboPCA3.Show()
self.ColumnLabel.Show()
self.Size = (401, 401)
if self.button.parameterVal == 'Phe':
self.comboPhe.Clear()
self.comboPhe.AppendItems(self.Columns)
self.comboPhe.Value = self.Columns[2]
self.comboPhe.Show()
self.PheLabel.Show()
self.Size = (402, 402)
def GetPanel(self, message, arg2=None):
'''Gets panel to display graph.'''
print("HI")
self._panel = message
class ChildFrame(wx.Frame):
'''
This is the primary admix frame for generating a new admix graph.
This contains functionality to generate the interactable window and is linked to
functions to fetch and process the input data
'''
def __init__(self, parent, title):
super(ChildFrame, self).__init__(parent,
title='Admix',
size=(300, 325))
#pan = wx.Panel(self,wx.ID_ANY)
self.currentDirectory = os.getcwd()
self.InitUI()
self.Centre()
self._DH = DataHolder
self._FI = FileImporter()
pub.subscribe(self.GetPanel, "GetPanelAdmix")
def InitUI(self):
'''Initilises user interface.'''
panel = wx.Panel(self, wx.ID_ANY)
self.Columns = []
self.m_textCtrl1 = wx.TextCtrl(panel, wx.ID_ANY, wx.EmptyString,
wx.DefaultPosition, wx.DefaultSize, 0)
self.m_textCtrl1.Value = "Name"
self.combo = wx.ComboBox(panel, choices=self.Columns)
self.combo.Bind(wx.EVT_COMBOBOX, self.OnCombo)
ColumnLabel = wx.StaticText(panel, label="Phenotype Column")
hbox = wx.BoxSizer(wx.HORIZONTAL)
fgs = wx.FlexGridSizer(6, 2, 15,
15) #Wx.FlexiGridSizer(rows, cols, vgap, hgap)
fgsWhole = wx.FlexGridSizer(2, 1, 15, 15)
OpenFileBtn = wx.Button(panel, wx.ID_ANY, label='Import Data File')
OpenFileBtn.parameterVal = 'Data'
OpenFamBtn = wx.Button(panel, wx.ID_ANY, label='Import Fam File')
OpenFamBtn.parameterVal = 'Fam'
OpenPheBtn = wx.Button(panel, wx.ID_ANY, label='Import Phe File')
OpenPheBtn.parameterVal = 'Phe'
AcceptBtn = wx.Button(panel, wx.ID_ANY, label='Accept')
ExitBtn = wx.Button(panel, wx.ID_EXIT, label='Exit')
OpenFileBtn.Bind(wx.EVT_BUTTON, self.onOpenFile)
OpenFamBtn.Bind(wx.EVT_BUTTON, self.onOpenFile)
OpenPheBtn.Bind(wx.EVT_BUTTON, self.onOpenFile)
AcceptBtn.Bind(wx.EVT_BUTTON, self.onAcceptFile)
ExitBtn.Bind(wx.EVT_BUTTON, self.Quit)
self.tc1 = wx.TextCtrl(panel)
self.tc2 = wx.TextCtrl(panel)
self.tc3 = wx.TextCtrl(panel)
fgs.AddMany([(OpenFileBtn), (self.tc1, 1, wx.EXPAND), (OpenFamBtn),
(self.tc2, 1, wx.EXPAND), (OpenPheBtn, 1, wx.EXPAND),
(self.tc3, 1, wx.EXPAND), (ColumnLabel, 1, wx.EXPAND),
(self.combo, 1, wx.EXPAND), (AcceptBtn), (ExitBtn)])
fgsWhole.AddMany([(self.m_textCtrl1, 1, wx.EXPAND),
(fgs, 1, wx.EXPAND)])
#fgs.AddGrowableRow(1, 2)
fgsWhole.AddGrowableCol(0, 2)
#fgs.AddGrowableRow(2, 3)
fgs.AddGrowableCol(1, 0)
hbox.Add(fgsWhole, proportion=2, flag=wx.ALL | wx.EXPAND, border=15)
panel.SetSizer(hbox)
def Quit(self, event):
''' Exits frame.'''
pub.sendMessage('panelListener', message=self._FI)
self.Destroy()
def AppearFrame(self, event):
'''Opens appearence settings.'''
self.child = PCAAppearFrame(self, title='Appearance')
#self.child.ShowModal()
self.child.Show()
def OnCombo(self, event):
'''Gets values from combobox.'''
print(self.combo.GetValue())
# self.label.SetLabel("selected "+ self.combo.GetValue() +" from Combobox")
def onAcceptFile(self, event):
'''Accepts input data'''
#get coloumn no. by spliting name
name = self.m_textCtrl1.Value
col = self.combo.Value.split(' ')
#check for phen data and making sure that data has been inputted
if (self.tc1.Value != "" and self.tc2.Value != ""):
try:
if (self.tc3.Value != ""):
self._FI.CreateAdmix(self._FI, self.tc1.Value,
self.tc2.Value, self.tc3.Value, name,
int(col[1]), self._panel)
else:
self._FI.CreateAdmix(self._FI, self.tc1.Value,
self.tc2.Value, None, name, 3,
self._panel)
except IndexError:
print("Index Error")
else:
print("No Fam and Data File")
plt.show()
self.Destroy()
def onOpenFile(self, event):
'''Opens file dialog to get input data.'''
button = event.GetEventObject()
if button.parameterVal == 'Data':
wildcard = admixWildcard
if button.parameterVal == 'Fam':
wildcard = famWildcard
if button.parameterVal == 'Phe':
wildcard = pheWildcard
self.CountColumns()
dlg = wx.FileDialog(self,
message="Choose a file",
defaultDir=self.currentDirectory,
defaultFile="",
wildcard=wildcard,
style=wx.FD_OPEN | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
self.DataFilePath = dlg.GetPath()
print('You chose the following file:')
print(self.DataFilePath)
# windowClass.AdmixPath = DataFilePath
if button.parameterVal == 'Data':
if (VC.CheckAdmixValid(self.DataFilePath)):
self.tc1.SetValue(self.DataFilePath)
#self.CountColumns()
else:
dlg = wx.MessageDialog(None, "Invalid Admix File", "ERROR",
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
if button.parameterVal == 'Fam':
if (VC.CheckFamValid(self.DataFilePath)):
self.tc2.SetValue(self.DataFilePath)
# self.CountColumns()
else:
dlg = wx.MessageDialog(None, "Invalid Fam File", "ERROR",
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
if button.parameterVal == 'Phe':
if (VC.CheckPhenValid(self.DataFilePath)):
self.tc3.SetValue(self.DataFilePath)
self.CountColumns()
else:
dlg = wx.MessageDialog(None, "Invalid Phe File", "ERROR",
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
print(button.parameterVal)
dlg.Destroy()
def CountColumns(self):
'''Counts number of columns in input file.'''
with open(self.DataFilePath) as myFile:
reader = csv.reader(myFile, delimiter=' ', skipinitialspace=True)
first_row = next(reader)
num_cols = len(first_row)
print(num_cols)
for index in range(0, num_cols):
self.Columns.insert(index, 'Column ' + str(index + 1))
print(self.Columns)
self.combo.Clear()
self.combo.AppendItems(self.Columns)
self.combo.Value = self.Columns[2]
#self.Columns = ['none']
def GetPanel(self, message, arg2=None):
print("HI")
self._panel = message