# Path: module/plotter.py
# class Plotter(QtCore.QThread):
#     def __init__(self, parent=None):
#     def topologyDonut(self, title, labels, sizes, donut_colors, subplotPosition=111):
#     def topologyScatter(self, title, wins_to_tops, scatter_colors, y, subplotPosition=111):
#     def sorted_scatter(self, lWindows, sigArray, title, xlab, ylab, subplotPosition=111):
#     def stat_scatter(self, dataMap, title, xLabel, yLabel, subplotPosition=111):
#     def barPlot(self, title, data, xLabel='', yLabel='', groupLabels=(), heightLabels=False, subplotPosition=111):
#     def heatMap(self, title, mapping, subplotPosition=111):
#     def treeImage(self, newick, rooted=False, outgroup=False):
#     def topologyColorizer(self, title, newicksToColors, topologies_to_counts, rooted=False, outgroup=False):
#     def doubleLineGraph(self, list1, list2, confidenceThreshold, xLabel='', yLabel=''):
#     def nlineGraph(self, dataSet, title, xLabel='', yLabel='', subplotPosition=111, groupLabels1=()):
#     def lineGraph(self, data, title, xLabel='', yLabel='', subplotPosition=111):
#     def tmrca_graph(self, sites_to_newick_mappings, labels, topology_only=False, subplotPosition=111):
#     def generateCircleGraph(self, file, windows_to_top_topologies, topologies_to_colors, window_size, window_offset, sites_to_informative):
#     def run(self):


import sys
import matplotlib
from module import plotter
from matplotlib import pyplot as plt
from matplotlibCustomBackend.customToolbar import CustomToolbar
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.qt_compat import QtCore, QtGui

        QtCore.QMetaObject.connectSlotsByName(self)

        # get arguments
        self.windowTitle = windowTitle

        # moves menu bar into application -- mac only windows sux
        self.menubar.setNativeMenuBar(False)

        # set window title
        self.setWindowTitle(self.windowTitle)

        self.initCanvas()

        self.toolbar = CustomToolbar(self.canvas, self)
        self.verticalLayout.addWidget(self.toolbar)

        self.setWindowPosition(x, y)

        # bind file menu actions
        self.connect(self.actionSaveAs, QtCore.SIGNAL('triggered()'), self.toolbar.save_figure)

        # bind configure menu actions
        self.connect(self.actionConfigureSubplots, QtCore.SIGNAL('triggered()'), self.toolbar.configure_subplots)
        self.connect(self.actionConfigureAxis, QtCore.SIGNAL('triggered()'), self.toolbar.edit_parameters)

        if legend:
            self.generateLegendMenu()

        # create instance of Plotter class

# Path: module/plotter.py
# class Plotter(QtCore.QThread):
#     def __init__(self, parent=None):
#     def topologyDonut(self, title, labels, sizes, donut_colors, subplotPosition=111):
#     def topologyScatter(self, title, wins_to_tops, scatter_colors, y, subplotPosition=111):
#     def sorted_scatter(self, lWindows, sigArray, title, xlab, ylab, subplotPosition=111):
#     def stat_scatter(self, dataMap, title, xLabel, yLabel, subplotPosition=111):
#     def barPlot(self, title, data, xLabel='', yLabel='', groupLabels=(), heightLabels=False, subplotPosition=111):
#     def heatMap(self, title, mapping, subplotPosition=111):
#     def treeImage(self, newick, rooted=False, outgroup=False):
#     def topologyColorizer(self, title, newicksToColors, topologies_to_counts, rooted=False, outgroup=False):
#     def doubleLineGraph(self, list1, list2, confidenceThreshold, xLabel='', yLabel=''):
#     def nlineGraph(self, dataSet, title, xLabel='', yLabel='', subplotPosition=111, groupLabels1=()):
#     def lineGraph(self, data, title, xLabel='', yLabel='', subplotPosition=111):
#     def tmrca_graph(self, sites_to_newick_mappings, labels, topology_only=False, subplotPosition=111):
#     def generateCircleGraph(self, file, windows_to_top_topologies, topologies_to_colors, window_size, window_offset, sites_to_informative):
#     def run(self):


# Path: raxmlOutputWindows/standardWindow.py
import sys
import matplotlib
from module import plotter
from matplotlib import pyplot as plt
from matplotlibCustomBackend.customToolbar import CustomToolbar
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.qt_compat import QtCore, QtGui


        QtCore.QMetaObject.connectSlotsByName(self)

        # get arguments
        self.windowTitle = windowTitle

        # moves menu bar into application -- mac only windows sux
        self.menubar.setNativeMenuBar(False)

        # set window title
        self.setWindowTitle(self.windowTitle)

        self.initCanvas()

        self.toolbar = CustomToolbar(self.canvas, self)
        self.verticalLayout.addWidget(self.toolbar)

        self.setWindowPosition(x, y)

        # bind file menu actions
        self.connect(self.actionSaveAs, QtCore.SIGNAL('triggered()'), self.toolbar.save_figure)

        # bind configure menu actions
        self.connect(self.actionConfigureSubplots, QtCore.SIGNAL('triggered()'), self.toolbar.configure_subplots)
        self.connect(self.actionConfigureAxis, QtCore.SIGNAL('triggered()'), self.toolbar.edit_parameters)

        if legend:
            self.generateLegendMenu()

        # create instance of Plotter class

        self.plotter = plotter.Plotter()