def add_text_to_canvas(x,
y,
text,
anchor=None,
font_color="black",
font_size=6,
html_font_size=10):
_text = str(text)
text_item = self.canvas_plot_scene.addText(_text)
w = text_item.boundingRect().width()
h = text_item.boundingRect().height()
text_item.setPos(int(x - w / 2.5), int(y - h / 2.5))
text_item.setFont(QtGui.QFont(text_item.font().family(),
font_size))
def __init__(self,
data,
parent,
sortable=False,
column_labels=None,
row_labels=None,
row_labels_height=25,
*args):
self.data = data
self.column_labels = column_labels
self.row_labels = row_labels
self.row_labels_height = row_labels_height
# Get a set with the length of each column.
rows_number = len(self.data)
columns_number = len(self.data[0])
QtWidgets.QTableWidget.__init__(self,
parent=parent,
columnCount=columns_number,
rowCount=rows_number,
sortingEnabled=sortable,
*args)
self.set_data()
self.resizeColumnsToContents()
# self.resizeRowsToContents()
self.setStyleSheet(
"QTableView::item {border: 0px; padding: 0px; margin: 0px;}")
# self.itemDoubleClicked.connect(self.on_click)
default_font = QtGui.QFont()
default_font.setPointSize(default_font.pointSize() - 1)
self.setFont(default_font)
def build_plotting_area(self,
use_controls=True,
use_all_controls_buttons=True,
messagebar_initial_text=None,
update_messagebar=False,
messagebar_text_on_update="",
messagebar_vars_on_update=(),
on_click_action=None,
x_label_text="x",
y_label_text="y",
label_size=None,
use_save_to_csv=True,
hide_x_ticks=False,
hide_y_ticks=False,
# hide_x_label=False,
# hide_y_label=False,
highlight_points=True,
):
"""
Configures the plotting area of the window.
# Arguments
use_controls: adds to the plotting window a right column with checkbuttons
to show/hide the lines plots in the drawing area.
use_all_controls_buttons: adds to the plotting control column 'Show All'
and 'Hide All' buttons.
messagebar_initial_text: initial text to be displayed in the messagebar
of the plotting window.
update_messagebar: if 'True', the messagebar will be updated when clicking
some point of the scatterplots.
messagebar_text_on_update: text to be shown when the messagebar is update.
If it contains the "__plot_name__", "__x__", "__y__" string, they
will be substituted with the name of the plot, the x value and y value
of the point respectively. If some 'additional_data' is provided
for a plot, its data will also be used to update the messagebar.
Each element of an 'additional_data' list has to correspond to a
data point of a plot and must be a dictionary in which the keys are
strings representing the names of the additional data series. If,
for example, these dictionaries have a key named 'info' and if the
'messagebar_text_on_update' contains the string "__info__", it will
be substituted with the value associated to the 'info' key of that
'additional_data' point.
on_click_action: function to be called when a point of a scatterplot
is clicked. This function must have the following argument:
point_data: a dictionary with additional data for the point
or a 'None' value.
x_label_text: text for the x-axis label.
y_label_text: text for the y-axis label.
label_size: font size for the axis labels.
use_save_to_csv: if 'True' add to the plotting window menu a command
to save data in the csv format.
hide_x_ticks: if 'True', hide the ticks and numbers of the x-axis.
hide_y_ticks: if 'True', hide the ticks and numbers of the y-axis.
highlight_points: if 'True', the scatterplot points will be highlighted
when they are clicked with the mouse.
"""
# Stores the arguments.
self.use_controls = use_controls
if self.use_controls:
self.upper_frame_layout.addWidget(self.info_frame, 0, 0)
self.middle_splitter.addWidget(self.plot_frame)
self.middle_splitter.addWidget(self.controls_scrollarea)
self.upper_frame_layout.addWidget(self.middle_splitter, 1, 0)
self.controls_scrollarea.resize(230, self.controls_scrollarea.sizeHint().height())
self.controls_frame_layout.addWidget(self.labels_title, 0, 0, 1, 2)
self.lower_frame_layout.addWidget(self.on_click_label, 0, 2)
self.lower_frame_layout.addWidget(self.interact_button, 0, 3)
self.lower_frame_layout.addWidget(self.no_interaction_button, 0, 4)
else:
self.upper_frame_layout.addWidget(self.plot_frame, 0, 0)
self.use_all_controls_buttons = use_all_controls_buttons
if self.use_controls and self.use_all_controls_buttons:
self.lower_frame_layout.addWidget(self.show_label, 0, 5)
self.lower_frame_layout.addWidget(self.show_all_button, 0, 6)
self.lower_frame_layout.addWidget(self.hide_all_button, 0, 7)
self.messagebar_initial_text = messagebar_initial_text
if self.messagebar_initial_text is not None:
self.info_label.setText(self.messagebar_initial_text)
self.update_messagebar = update_messagebar
self.on_click_action = on_click_action
if self.on_click_action is not None:
if not hasattr(self.on_click_action, "__call__"):
raise TypeError("'on_click_action' must be a function.")
self.messagebar_text_on_update = messagebar_text_on_update
self.messagebar_vars_on_update = messagebar_vars_on_update
self.use_save_to_csv = use_save_to_csv
if self.use_save_to_csv:
self.file_menu.addAction(self.save_to_csv_action)
self.file_menu.addAction(self.save_to_png_action)
self.highlight_points = highlight_points
# Configure the PlotWidget.
self.graphWidget.setMenuEnabled(False)
if label_size is not None:
kwargs = {"font-size": "%spx" % label_size}
font = QtGui.QFont()
font.setPixelSize(label_size)
# curve_pen = pyqtgraph.mkPen(width=2, color="r") # Color and width of the curve.
else:
kwargs = {}
self.graphWidget.setLabel("left", y_label_text, **kwargs)
self.graphWidget.setLabel("bottom", x_label_text, **kwargs)
if label_size is not None:
self.graphWidget.getAxis("left").tickFont = font
self.graphWidget.getAxis("bottom").tickFont = font
# self.graphWidget.getAxis("left").setPen(curve_pen)
if hide_x_ticks:
self.graphWidget.getAxis("bottom").setStyle(showValues=False, tickLength=0)
if hide_y_ticks:
self.graphWidget.getAxis("left").setStyle(showValues=False, tickLength=0)
if self.on_click_action is not None:
self.graphWidget.getViewBox().scene().sigMouseClicked.connect(self.on_scene_click)
'''
Simple Text Editor
'''
import os
import sys
import importlib
try:
from pymol.Qt import QtCore, QtWidgets, QtGui
from pymol.Qt.utils import connectFontContextMenu, getMonospaceFont
except ImportError:
from PyQt5 import QtCore, QtWidgets, QtGui
connectFontContextMenu = lambda *a: None
getMonospaceFont = lambda: QtGui.QFont()
class TextEditor(QtWidgets.QMainWindow):
def sizeHint(self):
return QtCore.QSize(600, 400)
def _write(self, handle):
content = self._get()
handle.write(content)
self._savedcontent = content
def _open(self, filename):
self.filename = filename or ''
if filename and os.path.exists(filename):
with open(filename, 'r') as handle:
content = handle.read()
def set_input_widget_width(self, width):
pass
def set_auto_input_widget_width(self, width):
pass
def get_width_hint(self):
return self.slider.sizeHint().width() + self.slider_label.sizeHint(
).width()
###############################################################################
# CSS Styles used in PyMod. #
###############################################################################
default_pt_size = QtGui.QFont().pointSize()
active_entry_style = "background-color: white; color: #333333"
inactive_entry_style = "background-color: #ccc; color: #7c7c7c"
inactive_bg_color = "#e3e3e3"
success_bg_color = "#98fb98"
failure_bg_color = "#f08080"
highlight_color = "#5ac8ff"
options_title_style = "font-size: %spt; color: %s" % (default_pt_size + 1,
highlight_color)
small_font_style = "font-size: %spt" % (default_pt_size - 1)
large_font_style = "font-size: %spt" % (default_pt_size + 1)
def __init__(self, parent, protocol):
super(Hmmscan_results_window_qt, self).__init__(parent)
self.protocol = protocol
self.query_len = len(
self.protocol.query_element.my_sequence.replace('-', ''))
#########################
# Configure the window. #
#########################
self.setWindowTitle("HMMSCAN Results")
# Sets the central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
# The window has a main vbox layout.
self.main_vbox = QtWidgets.QVBoxLayout()
# Parameters used to draw the 'QGraphicsView' widgets for showing domains.
self.preferred_size_policy = QtWidgets.QSizePolicy(
QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
self.view_bg_color = "transparent"
self.full_seq_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 0), 2)
self.full_seq_color = "#7f7f7f"
qcolor = QtGui.QColor(0, 0, 0)
qcolor.setNamedColor(self.full_seq_color)
self.full_seq_brush = QtGui.QBrush(qcolor)
self.font_qcolor = QtGui.QColor(220, 220, 220, 255)
self.font_size = 7
################
# Upper frame. #
################
self.upper_frame = QtWidgets.QFrame()
self.upper_frame_layout = QtWidgets.QGridLayout()
self.upper_frame.setLayout(self.upper_frame_layout)
self.main_vbox.addWidget(self.upper_frame)
if 'query_descr' in self.protocol.parsed_res[
0] and self.protocol.parsed_res[0]['query_descr']:
labelseq = self.protocol.query_element.my_header # + '\n' + querydescr
else:
try:
if len(self.protocol.query_element.description) > 79:
labelseq = self.protocol.query_element.description[:78] + '...'
else:
labelseq = self.protocol.query_element.description
except TypeError:
labelseq = self.protocol.query_element.my_header
self.upper_frame_title = QtWidgets.QLabel(
"HMMSCAN search results for " + labelseq)
self.upper_frame_layout.addWidget(self.upper_frame_title)
#-------------------------
# Domain graphics frame. -
#-------------------------
# Builds the scene where to draw the domain representations.
self.canvas_plot_scene = QtWidgets.QGraphicsScene()
self.canvas_plot_view = QtWidgets.QGraphicsView(self.canvas_plot_scene)
self.canvas_plot_view.setFixedHeight(120)
self.canvas_plot_view.setSizePolicy(self.preferred_size_policy)
self.canvas_plot_view.setStyleSheet("background: %s" %
self.view_bg_color)
self.upper_frame_layout.addWidget(self.canvas_plot_view)
# Draw a rectangle with the full sequence.
self.x_init = 10
y_init = 95 # 95
self.domain_y_init = y_init - 7
self.full_seq_rect_w = 800
full_seq_rect_h = 10
self.canvas_plot_scene.addRect(self.x_init, y_init,
self.full_seq_rect_w, full_seq_rect_h,
self.full_seq_pen, self.full_seq_brush)
# Draw the labels for the N- and C-terminal residues.
text_offset_y = 15
text_offset_x = 10
text_n = self.canvas_plot_scene.addText("1")
text_n.setPos(self.x_init - text_offset_x, y_init + text_offset_y)
text_n.setDefaultTextColor(self.font_qcolor)
text_n.setFont(QtGui.QFont(text_n.font().family(), self.font_size))
c_label = str(self.query_len)
text_c = self.canvas_plot_scene.addText(c_label)
text_offset_x_add = 5
if len(c_label) > 2:
text_offset_x_add = 10
text_c.setPos(
self.x_init + self.full_seq_rect_w - text_offset_x -
text_offset_x_add, y_init + text_offset_y)
text_c.setDefaultTextColor(self.font_qcolor)
text_c.setFont(QtGui.QFont(text_c.font().family(), self.font_size))
#################
# Middle frame. #
#################
# Scroll area which contains the widgets, set as the centralWidget.
self.middle_scroll = QtWidgets.QScrollArea()
self.main_vbox.addWidget(self.middle_scroll)
# Widget that contains the collection of Vertical Box.
self.middle_widget = QtWidgets.QWidget()
# Scroll area properties.
self.middle_scroll.setWidgetResizable(True)
self.middle_scroll.setWidget(self.middle_widget)
# QFormLayout in the middle frame.
self.middle_formlayout = QtWidgets.QFormLayout()
self.middle_widget.setLayout(self.middle_formlayout)
#-----------------
# Results frame. -
#-----------------
# Set the frame and its layout.
self.results_frame = QtWidgets.QFrame()
self.middle_formlayout.addRow(self.results_frame)
self.results_grid = QtWidgets.QGridLayout()
self.results_frame.setLayout(self.results_grid)
# Calls a method which actually displays the similarity searches results.
self.display_hmmscan_hits()
# Align the gridded widgets to the left.
self.results_grid.setAlignment(QtCore.Qt.AlignLeft)
self.results_grid.setHorizontalSpacing(30)
#################
# Bottom frame. #
#################
self.main_button = QtWidgets.QPushButton("Submit")
self.main_button.clicked.connect(
lambda a=None: self.protocol.hmmer_results_state())
self.main_vbox.addWidget(self.main_button)
self.main_button.setFixedWidth(self.main_button.sizeHint().width())
# Sets the main vertical layout.
self.central_widget.setLayout(self.main_vbox)
self.main_vbox.setAlignment(self.main_button, QtCore.Qt.AlignCenter)
def setupUi(self, UpdateDialog):
UpdateDialog.setObjectName("UpdateDialog")
UpdateDialog.resize(950, 470)
self.verticalLayout = QtWidgets.QVBoxLayout(UpdateDialog)
self.verticalLayout.setObjectName("verticalLayout")
self.select_comp_label = QtWidgets.QLabel(UpdateDialog)
self.select_comp_label.setObjectName("select_comp_label")
self.verticalLayout.addWidget(self.select_comp_label)
self.components_tableWidget = QtWidgets.QTableWidget(UpdateDialog)
default_font = QtGui.QFont()
default_font.setPointSize(default_font.pointSize()-1)
self.components_tableWidget.setFont(default_font)
self.components_tableWidget.setProperty("showDropIndicator", False)
self.components_tableWidget.setDragDropOverwriteMode(False)
self.components_tableWidget.setAlternatingRowColors(True)
self.components_tableWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.components_tableWidget.setGridStyle(QtCore.Qt.NoPen)
self.components_tableWidget.setColumnCount(self.n_cols)
self.components_tableWidget.setObjectName("components_tableWidget")
self.components_tableWidget.setRowCount(1)
vertical_header_item = QtWidgets.QTableWidgetItem()
self.components_tableWidget.setVerticalHeaderItem(0, vertical_header_item)
for i in range(self.n_cols):
item = QtWidgets.QTableWidgetItem()
self.components_tableWidget.setHorizontalHeaderItem(i, item)
item = QtWidgets.QTableWidgetItem()
self.components_tableWidget.setItem(0, self.component_col_idx, item)
item = QtWidgets.QTableWidgetItem()
self.components_tableWidget.setItem(0, self.databases_col_idx, item)
self.components_tableWidget.horizontalHeader().setVisible(True)
self.components_tableWidget.horizontalHeader().setCascadingSectionResizes(False)
self.components_tableWidget.setColumnWidth(self.component_col_idx, 210)
self.components_tableWidget.setColumnWidth(self.databases_col_idx, 180)
self.components_tableWidget.setColumnWidth(self.status_col_idx, 190)
# self.components_tableWidget.setColumnWidth(self.source_col_idx, 390)
# self.components_tableWidget.setColumnWidth(self.last_download_col_idx, 250)
self.components_tableWidget.horizontalHeader().setStretchLastSection(True)
self.components_tableWidget.verticalHeader().setVisible(False)
self.components_tableWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.verticalLayout.addWidget(self.components_tableWidget)
self.statusLabel = QtWidgets.QLabel(UpdateDialog)
self.statusLabel.setObjectName("statusLabel")
self.verticalLayout.addWidget(self.statusLabel)
self.installation_progressBar = QtWidgets.QProgressBar(UpdateDialog)
self.installation_progressBar.setEnabled(True)
self.installation_progressBar.setProperty("value", 10)
self.installation_progressBar.setObjectName("installation_progressBar")
self.verticalLayout.addWidget(self.installation_progressBar)
self.buttonsHorizontalLayout = QtWidgets.QHBoxLayout()
self.buttonsHorizontalLayout.setObjectName("buttonsHorizontalLayout")
self.installSel_button = QtWidgets.QPushButton(UpdateDialog)
self.installSel_button.setObjectName("installSel_button")
self.buttonsHorizontalLayout.addWidget(self.installSel_button)
spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.buttonsHorizontalLayout.addItem(spacerItem)
self.cancel_button = QtWidgets.QPushButton(UpdateDialog)
self.cancel_button.setObjectName("cancel_button")
self.buttonsHorizontalLayout.addWidget(self.cancel_button)
self.verticalLayout.addLayout(self.buttonsHorizontalLayout)
UpdateDialog.setWindowTitle("Install and update databases")
self.select_comp_label.setText("Select components to install or update")
self.components_tableWidget.setSortingEnabled(True)
self.components_tableWidget.horizontalHeaderItem(self.component_col_idx).setText("Component")
self.components_tableWidget.horizontalHeaderItem(self.databases_col_idx).setText("Databases Names")
self.components_tableWidget.horizontalHeaderItem(self.status_col_idx).setText("Status")
self.components_tableWidget.horizontalHeaderItem(self.source_col_idx).setText("Source")
self.components_tableWidget.horizontalHeaderItem(self.last_download_col_idx).setText("Last Downloaded")
__sortingEnabled = self.components_tableWidget.isSortingEnabled()
self.components_tableWidget.setSortingEnabled(False)
self.components_tableWidget.setSortingEnabled(__sortingEnabled)
self.statusLabel.setText("")
self.cancel_button.setText("Cancel")
self.installSel_button.setText("Install Selected")
QtCore.QMetaObject.connectSlotsByName(UpdateDialog)
def update_qt_font(self):
"""
Updates the font of the PyMod Qt main window.
"""
self.qfont = QtGui.QFont(self.font, self.font_size)
self.fm = QtGui.QFontMetrics(self.qfont)
