def startDrag(self):
""" this method is called whenever a user start to drag one of the label """
#D( ALL, "dragging started..." )
v = self._view
lp = v.painter()
fm = lp.fontmetrics()
idx, _ = v.xy2coord( 0, self._startpos.y() )
self._dragidx = idx
label = self.model()[idx].label
lineheight = v.lineheight()
baseline = (lineheight + fm.ascent())/2
width = fm.width(label)
hotspot = QtCore.QPoint( width/2, lineheight/2 )
drag = QtGui.QDrag(v)
pixmap = QtGui.QPixmap(width, lineheight)
p = QtGui.QPainter(pixmap)
p.fillRect(pixmap.rect(), QtGui.QColor(191, 191, 127))
p.setPen( QtCore.Qt.white )
p.setFont( lp.font() )
p.drawText(0, baseline, label)
p.end()
# fill in the data
seq = self.model()[idx]
mimedata = QtCore.QMimeData()
text_data = ">%s\n%s\n" % (seq.label, seq.seq)
mimedata.setText( text_data )
mimedata.setData("application/x-fasta", text_data.encode('UTF-8'))
drag.setMimeData(mimedata)
drag.setPixmap(pixmap)
drag.setHotSpot(hotspot)
drag.exec_(QtCore.Qt.CopyAction)
def start_app(arg):
global app
cout("Starting GUI\n")
if not app:
app = QtGui.QApplication.instance()
if not app:
if type(arg) == list:
app = QtGui.QApplication(arg)
else:
app = QtGui.QApplication(['__builtin__'])
w = IMainWindow()
if type(arg) == list and len(arg) >= 2:
w.load(arg[1])
elif type(arg) == str:
w.load(arg)
else:
cout('viewing...')
w.view(arg)
#w.setFocus()
w.show()
app.exec_()
try:
w.hide()
del w
except RuntimeError:
pass
def __init__(self,
typeface='Monospace',
fontsize=6,
charwidth=8,
lineheight=12):
self.typeface = typeface
self.fontsize = fontsize
self.charwidth = charwidth
self.lineheight = lineheight
self.font = QtGui.QFont(typeface, fontsize)
self.fontmetrics = QtGui.QFontMetrics(self.font)
def decrease_font(self):
self.set_lineheight( self.lineheight() - 3 )
self.set_charwidth( self.charwidth() - 2 )
self.fonts = {
'sequence': ('Monospace', self.fonts['sequence'][1] - 2 ),
'label': QtGui.QFont('Monospace', self.fonts['label'].pointSize() - 2 )
}
def __init__(self, label_pane, label_font, offset_x=0):
self._label_pane = label_pane
self._font = label_font
self._fontmetrics = QtGui.QFontMetrics(label_font)
self._offset_x = offset_x or self._fontmetrics.width('0000: ')
self._margin = 5
def paintEvent(self, ev):
# get the rectanguler area of visible view
r = ev.rect()
x, y, w, h = r.x(), r.y(), r.width(), r.height()
y_end = y + h
# prepare painter & other variables
p = QtGui.QPainter(self)
model = self.model()
lineheight = self.lineheight()
lp = self.painter()
# prepare font and painter state
p.setFont(lp.font())
baseline = (lineheight + lp.fontmetrics().ascent()) / 2
# check the visible sequences
start_idx, _ = self.xy2coord(0, y)
stop_idx, _ = self.xy2coord(0, y_end)
# iterate to paint the label
selection = self.selection() if isinstance(self.selection(),
LabelSelection) else None
for i in range(max(0, start_idx - 1), min(stop_idx + 1, len(model))):
p.save()
p.translate(0, i * lineheight)
if selection and i in selection:
lp.draw_label(p, i, baseline, model[i].label, selected=True)
else:
lp.draw_label(p, i, baseline, model[i].label)
p.restore()
def init_toolbar(self):
self._xscale_slider = PopupSlider( orientation = QtCore.Qt.Horizontal )
xslider = self._xscale_slider.slider()
xslider.setRange(2, 42)
xslider.setSingleStep(1)
xslider.valueChanged.connect( self.set_xscale )
xslider.setValue(10)
self.add_popup( '\u2194', self._xscale_slider )
self._yscale_slider = PopupSlider( orientation = QtCore.Qt.Vertical )
yslider = self._yscale_slider.slider()
yslider.setRange(1, 21)
yslider.setSingleStep(1)
yslider.valueChanged.connect( self.set_yscale )
yslider.setValue(10)
self.add_popup( '\u2195', self._yscale_slider )
self._searchbox = QtGui.QLineEdit('Search')
self._searchbox.setMaxLength(32)
self._searchbox.returnPressed.connect( self.do_search )
self._toolbar.addWidget( self._searchbox )
self._prevsearch = self._toolbar.addAction( '\u226a', self.do_prevsearch)
self._prevsearch.setEnabled(False)
self._nextsearch = self._toolbar.addAction( '\u226b', self.do_nextsearch)
self._nextsearch.setEnabled(False)
self._panesplit = QtGui.QSpinBox()
self._panesplit.setRange(1, 8)
self._panesplit.setSingleStep(1)
self._panesplit.valueChanged.connect( self.set_split )
self._panesplit.setValue( 4 )
self._toolbar.addWidget( self._panesplit )
self._peaks = {}
for i in range(len(trace_set)):
tb = QtGui.QToolButton()
tb.setText(trace_set[i])
tb.setDown(True)
self._toolbar.addWidget( tb )
self._peaks[i] = tb
tb.clicked.connect( lambda x, button_no = i: self.tracebutton_changed( x, button_no ) )
def paintEvent(self, ev):
r = ev.rect()
x, y, w, h = r.x(), r.y(), r.width(), r.height()
evrect = (x, y, w, h)
p = QtGui.QPainter(self)
# drawing sequence
self.draw_region(evrect, p, self.caret())
# drawing auxiliary region (such as selection, markers, etc)
self.draw_region_aux(r, p)
def test_tracepane():
import sys
import ienv
app = QtGui.QApplication( sys.argv )
tracedata = trace.open_trace( sys.argv[1] ).tracedata()
pane = TracePane( tracedata, TraceView )
pane.set_env( ienv.IEnv() )
pane.init_layout()
pane.set_split(4)
pane.show()
app.exec_()
def test_labelpane():
import sys
import msa
import ienv
app = QtGui.QApplication(sys.argv)
msa = msa.MSA()
msa.open(sys.argv[1])
msa.set_type()
pane = LabelPane(msa, LabelView)
pane.set_env(ienv.IEnv())
pane.init_layout()
pane.show()
app.exec_()
def test_sequencepane():
import sys
import msa
import ienv
app = QtGui.QApplication(sys.argv)
msa = msa.MSA()
msa.open(sys.argv[1])
msa.set_type()
pane = SequencePane(msa, SequenceView)
pane.set_env(ienv.IEnv())
pane.init_layout(header=RulerView(pane))
pane.show()
app.exec_()
def create_action(self, text, slot=None, shortcut=None, icon=None,
tip=None, checkable=False):
action = QtWidgets.QAction(text, self.pane())
if icon is not None:
action.setIcon( QtGui.QIcon(":/images%s.png" % icon) )
if shortcut is not None:
action.setShortcut( shortcut )
if tip is not None:
action.setToolTip( tip )
action.setStatusTip( tip )
if slot is not None:
action.triggered.connect( slot )
if checkable:
action.setCheckable( True )
return action
def __init__(self):
# for A, C, G, T, N
self.base_colors = [ QtGui.QColor(x) for x in ('forestgreen', 'blue', ' black',
'red', 'grey') ]
self.trace_pens = [ QtGui.QPen(x, 1) for x in self.base_colors ]
self.quality_pens = [ QtGui.QPen(
QtGui.QColor(*x), 5, QtCore.Qt.SolidLine, QtCore.Qt.FlatCap )
for x in ( (255,20,255), (255,25,25), (20,155,20) ) ]
self.ruler_pen = QtGui.QPen( QtGui.QColor('black'))
self.ruler_font = QtGui.QFont('Monospace', 8)
self.ruler_fontmetrics = QtGui.QFontMetrics( self.ruler_font )
self.ruler_fontmetrics_halfwidth = self.ruler_fontmetrics.width('A')/2
self._show = [ True, True, True, True ]
def paintEvent(self, ev):
# print '<RulerView>.paintEvent'
r = ev.rect()
x, w = r.x(), r.width()
height = self.height()
# print x,w,height
model = self.model()
p = QtGui.QPainter(self)
cw = self.pane().charwidth()
start = x // cw
end = start + w // cw
midl = cw // 2
p.setFont(self._font)
p.translate(0, height - 4)
# print "ruler from %d -> %d" % (start, end)
# print ticks
for i in range(start - 10, end + 10):
pos = i + self.pane().ruler_startpos()
line_x = i * cw + midl
if self.pane().ruler_atgframe() > 0:
if pos % 3 == self.pane().ruler_atgframe():
p.setPen(QtCore.Qt.red)
else:
p.setPen(QtCore.Qt.black)
if pos % 5 == 0:
if pos % 10 == 0:
text = str(pos)
tw = self._fontmetrics.width(text)
p.setPen(QtCore.Qt.black)
p.drawText(line_x - tw - 2, -self.smalltick - 3, text)
p.drawLine(line_x, 0, line_x, -13)
else:
p.drawLine(line_x, 0, line_x, -self.bigtick)
else:
p.drawLine(line_x, 0, line_x, -self.smalltick)
def _create_image(self, c, color):
p = QtGui.QPixmap(self.charwidth(), self.lineheight())
painter = QtGui.QPainter(p)
#painter.translate(0, self.font_height - 2)
if self.shaded:
fg_color = QtGui.QColor(*color[1])
bg_color = QtGui.QColor(*color[0])
else:
fg_color = QtGui.QColor(*color[0])
bg_color = QtGui.QColor(255, 255, 255)
bg_brush = QtGui.QBrush(bg_color)
painter.setBackground(bg_brush)
painter.setBrush(bg_brush)
painter.setPen(bg_color)
painter.drawRect(0, 0, self.charwidth(), self.lineheight())
painter.setPen(fg_color)
painter.setFont(self.seqfont.font)
painter.drawText(
1, (self.lineheight() + self.seqfont.fontmetrics.ascent()) / 2,
chr(c))
painter.end()
return p
def paintEvent(self, ev):
r = ev.rect()
x,y,w,h = r.x(), r.y(), r.width(), r.height()
D(INFO, "(%s) -> [%d,%d,%d,%d]" % ( self, x,y,w,h ) )
p = QtGui.QPainter(self)
# below makes the trace pretty, but consume more time to display
p.setRenderHint( QtGui.QPainter.Antialiasing )
p.setRenderHint( QtGui.QPainter.TextAntialiasing )
caret_box = self.caret().box()
if caret_box:
intersection = r.intersected( caret_box )
p.fillRect( intersection, self.env().brushes['trace-selection'] )
selection = self.selection()
if selection:
intersection = r.intersected( selection.box(self) )
p.fillRect( intersection, self.env().brushes['trace-selection'] )
height = self._scrollarea.height()
self.painter().draw_region( self.model(), x, w, height, p )
def paintEvent(self, ev):
r = ev.rect()
x, w = r.x(), r.width()
height = self.height()
model = self.model()
p = QtGui.QPainter()
start = max(0, x // cw - 1)
end = min(len(model[0]), start + w // cw + 1)
midl = cw // 2
p.setFont(self._font)
p.translate(0, height - 4)
p.rotate(90)
th = self._fontmetrics.height('0')
for i in range(start, end):
line_y = i * cw + midl
text = str(i)
p.setPen(QtCore.Qt.black)
p.drawText(0, line_y - th - 2, text)
def __init__(self):
super(IEnv, self).__init__()
self._lineheight = LINEHEIGHT # global lineheight
self._charwidth = CHARWIDTH # global charwidth
self._nascheme = EasyNA() # default NA scheme
self._aascheme = AESSN3() # default AA scheme
self._header = True
self._footer = False
self._split = 1
self._panesplit = 1
self._activeview = None
self._tracesplit = 4
# basic preference
self.fonts = {
'sequence': ('Monospace', 7 ),
'label': QtGui.QFont('Monospace', 8 )
}
# colors
self.colors = {
'general-background': QtGui.QColor( 244, 244, 232 ),
'sequence-selection': QtGui.QColor( 191, 191, 191, 64 ),
'trace-selection': QtGui.QColor( 'lightblue' ),
}
# brush
self.brushes = {
'sequence-selection': QtGui.QBrush( self.colors['sequence-selection'] ),
'trace-selection': QtGui.QBrush( self.colors['trace-selection'] ),
}
# pens
self.pens = {
'sequence-selection': QtGui.QPen( self.brushes['sequence-selection'], 0 )
}
def width_hint(self):
""" return the width of vertical scroll bar """
if self.__width_hint < 0:
self.__width_hint = QtGui.QScrollBar(
QtCore.Qt.Vertical).sizeHint().width()
return self.__width_hint
def __init__(self, pane, parent=None):
super().__init__(pane, parent)
self._font = QtGui.QFont('Monospace', 4)
self._fontmetrics = QtGui.QFontMetrics(self._font)
def prepare_statusbar(self, ):
self._statusbar = QtGui.QStatusBar()
self.init_statusbar()
def xxx_ContextMenuEvent(self, ev):
menu = QtGui.QMenu()
self.pane().custom_actions().populate_contextmenu(menu)
menu.exec_(ev.globalPos())
def __init__(self, pane, parent=None):
super(RulerView, self).__init__(pane, parent)
self.setFocusPolicy(QtCore.Qt.StrongFocus)
self._font = QtGui.QFont('Monospace', 7)
self._fontmetrics = QtGui.QFontMetrics(self._font)
def prepare_toolbar(self, title):
if title:
self._toolbar = QtGui.QToolBar( title )
else:
self._toolbar = QtGui.QToolBar()
self.init_toolbar()
def draw_single_trace(self, minTp, maxTp, data, pen, p, scaleX, scaleY):
p.setPen( pen )
points = [ QtCore.QPoint( x * scaleX, data[x] * scaleY)
for x in range(max(0, minTp - 5), min(maxTp+5, len(data))) ]
p.drawPolyline( QtGui.QPolygon(points) )
def prepare_menu(self):
self._menubar = QtGui.QMenuBar()
self.init_menu()