def __init__(self, dProject, parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(
self.tr("<center><b>MANUAL SIGNAL ALGINMENT</b></center>"))
self.name = "Manual Signal Alignment"
self.toolID = 1
self.dProject = dProject
self.dProjOut = deepcopy(dProject)
self.linkXR, self.linkXS = np.array([]), np.array([])
self.dataR, self.dataS = np.array([]), np.array([])
self.isToolApplied = False
label0 = QtGui.QLabel('Reference Channel')
self.comboBox0 = QtGui.QComboBox()
self.comboBox0.addItems(dProject['chKeyRS'])
label1 = QtGui.QLabel('Sample Channel')
self.comboBox1 = QtGui.QComboBox()
self.comboBox1.addItems(dProject['chKeyRS'])
self.comboBox1.setCurrentIndex(1)
layout0 = myGridLayout()
layout0.addWidget(label0, 0, 0)
layout0.addWidget(self.comboBox0, 0, 1)
layout0.addWidget(label1, 1, 0)
layout0.addWidget(self.comboBox1, 1, 1)
self.groupBox0 = QtGui.QGroupBox("Select Channels")
self.groupBox0.setLayout(layout0)
self.groupBox0.setCheckable(True)
self.button0 = QtGui.QPushButton('Modify Matched Peaks')
self.button0.setEnabled(False)
self.buttonBox = ToolButton()
self.applyChannel = ApplyChannel(self.dProject)
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.groupBox0)
mainLayout.addWidget(self.button0)
mainLayout.addStretch()
mainLayout.addWidget(self.applyChannel.groupBox)
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.refKey = 'RXS1'
self.sampleKey = 'BGS1'
def __init__(self, dProject, parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(
self.tr("<center><b>CHANNEL SWAP</b></center>"))
self.name = "Swap"
self.toolID = 1
self.dProject = dProject
self.dProjOut = dProject.copy()
self.label0 = {}
self.comboBox0 = {}
for key in self.dProject['chKeyRS']:
self.label0[key] = QtGui.QLabel(key)
self.comboBox0[key] = QtGui.QComboBox()
self.comboBox0[key].addItems(self.dProject['chKeyRS'])
self.comboBox0[key].setCurrentIndex(
self.dProject['chKeyRS'].index(key))
vbox = myGridLayout()
vbox.addWidget(self.label0['RX'], 0, 0)
vbox.addWidget(self.comboBox0['RX'], 0, 1)
vbox.addWidget(self.label0['BG'], 1, 0)
vbox.addWidget(self.comboBox0['BG'], 1, 1)
vbox.addWidget(self.label0['RXS1'], 2, 0)
vbox.addWidget(self.comboBox0['RXS1'], 2, 1)
vbox.addWidget(self.label0['BGS1'], 3, 0)
vbox.addWidget(self.comboBox0['BGS1'], 3, 1)
if self.dProject['isSeq2']:
vbox.addWidget(self.label0['RXS2'], 4, 0)
vbox.addWidget(self.comboBox0['RXS2'], 4, 1)
vbox.addWidget(self.label0['BGS2'], 5, 0)
vbox.addWidget(self.comboBox0['BGS2'], 5, 1)
self.groupBox0 = QtGui.QGroupBox()
self.groupBox0.setLayout(vbox)
### Button Box
self.buttonBox = ToolButton()
## Main Layout
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.groupBox0)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isToolApplied = False
def __init__(self, dVar, chKeyRS, parent=None):
super(DlgLineProps, self).__init__(parent)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setModal(False)
self.labelTitle = QtGui.QLabel(
self.tr("<center><b>CHANNEL ATTRIBUTES</b></center>"))
self.name = "Channel Attributes"
self.toolID = 3
self.dVar = dVar.copy()
self.chKeyRS = chKeyRS
labels = ["Channel", "Color", "Line", "Marker", "Width"]
self.label = {}
self.checkBox0 = {}
self.pushButton0 = {}
self.comboBoxLineStyle = {}
lineStyles = ["solid", "dashed", "dash_dot", "dotted"]
self.lineStyles = ['-', '--', '-.', ':']
self.comboBoxMarkerStyle = {}
markerStyles = [
"none", "point", "circle", "star", "square", "plus", "X", "diamond"
]
self.markerStyles1 = ['', '.', 'o', '*', 's', '+', 'x', 'D']
self.doubleSpinBoxLW = {}
for key in chKeyRS:
self.checkBox0[key] = QtGui.QCheckBox(key)
self.checkBox0[key].setChecked(self.dVar['lineVisible'][key])
self.pushButton0[key] = QtGui.QPushButton()
self.pushButton0[key].setStyleSheet(
"QWidget { background-color: %s }" %
self.dVar['lineColor'][key])
self.comboBoxLineStyle[key] = QtGui.QComboBox()
self.comboBoxLineStyle[key].addItems(lineStyles)
self.comboBoxMarkerStyle[key] = QtGui.QComboBox()
self.comboBoxMarkerStyle[key].addItems(markerStyles)
self.doubleSpinBoxLW[key] = QtGui.QDoubleSpinBox()
self.doubleSpinBoxLW[key].setValue(1.0)
self.doubleSpinBoxLW[key].setSingleStep(0.1)
layout0 = myGridLayout()
for i in range(len(labels)):
self.label[i] = QtGui.QLabel(labels[i])
layout0.addWidget(self.label[i], 0, i)
for key in chKeyRS: #self.dChKeys['RS']:
index = chKeyRS.index(key) + 1
layout0.addWidget(self.checkBox0[key], index, 0)
layout0.addWidget(self.pushButton0[key], index, 1)
layout0.addWidget(self.comboBoxLineStyle[key], index, 2)
layout0.addWidget(self.comboBoxMarkerStyle[key], index, 3)
layout0.addWidget(self.doubleSpinBoxLW[key], index, 4)
self.buttonBox = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Apply
| QtGui.QDialogButtonBox.Close)
self.connect(self.pushButton0['RX'], QtCore.SIGNAL("clicked()"),
self.changeColorRX)
self.connect(self.pushButton0['RXS1'], QtCore.SIGNAL("clicked()"),
self.changeColorRXS1)
self.connect(self.pushButton0['BG'], QtCore.SIGNAL("clicked()"),
self.changeColorBG)
self.connect(self.pushButton0['BGS1'], QtCore.SIGNAL("clicked()"),
self.changeColorBGS1)
if 'RXS2' in chKeyRS:
self.connect(self.pushButton0['RXS2'], QtCore.SIGNAL("clicked()"),
self.changeColorRXS2)
if 'BGS2' in chKeyRS:
self.connect(self.pushButton0['BGS2'], QtCore.SIGNAL("clicked()"),
self.changeColorBGS2)
self.connect(self.buttonBox.button(QtGui.QDialogButtonBox.Apply),
QtCore.SIGNAL("clicked()"), self.apply)
self.connect(self.buttonBox, QtCore.SIGNAL("rejected()"), self.reject)
mainLayout = QtGui.QVBoxLayout()
mainLayout.addLayout(layout0)
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.title = "Channel Attributes"
self.setWindowTitle(self.title)
def __init__(self, dVar, chKeyRS, parent=None):
super(DlgFigureSet, self).__init__(parent)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setModal(False)
self.labelTitle = QtGui.QLabel(
self.tr("<center><b>FIGURE SETTING</b></center>"))
self.name = "Figure Setting"
self.toolID = 3
self.dVar = dVar.copy()
self.chKeyRS = chKeyRS
# Size, width, height, resolution,
labelT = QtGui.QLabel('Size style')
self.comboBox0 = QtGui.QComboBox()
self.comboBox0.addItems(['Percentage', 'Inches'])
labelW = QtGui.QLabel("Width")
self.spinBoxWidth = QtGui.QSpinBox()
self.spinBoxWidth.setRange(10, 200)
self.spinBoxWidth.setValue(100)
self.spinBoxWidth.setSingleStep(10)
self.spinBoxWidth.setSuffix(" %")
labelH = QtGui.QLabel("Height")
self.spinBoxHeight = QtGui.QSpinBox()
self.spinBoxHeight.setRange(10, 200)
self.spinBoxHeight.setValue(100)
self.spinBoxHeight.setSingleStep(10)
self.spinBoxHeight.setSuffix(" %")
self.checkBoxFitWindow = QtGui.QCheckBox("Fit into Window")
labelR = QtGui.QLabel("Zoom")
self.spinBoxR = QtGui.QSpinBox()
self.spinBoxR.setRange(10, 1000)
self.spinBoxR.setValue(100)
self.spinBoxR.setSingleStep(50)
layout0 = myGridLayout()
layout0.addWidget(self.checkBoxFitWindow, 0, 0, 1, 2)
layout0.addWidget(labelT, 1, 0)
layout0.addWidget(self.comboBox0, 1, 1)
layout0.addWidget(labelW, 2, 0)
layout0.addWidget(self.spinBoxWidth, 2, 1)
layout0.addWidget(labelH, 3, 0)
layout0.addWidget(self.spinBoxHeight, 3, 1)
layout0.addWidget(labelR, 4, 0)
layout0.addWidget(self.spinBoxR, 4, 1)
groupBox0 = QtGui.QGroupBox(self.tr('Figure Options'))
groupBox0.setLayout(layout0)
labelSubs = {}
self.spinBoxSubs = {}
self.keySubs = ['top', 'bottom', 'left', 'right'] #,'wspace','hspace']
for key in self.keySubs:
labelSubs[key] = QtGui.QLabel(key)
self.spinBoxSubs[key] = QtGui.QDoubleSpinBox()
self.spinBoxSubs[key].setRange(0, 1)
self.spinBoxSubs[key].setValue(self.dVar[key])
self.spinBoxSubs[key].setSingleStep(0.01)
layout1 = myGridLayout()
i = 0
while i < len(self.keySubs):
key = self.keySubs[i]
layout1.addWidget(labelSubs[key], i, 0)
layout1.addWidget(self.spinBoxSubs[key], i, 1)
i += 1
key = self.keySubs[i]
layout1.addWidget(labelSubs[key], i - 1, 2)
layout1.addWidget(self.spinBoxSubs[key], i - 1, 3)
i += 1
groupBox1 = QtGui.QGroupBox(self.tr('Subplot Configuration'))
groupBox1.setLayout(layout1)
self.checkBoxSatd = QtGui.QCheckBox('Draw Saturated Points')
self.lanelXLim = QtGui.QLabel('Set Xlim')
self.fromSpinBox = QtGui.QSpinBox()
self.toSpinBox = QtGui.QSpinBox()
fromLabel = QtGui.QLabel('From')
toLabel = QtGui.QLabel('To')
self.buttonBox = QtGui.QDialogButtonBox(QtGui.QDialogButtonBox.Apply
| QtGui.QDialogButtonBox.Close)
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(groupBox0)
mainLayout.addWidget(groupBox1)
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.title = "Channel Attributes"
self.setWindowTitle(self.title)
def __init__(self, dProject,parent=None):
QtGui.QWidget.__init__(self, parent)
self.title = QtGui.QLabel(self.tr("<center><b>SIGNAL ALIGNMENT</b></center>"))
self.name="Signal Alignment"
self.toolID=4
self.dProject=dProject
self.dOutput=dProject['dData'].copy()
self.dProjOut=deepcopy(dProject)
self.linkXR,self.linkXS=np.array([]),np.array([])
self.dataR,self.dataS=np.array([]),np.array([])
self.isToolApplied=False
### Group of ComboBoxes
label1=QtGui.QLabel("Seq. Channels")
self.comboBox0=QtGui.QComboBox()
self.comboBox0.setCurrentIndex(0)
if self.dProject['isSeq2']:
choices0= ['RXS1 - BGS1','RXS2 - BGS2']
else:
choices0= ['RXS1 - BGS1']
self.comboBox0.addItems(choices0)
gridLayout0 = QtGui.QGridLayout()
gridLayout0.addWidget(label1, 0, 0)
gridLayout0.addWidget(self.comboBox0, 0, 1)
groupBox1=QtGui.QGroupBox('Select Channels to be aligned')
groupBox1.setLayout(gridLayout0)
self.button0=peakMatchModifyButton()
text=self.tr("HINT: When the matched peaks are modified; Key 'A' to add a Peak. Key 'D' to delete a Peak. Key 'Shift' to change position. ")
self.hint = hintLabel(text)
# self.button0=QtGui.QPushButton('Modify Matched Peaks')
# self.button0.setEnabled(False)
#
# self.hint = QtGui.QLabel(self.tr("HINT: When the matched peaks are modified,"
# "Press Key 'A' button and click both plots to add a Peak. "
# "Press Key 'D' button and click to delete a Peak. "
# "Press Key 'Shift' button and select a peak in BGS to change position. "
# ))
# self.font = QtGui.QFont()
# self.font.setPointSize(9)
# self.hint.setFont(self.font)
# self.hint.setWordWrap(True)
### Button Box
self.buttonBox = ToolButton()
## Main Layout
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget( self.title)
mainLayout.addWidget(groupBox1)
mainLayout.addWidget(self.button0)
mainLayout.addWidget(self.hint)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isToolAppliedSigAlign=False
self.connect(self.comboBox0,QtCore.SIGNAL('currentIndexChanged(int)'), self.comboChanged)
def __init__(self,dProject,parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(self.tr("<center><b>MOBILITY SHIFT</b></center>"))
self.name="Mobility Shift"
self.toolID=4
self.dProject=dProject
self.dProjOut=deepcopy(dProject)
self.dProject=dProject.copy()
self.isToolApplied=False
self.radioButton0=QtGui.QRadioButton('Position Similarity')
self.radioButton1=QtGui.QRadioButton('Dynamic Programming')
self.radioButton0.setChecked(True)
layoutMethod=myVBoxLayout()
layoutMethod.addWidget((self.radioButton0))
layoutMethod.addWidget(self.radioButton1)
self.groupBoxMethod=QtGui.QGroupBox('Select a method')
self.groupBoxMethod.setLayout(layoutMethod)
self.comboBox0={}
self.label0={}
for key in dProject['chKeyRS']:
self.label0[key] = QtGui.QLabel(key)
self.comboBox0[key]=QtGui.QComboBox()
self.comboBox0[key].addItems(dyesName)
try:
self.comboBox0[key].setCurrentIndex(dyesName.index(dProject['dyeN'][key]))
except:
pass
if len(self.dProject['dData'][key])==0:
self.comboBox0[key].setEnabled(False)
self.groupBoxRX=QtGui.QGroupBox(self.tr('(+) Reagent'))
self.groupBoxRX.setCheckable(True)
self.groupBoxRX.setChecked(True)
layoutRX = myGridLayout()
layoutRX.addWidget(self.label0['RX'], 0, 0)
layoutRX.addWidget(self.comboBox0['RX'], 0, 1)
layoutRX.addWidget(self.label0['RXS1'], 1, 0)
layoutRX.addWidget(self.comboBox0['RXS1'], 1, 1)
if self.dProject['isSeq2']:
layoutRX.addWidget(self.label0['RXS2'], 2, 0)
layoutRX.addWidget(self.comboBox0['RXS2'], 2, 1)
self.groupBoxRX.setLayout(layoutRX)
self.groupBoxBG=QtGui.QGroupBox(self.tr('(-) Reagent)'))
self.groupBoxBG.setCheckable(True)
self.groupBoxBG.setChecked(True)
layoutBG = myGridLayout()
layoutBG.addWidget(self.label0['BG'], 0, 0)
layoutBG.addWidget(self.comboBox0['BG'], 0, 1)
layoutBG.addWidget(self.label0['BGS1'], 1, 0)
layoutBG.addWidget(self.comboBox0['BGS1'], 1, 1)
if self.dProject['isSeq2']:
layoutBG.addWidget(self.label0['BGS2'], 2, 0)
layoutBG.addWidget(self.comboBox0['BGS2'], 2, 1)
self.groupBoxBG.setLayout(layoutBG)
### Button Box
self.buttonBox = ToolButton()
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.groupBoxMethod)
mainLayout.addWidget(self.groupBoxRX)
mainLayout.addWidget(self.groupBoxBG)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
def __init__(self, dProject, parent=None):
QtGui.QWidget.__init__(self, parent)
self.title = QtGui.QLabel(
self.tr("<center><b>SEQUENCE ALIGNMENT</b></center>"))
self.name = "Sequence Alignment"
self.toolID = 1
self.dProject = dProject
self.dProjOut = deepcopy(dProject)
self.fileReadSeq = DlgSelectFile(
'Seq. File', "Base Files (*.txt *.fasta *.gbk *.seq )",
self.dProject['dir'])
self.fileReadSeq.lineEdit0.setText(self.dProject['fNameSeq'])
self.seqRNA3to5 = self.dProjOut['RNA'][::-1]
self.seqRNA3to5N = changeNucToN(self.seqRNA3to5, self.dProjOut)
self.NSeqRNA = len(self.dProjOut['RNA'])
### SEQUENCE FIND
label0 = QtGui.QLabel("Channel")
label1 = QtGui.QLabel("ddNTP")
label2 = QtGui.QLabel('Thres')
self.comboBox0 = QtGui.QComboBox()
self.comboBox1 = QtGui.QComboBox()
self.comboBox2 = QtGui.QComboBox()
self.comboBox3 = QtGui.QComboBox()
self.spinBox0 = QtGui.QDoubleSpinBox()
self.spinBox0.setRange(-3, 3)
self.spinBox0.setValue(0.5)
self.spinBox0.setSingleStep(0.1)
choices0 = ['BGS1', 'RXS1']
self.choicesNuc = ['ddC', 'ddG', 'ddA', 'ddT']
self.nucNames = ['G', 'C', 'U', 'A']
self.comboBox0.addItems(choices0)
self.comboBox1.addItems(self.choicesNuc)
self.comboBox1.setCurrentIndex(
self.nucNames.index(self.dProject['nuc1']))
self.radioSeqFind0 = QtGui.QRadioButton('Histogram')
self.radioSeqFind1 = QtGui.QRadioButton('Background')
layoutMethod = myHBoxLayout()
layoutMethod.addWidget(self.radioSeqFind0)
layoutMethod.addWidget(self.radioSeqFind1)
gridLayout = myGridLayout()
gridLayout.addWidget(label0, 0, 0)
gridLayout.addWidget(label1, 0, 1)
# gridLayout.addWidget(label2, 0, 2)
gridLayout.addWidget(self.comboBox0, 1, 0)
gridLayout.addWidget(self.comboBox1, 1, 1)
# gridLayout.addWidget(self.spinBox0, 1, 2)
if self.dProject[
'isSeq2']: #('RXS2' in self.dInput.keys()) and ('BGS2' in self.dInput.keys()):
choices2 = ['BGS2', 'RXS2']
self.comboBox2.addItems(choices2)
self.comboBox3.addItems(self.choicesNuc)
self.comboBox3.setCurrentIndex(
self.nucNames.index(self.dProject['nuc2']))
self.spinBox1 = QtGui.QDoubleSpinBox()
self.spinBox1.setRange(-3, 3)
self.spinBox1.setValue(0.5)
self.spinBox1.setSingleStep(0.1)
gridLayout.addWidget(self.comboBox2, 2, 0)
gridLayout.addWidget(self.comboBox3, 2, 1)
# gridLayout.addWidget(self.spinBox1, 2, 2)
self.checkBox0 = QtGui.QCheckBox('Check for high BG peaks')
self.groupBoxBaseCall = QtGui.QGroupBox('Base Calling')
self.groupBoxBaseCall.setLayout(gridLayout)
self.groupBoxBaseCall.setCheckable(True)
## LAYOUTS
labelSetting2 = QtGui.QLabel("Seq Range: From")
labelSetting3 = QtGui.QLabel("To:")
labelSetting4 = QtGui.QLabel("Seq Start: ")
self.spinBoxSeqRangeFrom = QtGui.QSpinBox()
self.spinBoxSeqRangeTo = QtGui.QSpinBox()
try:
self.setSpinBoxSeq()
except:
pass
self.spinBoxSeqOffset = QtGui.QSpinBox()
self.spinBoxSeqOffset.setRange(0, len(self.dProject['RNA']))
self.checkBoxLineDraw = QtGui.QCheckBox('Draw peak match lines')
self.checkBoxLineDraw.setChecked(True)
layoutSetting = myGridLayout()
layoutSetting.addWidget(labelSetting2, 0, 0)
layoutSetting.addWidget(self.spinBoxSeqRangeFrom, 0, 1)
layoutSetting.addWidget(labelSetting3, 0, 2)
layoutSetting.addWidget(self.spinBoxSeqRangeTo, 0, 3)
# layoutSetting.addWidget(self.checkBoxLineDraw,1,0,1,2)
self.groupBoxSettings = QtGui.QGroupBox('Settings')
self.groupBoxSettings.setLayout(layoutSetting)
text = "HINT: Click a Nuc to change the type. \
Press Key 'A' button and click to add a Nuc.\
Press Key 'D' button and click to delete a Nuc. \
Press Key 'Shift' button and select a peak to change position. "
self.hint = hintLabel(text)
self.connect(self.fileReadSeq.pushButton0, QtCore.SIGNAL("clicked()"),
self.changeSeqFile)
self.buttonBox = ToolButton()
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.title)
mainLayout.addWidget(self.fileReadSeq)
mainLayout.addWidget(self.groupBoxBaseCall)
mainLayout.addWidget(self.groupBoxSettings)
mainLayout.addWidget(self.hint)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isToolApplied = False
def __init__(self, dProject, dProjRef, parent=None):
QtGui.QWidget.__init__(self, parent)
self.title = QtGui.QLabel(
self.tr("<center><b>SEQUENCE ALIGNMENT BY REFERENCE</b></center>"))
self.name = "Sequence Alignment by Reference"
self.toolID = 1
self.dProject = dProject
self.dProjRef = dProjRef
self.linkXR, self.linkXS = np.array([]), np.array([])
self.linkYR, self.linkYS = np.array([]), np.array([])
self.dataR, self.dataS = np.array([]), np.array([])
#### BY REFERENCE
self.fileReadRef = DlgSelectFile(
'Ref. Proj.', "Reference Project (*.pyShape *.qushape)",
self.dProject['dir'])
if 'fNameRef' in self.dProject.keys():
self.fileReadRef.lineEdit0.setText(self.dProject['fNameRef'])
self.connect(self.fileReadRef.pushButton0, QtCore.SIGNAL("clicked()"),
self.changeRefFile)
label10 = QtGui.QLabel("Ref. Channel")
self.comboBox10 = QtGui.QComboBox()
self.comboBox10.addItems(chKeysRS)
self.comboBox10.setCurrentIndex(3)
label11 = QtGui.QLabel("Sample Channel")
self.comboBox11 = QtGui.QComboBox()
self.comboBox11.addItems(chKeysRS)
self.comboBox11.setCurrentIndex(3)
layout0 = myGridLayout()
layout0.addWidget(self.fileReadRef, 0, 0, 1, 2)
layout0.addWidget(label10, 1, 0)
layout0.addWidget(self.comboBox10, 1, 1)
layout0.addWidget(label11, 2, 0)
layout0.addWidget(self.comboBox11, 2, 1)
self.groupBox0 = QtGui.QGroupBox(self.tr('Signal Alignment'))
self.groupBox0.setLayout(layout0)
self.groupBox0.setCheckable(True)
labelRX = QtGui.QLabel('Scale Factor for RX')
labelBG = QtGui.QLabel('Scale Factor for BG')
self.spinBoxRX = QtGui.QDoubleSpinBox()
self.spinBoxRX.setRange(0.01, 100.00)
self.spinBoxRX.setValue(1.00)
self.spinBoxRX.setSingleStep(0.01)
self.spinBoxBG = QtGui.QDoubleSpinBox()
self.spinBoxBG.setRange(0.01, 100.00)
self.spinBoxBG.setValue(1.00)
self.spinBoxBG.setSingleStep(0.01)
self.checkBoxScale0 = QtGui.QCheckBox('Scale by windowing')
layout1 = myGridLayout()
layout1.addWidget(labelRX, 0, 0)
layout1.addWidget(self.spinBoxRX, 0, 1)
layout1.addWidget(labelBG, 1, 0)
layout1.addWidget(self.spinBoxBG, 1, 1)
layout1.addWidget(self.checkBoxScale0, 2, 0, 1, 2)
self.groupBox1 = QtGui.QGroupBox(self.tr('Scale RX and BG'))
self.groupBox1.setLayout(layout1)
# self.groupBox1.setCheckable(True)
# self.button0=QtGui.QPushButton('Modify Matched Peaks')
# self.button0.setEnabled(False)
self.button0 = peakMatchModifyButton()
self.button1 = QtGui.QPushButton('Modify Peak Link by Reference')
self.button1.setEnabled(False)
self.button1.setWhatsThis(
self.
tr(" Check the accuracy of linked peaks"
" by C\changing the peak position in the sample RX and BG peaks."
" Press Key 'Shift' button and select a sample peak to change position. "
))
text = self.tr(
"HINT: When the matched peaks are modified; Key 'A' to add a Peak. Key 'D' to delete a Peak. Key 'Shift' to change position. "
)
self.hint = hintLabel(text)
### BUTTON BOX
self.buttonBox = ToolButton()
## MAIN LAYOUT
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.title)
mainLayout.addWidget(self.groupBox0)
mainLayout.addWidget(self.button0)
mainLayout.addWidget(self.button1)
mainLayout.addWidget(self.hint)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isClickedModifyMatchedPeaks = True
self.isToolApplied = False
self.isMatchedPeaksChanged = True
def __init__(self, dProject,parent=None):
QtGui.QDialog.__init__(self, parent)
self.name='New Project'
self.title = QtGui.QLabel(self.tr("<center><b>CREATE NEW PROJECT - STEP 3 OF 3</b></center>"))
self.dProject=dProject
self.isApplied=False
self.label0={}
self.comboBox0={}
choices0=['Channel 1','Channel 2', 'Channel 3','Channel 4']
for key in self.dProject['chKeyRS']:
self.label0[key]=QtGui.QLabel(key)
self.comboBox0[key]=QtGui.QComboBox()
self.comboBox0[key].addItems(choices0)
self.comboBox0[key].setCurrentIndex(self.dProject['chIndex'][key])
choices2=['ddC','ddG', 'ddA', 'ddT']
self.comboBox1={}
self.comboBox1['RXS1']=QtGui.QComboBox()
self.comboBox1['RXS1'].addItems(choices2)
self.comboBox1['BGS1']=QtGui.QComboBox()
self.comboBox1['BGS1'].addItems(choices2)
if self.dProject['isSeq2']:
self.comboBox1['RXS2']=QtGui.QComboBox()
self.comboBox1['RXS2'].addItems(choices2)
self.comboBox1['BGS2']=QtGui.QComboBox()
self.comboBox1['BGS2'].addItems(choices2)
self.comboBox1['RXS2'].setCurrentIndex(1)
self.comboBox1['BGS2'].setCurrentIndex(1)
layout1 = QtGui.QGridLayout()
layout1.addWidget(self.label0['RX'], 0, 0)
layout1.addWidget(self.comboBox0['RX'], 0, 1)
layout1.addWidget(self.label0['RXS1'], 1, 0)
layout1.addWidget(self.comboBox0['RXS1'], 1, 1)
layout1.addWidget(self.comboBox1['RXS1'], 1, 2)
if self.dProject['isSeq2']:
layout1.addWidget(self.label0['RXS2'], 2, 0)
layout1.addWidget(self.comboBox0['RXS2'], 2, 1)
layout1.addWidget(self.comboBox1['RXS2'], 2, 2)
groupBox1=QtGui.QGroupBox('Select (+) Reaction Channels')
groupBox1.setLayout(layout1)
layout2 = QtGui.QGridLayout()
layout2.addWidget(self.label0['BG'], 0, 0)
layout2.addWidget(self.comboBox0['BG'], 0, 1)
layout2.addWidget(self.label0['BGS1'], 1, 0)
layout2.addWidget(self.comboBox0['BGS1'], 1, 1)
layout2.addWidget(self.comboBox1['BGS1'], 1, 2)
if self.dProject['isSeq2']:
layout2.addWidget(self.label0['BGS2'], 2, 0)
layout2.addWidget(self.comboBox0['BGS2'], 2, 1)
layout2.addWidget(self.comboBox1['BGS2'], 2, 2)
groupBox2=QtGui.QGroupBox('Select (-) Reaction Channels')
groupBox2.setLayout(layout2)
self.buttonBox=ButtonWizard()
self.buttonBox.nextButton.setText('Apply')
self.buttonBox.doneButton.setEnabled(False)
self.buttonBox.nextButton.setDefault(True)
self.connect(self.buttonBox.backButton,QtCore.SIGNAL("clicked()"),self.clickBack2)
self.connect(self.buttonBox.nextButton,QtCore.SIGNAL("clicked()"),self.clickNext2)
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.title)
mainLayout.addWidget(groupBox1)
mainLayout.addWidget(groupBox2)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.connect(self.comboBox0['RX'],QtCore.SIGNAL("currentIndexChanged(int)"),self.changeCombo00)
self.connect(self.comboBox0['RXS1'],QtCore.SIGNAL("currentIndexChanged(int)"),self.changeCombo01)
self.connect(self.comboBox1['RXS1'],QtCore.SIGNAL("currentIndexChanged(int)"),self.changeCombo10)
if self.dProject['isSeq2']:
self.connect(self.comboBox0['RXS2'],QtCore.SIGNAL("currentIndexChanged(int)"),self.changeCombo02)
self.connect(self.comboBox1['RXS2'],QtCore.SIGNAL("currentIndexChanged(int)"),self.changeCombo11)