def __init__(self, dProject, parent=None):
QtGui.QWidget.__init__(self, parent)
## Region of Interest
self.fromSpinBox = QtGui.QSpinBox()
self.fromSpinBox.setRange(0, len(dProject['dData']['RX']))
self.fromSpinBox.setValue(0)
self.fromSpinBox.setSingleStep(1)
self.toSpinBox = QtGui.QSpinBox()
self.toSpinBox.setRange(0, len(dProject['dData']['RX']))
self.toSpinBox.setValue(len(dProject['dData']['RX']))
self.toSpinBox.setSingleStep(1)
fromLabel = QtGui.QLabel('From')
toLabel = QtGui.QLabel('To')
self.groupBox = QtGui.QGroupBox(self.tr('Region of Interest'))
self.groupBox.setCheckable(True)
self.groupBox.setChecked(False)
layoutRoi = myHBoxLayout()
layoutRoi.addWidget(fromLabel)
layoutRoi.addWidget(self.fromSpinBox)
layoutRoi.addWidget(toLabel)
layoutRoi.addWidget(self.toSpinBox)
self.groupBox.setLayout(layoutRoi)
def __init__(self, dProject,parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(self.tr("<center><b>SMOOTHING</b></center>"))
self.name="Smooth"
self.toolID=2
self.dProject=dProject
self.dProjOut=deepcopy(dProject)
self.isToolApplied=False
#Saturation Correction: Analysis of saturated data points by creating a synthetic peak based upon the peak shape before and after saturation.
self.checkBoxSatd=QtGui.QCheckBox('Saturation Correction')
self.checkBoxSatd.setChecked(True)
#### Group Box Radio
self.radioButton0 = QtGui.QRadioButton(self.tr("Triangular Moving Aver."))
self.radioButton1 = QtGui.QRadioButton(self.tr("Rectangular Moving Aver."))
self.radioButton2 = QtGui.QRadioButton(self.tr("Gaussian"))
self.radioButton0.setChecked(True)
#### Window Size
windowSizeLabel = QtGui.QLabel("Window Size:")
self.spinBox1 = QtGui.QSpinBox()
self.spinBox1.setRange(1, 10)
self.spinBox1.setValue(1)
self.spinBox1.setSingleStep(1)
layout1 = myGridLayout()
layout1.addWidget(self.radioButton0,0,0,1,2)
layout1.addWidget(self.radioButton1,1,0,1,2)
layout1.addWidget(self.radioButton2,2,0,1,2)
layout1.addWidget(windowSizeLabel,3,0)
layout1.addWidget(self.spinBox1,3,1)
self.groupBox0 = QtGui.QGroupBox(self.tr("Smoothing"))
self.groupBox0.setCheckable(True)
self.groupBox0.setLayout(layout1)
### Button Box
self.buttonBox =ToolButton()
self.groupBoxROI=GroupBoxROI(self.dProject)
self.applyChannel=ApplyChannel(self.dProject)
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.checkBoxSatd)
mainLayout.addWidget(self.groupBox0)
mainLayout.addWidget(self.groupBoxROI.groupBox)
mainLayout.addWidget(self.applyChannel.groupBox)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
def __init__(self, dProject,parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(self.tr("<center><b>BASELINE ADJUSTMENT</b></center>"))
self.name="Baseline Adjustment"
self.toolID=3
self.dProject=dProject
self.isToolApplied=False
#### Window Size
windowLabel = QtGui.QLabel("Baseline Window:")
self.spinBox0 = QtGui.QSpinBox()
self.spinBox0.setRange(0,200)
self.spinBox0.setValue(60)
self.spinBox0.setSingleStep(1)
self.smoothCheckBox = QtGui.QCheckBox("Smooth the Baseline Drift")
#self.smoothCheckBox.setChecked(True)
layout2=myGridLayout()
layout2.addWidget(windowLabel,0,0)
layout2.addWidget(self.spinBox0,0,1)
layout2.addWidget(self.smoothCheckBox,1,0)
groupBoxParameter = QtGui.QGroupBox()
groupBoxParameter.setLayout(layout2)
### Button Box
self.buttonBox = ToolButton()
self.groupBoxROI=GroupBoxROI(self.dProject)
self.applyChannel=ApplyChannel(self.dProject)
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(groupBoxParameter)
mainLayout.addWidget(self.groupBoxROI.groupBox)
mainLayout.addWidget(self.applyChannel.groupBox)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
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,dProjRef,parent=None):
QtGui.QWidget.__init__(self, parent)
self.labelTitle = QtGui.QLabel(self.tr("<center><b>APPLY ALL TOOLS</b></center>"))
self.name="Apply All Tools"
self.toolID=1
self.dProject=dProject
self.dProjOut=deepcopy(dProject)
self.dProjRef=deepcopy(dProjRef)
label0 = QtGui.QLabel("Start Point")
label1 = QtGui.QLabel("End Point")
start,end=0,len(self.dProject['dData']['RX']) # findRoi(self.dCurData['RXS'])
self.spinBox0 = QtGui.QSpinBox()
self.spinBox0.setRange(0, len(self.dProject['dData']['RX']))
self.spinBox0.setValue(start)
self.spinBox0.setSingleStep(1)
self.spinBox1 = QtGui.QSpinBox()
self.spinBox1.setRange(0, len(self.dProject['dData']['RX']))
self.spinBox1.setValue(end)
self.spinBox1.setSingleStep(1)
layout0=QtGui.QHBoxLayout()
layout0.addWidget(label0)
layout0.addWidget(self.spinBox0)
layout0.addWidget(label1)
layout0.addWidget(self.spinBox1)
groupBox0=QtGui.QGroupBox('Select Region of Interest')
groupBox0.setLayout(layout0)
self.checkBox01=QtGui.QCheckBox("Saturation Correction")
self.checkBox0=QtGui.QCheckBox("Smoothing Windows Size")
self.checkBox1=QtGui.QCheckBox("Mobility Shift")
self.checkBox2=QtGui.QCheckBox("Baseline Adjustment Window")
self.checkBox3=QtGui.QCheckBox("Signal Decay Correction")
self.checkBox4=QtGui.QCheckBox("Signal Alignment")
self.checkBox01.setChecked(True)
self.checkBox0.setChecked(True)
self.checkBox1.setChecked(True)
self.checkBox2.setChecked(True)
self.checkBox3.setChecked(True)
self.checkBox4.setChecked(True)
self.spinBox2 = QtGui.QSpinBox()
self.spinBox2.setRange(0, 10)
self.spinBox2.setValue(1)
self.spinBox2.setSingleStep(1)
self.spinBox4 = QtGui.QSpinBox()
self.spinBox4.setRange(0, 500)
self.spinBox4.setValue(60)
self.spinBox4.setSingleStep(1)
layout1=QtGui.QGridLayout()
layout1.addWidget(self.checkBox01,0,0)
layout1.addWidget(self.checkBox0,1,0)
layout1.addWidget(self.spinBox2,1,1)
layout1.addWidget(self.checkBox1,2,0)
layout1.addWidget(self.checkBox2,3,0)
layout1.addWidget(self.spinBox4,3,1)
layout1.addWidget(self.checkBox3,4,0)
layout1.addWidget(self.checkBox4,5,0)
groupBox1=QtGui.QGroupBox('Select Tools')
groupBox1.setLayout(layout1)
### Button Box
self.buttonBox = ToolButton()
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(groupBox0)
mainLayout.addWidget(groupBox1)
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.labelTitle = QtGui.QLabel(self.tr("<center><b>REGION OF INTEREST</b></center>"))
self.name="Region of Interest"
self.toolID=1
self.hint = QtGui.QLabel(self.tr("HINT: Press Key 'F' button and click the axes to set From. "
"Press Key 'T' button and click the axes to set To"
))
self.hint.setWordWrap(True)
self.font = QtGui.QFont()
self.font.setPointSize(10)
self.hint.setFont(self.font)
self.dProject=dProject
self.dProjRef=dProjRef
self.dProjOut=deepcopy(dProject)
self.isToolApplied=False
self.roi={}
for key in self.dProject['chKeyRS']:
self.roi[key]=[0,len(self.dProject['dData'][key])]
labelFrom = QtGui.QLabel("From ")
labelTo = QtGui.QLabel("To ")
labelPlus=QtGui.QLabel('(+) Reaction')
self.spinBoxPlusFrom=QtGui.QSpinBox()
self.spinBoxPlusTo=QtGui.QSpinBox()
self.spinBoxPlusFrom.setRange(0,len(self.dProject['dData']['RX']))
self.spinBoxPlusTo.setRange(0,len(self.dProject['dData']['RX']))
self.spinBoxPlusTo.setValue(len(self.dProject['dData']['RX']))
labelMinus=QtGui.QLabel('(-) Reaction')
self.spinBoxMinusFrom=QtGui.QSpinBox()
self.spinBoxMinusTo=QtGui.QSpinBox()
self.spinBoxMinusFrom.setRange(0,len(self.dProject['dData']['BG']))
self.spinBoxMinusTo.setRange(0,len(self.dProject['dData']['BG']))
self.spinBoxMinusTo.setValue(len(self.dProject['dData']['BG']))
layout0=myGridLayout()
layout0.addWidget(labelFrom,0,1)
layout0.addWidget(labelTo,0,2)
layout0.addWidget(labelPlus,1,0)
layout0.addWidget( self.spinBoxPlusFrom,1,1)
layout0.addWidget( self.spinBoxPlusTo,1,2)
layout0.addWidget(labelMinus,2,0)
layout0.addWidget( self.spinBoxMinusFrom,2,1)
layout0.addWidget( self.spinBoxMinusTo,2,2)
self.groupBox0=QtGui.QGroupBox()
self.groupBox0.setLayout(layout0)
self.buttunAuto=QtGui.QPushButton('Auto ROI by Reference')
self.connect(self.buttunAuto,QtCore.SIGNAL("clicked()"),self.autoFindROI)
if not self.dProject['isRef']:
self.buttunAuto.setEnabled(False)
self.buttonBox = ToolButton()
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.groupBox0)
mainLayout.addWidget(self.buttunAuto)
mainLayout.addWidget(self.hint)
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
