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.QDialog.__init__(self, parent)
self.dProject=dProject
self.isApplied=False
self.title = QtGui.QLabel(self.tr("<center><b>CREATE NEW PROJECT - STEP 1 OF 3</b></center>"))
self.name='New Project'
label0=QtGui.QLabel('Project Name')
self.lineEdit0=QtGui.QLineEdit()
self.lineEdit0.setText(self.dProject['name'])
self.selectDir0=DlgSelectDir('Directory')
self.selectDir0.lineEdit0.setText(self.dProject['dir'])
self.radioButton0=QtGui.QRadioButton('One Sequencing Channel')
self.radioButton1=QtGui.QRadioButton('Two Sequencing Channels ')
if self.dProject['isSeq2']:
self.radioButton1.setChecked(True)
else:
self.radioButton0.setChecked(True)
self.groupBox = QtGui.QGroupBox(self.tr("Choose the Project Type"))
layout0=QtGui.QVBoxLayout()
layout0.addWidget(self.radioButton0)
layout0.addWidget(self.radioButton1)
self.groupBox.setLayout(layout0)
layout0=QtGui.QGridLayout()
layout0.addWidget(label0,1,0)
layout0.addWidget(self.lineEdit0,1,1)
layout0.addWidget(self.selectDir0,2,0,1,2)
layout0.addWidget(self.groupBox,3,0,1,2)
self.buttonBox=ButtonWizard()
self.buttonBox.backButton.setEnabled(False)
self.buttonBox.doneButton.setEnabled(False)
self.buttonBox.nextButton.setDefault(True)
self.connect(self.buttonBox.nextButton,QtCore.SIGNAL("clicked()"),self.clickNext0)
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.title)
mainLayout.addLayout(layout0)
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>SIGNAL DECAY CORRECTION</b></center>"))
self.name="Signal Decay Correction"
self.toolID=4
self.dProject=dProject
self.dOutput=dProject['dData'].copy()
self.dProjOut=deepcopy(dProject)
self.isToolApplied=False
self.spinBox0=QtGui.QDoubleSpinBox()
self.spinBox0.setRange(0,2.0)
self.spinBox0.setValue(0.2)
self.spinBox0.setSingleStep(0.1)
#### Group Box Radio
self.radioButton0 = QtGui.QRadioButton(self.tr(" Automatic Summation "))
self.radioButton1 = QtGui.QRadioButton(self.tr("Exponential"))
self.radioButton2 = QtGui.QRadioButton(self.tr("Summation - Factor"))
self.radioButton0.setChecked(True)
layout0 = myGridLayout()
layout0.addWidget(self.radioButton0,0,0)
layout0.addWidget(self.radioButton1,1,0)
layout0.addWidget(self.radioButton2,2,0)
layout0.addWidget(self.spinBox0,2,1)
groupBox0 = QtGui.QGroupBox(self.tr("Select a method"))
groupBox0.setLayout(layout0)
### Button Box
self.buttonBox = ToolButton()
self.groupBoxROI=GroupBoxROI(self.dProject)
self.applyChannel=ApplyChannel(self.dProject)
### Main Layout
mainLayout=QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(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>SOME FUNCTIONS</b></center>"))
self.name = "Various Tools"
self.toolID = 1
self.dProject = dProject
self.isToolApplied = False
#### Group Box Radio
groupBoxRadio = QtGui.QGroupBox(self.tr("Select a Tool"))
self.radioButton0 = QtGui.QRadioButton(
self.tr("Resolution Enhancement"))
self.radioButton1 = QtGui.QRadioButton(self.tr("First Derivative"))
self.radioButton2 = QtGui.QRadioButton(self.tr("Stat Normalization"))
self.radioButton3 = QtGui.QRadioButton(self.tr("Fourier Transform"))
self.radioButton0.setChecked(True)
vbox = myVBoxLayout()
vbox.addWidget(self.radioButton0)
vbox.addWidget(self.radioButton1)
vbox.addWidget(self.radioButton2)
vbox.addWidget(self.radioButton3)
groupBoxRadio.setLayout(vbox)
### Button Box
self.buttonBox = ToolButton()
self.groupBoxROI = GroupBoxROI(self.dProject)
self.applyChannel = ApplyChannel(self.dProject)
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(groupBoxRadio)
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>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.labelTitle = QtGui.QLabel(
self.tr("<center><b>REACTIVITY</b></center>"))
self.name = "Reactivity"
self.toolID = 1
self.dProject = dProject
self.dProjRef = dProjRef
self.dProjOut = deepcopy(self.dProject)
self.scaleFactor = 1
self.checkBox0 = QtGui.QCheckBox('Scale and Normalize with Reference')
## SCALE
self.groupBox1 = scaleGroupBox("Scale BG")
## NORMALIZATION
label0 = QtGui.QLabel('Outlier')
label1 = QtGui.QLabel('Average')
self.spinBox0 = QtGui.QDoubleSpinBox()
self.spinBox1 = QtGui.QDoubleSpinBox()
self.spinBox0.setRange(0, 9)
self.spinBox1.setRange(0, 15)
self.spinBox0.setSuffix("%")
self.spinBox1.setSuffix("%")
self.spinBox0.setSingleStep(0.25)
self.spinBox1.setSingleStep(0.25)
self.spinBox0.setValue(2.0)
self.spinBox1.setValue(10.0)
self.checkBox1 = QtGui.QCheckBox("Set Negative Value to Zero")
layout2 = myHBoxLayout()
layout2.addWidget(label0)
layout2.addWidget(self.spinBox0)
# layout2.addWidget(label1)
# layout2.addWidget(self.spinBox1)
layout21 = myVBoxLayout()
# layout21.addWidget(self.radioNormCluster)
layout21.addLayout(layout2)
layout21.addWidget(self.checkBox1)
self.groupBox2 = QtGui.QGroupBox(self.tr('Normalization'))
self.groupBox2.setLayout(layout21)
# self.groupBox2.setEnabled(False)
self.radio3to5 = QtGui.QRadioButton("3' to 5'")
self.radio5to3 = QtGui.QRadioButton("5' to 3'")
self.radio3to5.setChecked(True)
self.pushButton0 = QtGui.QPushButton('Reactivity')
self.pushButton1 = QtGui.QPushButton('Peak Area')
self.pushButton2 = QtGui.QPushButton('Data')
layout3 = myGridLayout()
layout3.addWidget(self.radio3to5, 0, 0)
layout3.addWidget(self.radio5to3, 0, 1)
layout3.addWidget(self.pushButton0, 1, 0)
layout3.addWidget(self.pushButton1, 1, 1)
layout3.addWidget(self.pushButton2, 1, 3)
self.groupBox3 = QtGui.QGroupBox(self.tr('Select Plot Type'))
self.groupBox3.setLayout(layout3)
# self.groupBox3.setEnabled(False)
self.buttonBox = ToolButton()
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.groupBox1)
mainLayout.addWidget(self.groupBox2)
mainLayout.addWidget(self.groupBox3)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isToolApplied = False