def __init__(self, dProject, parent=None):
QtGui.QWidget.__init__(self, parent)
self.title = QtGui.QLabel(self.tr("<center><b>SCALE</b></center>"))
self.name = "Scale"
self.toolID = 1
self.dProject = dProject
self.dOutput = dProject['dData'].copy()
self.label0 = {}
self.doubleSpinBox0 = {}
for key in self.dProject['chKeyRS']:
self.label0[key] = QtGui.QLabel(key)
self.doubleSpinBox0[key] = QtGui.QDoubleSpinBox()
self.doubleSpinBox0[key].setRange(0.01, 100.00)
self.doubleSpinBox0[key].setValue(1.00)
self.doubleSpinBox0[key].setSingleStep(0.01)
self.groupBox1 = QtGui.QGroupBox(self.tr('Enter Scale Factor'))
vbox = QtGui.QGridLayout()
vbox.addWidget(self.label0['RX'], 0, 0)
vbox.addWidget(self.doubleSpinBox0['RX'], 0, 1)
vbox.addWidget(self.label0['BG'], 1, 0)
vbox.addWidget(self.doubleSpinBox0['BG'], 1, 1)
vbox.addWidget(self.label0['RXS1'], 2, 0)
vbox.addWidget(self.doubleSpinBox0['RXS1'], 2, 1)
vbox.addWidget(self.label0['BGS1'], 3, 0)
vbox.addWidget(self.doubleSpinBox0['BGS1'], 3, 1)
if self.dProject['isSeq2']:
vbox.addWidget(self.label0['RXS2'], 4, 0)
vbox.addWidget(self.doubleSpinBox0['RXS2'], 4, 1)
vbox.addWidget(self.label0['BGS2'], 5, 0)
vbox.addWidget(self.doubleSpinBox0['BGS2'], 5, 1)
vbox.setContentsMargins(0, 0, 0, 0)
self.groupBox1.setLayout(vbox)
self.pushButton0 = QtGui.QPushButton('Scale All to BG')
self.connect(self.pushButton0, QtCore.SIGNAL("clicked()"),
self.autoScale)
### Button Box
self.buttonBox = ToolButton()
## Main Layout
self.groupBoxROI = GroupBoxROI(self.dProject)
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.title)
mainLayout.addWidget(self.groupBox1)
mainLayout.addWidget(self.pushButton0)
mainLayout.addWidget(self.groupBoxROI.groupBox)
mainLayout.addStretch()
mainLayout.addWidget(self.buttonBox)
self.setLayout(mainLayout)
self.isToolApplied = False
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,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,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.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)