def clickNext0(self):
if self.lineEdit0.text()=='':
QtGui.QMessageBox.warning(self,'Warning', 'Write a project Name')
elif self.selectDir0.lineEdit0.text()=='':
QtGui.QMessageBox.warning(self,'Warning', 'Select Project Directory')
else:
self.dProject['name']=str(self.lineEdit0.text())
self.dProject['dir']=str(self.selectDir0.lineEdit0.text())
self.dProject['fName']=self.dProject['dir']+'/'+self.dProject['name']+'.qushape'
if self.radioButton1.isChecked():
self.dProject['isSeq2']=True
self.dProject['chKeyRS']=['RX', 'BG', 'RXS1', 'BGS1','RXS2','BGS2']
self.dProject['chKeyCC']=['RX', 'RXS1','RXS2','BG', 'BGS1','BGS2']
self.dProject['chKeyRX']=['RX', 'RXS1','RXS2']
self.dProject['chKeyBG']=['BG', 'BGS1','BGS2']
else:
self.dProject['isSeq2']=False
self.dProject['chKeyRS']=['RX', 'BG', 'RXS1', 'BGS1']
self.dProject['chKeyCC']=['RX', 'RXS1','BG', 'BGS1']
self.dProject['chKeyRX']=['RX', 'RXS1']
self.dProject['chKeyBG']=['BG', 'BGS1']
if QtCore.QFile(self.dProject['fName']).exists():
reply=QtGui.QMessageBox.question(self,"QuShape",
"Saving the file will overwrite the original file on the disk.\n"
"Do you really want to save?",
QtGui.QMessageBox.Yes| QtGui.QMessageBox.Cancel)
if reply==QtGui.QMessageBox.Cancel:
return False
elif reply==QtGui.QMessageBox.Yes:
QtCore.QFile(self.dProject['fName']).remove()
self.isApplied=True
def __init__(self,
label,
fileType,
path=QtCore.QDir.homePath(),
parent=None):
QtGui.QWidget.__init__(self, parent)
self.label = label
self.fileType = fileType
self.path = path
self.label0 = QtGui.QLabel(label)
self.label0.setFixedWidth(80)
self.lineEdit0 = QtGui.QLineEdit()
self.lineEdit0.setReadOnly(True)
self.pushButton0 = QtGui.QPushButton('Browse')
self.layout0 = QtGui.QHBoxLayout()
self.layout0.addWidget(self.label0)
self.layout0.addWidget(self.lineEdit0)
self.layout0.addWidget(self.pushButton0)
self.layout0.setContentsMargins(0, 0, 0, 0)
self.layout0.setSpacing(1)
self.setLayout(self.layout0)
self.connect(self.pushButton0, QtCore.SIGNAL("clicked()"),
self.fileBrowse)
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.name='New Project'
self.title = QtGui.QLabel(self.tr("<center><b>CREATE NEW PROJECT - STEP 2 OF 3</b></center>"))
self.dProject=dProject
self.isApplied=False
self.fileRead0=DlgSelectFile('(+) Reaction',"ABIF or Text File (*.ab1 *.fsa *.txt)",self.dProject['dir'])
self.fileRead1=DlgSelectFile('(-) Reaction',"ABIF or Text File (*.ab1 *.fsa *.txt)",self.dProject['dir'])
self.fileRead2=DlgSelectFile('Sequence',"Base Files (*.txt *.fasta *.gbk *.seq )",self.dProject['dir'])
self.fileRead3=DlgSelectFile('Ref. Proj.',"Reference Project (*.pyshape *.qushape)",self.dProject['dir'])
self.fileRead0.lineEdit0.setText(self.dProject['fNameRX'])
self.fileRead1.lineEdit0.setText(self.dProject['fNameBG'])
self.fileRead2.lineEdit0.setText(self.dProject['fNameSeq'])
self.fileRead3.lineEdit0.setText(self.dProject['fNameRef'])
text="HINT: Select either Sequence or Reference Project"
self.hint = hintLabel(text)
layout0 = QtGui.QVBoxLayout()
layout0.addWidget(self.fileRead0)
layout0.addWidget(self.fileRead1)
layout0.addWidget(self.fileRead2)
layout0.addWidget(self.fileRead3)
layout0.addWidget(self.hint)
self.buttonBox=ButtonWizard()
self.buttonBox.doneButton.setEnabled(False)
self.buttonBox.nextButton.setDefault(True)
self.connect(self.buttonBox.backButton,QtCore.SIGNAL("clicked()"),self.clickBack1)
self.connect(self.buttonBox.nextButton,QtCore.SIGNAL("clicked()"),self.clickNext1)
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>REPORT</b></center>"))
self.name = "Report"
self.toolID = 1
self.dProject = dProject
self.dReport = createDReport(dProject)
for key in self.dReport.keys():
self.dReport[key] = self.dReport[key][::-1]
self.saveTextButton = QtGui.QPushButton("Save as Text")
self.connect(self.saveTextButton, QtCore.SIGNAL('clicked()'),
self.saveTextReport)
self.layout0 = QtGui.QHBoxLayout()
self.layout0.addWidget(self.saveTextButton)
self.layout0.addStretch()
N = len(self.dReport['seqNum'])
self.table = QtGui.QTableWidget()
self.table.setRowCount(N)
self.table.setColumnCount(len(reportKeys))
self.table.setHorizontalHeaderLabels(reportKeys)
self.table.setSelectionBehavior(QtGui.QTableWidget.SelectRows)
self.table.setSelectionMode(QtGui.QTableWidget.SingleSelection)
self.font = QtGui.QFont()
self.font.setPointSize(9)
self.table.setFont(self.font)
for i in range(N):
for key in reportKeys:
if key == 'seqRNA':
item = QtGui.QTableWidgetItem(self.dReport[key][i])
elif key in ['seqNum', 'posSeq', 'posRX', 'posBG']:
item = QtGui.QTableWidgetItem("%d" % self.dReport[key][i])
else:
item = QtGui.QTableWidgetItem("%.2f" %
self.dReport[key][i])
col = reportKeys.index(key)
self.table.setItem(int(i), int(col), item)
self.table.resizeColumnsToContents()
self.table.resizeRowsToContents()
mainLayout = QtGui.QVBoxLayout()
mainLayout.addWidget(self.labelTitle)
mainLayout.addWidget(self.table)
mainLayout.addLayout(self.layout0)
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, label, parent=None):
QtGui.QWidget.__init__(self, parent)
type = 'file' # dir, save,
label0 = QtGui.QLabel(label)
self.lineEdit0 = QtGui.QLineEdit()
self.lineEdit0.setReadOnly(True)
self.pushButton0 = QtGui.QPushButton('Browse')
self.connect(self.pushButton0, QtCore.SIGNAL("clicked()"),
self.dirBrowse0)
layout0 = myGridLayout()
layout0.addWidget(label0, 1, 0)
layout0.addWidget(self.lineEdit0, 1, 1)
layout0.addWidget(self.pushButton0, 1, 2)
self.setLayout(layout0)
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 setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow")
MainWindow.setFixedSize(350, 450)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
self.label = QtWidgets.QLabel(self.centralwidget)
self.label.setGeometry(QtCore.QRect(0, 0, 350, 41))
font = QtGui.QFont()
font.setPointSize(20)
font.setBold(True)
font.setUnderline(False)
font.setWeight(75)
self.label.setFont(font)
self.label.setScaledContents(False)
self.label.setAlignment(QtCore.Qt.AlignCenter)
self.label.setObjectName("label")
self.label_2 = QtWidgets.QLabel(self.centralwidget)
self.label_2.setEnabled(True)
self.label_2.setGeometry(QtCore.QRect(25, 330, 300, 61))
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(12)
sizePolicy.setVerticalStretch(12)
sizePolicy.setHeightForWidth(self.label_2.sizePolicy().hasHeightForWidth())
self.label_2.setSizePolicy(sizePolicy)
font = QtGui.QFont()
font.setStrikeOut(False)
font.setKerning(True)
self.label_2.setFont(font)
self.label_2.setAutoFillBackground(False)
self.label_2.setStyleSheet("color: rgb(130, 142, 155);")
self.label_2.setLocale(QtCore.QLocale(QtCore.QLocale.Ukrainian, QtCore.QLocale.Ukraine))
self.label_2.setFrameShape(QtWidgets.QFrame.NoFrame)
self.label_2.setFrameShadow(QtWidgets.QFrame.Plain)
self.label_2.setLineWidth(0)
self.label_2.setMidLineWidth(0)
self.label_2.setScaledContents(True)
self.label_2.setAlignment(QtCore.Qt.AlignHCenter|QtCore.Qt.AlignTop)
self.label_2.setWordWrap(True)
self.label_2.setIndent(-1)
self.label_2.setTextInteractionFlags(QtCore.Qt.NoTextInteraction)
self.label_2.setObjectName("label_2")
self.pushButton = QtWidgets.QPushButton(self.centralwidget)
self.pushButton.setGeometry(QtCore.QRect(115, 290, 120, 32))
self.pushButton.setObjectName("pushButton")
self.pushButton_2 = QtWidgets.QPushButton(self.centralwidget)
self.pushButton_2.setGeometry(QtCore.QRect(115, 400, 120, 32))
self.pushButton_2.setObjectName("pushButton_2")
self.frame = QtWidgets.QFrame(self.centralwidget)
self.frame.setGeometry(QtCore.QRect(0, 42, 351, 241))
self.frame.setAcceptDrops(False)
self.frame.setStyleSheet("image: url(:/logo/color.png);")
self.frame.setFrameShape(QtWidgets.QFrame.NoFrame)
self.frame.setFrameShadow(QtWidgets.QFrame.Raised)
self.frame.setObjectName("frame")
MainWindow.setCentralWidget(self.centralwidget)
self.pushButton_2.hide()
self.retranslateUi(MainWindow)
self.app_functions(MainWindow)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
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,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
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)