def loadTemp(self):
if self.savedFlag == False:
self.warningDialog = WarningDialog('Any unsaved data will be lost.'\
+'Do you wish to proceed?', self.loadApproved)
self.warningDialog.show()
else:
self.loadApproved()
def saveTemp(self):
if self.saveEnable == True:
if self.openPath == None:
self.saveTempAs()
else:
self.saveFile(self.openPath)
else:
self.warningDialog = WarningDialog('Make sure no sequences are'\
+' less than 20 bp in length', None)
self.warningDialog.show()
def saveTempAs(self):
if self.saveEnable == True:
self.openPath = QFileDialog.getSaveFileName(self, \
"Save File As", _root_dir + '/templateSchemes/' , \
QString("Schemes (*.cfg)"))
try:
self.saveFile(self.openPath)
except:
pass
else:
self.warningDialog = WarningDialog('Make sure no sequences are'\
+' less than 20 bp in length', None)
self.warningDialog.show()
class TDController(QMainWindow, ui_tempDesign.Ui_Dialog):
def __init__(self, parent=None):
super(TDController, self).__init__(parent)
self.setupUi(self)
self.openPath = None
self.warningDialog = None
self.tempDesignTable.setColumnWidth(2, 290)
self.setWindowTitle('Template Design')
# self.tempDesignTable.setDragEnabled(True)
# self.tempDesignTable.setDragDropOverwriteMode(False)
# self.tempDesignTable.DropIndicatorPosition(QAbstractItemView.BelowItem)
# self.tempDesignTable.setDragDropMode(QAbstractItemView.DragDrop)
# self.tempDesignTable.setSelectionBehavior(QAbstractItemView.SelectRows)
self.establishConnections()
self.addNewSequence('NNNNNNNNNNNNNNNNNNNN', 'S')
self.savedFlag = True
self.saveEnable = True
self.editPosCB.setCurrentIndex(self.editPosCB.currentIndex() + 1)
def establishConnections(self):
self.addSeqPB.pressed.connect(self.addSeq)
self.rmSeqPB.pressed.connect(self.rmSeq)
self.newTempPB.pressed.connect(self.newTemp)
self.loadTempPB.pressed.connect(self.loadTemp)
self.saveTempPB.pressed.connect(self.saveTemp)
self.saveTempAsPB.pressed.connect(self.saveTempAs)
self.tempDesignTable.cellChanged.connect(self.cellChangeEvent)
def cellChangeEvent(self, row, column):
self.savedFlag = False
self.saveEnable = True
if column == 2 and \
len(self.tempDesignTable.item(row, column).text()) < 20:
self.tempDesignTable.item(row, column).setBackground(QBrush(QColor(200, 35, 35)))
self.saveEnable = False
else:
self.tempDesignTable.item(row, column).setBackground(QBrush(QColor(255, 255, 255)))
def primerLabelUpdate(self):
index = 65
for row in range(self.tempDesignTable.rowCount()):
if index >= 65 + 26:
self.tempDesignTable.cellWidget(row, 0).setCurrentIndex(0)
if self.tempDesignTable.cellWidget(row, 0).currentIndex() == 1:
self.tempDesignTable.item(row, 1).setText(chr(index))
index = index + 1
self.savedFlag = False
def addSeq(self):
self.addNewSequence('NNNNNNNNNNNNNNNNNNNN', 'S')
def addNewSequence(self, sequence, seqType):
row = self.editPosCB.currentIndex() + 1
self.tempDesignTable.insertRow(row)
self.editPosCB.addItem(QString(str(self.tempDesignTable.rowCount())))
self.editPosCB.setCurrentIndex(self.editPosCB.currentIndex() + 1)
setattr(self, str(row)+'1', QTableWidgetItem(QString(''), QTableWidgetItem.Type))
setattr(self, str(row)+'2', QTableWidgetItem(QString(sequence), QTableWidgetItem.Type))
getattr(self, str(row)+'1').setFlags(Qt.NoItemFlags)
self.tempDesignTable.setItem(row, 1, getattr(self, str(row)+'1'))
self.tempDesignTable.setItem(row, 2, getattr(self, str(row)+'2'))
self.tempDesignTable.setCellWidget(row , 0, typeCB(row, self))
#Reassign Class Names to reflect rearrangement
if row + 1 < self.tempDesignTable.rowCount():
for missRow in range(self.tempDesignTable.rowCount() - row):
newRow = self.tempDesignTable.rowCount() - missRow - 1
setattr(self, str(newRow) + '1', getattr(self, str(newRow - 1)+'1'))
setattr(self, str(newRow) +'2', getattr(self, str(newRow - 1)+'2'))
self.tempDesignTable.cellWidget(newRow, 0).row = newRow
if seqType == 'P':
self.tempDesignTable.cellWidget(row, 0).setCurrentIndex(1)
self.savedFlag = False
def rmSeq(self):
row = self.editPosCB.currentIndex()
if self.tempDesignTable.rowCount() > 1:
self.tempDesignTable.removeRow(row)
self.editPosCB.removeItem(self.editPosCB.count()-1)
#Reassign Class Names to reflect rearrangement
if row + 1 < self.tempDesignTable.rowCount():
for missRow in range(self.tempDesignTable.rowCount() - row):
newRow = self.tempDesignTable.rowCount() - missRow - 1
setattr(self, str(newRow) + '1', getattr(self, str(newRow - 1)+'1'))
setattr(self, str(newRow) +'2', getattr(self, str(newRow - 1)+'2'))
self.tempDesignTable.cellWidget(newRow, 0).row = newRow
self.primerLabelUpdate()
self.savedFlag = False
def newTemp(self):
if self.savedFlag == False:
self.warningDialog = WarningDialog('Any unsaved data will be lost.'\
+'Do you wish to proceed?', self.newTempApproved)
self.warningDialog.show()
else:
self.newTempApproved()
def newTempApproved(self):
self.tempDesignTable.setRowCount(0)
self.addSeq()
self.savedFlag = True
def loadTemp(self):
if self.savedFlag == False:
self.warningDialog = WarningDialog('Any unsaved data will be lost.'\
+'Do you wish to proceed?', self.loadApproved)
self.warningDialog.show()
else:
self.loadApproved()
def loadApproved(self):
self.openPath = QFileDialog.getOpenFileName(self, \
"Open File", _root_dir + '/templateSchemes/' , \
QString("Schemes (*.cfg)"))
self.tempDesignTable.setRowCount(0)
f = file(self.openPath, 'r')
seqList = json.load(f)[1]
for row in range(len(seqList)):
self.addNewSequence(seqList[row][1:], seqList[row][0])
self.primerLabelUpdate()
self.savedFlag = True
def saveTemp(self):
if self.saveEnable == True:
if self.openPath == None:
self.saveTempAs()
else:
self.saveFile(self.openPath)
else:
self.warningDialog = WarningDialog('Make sure no sequences are'\
+' less than 20 bp in length', None)
self.warningDialog.show()
def saveTempAs(self):
if self.saveEnable == True:
self.openPath = QFileDialog.getSaveFileName(self, \
"Save File As", _root_dir + '/templateSchemes/' , \
QString("Schemes (*.cfg)"))
try:
self.saveFile(self.openPath)
except:
pass
else:
self.warningDialog = WarningDialog('Make sure no sequences are'\
+' less than 20 bp in length', None)
self.warningDialog.show()
def saveFile(self, path):
seqList = []
for row in range(self.tempDesignTable.rowCount()):
seq = ''
if self.tempDesignTable.cellWidget(row, 0).currentIndex() == 1:
seq = 'P'
else:
seq = 'S'
seq = seq + str(self.tempDesignTable.item(row, 2).text())
seqList.append(seq)
f = file(path, 'w')
json.dump(('None', seqList), f)
self.savedFlag = True
class seqTab:
def __init__(self, mainWin, parent=None):
self.mainWin = mainWin
self.functions = SeqTabFunctions(self)
self.seqStartPB = self.mainWin.seqStartPB
self.seqStartPB.setEnabled(False)
self.includeHomeAxisRB = self.mainWin.includeHomeAxisRB
self.cycleEntryValidatePB = self.mainWin.cycleEntryValidatePB
self.clearSelectionPB = self.mainWin.clearSelectionPB
self.applyPB = self.mainWin.applyPB
self.applyRepeatPB = self.mainWin.applyRepeatPB
self.applyPB.setEnabled(False)
self.applyRepeatPB.setEnabled(False)
self.warningDialog = None
self.touchFlagCB = self.mainWin.touchFlagCB
self.cycleTable = self.mainWin.cycleTable
self.sequenceGraphicsView = self.mainWin.sequenceGraphicsView
self.baseClassL = []
self.sortBaseL = []
self.sortedCyclesL = []
self.sortCycleD = {}
self.seqList = []
self.polonatorCycleListVector = self.mainWin.polonatorCycleListVector
self.seqScene = QGraphicsScene()
self.seqScene.setSceneRect(QRectF(0, 0, self.sequenceGraphicsView.width(), self.sequenceGraphicsView.height()))
self.sequenceGraphicsView.setDragMode(QGraphicsView.RubberBandDrag)
self.sequenceGraphicsView.setScene(self.seqScene)
self.sequenceGraphicsView.mouseReleaseEvent = self.graphicsViewMouseRelease
self.sequenceGraphicsView.setRubberBandSelectionMode(Qt.ContainsItemBoundingRect)
#load most recent template
f = file(_root_dir + "/.config/.polGV.cfg", 'r')
path = json.load(f)
if path != 'None':
try:
self.functions.addSequence(path)
except:
f = file(_root_dir + "/.config/.polGV.cfg", 'w')
json.dump('None', f)
#initialize table widget
self.functions.updateCycleList(True)
self.establishConnections()
def establishConnections(self):
self.seqStartPB.pressed.connect(self.start)
self.cycleEntryValidatePB.pressed.connect(self.validate)
self.clearSelectionPB.pressed.connect(self.clear)
self.applyPB.pressed.connect(self.applySeq)
self.applyRepeatPB.pressed.connect(self.applyRepeatSeq)
#prevent user from starting invalid cycle
self.cycleTable.cellChanged.connect(self.disableStart)
def disableStart(self):
self.seqStartPB.setEnabled(False)
def start(self):
print 'start'
touchFlag = "0"
for i in range(self.cycleTable.rowCount()):
if self.cycleTable.item(i,0).text() != '':
print self.cycleTable.item(i,0).text() + \
self.cycleTable.item(i,1).text() + \
self.cycleTable.item(i,2).text()
cmd = 'python ' + _root_dir + '/pol_API/G.007_fluidics/src/polonator_main.py ' + touchFlag
# os.system(cmd)
print cmd
'''
try:
with open("/home/polonator/G.007/G.007_fluidics/src/cycle_list", "w") as outfile:
for i in range(len(entry)):
outfile.write(str(self.polonatorCycleListVector[i][0]+self.polonatorCycleListVector[i][1]+self.polonatorCycleListVector[i][2]))
outfile.write('\n')
if self.touchFlagCB.currentIndex() == 1:
touchFlag = "1"
cmd = "python /home/polonator/G.007/G.007_fluidics/src/polonator_main.py "+ touchFlag
#os.system(cmd)
except IOError: #as (errno, strerror):
print "Error writing to cycle_list file, I/O error" #: ({0}): {1}".format(errno, strerror)
# self.process_start(cmd, ['pass'], "self.process_pass()")
'''
def validate(self):
self.seqStartPB.setEnabled(True)
self.functions.executeValidation()
def clear(self):
self.warningDialog = WarningDialog('Are you sure that you want to'+\
' clear the cycle list?', self.okClear)
self.warningDialog.show()
def okClear(self):
self.cycleTable.clearContents()
while len(self.baseClassL) != 0:
#Make sure to remove all repeats, base select turns bases purple
self.baseClassL[0].fill = self.baseClassL[0].red
self.baseClassL[0].baseSelect()
self.functions.updateCycleList(True)
self.applyPB.setEnabled(False)
self.applyRepeatPB.setEnabled(False)
self.warningDialog = None
def applySeq(self):
self.functions.updateCycleList(True)
self.applyPB.setEnabled(False)
self.applyRepeatPB.setEnabled(True)
def applyRepeatSeq(self):
baseClassLPreserve = []
for base in self.baseClassL:
if baseClassLPreserve.count(base) == 0:
baseClassLPreserve.append(base)
for base in baseClassLPreserve:
self.baseClassL.append(base)
self.functions.updateCycleList(True)
def graphicsViewMouseRelease(self, event):
#Create cycle name from base
if len(self.sortBaseL) != 0:
sortCycleL = []
for base in self.sortBaseL:
cycle = base.primer.primerLetter
if base.parentItem().pos().x() > base.primer.pos().x():
cycle = cycle + 'P'
else:
cycle = cycle + 'M'
cycle = cycle + base.position
self.sortCycleD.update({cycle : base})
sortCycleL.append(cycle)
#Create a plus list and a minus list
plusL = []
minusL = []
maxPos = 1
cycleCount = 0
for cycle in sortCycleL:
if cycle[1] == 'P':
plusL.append(cycle)
if cycle[1] == 'M':
minusL.append(cycle)
#Sort Plus
sortL = []
for cycle in plusL:
pos = int(cycle[2:])
if sortL.count(pos) == 0:
sortL.append(pos)
sortL.sort()
sortL.reverse()
for num in sortL:
for cycle in plusL:
pos = int(cycle[2:])
if pos == num:
self.sortedCyclesL.append(cycle)
#Sort Minus
sortL = []
for cycle in minusL:
pos = int(cycle[2:])
if sortL.count(pos) == 0:
sortL.append(pos)
sortL.sort()
sortL.reverse()
for num in sortL:
for cycle in minusL:
pos = int(cycle[2:])
if pos == num:
self.sortedCyclesL.append(cycle)
for cycle in self.sortedCyclesL:
self.baseClassL.append(self.sortCycleD[cycle])
#Reinitialize data structures
self.sortedCyclesL = []
self.sortCycleD = {}
#Empty list without jeapordizing data structure location
while len(self.sortBaseL) != 0:
self.sortBaseL.pop()
self.applyPB.setEnabled(True)
def clear(self):
self.warningDialog = WarningDialog('Are you sure that you want to'+\
' clear the cycle list?', self.okClear)
self.warningDialog.show()
