def __init__(self,nb_sc,label,next_widget,next_title,nb_min_sel,analysis,parent):
super(GenericScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.nb_min_sel = nb_min_sel
self.next_widget = next_widget
self.next_title = next_title
self.checklist = []
self.createWidgets()
self.ui.selectionLabel.setText(label)
self.ui.analysisTypeLabel.setText(self.next_title)
self.ui.projectDirEdit.setText(self.parents.dir)
self.putChoices()
self.ui.verticalLayout_3.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_3.setAlignment(Qt.AlignTop)
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.ui.verticalLayout.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
def __init__(self,nb_sc,analysis,parent=None):
super(ConfidenceTypeSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.createWidgets()
self.restoreAnalysisValues()
def __init__(self,analysis,parent=None):
super(SetupComparisonConfidence,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.scNumList = []
self.dico_values = {}
self.createWidgets()
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
self.parents.updateDoc(self)
def __init__(self,analysis,parent=None):
super(HistFixed,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.sc_to_show = self.analysis.chosenSc
self.list_selected_evaluate_sc = self.analysis.candidateScList
self.paramList = []
self.condList = []
self.param_info_dico = {}
self.createWidgets()
self.addTheSc()
self.addTheParams()
self.restoreAnalysisValues()
def __init__(self,nb_sc,analysis,parent=None):
super(BiasNConfidenceScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.checklist = []
self.radiolist = []
self.createWidgets()
self.putChoices()
self.ui.verticalLayout_3.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_3.setAlignment(Qt.AlignTop)
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.ui.verticalLayout.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
def __init__(self,parent=None):
super(SetGeneticData,self).__init__(parent)
self.parent=parent
self.parents=Parents(self.parent)
# liste des box
self.groupList = []
# dicos de frames indexé par les box
self.setMutation_dico = {}
self.setMutationSeq_dico = {}
self.setSum_dico = {}
self.setSumSeq_dico = {}
# dicos de booleens indexé par les box
self.setMutationValid_dico = {}
self.setMutationSeqValid_dico = {}
# dico indexé par la box du groupe
self.group_info_dico = {}
self.nbLocusGui = 0
# dico indexé par les noms de locus, qui donne le numero du locus et le groupe du locus
self.dico_num_and_numgroup_locus = {}
self.createWidgets()
class SetGeneticData(formGenData,baseGenData):
""" Frame qui est créée pour faire des groupes de locus,
déterminer leur modèle mutationnel et leur summary statistics
"""
def __init__(self,parent=None):
super(SetGeneticData,self).__init__(parent)
self.parent=parent
self.parents=Parents(self.parent)
# liste des box
self.groupList = []
# dicos de frames indexé par les box
self.setMutation_dico = {}
self.setMutationSeq_dico = {}
self.setSum_dico = {}
self.setSumSeq_dico = {}
# dicos de booleens indexé par les box
self.setMutationValid_dico = {}
self.setMutationSeqValid_dico = {}
# dico indexé par la box du groupe
self.group_info_dico = {}
self.nbLocusGui = 0
# dico indexé par les noms de locus, qui donne le numero du locus et le groupe du locus
self.dico_num_and_numgroup_locus = {}
self.createWidgets()
def createWidgets(self):
#self.ui = Ui_Frame()
self.ui = self
self.ui.setupUi(self)
self.ui.verticalLayout_3.setAlignment(QtCore.Qt.AlignTop)
self.ui.tableWidget.setColumnWidth(0,230)
self.ui.tableWidget.setColumnWidth(1,60)
self.ui.tableWidget.setColumnWidth(2,60)
self.ui.tableWidget.setColumnWidth(3,60)
QObject.connect(self.ui.addGroupButton,SIGNAL("clicked()"),self.addGroup)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.clearButton,SIGNAL("clicked()"),self.clear)
self.ui.analysisFrame.hide()
self.ui.autoGroupButton.hide()
def updateDoc(self,obj=None):
""" Met à jour la doc uniquement pour les fils de l'objet obj.
Fonctionne tant que les instances de SetGeneticData ont pour parent.parent
l'objet Diyabc
"""
self.parents.updateDoc(obj)
def fillLocusTableFromData(self):
""" rempli le tableau des locus en consultant l'instance de Data
On ne peut pas le faire à l'instanciation de l'objet SetGeneticData car on a pas
encore lu le fichier de conf dans le cas d'un load project
"""
data = self.parents.data
nb_m = 0
nb_s = 0
for i in range(data.nloc):
if data.locuslist[i].type > 4:
self.addRow(name=data.locuslist[i].name,type="S")
nb_s += 1
else:
self.addRow(name=data.locuslist[i].name,type="M")
nb_m += 1
self.dico_num_and_numgroup_locus[data.locuslist[i].name] = [i+1,0]
self.nbLocusGui+=1
# affichage du bon nombre de locus dans l'onglet principal du projet
self.majProjectGui(m=nb_m,s=nb_s)
def addRow(self,name="locus",type="M"):
""" ajoute un locus à la liste principale (de locus)
"""
self.ui.tableWidget.insertRow(self.ui.tableWidget.rowCount())
#self.ui.tableWidget.setCellWidget(self.ui.tableWidget.rowCount()-1,i,QPushButton("View"))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,0,QTableWidgetItem("%s"%(name)))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,1,QTableWidgetItem("%s"%type))
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).flags() & ~Qt.ItemIsEditable)
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).flags() & ~Qt.ItemIsEditable)
if type == "M":
#self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,QTableWidgetItem("2"))
#self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,QTableWidgetItem("40"))
#self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).setTextAlignment(Qt.AlignRight)
#self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).setTextAlignment(Qt.AlignRight)
dos = QTableWidgetItem("2")
tres = QTableWidgetItem("40")
dos.setTextAlignment(Qt.AlignRight|Qt.AlignTop)
tres.setTextAlignment(Qt.AlignRight|Qt.AlignTop)
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,dos)
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,tres)
log(3,"Adding a locus (%s)"%tres.textAlignment())
else:
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,2,QTableWidgetItem(" "))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,3,QTableWidgetItem(" "))
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,2).flags() & ~Qt.ItemIsEditable)
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,3).flags() & ~Qt.ItemIsEditable)
def addGroup(self):
""" dessine un nouveau groupe vide
"""
groupBox = QtGui.QGroupBox("Group %i"%(len(self.groupList)+1),self.ui.scrollAreaWidgetContents)
groupBox.setMinimumSize(QtCore.QSize(0, 200))
groupBox.setMaximumSize(QtCore.QSize(16777215, 200))
groupBox.setObjectName("groupBox")
horizontalLayout = QtGui.QHBoxLayout(groupBox)
horizontalLayout.setObjectName("horizontalLayout")
verticalLayout = QtGui.QVBoxLayout()
verticalLayout.setObjectName("verticalLayout")
addToButton = QtGui.QPushButton(">>",groupBox)
addToButton.setObjectName("addToGroupButton")
verticalLayout.addWidget(addToButton)
rmFromButton = QtGui.QPushButton("<<",groupBox)
rmFromButton.setObjectName("rmFromGroupButton")
verticalLayout.addWidget(rmFromButton)
horizontalLayout.addLayout(verticalLayout)
verticalLayout_3 = QtGui.QVBoxLayout()
verticalLayout_3.setObjectName("verticalLayout_3")
rmButton = QtGui.QPushButton("Remove group",groupBox)
rmButton.setObjectName("rmLocusGroupButton")
verticalLayout_3.addWidget(rmButton)
listWidget = QtGui.QListWidget(groupBox)
listWidget.setObjectName("locusGroupList")
verticalLayout_3.addWidget(listWidget)
horizontalLayout.addLayout(verticalLayout_3)
listWidget.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
verticalLayout_2 = QtGui.QVBoxLayout()
verticalLayout_2.setObjectName("verticalLayout_2")
setMutationButton = QtGui.QPushButton("Set mutation\nModel",groupBox)
setMutationButton.setObjectName("setMutationButton")
verticalLayout_2.addWidget(setMutationButton)
setSumButton = QtGui.QPushButton("Set Summary\nStatistics",groupBox)
setSumButton.setObjectName("setSumButton")
verticalLayout_2.addWidget(setSumButton)
horizontalLayout.addLayout(verticalLayout_2)
self.ui.verticalLayout_3.addWidget(groupBox)
QObject.connect(addToButton,SIGNAL("clicked()"),self.addToGroup)
QObject.connect(rmFromButton,SIGNAL("clicked()"),self.rmFromGroup)
QObject.connect(rmButton,SIGNAL("clicked()"),self.rmGroup)
QObject.connect(setMutationButton,SIGNAL("clicked()"),self.setMutation)
QObject.connect(setSumButton,SIGNAL("clicked()"),self.setSum)
self.groupList.append(groupBox)
self.group_info_dico[groupBox] = [ "" , [] ]
self.majProjectGui(g=len(self.groupList))
return groupBox
def switchTo(self,widget):
""" methode virtuelle a redefinir
"""
pass
def setMutation(self,box=None):
""" déclenché par le clic sur le bouton 'set mutation model' ou par le clic sur 'clear'
dans 'set mutation model'. bascule vers la saisie du modèle mutationnel
"""
if box == None:
box = self.sender().parent()
title = str(box.title())
if "Microsatellites" in title:
#self.parent.addTab(self.setMutation_dico[box],"Set mutation model")
#self.parent.setTabEnabled(self.parent.indexOf(self),False)
#self.parent.setCurrentWidget(self.setMutation_dico[box])
self.switchTo(self.setMutation_dico[box])
# maj du titre de la frame
lab = self.setMutation_dico[box].ui.setMutMsLabel
lab.setText("Set mutation model of %s (microsatellites)"%(" ".join(str(box.title()).split()[:2])))
# on considère que le setmutation n'est plus valide, il faut le revalider
self.setMutationValid_dico[box] = False
elif "Sequences" in title:
#self.parent.addTab(self.setMutationSeq_dico[box],"Set mutation model")
#self.parent.setTabEnabled(self.parent.indexOf(self),False)
#self.parent.setCurrentWidget(self.setMutationSeq_dico[box])
self.switchTo(self.setMutationSeq_dico[box])
# maj du titre de la frame
lab = self.setMutationSeq_dico[box].ui.setMutSeqLabel
lab.setText("Set mutation model of %s (sequences)"%(" ".join(str(box.title()).split()[:2])))
# on considère que le setmutation n'est plus valide, il faut le revalider
self.setMutationSeqValid_dico[box] = False
else:
output.notify(self,"Set Mutation Model error","Add locus to a group before setting the mutation model")
def rmGroup(self,box=None):
""" Enlève les loci présents dans le groupe et supprime le groupe
"""
if (box == None):
box = self.sender().parent()
lw = box.findChild(QListWidget,"locusGroupList")
lw.selectAll()
self.rmFromGroup(box)
# suppression de la box
box.hide()
self.groupList.remove(box)
del self.group_info_dico[box]
# renommage des groupes
for i,box in enumerate(self.groupList):
old_title = str(box.title())
box.setTitle("Group %i %s"%(i+1,' '.join(old_title.split()[2:])))
# pour chaque groupe, on maj le numero de groupe de tous les locus du groupe
lw = box.findChild(QListWidget,"locusGroupList")
for j in range(lw.count()):
itemtxt = str(lw.item(j).text())
self.dico_num_and_numgroup_locus[itemtxt][1] = i+1
self.majProjectGui(g=len(self.groupList))
def addToGroup(self,box=None):
""" ajoute les loci selectionnés au groupe du bouton pressé
"""
all_similar = True
first_type_found = ""
if box == None:
box = self.sender().parent()
listwidget = box.findChild(QListWidget,"locusGroupList")
row_list = []
selection = self.ui.tableWidget.selectedIndexes()
selection.sort()
for it in selection:
if it.row() not in row_list:
row_list.append(it.row())
# verif que tous les loci selectionnés ont le meme type
if first_type_found == "":
first_type_found = str(self.ui.tableWidget.item(it.row(),1).text())
else:
if first_type_found != str(self.ui.tableWidget.item(it.row(),1).text()):
all_similar = False
# verif que les loci deja dans le groupe sont du même type que ceux sélectionnés
# on compare le premier type trouvé dans la selection avec le type du premier
# élément du groupe
if listwidget.count() > 0:
if all_similar:
name = str(listwidget.item(0).text())
#num = int(name.split(' ')[1])
num = self.dico_num_and_numgroup_locus[name][0]
# info sur le premier locus du groupe
type = str(self.ui.tableWidget.item(num-1,1).text())
#print "\ntype deja present : %s"%type
if type != first_type_found:
all_similar = False
else:
if all_similar:
# le groupe est vide, on set le nom avec le type
old_title = str(box.title())
tt = ''
if first_type_found == 'M':
tt = "Microsatellites"
elif first_type_found == 'S':
tt = "Sequences"
if tt != '':
box.setTitle("%s %s : %s"%(old_title.split()[0],old_title.split()[1],tt))
# on met à jour le dico des groupes
self.group_info_dico[box][0] = tt
if all_similar:
# déselection des présents
for ind_to_unselect in range(listwidget.count()):
listwidget.item(ind_to_unselect).setSelected(False)
# ajout des nouveaux
for row in row_list:
name = self.ui.tableWidget.item(row,0).text()
# ajout trié dans le groupe
i = 0
#num_to_insert = int(name.split(' ')[1])
num_to_insert = row+1
while i < listwidget.count() and self.dico_num_and_numgroup_locus[str(listwidget.item(i).text())][0] < num_to_insert :
i+=1
#box.findChild(QListWidget,"locusGroupList").addItem(name)
box.findChild(QListWidget,"locusGroupList").insertItem(i,name)
box.findChild(QListWidget,"locusGroupList").item(i).setSelected(True)
# on cache la ligne
self.ui.tableWidget.setRowHidden(row,True)
# on met à jour le dico des groupes
self.group_info_dico[box][1].append(num_to_insert)
# on met à jour le numero du groupe pour ce locus
self.dico_num_and_numgroup_locus[str(name)][1] = (self.groupList.index(box)+1)
else:
output.notify(self,"Group error","In a group, all the loci must have the same type")
def rmFromGroup(self,box=None):
""" retire les loci selectionnés du groupe du bouton pressé
"""
if box == None:
box = self.sender().parent()
listw_of_group = box.findChild(QListWidget,"locusGroupList")
row_list = []
selection = listw_of_group.selectedIndexes()
for it in selection:
if it.row() not in row_list:
row_list.append(int(it.row()))
row_list.sort()
row_list.reverse()
for row in row_list:
name = str(listw_of_group.item(row).text())
#num = int(name.split(' ')[1])
num = self.dico_num_and_numgroup_locus[name][0]
# retrait du groupe
#item = listw_of_group.takeItem(row)
listw_of_group.takeItem(row)
# on decouvre la ligne
self.ui.tableWidget.setRowHidden(num-1,False)
# on met à jour le dico des groupes
self.group_info_dico[box][1].remove(num)
self.dico_num_and_numgroup_locus[name][1] = 0
# si le groupe devient vide, on enleve le type dans le nom
if listw_of_group.count() == 0:
old_title = str(box.title())
box.setTitle("%s %s"%(old_title.split()[0],old_title.split()[1]))
# on met à jour le dico des groupes
self.group_info_dico[box][0] = ""
## on remet en gras les boutons de mutation model et sum stats
#set_mut_button = box.findChild(QPushButton,"setMutationButton")
#set_sum_button = box.findChild(QPushButton,"setSumButton")
#set_mut_button.setStyleSheet("background-color: #EFB1B3")
#set_sum_button.setStyleSheet("background-color: #EFB1B3")
#fontt = set_mut_button.font()
#fontt.setBold(True)
#set_mut_button.setFont(fontt)
#set_sum_button.setFont(fontt)
def getNbSumStats(self):
""" retourne le nombre total de summary statistics (nb de cases cochées)
"""
nb_sum_stats = 0
for box in self.groupList:
if "Microsatellites" in str(box.title()):
(nstat,stat_txt) = self.setSum_dico[box].getSumConf()
nb_sum_stats += nstat
elif "Sequences" in str(box.title()):
(nstat,stat_txt) = self.setSumSeq_dico[box].getSumConf()
nb_sum_stats += nstat
return nb_sum_stats
def getNbParam(self):
""" retourne le nombre de paramètres mutationnels réels (qui varient. min<max pour le MEAN)
"""
nb_param = 0
for box in self.groupList:
if "Microsatellites" in str(box.title()):
nb_param += self.setMutation_dico[box].getNbParam()
elif "Sequences" in str(box.title()):
nb_param += self.setMutationSeq_dico[box].getNbParam()
return nb_param
def getParamTableHeader(self):
""" retourne la chaine des noms des paramètres pour le conf.th.tmp
"""
result = u""
for box in self.groupList:
if "Microsatellites" in str(box.title()):
params_txt = self.setMutation_dico[box].getParamTableHeader()
elif "Sequences" in str(box.title()):
params_txt = self.setMutationSeq_dico[box].getParamTableHeader()
result += params_txt
return result
def getConstantParameters(self):
""" retourne une liste de noms de paramètres mutationnels qui sont constants
pour chaque groupe, le tout rangé dans un dico indexé par le numero de groupe
"""
result = {}
for i,box in enumerate(self.groupList):
if "Microsatellites" in str(box.title()):
result[i] = self.setMutation_dico[box].getConstantParameters()
elif "Sequences" in str(box.title()):
result[i] = self.setMutationSeq_dico[box].getConstantParameters()
return result
def getSumStatsTableHeader(self):
""" retourne la partie sumstats du table header
"""
result = u""
for box in self.groupList:
if "Microsatellites" in str(box.title()):
sums_txt = self.setSum_dico[box].getSumStatsTableHeader()
elif "Sequences" in str(box.title()):
sums_txt = self.setSumSeq_dico[box].getSumStatsTableHeader()
result += sums_txt
return result
def clearSummaryStats(self,box):
""" vide les summary statistics des microsats
"""
self.setSum_dico[box].exit()
self.setSum_dico[box] = SetSummaryStatisticsMsat(self,box)
self.setSum(box)
def clearSummaryStatsSeq(self,box):
""" vide les summary statistics des sequences
"""
self.setSumSeq_dico[box].exit()
self.setSumSeq_dico[box] = SetSummaryStatisticsSeq(self,box)
self.setSum(box)
class HistDrawn(formHistModelDrawn,baseHistModelDrawn):
""" définition du modèle historique dans le cadre d'une analyse
les valeurs ne sont pas fixées
"""
def __init__(self,analysis,parent=None):
super(HistDrawn,self).__init__(parent)
self.parent=parent
self.parents = Parents(parent)
self.analysis = analysis
self.sc_to_show = self.analysis.chosenSc
self.list_selected_evaluate_sc = self.analysis.candidateScList
self.paramList = []
self.condList = []
self.param_info_dico = {}
self.createWidgets()
self.addTheSc()
self.addTheParams()
self.addTheConditions()
self.hideFixedParams()
self.restoreAnalysisValues()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
self.ui.clearButton.hide()
self.ui.frame_3.hide()
self.ui.frame_2.hide()
#self.ui.scrollArea_3.hide()
self.ui.defPrButton.hide()
self.ui.chkScButton.hide()
self.ui.addScButton.hide()
self.ui.drawPreviewsCheck.hide()
self.ui.refreshPreviewsButton.hide()
self.ui.verticalLayout_6.setAlignment(QtCore.Qt.AlignTop)
self.ui.horizontalLayout_6.setAlignment(QtCore.Qt.AlignLeft)
self.ui.horizontalLayout_2.setAlignment(QtCore.Qt.AlignLeft)
self.ui.horizontalLayout_3.setAlignment(QtCore.Qt.AlignLeft)
self.ui.analysisNameLabel.setText(self.analysis.name)
def restoreAnalysisValues(self):
if self.analysis.histParamsDrawn != None:
for p in self.analysis.histParamsDrawn.keys():
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
if pname == p:
param.findChild(QLineEdit,"minValueParamEdit").setText(self.analysis.histParamsDrawn[p][2])
param.findChild(QLineEdit,"maxValueParamEdit").setText(self.analysis.histParamsDrawn[p][3])
param.findChild(QLineEdit,"meanValueParamEdit").setText(self.analysis.histParamsDrawn[p][4])
param.findChild(QLineEdit,"stValueParamEdit").setText(self.analysis.histParamsDrawn[p][5])
law = self.analysis.histParamsDrawn[p][1]
if law == "LN":
param.findChild(QRadioButton,'logNormalRadio').setChecked(True)
elif law == "NO":
param.findChild(QRadioButton,'normalRadio').setChecked(True)
elif law == "UN":
param.findChild(QRadioButton,'uniformParamRadio').setChecked(True)
elif law == "LU":
param.findChild(QRadioButton,'logUniformRadio').setChecked(True)
def hideFixedParams(self):
fixed_params_list = self.parents.hist_model_win.getFixedParamList()
for box in self.paramList:
name = str(box.findChild(QLabel,"paramNameLabel").text())
if name in fixed_params_list:
box.hide()
log(3,"Hiding parameter %s because its value is fixed"%name)
def addTheSc(self):
# creation de la groupbox a ajouter
groupBox = QtGui.QGroupBox(self.ui.scScrollContent)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Maximum, QtGui.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox.sizePolicy().hasHeightForWidth())
groupBox.setSizePolicy(sizePolicy)
groupBox.setObjectName("groupBox_"+str(self.sc_to_show))
verticalLayout_6 = QtGui.QVBoxLayout(groupBox)
verticalLayout_6.setObjectName("verticalLayout_6")
horizontalLayout_6 = QtGui.QHBoxLayout()
horizontalLayout_6.setObjectName("horizontalLayout_6")
label_3 = QtGui.QLabel("scenario %i"%self.sc_to_show,groupBox)
# ne mettre qu'un seul label du nom scLabel pour pouvoir le retrouver avec findChild()
label_3.setObjectName("scLabel")
horizontalLayout_6.addWidget(label_3)
verticalLayout_6.addLayout(horizontalLayout_6)
plainTextEdit = QtGui.QPlainTextEdit(groupBox)
plainTextEdit.setLineWrapMode(QtGui.QPlainTextEdit.NoWrap)
plainTextEdit.setObjectName("scplainTextEdit")
verticalLayout_6.addWidget(plainTextEdit)
# ajout de la groupbox
self.ui.horizontalLayout_3.addWidget(groupBox)
# recup du texte du scenario
plainTextEdit.setPlainText(self.getScText())
plainTextEdit.setReadOnly(True)
def getScText(self):
""" récupère le texte du scenario concerné dans le modèle historique de la reftable
"""
return self.parents.hist_model_win.scList[self.sc_to_show-1].findChild(QPlainTextEdit,"scplainTextEdit").toPlainText()
def addTheParams(self):
""" trouve et ajoute les paramètres du scenario concerné
"""
try:
sc = str(self.getScText())
scChecker = Scenario(number=self.sc_to_show)
scChecker.checkread(sc.strip().split('\n'),self.parents.data)
scChecker.checklogic()
dico_sc_infos = {}
dico_sc_infos["text"] = sc.strip().split('\n')
dico_sc_infos["checker"] = scChecker
#print "nb param du sc ",num," ",scChecker.nparamtot
except Exception as e:
output.notify(self,"Unexpected Error",str(e))
self.exit()
return
# calcul des infos pour savoir si on peut setCondition sur ce param
dico_cat = {}
lprem = []
for param in scChecker.parameters:
if dico_cat.has_key(param.category):
dico_cat[param.category] += 1
else:
lprem.append(param.name)
dico_cat[param.category] = 1
dico_param = self.parents.hist_model_win.param_info_dico
for param in scChecker.parameters:
pname = param.name
pcat = param.category
visible = False
if pname not in lprem and dico_cat[pcat] > 1:
visible = True
elem = dico_param[pname]
self.addParamGui(pname,elem[1],elem[2],elem[3],elem[4],elem[5],visible)
self.param_info_dico[pname] = [pcat]
def addTheConditions(self):
""" récupère les conditions du modèle historique de la reftable contenant
uniquement des paramètre du scenarion concerné
"""
self.majParamInfoDico()
for condbox in self.parents.hist_model_win.condList:
txt = str(condbox.findChild(QLabel,"condLabel").text())
if "<=" in txt:
sep = "<="
elif ">=" in txt:
sep = ">="
elif ">" in txt:
sep = ">"
elif "<" in txt:
sep = "<"
termes = txt.split(sep)
if termes[0] in self.param_info_dico.keys() and termes[1] in self.param_info_dico.keys():
self.addCondition(txt)
def addParamGui(self,name,law,min,max,mean,stdev,visible):
""" ajoute un paramètre à la GUI et à la liste locale de paramètres
et retourne la groupBox créée
"""
groupBox_8 = QtGui.QFrame(self.ui.scrollArea)
#groupBox_8.setFrameShape(QtGui.QFrame.StyledPanel)
#groupBox_8.setFrameShadow(QtGui.QFrame.Raised)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_8.sizePolicy().hasHeightForWidth())
groupBox_8.setSizePolicy(sizePolicy)
groupBox_8.setMinimumSize(QtCore.QSize(0, 26))
groupBox_8.setMaximumSize(QtCore.QSize(16777215, 26))
groupBox_8.setObjectName("groupBox_8")
horizontalLayout_13 = QtGui.QHBoxLayout(groupBox_8)
horizontalLayout_13.setObjectName("horizontalLayout_13")
horizontalLayout_13.setContentsMargins(-1, 1, -1, 1)
groupBox_9 = QtGui.QGroupBox(groupBox_8)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_9.sizePolicy().hasHeightForWidth())
groupBox_9.setSizePolicy(sizePolicy)
groupBox_9.setMinimumSize(QtCore.QSize(140, 25))
groupBox_9.setMaximumSize(QtCore.QSize(140, 25))
groupBox_9.setObjectName("groupBox_9")
horizontalLayout_8 = QtGui.QHBoxLayout(groupBox_9)
horizontalLayout_8.setObjectName("horizontalLayout_8")
horizontalLayout_8.setContentsMargins(-1, 1, -1, 1)
paramNameLabel = QtGui.QLabel(name,groupBox_9)
paramNameLabel.setObjectName("paramNameLabel")
horizontalLayout_8.addWidget(paramNameLabel)
setCondButton = QtGui.QPushButton("set condition",groupBox_9)
setCondButton.setObjectName("setCondButton")
setCondButton.setMinimumSize(QtCore.QSize(80, 20))
setCondButton.setMaximumSize(QtCore.QSize(80, 20))
if not visible:
setCondButton.hide()
else:
QObject.connect(setCondButton,SIGNAL("clicked()"),self.setConditionAction)
if "darwin" in sys.platform:
ff = setCondButton.font()
ff.setPointSize(10)
setCondButton.setFont(ff)
else:
ff = setCondButton.font()
ff.setPointSize(8)
setCondButton.setFont(ff)
horizontalLayout_8.addWidget(setCondButton)
horizontalLayout_13.addWidget(groupBox_9)
groupBox_10 = QtGui.QGroupBox(groupBox_8)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_10.sizePolicy().hasHeightForWidth())
groupBox_10.setSizePolicy(sizePolicy)
groupBox_10.setMinimumSize(QtCore.QSize(290, 25))
groupBox_10.setMaximumSize(QtCore.QSize(290, 25))
groupBox_10.setObjectName("groupBox_10")
horizontalLayout_9 = QtGui.QHBoxLayout(groupBox_10)
horizontalLayout_9.setObjectName("horizontalLayout_9")
horizontalLayout_9.setContentsMargins(-1, 1, -1, 1)
uniformParamRadio = QtGui.QRadioButton(groupBox_10)
uniformParamRadio.setChecked(True)
uniformParamRadio.setObjectName("uniformParamRadio")
uniformParamRadio.setMinimumSize(QtCore.QSize(20, 0))
horizontalLayout_9.addWidget(uniformParamRadio)
logUniformRadio = QtGui.QRadioButton(groupBox_10)
logUniformRadio.setObjectName("logUniformRadio")
logUniformRadio.setMinimumSize(QtCore.QSize(20, 0))
horizontalLayout_9.addWidget(logUniformRadio)
normalRadio = QtGui.QRadioButton(groupBox_10)
normalRadio.setObjectName("normalRadio")
normalRadio.setMinimumSize(QtCore.QSize(20, 0))
horizontalLayout_9.addWidget(normalRadio)
logNormalRadio = QtGui.QRadioButton(groupBox_10)
logNormalRadio.setObjectName("logNormalRadio")
logNormalRadio.setMinimumSize(QtCore.QSize(20, 0))
## alignement des radio
#uniformParamRadio.setAlignment(QtCore.Qt.AlignCenter)
#logUniformRadio.setAlignment(QtCore.Qt.AlignCenter)
#normalRadio.setAlignment(QtCore.Qt.AlignCenter)
#logNormalRadio.setAlignment(QtCore.Qt.AlignCenter)
horizontalLayout_9.addWidget(logNormalRadio)
horizontalLayout_9.insertStretch(4)
horizontalLayout_9.insertStretch(3)
horizontalLayout_9.insertStretch(2)
horizontalLayout_9.insertStretch(1)
horizontalLayout_9.insertStretch(0)
horizontalLayout_13.addWidget(groupBox_10)
groupBox_14 = QtGui.QGroupBox(groupBox_8)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_14.sizePolicy().hasHeightForWidth())
groupBox_14.setSizePolicy(sizePolicy)
groupBox_14.setMinimumSize(QtCore.QSize(0, 25))
groupBox_14.setMaximumSize(QtCore.QSize(16777215,25))
groupBox_14.setObjectName("groupBox_14")
horizontalLayout_10 = QtGui.QHBoxLayout(groupBox_14)
horizontalLayout_10.setObjectName("horizontalLayout_10")
horizontalLayout_10.setContentsMargins(-1, 1, -1, 1)
minValueParamEdit = QtGui.QLineEdit(groupBox_14)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(minValueParamEdit.sizePolicy().hasHeightForWidth())
minValueParamEdit.setSizePolicy(sizePolicy)
minValueParamEdit.setMinimumSize(QtCore.QSize(60, 0))
minValueParamEdit.setMaximumSize(QtCore.QSize(60, 16777215))
minValueParamEdit.setObjectName("minValueParamEdit")
horizontalLayout_10.addWidget(minValueParamEdit)
maxValueParamEdit = QtGui.QLineEdit(groupBox_14)
maxValueParamEdit.setMinimumSize(QtCore.QSize(60, 0))
maxValueParamEdit.setMaximumSize(QtCore.QSize(60, 16777215))
maxValueParamEdit.setObjectName("maxValueParamEdit")
horizontalLayout_10.addWidget(maxValueParamEdit)
meanValueParamEdit = QtGui.QLineEdit(groupBox_14)
meanValueParamEdit.setMinimumSize(QtCore.QSize(60, 0))
meanValueParamEdit.setMaximumSize(QtCore.QSize(60, 16777215))
meanValueParamEdit.setObjectName("meanValueParamEdit")
horizontalLayout_10.addWidget(meanValueParamEdit)
stValueParamEdit = QtGui.QLineEdit(groupBox_14)
stValueParamEdit.setMinimumSize(QtCore.QSize(60, 0))
stValueParamEdit.setMaximumSize(QtCore.QSize(60, 16777215))
stValueParamEdit.setObjectName("stValueParamEdit")
horizontalLayout_10.addWidget(stValueParamEdit)
horizontalLayout_13.addWidget(groupBox_14)
self.ui.verticalLayout_6.addWidget(groupBox_8)
# liste locale des paramètres
self.paramList.append(groupBox_8)
minValueParamEdit.setText(min)
maxValueParamEdit.setText(max)
meanValueParamEdit.setText(mean)
stValueParamEdit.setText(stdev)
if law == "UN":
uniformParamRadio.setChecked(True)
elif law == "NO":
normalRadio.setChecked(True)
elif law == "LN":
logNormalRadio.setChecked(True)
elif law == "LU":
logUniformRadio.setChecked(True)
return groupBox_8
def setConditionAction(self):
""" methode qui receptionne l'evennement du clic sur "set condition"
ajout d'une condition sur un paramètre ou une paire de paramètres
"""
param_src = self.sender().parent().findChild(QLabel,"paramNameLabel").text()
# construction de la liste des params qui sont dans la même catégorie que le notre
target_list = []
for pname in self.param_info_dico.keys():
if pname != param_src and self.param_info_dico[str(pname)][0] == self.param_info_dico[str(param_src)][0]:
target_list.append(pname)
self.setCondition = SetCondition(self.sender().parent().findChild(QLabel,"paramNameLabel").text(),target_list,self)
self.setCondition.show()
def majParamInfoDico(self):
""" met a jour les infos des paramètres dans l'attribut param_info_dico
"""
# recup des valeurs pour les params
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
min = str(param.findChild(QLineEdit,"minValueParamEdit").text())
max = str(param.findChild(QLineEdit,"maxValueParamEdit").text())
mean = str(param.findChild(QLineEdit,"meanValueParamEdit").text())
stdev = str(param.findChild(QLineEdit,"stValueParamEdit").text())
if param.findChild(QRadioButton,'logNormalRadio').isChecked():
law = "LN"
elif param.findChild(QRadioButton,'normalRadio').isChecked():
law = "NO"
elif param.findChild(QRadioButton,'uniformParamRadio').isChecked():
law = "UN"
elif param.findChild(QRadioButton,'logUniformRadio').isChecked():
law = "LU"
visible = param.findChild(QPushButton,"setCondButton").isVisible()
self.param_info_dico[pname] = [self.param_info_dico[pname][0],law,min,max,mean,stdev,visible]
def addCondition(self,cond_str=""):
""" ajout d'une condition dans la zone du bas réservée à cet effet
"""
groupBox_cond = QtGui.QGroupBox(self.ui.scrollAreaWidgetContents_3)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Maximum, QtGui.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_cond.sizePolicy().hasHeightForWidth())
groupBox_cond.setSizePolicy(sizePolicy)
groupBox_cond.setTitle("")
groupBox_cond.setObjectName("groupBox_6")
groupBox_cond.setMaximumSize(QtCore.QSize(100, 44))
verticalLayout_2 = QtGui.QVBoxLayout(groupBox_cond)
verticalLayout_2.setObjectName("verticalLayout_2")
verticalLayout_2.setContentsMargins(-1, 1, -1, 1)
label_2 = QtGui.QLabel(cond_str,groupBox_cond)
label_2.setObjectName("condLabel")
label_2.setAlignment(QtCore.Qt.AlignCenter)
label_2.setMinimumSize(QtCore.QSize(52, 11))
label_2.setMaximumSize(QtCore.QSize(52, 11))
verticalLayout_2.addWidget(label_2)
pushButton_5 = QtGui.QPushButton("remove",groupBox_cond)
#sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Maximum, QtGui.QSizePolicy.Fixed)
#sizePolicy.setHorizontalStretch(0)
#sizePolicy.setVerticalStretch(0)
#sizePolicy.setHeightForWidth(pushButton_5.sizePolicy().hasHeightForWidth())
#pushButton_5.setSizePolicy(sizePolicy)
pushButton_5.setMinimumSize(QtCore.QSize(52, 17))
pushButton_5.setMaximumSize(QtCore.QSize(52, 17))
pushButton_5.setObjectName("rmCondButton")
verticalLayout_2.addWidget(pushButton_5)
# ajout dans la GUI
self.ui.horizontalLayout_2.addWidget(groupBox_cond)
# evennement de suppression de la condition
QObject.connect(pushButton_5,SIGNAL("clicked()"),self.rmCond)
self.condList.append(groupBox_cond)
def rmCond(self,condBox=None):
""" Suppression d'une condition sur les variables
dans l'affichage et dans la liste locale
"""
if condBox == None:
condBox = self.sender().parent()
condBox.hide()
self.condList.remove(condBox)
def checkAll(self):
""" verification de la coherence des valeurs du modèle historique
"""
# pour tous les params, min<=max, tout>0
problems = ""
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
try:
min = float(param.findChild(QLineEdit,"minValueParamEdit").text())
max = float(param.findChild(QLineEdit,"maxValueParamEdit").text())
mean = float(param.findChild(QLineEdit,"meanValueParamEdit").text())
stdev = float(param.findChild(QLineEdit,"stValueParamEdit").text())
#step = float(param.findChild(QLineEdit,"stepValueParamEdit").text())
if min > max or min < 0 or max < 0 or mean < 0 or stdev < 0:
problems += "Values for parameter %s are incoherent\n"%pname
except Exception as e:
problems += "%s\n"%e
if problems == "":
return True
else:
QMessageBox.information(self,"Value error","%s"%problems)
return False
def getNextWidgetSnp(self):
""" méthode appelée par ping pong
"""
if self.analysis.category == "bias":
#next_title = "bias and precision"
return SetupEstimationBias(self.analysis,self.parent)
else:
#next_title = "evaluate confidence"
return SetupComparisonConfidence(self.analysis,self.parent)
def getNextWidgetMsatSeq(self):
""" méthode appelée par ping pong
"""
return SetGeneticDataAnalysis(self.analysis,self.parent.parent)
def validate(self):
""" validation du historical model, nous n'avons ici que les valeurs à vérifier
"""
if self.checkAll():
self.majParamInfoDico()
self.analysis.histParamsDrawn = self.param_info_dico
lCond = []
for cb in self.condList:
lCond.append(str(cb.findChild(QLabel,"condLabel").text()))
self.analysis.condTxtList = lCond
# appel ping pong
next_widget = self.parents.getNextWidget(self)
self.ui.parents.analysisStack.addWidget(next_widget)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(next_widget)
self.parents.updateDoc(next_widget)
def exit(self):
## reactivation des onglets
#self.parent.parent.setTabEnabled(1,True)
#self.parent.parent.setTabEnabled(0,True)
#self.parent.parent.removeTab(self.parent.parent.indexOf(self))
#self.parent.parent.setCurrentIndex(1)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
def getNbParam(self):
return len(self.paramList)
class GenericScenarioSelection(formGenericScenarioSelection,baseGenericScenarioSelection):
""" Sélection du scenario dans la cadre d'une analyse de type comparison ou estimate
"""
def __init__(self,nb_sc,label,next_widget,next_title,nb_min_sel,analysis,parent):
super(GenericScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.nb_min_sel = nb_min_sel
self.next_widget = next_widget
self.next_title = next_title
self.checklist = []
self.createWidgets()
self.ui.selectionLabel.setText(label)
self.ui.analysisTypeLabel.setText(self.next_title)
self.ui.projectDirEdit.setText(self.parents.dir)
self.putChoices()
self.ui.verticalLayout_3.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_3.setAlignment(Qt.AlignTop)
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.ui.verticalLayout.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
self.ui.analysisNameLabel.setText(self.analysis.name)
def restoreAnalysisValues(self):
""" Si on est en edition d'analyse, elle possède déjà des valeurs que
l'on doit afficher
"""
if self.analysis.candidateScList != []:
for i,ch in enumerate(self.checklist):
ch.setChecked((i+1) in self.analysis.candidateScList)
def validate(self):
""" passe à l'étape suivante de définition de l'analyse
"""
if len(self.getListSelectedScenarios()) >= self.nb_min_sel:
self.analysis.candidateScList = self.getListSelectedScenarios()
self.next_widget.setScenarios(self.analysis.candidateScList)
analysis_in_edition = (self.analysis.computationParameters != "")
if self.analysis.category == "compare" and not analysis_in_edition:
self.next_widget.setRecordValues(self.analysis.candidateScList)
self.ui.parents.analysisStack.addWidget(self.next_widget)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(self.next_widget)
self.parents.updateDoc(self.next_widget)
else:
QMessageBox.information(self,"Selection error","At least %s scenarios have to be selected"%self.nb_min_sel)
def getListSelectedScenarios(self):
""" retourne la liste des scenarios choisis
"""
res = []
for i,ch in enumerate(self.checklist):
if ch.isChecked():
res.append(i+1)
return res
def putChoices(self):
""" met les choix de scenario en place
"""
bg = QButtonGroup(self)
left = True
for i in range(self.nb_sc):
num = i+1
if self.analysis.category == "modelChecking":
check = QRadioButton("Scenario %s"%num,self)
bg.addButton(check)
else:
check = QCheckBox("Scenario %s"%num,self)
if self.analysis.category == "compare":
check.setChecked(True)
self.checklist.append(check)
if left:
self.ui.verticalLayout.addWidget(check)
else:
self.ui.verticalLayout_2.addWidget(check)
left = not left
# les deux cas où on a pas le choix des scenarios parce qu'ils sont trop peu
if self.nb_sc == 1:
self.checklist[0].setChecked(True)
self.checklist[0].setDisabled(True)
self.next_widget.ui.redefButton.hide()
log(4,"type of next widget : %s"%type(self.next_widget))
if self.nb_sc == 2 and "Comparison" in str(type(self.next_widget)):
self.checklist[0].setChecked(True)
self.checklist[0].setDisabled(True)
self.checklist[1].setChecked(True)
self.checklist[1].setDisabled(True)
self.next_widget.ui.redefButton.hide()
def exit(self):
# reactivation des onglets
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
def __init__(self,parent,analysis):
super(ViewAnalysisParameters,self).__init__(parent)
self.parent = parent
self.analysis = analysis
self.parents = Parents(self.parent)
self.createWidgets()
class HistFixed(formHistModelFixed,baseHistModelFixed):
""" définition du modèle historique dans le cadre d'une analyse
les valeurs sont fixées
"""
def __init__(self,analysis,parent=None):
super(HistFixed,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.sc_to_show = self.analysis.chosenSc
self.list_selected_evaluate_sc = self.analysis.candidateScList
self.paramList = []
self.condList = []
self.param_info_dico = {}
self.createWidgets()
self.addTheSc()
self.addTheParams()
self.restoreAnalysisValues()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
self.ui.clearButton.hide()
self.ui.frame_3.hide()
self.ui.frame_2.hide()
self.ui.scrollArea_3.hide()
self.ui.defPrButton.hide()
self.ui.chkScButton.hide()
self.ui.addScButton.hide()
self.ui.groupBox_12.hide()
self.ui.maxLabel.hide()
self.ui.meanLabel.hide()
# self.ui.label_11.hide()
self.ui.stdevLabel.hide()
self.ui.minLabel.setText("Value")
self.ui.drawPreviewsCheck.hide()
self.ui.refreshPreviewsButton.hide()
self.ui.groupBox_13.setMinimumSize(QtCore.QSize(150, 20))
self.ui.groupBox_13.setMaximumSize(QtCore.QSize(150,20))
self.ui.verticalLayout_6.setAlignment(QtCore.Qt.AlignTop)
self.ui.horizontalLayout_5.setAlignment(QtCore.Qt.AlignLeft)
self.ui.horizontalLayout_6.setAlignment(QtCore.Qt.AlignLeft)
self.ui.horizontalLayout_2.setAlignment(QtCore.Qt.AlignLeft)
self.ui.horizontalLayout_3.setAlignment(QtCore.Qt.AlignLeft)
self.ui.analysisNameLabel.setText(self.analysis.name)
def restoreAnalysisValues(self):
if self.analysis.histParamsFixed != None:
for p in self.analysis.histParamsFixed.keys():
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
if pname == p:
param.findChild(QLineEdit,"meanValueParamEdit").setText(self.analysis.histParamsFixed[p][1])
def addTheSc(self):
# creation de la groupbox a ajouter
groupBox = QtGui.QGroupBox(self.ui.scScrollContent)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Maximum, QtGui.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox.sizePolicy().hasHeightForWidth())
groupBox.setSizePolicy(sizePolicy)
groupBox.setObjectName("groupBox_"+str(self.sc_to_show))
verticalLayout_6 = QtGui.QVBoxLayout(groupBox)
verticalLayout_6.setObjectName("verticalLayout_6")
horizontalLayout_6 = QtGui.QHBoxLayout()
horizontalLayout_6.setObjectName("horizontalLayout_6")
label_3 = QtGui.QLabel("scenario %i"%self.sc_to_show,groupBox)
# ne mettre qu'un seul label du nom scLabel pour pouvoir le retrouver avec findChild()
label_3.setObjectName("scLabel")
horizontalLayout_6.addWidget(label_3)
verticalLayout_6.addLayout(horizontalLayout_6)
plainTextEdit = QtGui.QPlainTextEdit(groupBox)
plainTextEdit.setLineWrapMode(QtGui.QPlainTextEdit.NoWrap)
plainTextEdit.setObjectName("scplainTextEdit")
verticalLayout_6.addWidget(plainTextEdit)
# ajout de la groupbox
self.ui.horizontalLayout_3.addWidget(groupBox)
# recup du texte du scenario
plainTextEdit.setPlainText(self.getScText())
plainTextEdit.setReadOnly(True)
def getScText(self):
""" récupère le texte du scenario concerné dans le modèle historique de la reftable
"""
return self.parents.hist_model_win.scList[self.sc_to_show-1].findChild(QPlainTextEdit,"scplainTextEdit").toPlainText()
def addTheParams(self):
""" trouve et ajoute les paramètres du scenario concerné
"""
try:
sc = str(self.getScText())
scChecker = Scenario(number=self.sc_to_show)
scChecker.checkread(sc.strip().split('\n'),self.parents.data)
scChecker.checklogic()
dico_sc_infos = {}
dico_sc_infos["text"] = sc.strip().split('\n')
dico_sc_infos["checker"] = scChecker
#print "nb param du sc ",num," ",scChecker.nparamtot
except Exception as e:
output.notify(str(e))
self.exit()
return
visible = False
dico_param = self.parents.hist_model_win.param_info_dico
for param in scChecker.parameters:
pname = param.name
pcat = param.category
elem = dico_param[pname]
val = (float(elem[2]) + float(elem[3])) / 2
self.addParamGui(pname,str(val),visible)
self.param_info_dico[pname] = [pcat]
def addParamGui(self,name,val,visible):
""" ajoute un paramètre à la GUI et à la liste locale de paramètres
et retourne la groupBox créée
"""
groupBox_8 = QtGui.QFrame(self.ui.scrollArea)
#groupBox_8.setFrameShape(QtGui.QFrame.StyledPanel)
#groupBox_8.setFrameShadow(QtGui.QFrame.Raised)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_8.sizePolicy().hasHeightForWidth())
groupBox_8.setSizePolicy(sizePolicy)
groupBox_8.setMinimumSize(QtCore.QSize(0, 26))
groupBox_8.setMaximumSize(QtCore.QSize(16777215, 26))
groupBox_8.setObjectName("groupBox_8")
horizontalLayout_13 = QtGui.QHBoxLayout(groupBox_8)
horizontalLayout_13.setAlignment(QtCore.Qt.AlignLeft)
horizontalLayout_13.setObjectName("horizontalLayout_13")
horizontalLayout_13.setContentsMargins(-1, 1, -1, 1)
groupBox_9 = QtGui.QGroupBox(groupBox_8)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_9.sizePolicy().hasHeightForWidth())
groupBox_9.setSizePolicy(sizePolicy)
groupBox_9.setMinimumSize(QtCore.QSize(140, 25))
groupBox_9.setMaximumSize(QtCore.QSize(140, 25))
groupBox_9.setObjectName("groupBox_9")
horizontalLayout_8 = QtGui.QHBoxLayout(groupBox_9)
horizontalLayout_8.setObjectName("horizontalLayout_8")
horizontalLayout_8.setContentsMargins(-1, 1, -1, 1)
paramNameLabel = QtGui.QLabel(name,groupBox_9)
paramNameLabel.setObjectName("paramNameLabel")
horizontalLayout_8.addWidget(paramNameLabel)
setCondButton = QtGui.QPushButton("set condition",groupBox_9)
setCondButton.setObjectName("setCondButton")
setCondButton.setMinimumSize(QtCore.QSize(80, 20))
setCondButton.setMaximumSize(QtCore.QSize(80, 20))
if not visible:
setCondButton.hide()
else:
QObject.connect(setCondButton,SIGNAL("clicked()"),self.setConditionAction)
if "darwin" in sys.platform:
ff = setCondButton.font()
ff.setPointSize(10)
setCondButton.setFont(ff)
else:
ff = setCondButton.font()
ff.setPointSize(8)
setCondButton.setFont(ff)
horizontalLayout_8.addWidget(setCondButton)
horizontalLayout_13.addWidget(groupBox_9)
groupBox_14 = QtGui.QGroupBox(groupBox_8)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(groupBox_14.sizePolicy().hasHeightForWidth())
groupBox_14.setSizePolicy(sizePolicy)
groupBox_14.setMinimumSize(QtCore.QSize(150, 25))
groupBox_14.setMaximumSize(QtCore.QSize(150,25))
groupBox_14.setObjectName("groupBox_14")
horizontalLayout_10 = QtGui.QHBoxLayout(groupBox_14)
horizontalLayout_10.setObjectName("horizontalLayout_10")
horizontalLayout_10.setContentsMargins(-1, 1, -1, 1)
meanValueParamEdit = QtGui.QLineEdit(groupBox_14)
meanValueParamEdit.setMinimumSize(QtCore.QSize(60, 0))
meanValueParamEdit.setMaximumSize(QtCore.QSize(60, 16777215))
meanValueParamEdit.setObjectName("meanValueParamEdit")
horizontalLayout_10.addWidget(meanValueParamEdit)
horizontalLayout_13.addWidget(groupBox_14)
self.ui.verticalLayout_6.addWidget(groupBox_8)
# liste locale des paramètres
self.paramList.append(groupBox_8)
meanValueParamEdit.setText(val)
return groupBox_8
def majParamInfoDico(self):
""" met a jour les infos des paramètres dans l'attribut param_info_dico
"""
# recup des valeurs pour les params
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
val = str(param.findChild(QLineEdit,"meanValueParamEdit").text())
self.param_info_dico[pname] = [self.param_info_dico[pname][0],val]
def checkAll(self):
""" verification de la coherence des valeurs du modèle historique. Vérification des conditions.
"""
problems = ""
conditions = defaultdict(set)
for cond in self.parents.findChildren(QtGui.QLabel, "condLabel") :
condText = str(cond.text()).strip()
for b in ['<=','<','>=','>'] :
if b in condText :
a,c = condText.split(b)
conditions[a].add((b,c))
break
paramValues = {}
for param in self.paramList:
pname = str(param.findChild(QLabel,"paramNameLabel").text())
try:
value = float(param.findChild(QLineEdit,"meanValueParamEdit").text())
paramValues[pname] = value
if value < 0:
problems += "Values for parameter %s are incoherent.\n"%pname
except Exception as e:
problems += "%s.\n"%e
for pname in paramValues.keys() :
for condition in conditions[pname] :
if not eval("{0} {1} {2}".format(paramValues[pname], condition[0], paramValues[condition[1]])) :
problems += "Parameter {0} ({1}) must be {2} to parameter {3} ({4}).\n".format(pname, paramValues[pname], condition[0], condition[1], paramValues[condition[1]])
if problems == "":
return True
else:
QMessageBox.information(self,"Value error","%s"%problems)
return False
def getNextWidgetSnp(self):
""" methode appelée par ping pong
"""
if self.analysis.category == "bias":
#next_title = "bias and precision"
return SetupEstimationBias(self.analysis,self.parent)
else:
#next_title = "evaluate confidence"
return SetupComparisonConfidence(self.analysis,self.parent)
def getNextWidgetMsatSeq(self):
""" methode appelée par ping pong
"""
return SetGeneticDataAnalysis(self.analysis,self.parent.parent)
def validate(self):
""" on vérifie ici que les valeurs sont bien des float et qu'elles sont bien supérieures à 0
"""
if self.checkAll():
self.majParamInfoDico()
self.analysis.histParamsFixed = self.param_info_dico
# appel ping pong
next_widget = self.parents.getNextWidget(self)
self.ui.parents.analysisStack.addWidget(next_widget)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(next_widget)
self.parents.updateDoc(next_widget)
def exit(self):
## reactivation des onglets
#self.parent.parent.setTabEnabled(1,True)
#self.parent.parent.setTabEnabled(0,True)
#self.parent.parent.removeTab(self.parent.parent.indexOf(self))
#self.parent.parent.setCurrentIndex(1)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
def getNbParam(self):
return len(self.paramList)
class ConfidenceTypeSelection(formConfidenceTypeSelection,baseConfidenceTypeSelection):
""" Selection du scenario dans la cadre d'une analyse de type bias ou confidence
"""
def __init__(self,nb_sc,analysis,parent=None):
super(ConfidenceTypeSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.createWidgets()
self.restoreAnalysisValues()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.posteriorConfidenceButton,SIGNAL("clicked()"),self.checkParameterValues)
QObject.connect(self.ui.priorConfidenceButton,SIGNAL("clicked()"),self.checkParameterValues)
QObject.connect(self.ui.priorGlobalConfidenceButton,SIGNAL("clicked()"),self.checkParameterValues)
QObject.connect(self.ui.priorSpecificConfidenceButton,SIGNAL("clicked()"),self.checkParameterValues)
if "confidence" in self.analysis.category :
pass
#self.ui.analysisTypeLabel.setText("Type based confidence")
else :
log(1,"Should found a confidence scenario but found : " % self.analysis.category)
raise Exception("Should found a confidence scenario but found : " % self.analysis.category)
self.ui.projectDirEdit.setText(self.parents.dir)
self.ui.analysisNameLabel.setText(self.analysis.name)
self.checkParameterValues()
def restoreAnalysisValues(self):
if self.analysis.category == "confidence_posterior_global":
self.ui.posteriorConfidenceButton.setChecked(True)
else :
if self.analysis.category == "confidence_prior_global":
self.ui.priorConfidenceButton.setChecked(True)
self.ui.priorGlobalConfidenceButton.setChecked(True)
elif self.analysis.category == "confidence_prior_specific" or \
(self.analysis.category == "confidence" and len(self.analysis.computationParameters) > 1) :
self.ui.priorConfidenceButton.setChecked(True)
self.ui.priorSpecificConfidenceButton.setChecked(True)
self.checkParameterValues(reset=False)
def checkParameterValues(self, reset=True):
self.ui.priorTypeFrame.hide()
if self.ui.posteriorConfidenceButton.isChecked() :
self.ui.priorGlobalConfidenceButton.setChecked(False)
self.ui.priorSpecificConfidenceButton.setChecked(False)
if self.ui.priorConfidenceButton.isChecked() :
self.ui.priorTypeFrame.show()
def validate(self):
""" passe à l'étape suivante de la définition de l'analyse
"""
next_widget = False
if self.ui.posteriorConfidenceButton.isChecked() :
self.analysis.category = "confidence_posterior_global"
next_widget = SetupComparisonConfidence(analysis=self.analysis, parent=self)
elif self.ui.priorConfidenceButton.isChecked() :
if self.ui.priorGlobalConfidenceButton.isChecked() :
self.analysis.category = "confidence_prior_global"
next_widget = SetupComparisonConfidence(analysis=self.analysis, parent=self)
elif self.ui.priorSpecificConfidenceButton.isChecked() :
self.analysis.category = "confidence_prior_specific"
next_widget = BiasNConfidenceScenarioSelection(len(self.parents.hist_model_win.scList),self.analysis,self)
else :
QMessageBox.information(self,"No prior selection error","You must choose a prior type : GLOBAL or SCENARIO SPECIFIC.")
return 0
else :
QMessageBox.information(self,"No type based selection error","You must choose a type based confidence : Posterior or Prior.")
return 0
self.ui.parents.analysisStack.addWidget(next_widget)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(next_widget)
# skip group loci selection for microsat and seqs analysis
self.parents.updateDoc(next_widget)
def exit(self):
## reactivation des onglets
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
def __init__(self,analysis,parent=None):
super(SetGeneticDataAnalysis,self).__init__(parent)
self.parent = parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.fsCoding = getFsEncoding(logLevel=False)
self.analysisFrame.show()
self.analysisNameLabel.setText(self.analysis.name)
self.ui.addGroupButton.hide()
self.ui.autoGroupButton.hide()
self.ui.clearButton.hide()
self.fillLocusTableFromData()
gen_data_ref = self.parents.gen_data_win
# copie des valeurs de range et size
for locusrow in range(gen_data_ref.ui.tableWidget.rowCount()):
self.ui.tableWidget.setItem(locusrow,2,QTableWidgetItem("%s"%gen_data_ref.ui.tableWidget.item(locusrow,2).text()))
self.ui.tableWidget.setItem(locusrow,3,QTableWidgetItem("%s"%gen_data_ref.ui.tableWidget.item(locusrow,3).text()))
# remplissage des groupes et set des mutation model et sum stats ac valeurs
for numgr,box in enumerate(gen_data_ref.groupList):
title = gen_data_ref.group_info_dico[box][0]
locus_list = gen_data_ref.group_info_dico[box][1]
self.addGroup()
self.groupList[-1].setTitle("Group %s : %s"%(len(self.groupList),title))
self.groupList[-1].findChild(QPushButton,"rmLocusGroupButton").hide()
# selection pour ajouter dans le groupe
for locus in locus_list:
#index = gen_data_ref.dico_num_and_numgroup_locus[locus]
self.ui.tableWidget.setItemSelected(self.ui.tableWidget.item(locus-1,0),True)
self.addToGroup(self.groupList[-1])
# creation des objets mutation model
if self.analysis.drawn :
# on instancie des mutationmodel normaux (mais fait pour analysis)
if "Microsatellites" in str(box.title()):
self.setMutation_dico[self.groupList[-1]] = SetMutationModelMsatAnalysis(self,self.groupList[-1])
self.setMutation_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutation_dico[box].getMutationConf()
if self.analysis.mutationModelDrawn != "":
self.setMutation_dico[self.groupList[-1]].setMutationConf(self.analysis.mutationModelDrawn[numgr].split('\n'))
else:
self.setMutation_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutation_dico[box].getMutationConf().split('\n'))
# on grise ce qui ne varie pas
self.setMutation_dico[self.groupList[-1]].hideFixedParameters()
self.setMutationValid_dico[self.groupList[-1]] = True
elif "Sequences" in str(box.title()):
self.setMutationSeq_dico[self.groupList[-1]] = SetMutationModelSequencesAnalysis(self,self.groupList[-1])
self.setMutationSeq_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutationSeq_dico[box].getMutationConf()
if self.analysis.mutationModelDrawn != "":
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(self.analysis.mutationModelDrawn[numgr].split('\n'))
else:
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutationSeq_dico[box].getMutationConf().split('\n'))
# on grise ce qui ne varie pas
self.setMutationSeq_dico[self.groupList[-1]].hideFixedParameters()
self.setMutationSeqValid_dico[self.groupList[-1]] = True
else:
# on instancie des mutationmodel fixed
if "Microsatellites" in str(box.title()):
self.setMutation_dico[self.groupList[-1]] = SetMutationModelMsatFixed(self,self.groupList[-1])
self.setMutation_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutation_dico[box].getMutationConf()
if self.analysis.mutationModelFixed != "":
self.setMutation_dico[self.groupList[-1]].setMutationConfFromAnalysisValues(self.analysis.mutationModelFixed[numgr])
else:
self.setMutation_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutation_dico[box].getMutationConf().split('\n'))
self.setMutationValid_dico[self.groupList[-1]] = True
# on grise ce qui ne varie pas
if float(str(gen_data_ref.setMutation_dico[box].mmrMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].mmrMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].mmrFrame.setDisabled(True)
if float(str(gen_data_ref.setMutation_dico[box].mcpMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].mcpMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].mcpFrame.setDisabled(True)
if float(str(gen_data_ref.setMutation_dico[box].msrMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].msrMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].msrFrame.setDisabled(True)
elif "Sequences" in str(box.title()):
self.setMutationSeq_dico[self.groupList[-1]] = SetMutationModelSequencesFixed(self,self.groupList[-1])
self.setMutationSeq_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutationSeq_dico[box].getMutationConf()
if self.analysis.mutationModelFixed != "":
self.setMutationSeq_dico[self.groupList[-1]].setMutationConfFromAnalysisValues(self.analysis.mutationModelFixed[numgr])
else:
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutationSeq_dico[box].getMutationConf().split('\n'))
self.setMutationSeqValid_dico[self.groupList[-1]] = True
# on grise ce qui ne varie pas
if float(str(gen_data_ref.setMutationSeq_dico[box].mmrMinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mmrMaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mmrFrame.setDisabled(True)
if float(str(gen_data_ref.setMutationSeq_dico[box].mc1MinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mc1MaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mc1Frame.setDisabled(True)
if float(str(gen_data_ref.setMutationSeq_dico[box].mc2MinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mc2MaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mc2Frame.setDisabled(True)
for box in self.groupList:
box.findChild(QPushButton,"addToGroupButton").hide()
box.findChild(QPushButton,"rmFromGroupButton").hide()
box.findChild(QPushButton,"setSumButton").hide()
class SetGeneticDataAnalysis(SetGeneticData):
""" set genetic data pour les informations concernant une analyse bias ou confidence
"""
def __init__(self,analysis,parent=None):
super(SetGeneticDataAnalysis,self).__init__(parent)
self.parent = parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.fsCoding = getFsEncoding(logLevel=False)
self.analysisFrame.show()
self.analysisNameLabel.setText(self.analysis.name)
self.ui.addGroupButton.hide()
self.ui.autoGroupButton.hide()
self.ui.clearButton.hide()
self.fillLocusTableFromData()
gen_data_ref = self.parents.gen_data_win
# copie des valeurs de range et size
for locusrow in range(gen_data_ref.ui.tableWidget.rowCount()):
self.ui.tableWidget.setItem(locusrow,2,QTableWidgetItem("%s"%gen_data_ref.ui.tableWidget.item(locusrow,2).text()))
self.ui.tableWidget.setItem(locusrow,3,QTableWidgetItem("%s"%gen_data_ref.ui.tableWidget.item(locusrow,3).text()))
# remplissage des groupes et set des mutation model et sum stats ac valeurs
for numgr,box in enumerate(gen_data_ref.groupList):
title = gen_data_ref.group_info_dico[box][0]
locus_list = gen_data_ref.group_info_dico[box][1]
self.addGroup()
self.groupList[-1].setTitle("Group %s : %s"%(len(self.groupList),title))
self.groupList[-1].findChild(QPushButton,"rmLocusGroupButton").hide()
# selection pour ajouter dans le groupe
for locus in locus_list:
#index = gen_data_ref.dico_num_and_numgroup_locus[locus]
self.ui.tableWidget.setItemSelected(self.ui.tableWidget.item(locus-1,0),True)
self.addToGroup(self.groupList[-1])
# creation des objets mutation model
if self.analysis.drawn :
# on instancie des mutationmodel normaux (mais fait pour analysis)
if "Microsatellites" in str(box.title()):
self.setMutation_dico[self.groupList[-1]] = SetMutationModelMsatAnalysis(self,self.groupList[-1])
self.setMutation_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutation_dico[box].getMutationConf()
if self.analysis.mutationModelDrawn != "":
self.setMutation_dico[self.groupList[-1]].setMutationConf(self.analysis.mutationModelDrawn[numgr].split('\n'))
else:
self.setMutation_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutation_dico[box].getMutationConf().split('\n'))
# on grise ce qui ne varie pas
self.setMutation_dico[self.groupList[-1]].hideFixedParameters()
self.setMutationValid_dico[self.groupList[-1]] = True
elif "Sequences" in str(box.title()):
self.setMutationSeq_dico[self.groupList[-1]] = SetMutationModelSequencesAnalysis(self,self.groupList[-1])
self.setMutationSeq_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutationSeq_dico[box].getMutationConf()
if self.analysis.mutationModelDrawn != "":
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(self.analysis.mutationModelDrawn[numgr].split('\n'))
else:
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutationSeq_dico[box].getMutationConf().split('\n'))
# on grise ce qui ne varie pas
self.setMutationSeq_dico[self.groupList[-1]].hideFixedParameters()
self.setMutationSeqValid_dico[self.groupList[-1]] = True
else:
# on instancie des mutationmodel fixed
if "Microsatellites" in str(box.title()):
self.setMutation_dico[self.groupList[-1]] = SetMutationModelMsatFixed(self,self.groupList[-1])
self.setMutation_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutation_dico[box].getMutationConf()
if self.analysis.mutationModelFixed != "":
self.setMutation_dico[self.groupList[-1]].setMutationConfFromAnalysisValues(self.analysis.mutationModelFixed[numgr])
else:
self.setMutation_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutation_dico[box].getMutationConf().split('\n'))
self.setMutationValid_dico[self.groupList[-1]] = True
# on grise ce qui ne varie pas
if float(str(gen_data_ref.setMutation_dico[box].mmrMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].mmrMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].mmrFrame.setDisabled(True)
if float(str(gen_data_ref.setMutation_dico[box].mcpMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].mcpMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].mcpFrame.setDisabled(True)
if float(str(gen_data_ref.setMutation_dico[box].msrMinEdit.text())) == float(str(gen_data_ref.setMutation_dico[box].msrMaxEdit.text())):
self.setMutation_dico[self.groupList[-1]].msrFrame.setDisabled(True)
elif "Sequences" in str(box.title()):
self.setMutationSeq_dico[self.groupList[-1]] = SetMutationModelSequencesFixed(self,self.groupList[-1])
self.setMutationSeq_dico[self.groupList[-1]].hide()
# on transfere la conf depuis le mutmod reftable
#print "mut conf : %s"%gen_data_ref.setMutationSeq_dico[box].getMutationConf()
if self.analysis.mutationModelFixed != "":
self.setMutationSeq_dico[self.groupList[-1]].setMutationConfFromAnalysisValues(self.analysis.mutationModelFixed[numgr])
else:
self.setMutationSeq_dico[self.groupList[-1]].setMutationConf(gen_data_ref.setMutationSeq_dico[box].getMutationConf().split('\n'))
self.setMutationSeqValid_dico[self.groupList[-1]] = True
# on grise ce qui ne varie pas
if float(str(gen_data_ref.setMutationSeq_dico[box].mmrMinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mmrMaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mmrFrame.setDisabled(True)
if float(str(gen_data_ref.setMutationSeq_dico[box].mc1MinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mc1MaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mc1Frame.setDisabled(True)
if float(str(gen_data_ref.setMutationSeq_dico[box].mc2MinEdit.text())) == float(str(gen_data_ref.setMutationSeq_dico[box].mc2MaxEdit.text())):
self.setMutationSeq_dico[self.groupList[-1]].mc2Frame.setDisabled(True)
for box in self.groupList:
box.findChild(QPushButton,"addToGroupButton").hide()
box.findChild(QPushButton,"rmFromGroupButton").hide()
box.findChild(QPushButton,"setSumButton").hide()
def majProjectGui(self,m=None,s=None,g=None,ss=None):
pass
# if m != None:
# self.parent.ui.nbMicrosatLabel.setText("%s microsatellite loci"%m)
# if s != None:
# self.parent.ui.nbSequencesLabel.setText("%s DNA sequence loci"%s)
# if g != None:
# self.parent.ui.nbGroupLabel.setText("%s locus groups"%g)
# if ss != None:
# self.parent.ui.nbSumStatsLabel.setText("%s summary statistics"%ss)
def setSum(self,box=None):
""" déclenché par le clic sur le bouton 'set summary statistics' ou par le clic sur 'clear'
dans 'set summary statistics'. bascule vers la saisie des summary statistics
"""
if box == None:
box = self.sender().parent()
title = str(box.title())
if "Microsatellites" in title:
#self.parent.addTab(self.setSum_dico[box],"Set summary statistics")
#self.parent.setTabEnabled(self.parent.indexOf(self),False)
#self.parent.setCurrentWidget(self.setSum_dico[box])
self.switchTo(self.setSum_dico[box])
# maj du titre de la frame
lab = self.setSum_dico[box].ui.sumStatLabel
lab.setText("Set summary statistics of %s (microsatellites)"%(" ".join(str(box.title()).split()[:2])))
elif "Sequences" in title:
#self.parent.addTab(self.setSumSeq_dico[box],"Set summary statistics")
#self.parent.setTabEnabled(self.parent.indexOf(self),False)
#self.parent.setCurrentWidget(self.setSumSeq_dico[box])
self.switchTo(self.setSumSeq_dico[box])
# maj du titre de la frame
lab = self.setSumSeq_dico[box].ui.sumStatLabel
lab.setText("Set summary statistics of %s (sequences)"%(" ".join(str(box.title()).split()[:2])))
else:
QMessageBox.information(self,"Set Summary statistics error","Add locus to a group before setting the summary statistics")
def switchTo(self,widget):
""" on switche dans la stack analysis
"""
self.ui.parents.analysisStack.addWidget(widget)
self.ui.parents.analysisStack.setCurrentWidget(widget)
def exit(self):
## reactivation des onglets
#self.parent.setTabEnabled(0,True)
#self.parent.setTabEnabled(1,True)
#self.parent.removeTab(self.parent.indexOf(self))
#self.parent.setCurrentIndex(1)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
def validate(self):
""" clic sur le bouton validate
verifie la validité de tous les groupes (mutmodel valide && nbsumstats > 0 && nblocus > 0)
si valide : sort , maj de l'icone de validité et sauve
si non valide : informe et sauve
"""
log(3,"Validation of Genetic Data of analysis")
#print self.group_info_dico
#print self.dico_num_and_numgroup_locus
mutconf_list = []
problem = u""
for i,box in enumerate(self.groupList):
title = str(box.title())
if "Microsatellites" in title:
mutconf_list.append(self.setMutation_dico[box].getMutationConf())
if box not in self.setMutationValid_dico.keys() or not self.setMutationValid_dico[box]:
problem += u"Mutation model of group %s is not considered as valid\n"%(i+1)
elif "Sequences" in title:
mutconf_list.append(self.setMutationSeq_dico[box].getMutationConf())
if box not in self.setMutationSeqValid_dico.keys() or not self.setMutationSeqValid_dico[box]:
problem += u"Mutation model of group %s is not considered as valid\n"%(i+1)
else:
problem += u"Group %s is empty\n"%(i+1)
if problem != u"":
QMessageBox.information(self,"Impossible to validate the genetic data",problem)
self.parents.setGenValid(False)
else:
# c'est valide, on passe à la dernière phase de paramètrage
if self.analysis.drawn:
self.analysis.mutationModelDrawn = mutconf_list
else:
self.analysis.mutationModelFixed = mutconf_list
if self.analysis.category == "bias":
#next_title = "bias and precision"
last_parametrisation = SetupEstimationBias(self.analysis,self)
else:
#next_title = "evaluate confidence"
last_parametrisation = SetupComparisonConfidence(self.analysis,self)
#self.parent.addTab(last_parametrisation,next_title)
#self.parent.removeTab(self.parent.indexOf(self))
#self.parent.setCurrentWidget(last_parametrisation)
self.ui.parents.analysisStack.addWidget(last_parametrisation)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(last_parametrisation)
#self.parent.addAnalysis(self.analysis)
#self.exit()
def clear(self):
""" On supprime tous les groupes
"""
#for i in range(len(self.groupList)):
# self.groupList[i].hide()
for box in self.groupList:
box.hide()
lw = box.findChild(QListWidget,"locusGroupList")
for row in range(lw.count()):
name = str(lw.item(row).text())
#num = int(name.split(' ')[1])
num = self.dico_num_and_numgroup_locus[name][0]
# on decouvre la ligne
self.ui.tableWidget.setRowHidden(num-1,False)
self.groupList = []
def writeGeneticConfFromGui(self):
""" on ecrit l'etat actuel des genetic data dans conf.gen.tmp
"""
if os.path.exists((u"%s/%s"%(self.parents.dir,self.parents.gen_conf_name)).encode(self.fsCoding)):
os.remove((u"%s/%s"%(self.parents.dir,self.parents.gen_conf_name)).encode(self.fsCoding))
f = codecs.open((u"%s/%s"%(self.parents.dir,self.parents.gen_conf_name)).encode(self.fsCoding),'w',"utf-8")
# partie description des locus
f.write("loci description (%i)\n"%self.nbLocusGui)
data = self.parents.data
for i in range(data.nloc):
name = data.locuslist[i].name
type = data.locuslist[i].type
group = self.dico_num_and_numgroup_locus[name][1]
if type > 4:
microSeq = "S"
typestr = LOC_TYP[type-5]
length = data.locuslist[i].dnalength
f.write("%s %s [%s] G%i %s\n"%(name.replace(' ','_'),typestr,microSeq,group,length))
else:
microSeq = "M"
typestr = LOC_TYP[type]
indice_dans_table = self.dico_num_and_numgroup_locus[name][0]
motif_size = str(self.ui.tableWidget.item(indice_dans_table-1,2).text())
motif_range = str(self.ui.tableWidget.item(indice_dans_table-1,3).text()).strip()
f.write("%s %s [%s] G%i %s %s\n"%(name.replace(' ','_'),typestr,microSeq,group,motif_size,motif_range))
# partie mutation model
f.write("\ngroup priors (%i)\n"%len(self.groupList))
if len(self.groupList) == 0:
f.write("\n")
else:
for i,box in enumerate(self.groupList):
if "Microsatellites" in str(box.title()):
f.write("group G%i [M]\n"%(i+1))
f.write(u'%s'%self.setMutation_dico[box].getMutationConf())
elif "Sequences" in str(box.title()):
f.write("group G%i [S]\n"%(i+1))
to_write = u'%s'%self.setMutationSeq_dico[box].getMutationConf()
f.write(to_write)
# partie sum stats
stat_txt_list = []
nstat_tot = 0
for i,box in enumerate(self.groupList):
stat_txt = ""
if "Microsatellites" in str(box.title()):
(nstat_tmp,stat_txt) = self.setSum_dico[box].getSumConf()
stat_header_txt = "group G%i [M] (%i)\n"%((i+1),nstat_tmp)
nstat_tot += nstat_tmp
# construction de la chaine a ecrire pour ce groupe
stat_to_write = stat_header_txt+stat_txt
elif "Sequences" in str(box.title()):
(nstat_tmp,stat_txt) = self.setSumSeq_dico[box].getSumConf()
stat_header_txt = "group G%i [S] (%i)\n"%((i+1),nstat_tmp)
nstat_tot += nstat_tmp
# construction de la chaine a ecrire pour ce groupe
stat_to_write = stat_header_txt+stat_txt
stat_txt_list.append(stat_to_write)
f.write("group summary statistics (%i)\n"%nstat_tot)
for txt in stat_txt_list:
f.write(txt)
#print txt
f.write('\n')
def loadGeneticConf(self):
""" Charge le fichier conf.gen.tmp
"""
# de toute façon, on rempli le tableau de locus
#self.fillLocusTableFromData()
if os.path.exists(str(self.parents.dir).encode(self.fsCoding)):
if os.path.exists((u"%s/%s"%(self.parents.dir,self.parents.gen_conf_name)).encode(self.fsCoding)):
f = codecs.open((u"%s/%s"%(self.parents.dir,self.parents.gen_conf_name)).encode(self.fsCoding),"rU","utf-8")
lines = f.readlines()
nloc = int(lines[0].split('(')[1].split(')')[0])
# determination du nombre de groupes
l = 1
gmax = 0
while l < nloc+1:
g = int(lines[l].split()[3].replace('G',''))
if g > gmax:
gmax = g
l+=1
# creation du bon nombre de groupes
for it in range(gmax):
self.addGroup()
# recup des infos de chaque locus
l = 1
while l < nloc+1:
lname = lines[l].split()[0].replace('_',' ')
#ltype = lines[l].split(' ')[1]
#ltype_num = LOC_TYP.index(ltype)
lmicroSeq = lines[l].split('[')[1].split(']')[0]
num_group = int(lines[l].split()[3].replace('G',''))
# maj du dico
self.dico_num_and_numgroup_locus[lname] = [l,num_group]
if lmicroSeq == 'M':
# ajout ds le groupe
if num_group != 0:
self.ui.tableWidget.setItemSelected(self.ui.tableWidget.item(l-1,0),True)
self.addToGroup(self.groupList[num_group-1])
# maj des infos dans le table
ranger = lines[l].split()[4]
motif = lines[l].split()[5]
self.ui.tableWidget.setItem(l-1,2,QTableWidgetItem("%s"%(ranger)))
self.ui.tableWidget.setItem(l-1,3,QTableWidgetItem("%s"%(motif)))
else:
# ajout ds le groupe
if num_group != 0:
self.ui.tableWidget.setItemSelected(self.ui.tableWidget.item(l-1,0),True)
self.addToGroup(self.groupList[num_group-1])
l+=1
# chargement des infos sur les groupes
l+=1
if l < len(lines):
#print 'ligne:',lines[l]
#nb_groupes = int(lines[l].split('(')[1].split(')')[0])
#num_group_max_done = 0
l+=1
# on va jusqu'à la prochaine ligne vide ou la fin du fichier
while l<len(lines) and lines[l].strip() != "":
#print 'prem ligne du groupe:',lines[l]
num_group = int(lines[l].split('group G')[1].split()[0])
#num_group_max_done = num_group
type_group = lines[l].split('[')[1].split(']')[0]
l+=1
if type_group == 'S':
self.setMutationSeq_dico[self.groupList[num_group-1]].setMutationConf(lines[l:(l+7)])
l+=7
else:
self.setMutation_dico[self.groupList[num_group-1]].setMutationConf(lines[l:(l+6)])
l+=6
# on avance jusqu'au summary stats
while l<len(lines) and "group summary statistics" not in lines[l]:
l+=1
# on est sur la première ligne
#nb_sum_stat = int(lines[l].split('(')[1].split(')')[0])
#print "nbsumstat %s"%nb_sum_stat
l+=1
# parcours de tous les groupes
while l<len(lines) and lines[l].strip() != "":
num_group = int(lines[l].split('group G')[1].split()[0])
type_group = lines[l].split('[')[1].split(']')[0]
l+=1
# parcours des lignes du groupe
lines_group = []
while l<len(lines) and "group" not in lines[l]:
lines_group.append(lines[l].strip())
l+=1
if len(lines_group) > 0:
if type_group == 'S':
self.setSumSeq_dico[self.groupList[num_group-1]].setSumConf(lines_group)
else:
self.setSum_dico[self.groupList[num_group-1]].setSumConf(lines_group)
self.majProjectGui(ss=self.getNbSumStats())
def clearMutationModel(self,box):
self.setMutation_dico[box].exit()
self.setMutation_dico[box] = SetMutationModelMsat(self,box)
self.setMutation(box)
def clearMutationModelSeq(self,box):
self.setMutationSeq_dico[box].exit()
self.setMutationSeq_dico[box] = SetMutationModelSequences(self,box)
self.setMutation(box)
class SetupComparisonConfidence(formSetupComparisonConfidence,baseSetupComparisonConfidence):
""" dernière étape de définition d'une analyse de type comparison ou confidence
"""
def __init__(self,analysis,parent=None):
super(SetupComparisonConfidence,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.scNumList = []
self.dico_values = {}
self.createWidgets()
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
self.parents.updateDoc(self)
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
self.deInterValuesW = []
self.lrInterValuesW = []
self.ui.projectNameEdit.setText(self.parents.dir)
self.ui.gridLayout.setAlignment(Qt.AlignTop)
self.ui.posteriorDistributionFrame.hide()
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.redefButton,SIGNAL("clicked()"),self.redefineScenarios)
QObject.connect(self.ui.numRegCombo,SIGNAL("currentIndexChanged(QString)"),self.updateInterValues)
QObject.connect(self.ui.deEdit,SIGNAL("textChanged(QString)"),self.updateInterValues)
QObject.connect(self.ui.lrEdit,SIGNAL("textChanged(QString)"),self.updateInterValues)
QObject.connect(self.ui.posteriorDistributionSampleSizeEdit,SIGNAL("textChanged(QString)"),self.updateInterValues)
QObject.connect(self.ui.logisticRegressioncheckBox,SIGNAL("stateChanged(int)"),self.updateInterValues)
if "confidence" in self.analysis.category :
self.ui.label.setText("Confidence in scenario choice")
self.setScenarios([self.analysis.chosenSc])
self.setCandidateScenarios(self.analysis.candidateScList)
self.setRecordValues(self.analysis.candidateScList)
self.ui.redefButton.hide()
self.ui.numRegCombo.clear()
self.ui.numRegCombo.addItem("0")
self.ui.numRegCombo.addItem("1")
#self.ui.notdsEdit.setText("500")
self.ui.intermediateValuesFrame.hide()
if self.analysis.category == "confidence_posterior_global" :
self.ui.posteriorDistributionFrame.show()
self.ui.notdsLabel.setText(self.ui.notdsLabel.text().replace("[TO-REPLACE]", "pseudo-observed"))
self.ui.scenarioProbaExplainLabel.setText(self.ui.scenarioProbaExplainLabel.text().replace("[TO-REPLACE]", "pseudo-observed"))
else: # assume self.analysis.category == "compare"
self.ui.logisticRegressioncheckBox.setChecked(True)
self.ui.logisticRegressioncheckBox.hide()
self.ui.notdsEdit.hide()
self.ui.notdsLabel.hide()
self.ui.candidateLabel.hide()
self.setScenarios([self.analysis.chosenSc])
self.setCandidateScenarios(self.analysis.candidateScList)
self.setRecordValues(self.analysis.candidateScList)
self.ui.notdsLabel.setText(self.ui.notdsLabel.text().replace("[TO-REPLACE]", "observed"))
self.ui.scenarioProbaExplainLabel.setText(self.ui.scenarioProbaExplainLabel.text().replace("[TO-REPLACE]", "observed"))
self.ui.numRegCombo.setCurrentIndex(1)
self.ui.deEdit.setText("500")
self.ui.analysisNameLabel.setText(self.analysis.name)
def updateInterValues(self,numstr):
if self.ui.logisticRegressioncheckBox.isChecked() :
self.lrEdit.setEnabled(True)
if "confidence" in self.analysis.category :
self.ui.numRegCombo.setCurrentIndex(self.ui.numRegCombo.findText("1"))
else :
self.lrEdit.setDisabled(True)
if "confidence" in self.analysis.category :
self.ui.numRegCombo.setCurrentIndex(self.ui.numRegCombo.findText("0"))
for w in self.lrInterValuesW:
w.hide()
self.ui.lrValLayout.removeWidget(w)
for w in self.deInterValuesW:
w.hide()
self.ui.deValLayout.removeWidget(w)
self.lrInterValuesW = []
self.deInterValuesW = []
try:
#de = int(self.ui.deEdit.text())
lr = int(self.ui.lrEdit.text())
numreg = int(self.ui.numRegCombo.currentText())
if numreg == 0:
self.ui.lrValuesFrame.setDisabled(True)
self.ui.lrEdit.setDisabled(True)
self.analysis.logreg = False
else :
self.ui.lrValuesFrame.setDisabled(False)
self.ui.lrEdit.setDisabled(False)
self.analysis.logreg = True
#dedec = de/numreg
lrdec = lr/numreg
for i in range(numreg):
lrlab = QLabel(str(lr))
#delab = QLabel(str(de))
self.lrInterValuesW.append(lrlab)
#self.deInterValuesW.append(delab)
self.ui.lrValLayout.addWidget(lrlab)
#self.ui.deValLayout.addWidget(delab)
#de -= dedec
lr -= lrdec
except Exception as e:
print e
def restoreAnalysisValues(self):
if self.analysis.computationParameters != "":
cp = self.analysis.computationParameters
self.ui.cnosdEdit.setText(cp.split('n:')[1].split(';')[0])
self.ui.deEdit.setText(cp.split('d:')[1].split(';')[0])
numreg = cp.split('m:')[1].split(';')[0]
self.ui.numRegCombo.setCurrentIndex(self.ui.numRegCombo.findText(numreg))
if numreg in [1, "1"] :
self.ui.logisticRegressioncheckBox.setChecked(True)
else :
self.ui.logisticRegressioncheckBox.setChecked(False)
self.ui.lrEdit.setText(cp.split('l:')[1].split(';')[0])
if "confidence" in self.analysis.category :
if self.analysis.category == "confidence_posterior_global":
if "z:" in cp :
self.ui.posteriorDistributionSampleSizeEdit.setText(cp.split('z:')[1].split(';')[0])
if "c:" in cp :
self.ui.notdsEdit.setText(cp.split('c:')[1].split(';')[0])
elif self.analysis.category == "confidence_prior_global":
if "b:" in cp :
self.ui.notdsEdit.setText(cp.split('b:')[1].split(';')[0])
elif self.analysis.category in ["confidence_prior_specific", "confidence"]:
if "t:" in cp :
self.ui.notdsEdit.setText(cp.split('t:')[1].split(';')[0])
def checkAll(self):
problems = ""
try:
if "confidence" in self.analysis.category :
notds = int(self.ui.notdsEdit.text())
if self.analysis.category == "confidence_posterior_global":
linearRegrassion = int(self.ui.posteriorDistributionSampleSizeEdit.text())
lr = int(self.ui.lrEdit.text())
de = int(self.ui.deEdit.text())
cnosd = int(self.ui.cnosdEdit.text())
except Exception as e:
problems += "Only non-empty integer values are accepted\n"
if problems == "":
return True
else:
output.notify(self,"value problem",problems)
return False
def validate(self):
""" defini les computation parameters de l'analyse et ajoute celle-ci au projet
"""
analysis_in_edition = (self.analysis.computationParameters != "")
self.analysis.candidateScList = self.scNumList
self.majDicoValues()
chosen_scs_txt = ""
for cs in self.scNumList:
chosen_scs_txt+="%s,"%str(cs)
chosen_scs_txt = chosen_scs_txt[:-1]
if self.checkAll():
if self.analysis.category == "compare":
self.analysis.computationParameters = "s:%s;n:%s;d:%s;l:%s;m:%s;f:%s"%(chosen_scs_txt,self.dico_values['choNumberOfsimData'],self.dico_values['de'],self.dico_values['lr'],self.dico_values['numReg'],self.analysis.fda)
elif "confidence" in self.analysis.category : # == "confidence":
# FIXED :
# "/home/dehneg/diyabc/src-JMC-C++/general"
# -p "/media/psf/Home/VMshare/example_2_microsat_sequence_data_complexe_scenarios_ghost_pop_project_2013_7_9-1/"
# -f "s:1,2;r:1;n:203900;m:1;d:501;l:2039;t:509;f:0;h:t2=25500.0 t1=5005.0 ra=0.5 NS1=25500.0 N1=25500.0 N2=25500.0
# N3=5005.0 NS2=25500.0 ta=5005.0;u:g1(0.00055 2 0.2 2 5.005e-06 2)*g2(0.00055 2 0.2 2 5.005e-06 2)*g3(0.00055
# 2 0.2 2 5.005e-06 2)*g4(5.5e-09 2 10.025 2)*g5(5.05e-08 2 10.025 2)"
# -i fixed
# -g 509
# -m
# -t 1
#PRIOR
#"/home/dehneg/diyabc/src-JMC-C++/general"
# -p "/media/psf/Home/VMshare/example_2_microsat_sequence_data_complexe_scenarios_ghost_pop_project_2013_7_9-1/"
# -f "s:1,2;r:1;n:203900;m:1;d:501;l:2039;t:509;f:0;h:t2=UN[1000,50000.0,0.0,0.0] t1=UN[10.0,10000.0,0.0,0.0] ra=UN[0.001,0.999,0.0,0.0]
# NS1=UN[1000,50000.0,0.0,0.0] N1=UN[1000,50000.0,0.0,0.0] N2=UN[1000,50000.0,0.0,0.0] N3=UN[10,10000.0,0.0,0.0]
# NS2=UN[1000,50000.0,0.0,0.0] ta=UN[10.0,10000.0,0.0,0.0] ta>t1 t2>ta;u:g1(UN[1.00E-004,1.00E-3,0.0005,2]
# GA[1.00E-005,1.00E-002,Mean_u,2] UN[1.00E-001,3.00E-001,0.22,2] GA[1.00E-002,9.00E-001,Mean_P,2]
# LU[1.00E-008,1.00E-005,1.00E-007,2] GA[1.00E-009,1.00E-004,Mean_u_SNI,2])*g2(UN[1.00E-004,1.00E-3,0.0005,2]
# GA[1.00E-005,1.00E-002,Mean_u,2] UN[1.00E-001,3.00E-001,0.22,2] GA[1.00E-002,9.00E-001,Mean_P,2]
# LU[1.00E-008,1.00E-005,1.00E-007,2] GA[1.00E-009,1.00E-004,Mean_u_SNI,2])*g3(UN[1.00E-004,1.00E-3,0.0005,2]
# GA[1.00E-005,1.00E-002,Mean_u,2] UN[1.00E-001,3.00E-001,0.22,2] GA[1.00E-002,9.00E-001,Mean_P,2]
# LU[1.00E-008,1.00E-005,1.00E-007,2]
# GA[1.00E-009,1.00E-004,Mean_u_SNI,2])*g4(UN[1.00E-9,1.00E-8,5E-9,2] GA[1.00E-10,1.00E-7,Mean_u,2] UN[0.050,20,10,2]
# GA[0.050,20,Mean_k1,2] UN[0.050,20,10,2] GA[0.050,20,Mean_k2,2])*g5(UN[1.00E-9,1.00E-7,5E-9,2] GA[1.00E-9,1.00E-6,Mean_u,2]
# UN[0.050,20,10,2] GA[0.050,20,Mean_k1,2] UN[0.050,20,10,2] GA[0.050,20,Mean_k2,2])"
# -i prior
# -g 509 -m -t 1
candListTxt = ""
for cs in self.analysis.candidateScList:
candListTxt+="%s,"%str(cs)
candListTxt = candListTxt[:-1]
strparam = ""
strparam += "n:%s;"%self.dico_values['choNumberOfsimData']
strparam += "m:%s;"%self.dico_values['numReg']
strparam += "d:%s;"%self.dico_values['de']
strparam += "f:%s;"%self.analysis.fda
if self.analysis.category == "confidence_posterior_global":
strparam += "z:%s;" % self.dico_values['linearRegression']
strparam += "l:%s;" % self.dico_values['lr']
strparam += "c:%s;"%self.dico_values['notds']
strparam += ""
elif self.analysis.category == "confidence_prior_global":
strparam += "l:%s;"%self.dico_values['lr']
strparam += "b:%s;"%self.dico_values['notds']
elif self.analysis.category == "confidence_prior_specific":
strparam += "s:%s;"%candListTxt
strparam += "r:%s;"%self.analysis.chosenSc
strparam += "l:%s;"%self.dico_values['lr']
strparam += "t:%s;"%self.dico_values['notds']
if self.analysis.drawn is 'posterior':
strparam += "po;z:%s;a:%s"% (self.dico_values['posteriorNumDataSets'], self.dico_values['posteriorSimNumDataSets'])
else :
strparam += "h:"
if self.analysis.drawn:
for paramname in self.analysis.histParamsDrawn.keys():
l = self.analysis.histParamsDrawn[paramname]
strparam += "%s="%paramname
strparam += "%s[%s,%s,%s,%s] "%(l[1],l[2],l[3],l[4],l[5])
for ctxt in self.analysis.condTxtList:
strparam += "%s "%ctxt
else:
for paramname in self.analysis.histParamsFixed.keys():
l = self.analysis.histParamsFixed[paramname]
strparam += "%s="%paramname
strparam += "%s "%l[1]
strparam = strparam[:-1]
if self.analysis.drawn:
mutmod = self.analysis.mutationModelDrawn
else:
mutmod = self.analysis.mutationModelFixed
if len(mutmod)>0:
strparam += ";u:"
if type(mutmod[0]) == type(u'plop'):
for ind,gr in enumerate(mutmod):
strparam += "g%s("%(ind+1)
strgr = gr.strip()
strgr = strgr.split('\n')
for j,elem in enumerate(strgr):
if elem.split()[0] != "MODEL":
to_add = strgr[j].split()[1]
strparam += "%s "%to_add
# virer le dernier espace
strparam = strparam[:-1]
strparam += ")*"
else:
for ind,gr in enumerate(mutmod):
strparam += "g%s("%(ind+1)
for num in gr:
strparam += "%s "%num
# virer le dernier espace
strparam = strparam[:-1]
strparam += ")*"
# virer le dernier '-'
strparam = strparam[:-1]
self.analysis.computationParameters = strparam
if not analysis_in_edition:
self.parents.addAnalysis(self.analysis)
self.exit()
def setRecordValues(self,scList):
if scList in [None, False, [None], [False]] or len(scList) == 0 :
scList = [x for x in range(1,self.parents.nb_sc+1)]
sumRec = 0
for i in scList:
sumRec+=self.parents.readNbRecordsOfScenario(int(i))
self.ui.cnosdEdit.setText(str(sumRec))
# total number of simulated data default
self.ui.totNumSimLabel.setText(str(sumRec))
# logistic regression default
onePc = sumRec / 100
if onePc < 1000:
if sumRec < 1000:
onePc = sumRec
else:
onePc = 1000
self.ui.lrEdit.setText(str(onePc))
# posteriorDistributionSampleSize default
#onePcScn = (sumRec / 100 ) / len(scList)
#self.ui.posteriorDistributionSampleSizeEdit.setText(str(onePcScn))
def setCandidateScenarios(self,scList):
""" ecrit la liste des scenarios candidats
"""
if scList in [None, False, [None], [False]] or len(scList) == 0 :
txt = ""
else :
plur= ""
if len(scList)>1:
plur = "s"
lstxt=""
self.scNumList = []
for i in scList:
lstxt+="%s, "%i
self.scNumList.append(i)
lstxt = lstxt[:-2]
txt = "Candidate scenario%s : %s"%(plur,lstxt)
self.ui.candidateLabel.setText(txt)
def setScenarios(self,scList):
""" ecrit la liste des scenarios à comparer
"""
if scList in [None, False, [None], [False]] or len(scList) == 0 :
txt = ""
else :
plur= ""
if len(scList)>1:
plur = "s"
lstxt=""
self.scNumList = []
for i in scList:
lstxt+="%s, "%i
self.scNumList.append(i)
lstxt = lstxt[:-2]
txt = "Chosen scenario%s : %s"%(plur,lstxt)
self.ui.scenariosLabel.setText(txt)
def redefineScenarios(self):
""" retourne au choix des scenarios en lui redonnant moi même comme next_widget
"""
compFrame = self
genSel = GenericScenarioSelection(len(self.parents.hist_model_win.scList),"Select the scenarios that you wish to compare",compFrame,"Comparison of scenarios",2,self.analysis,self.parent)
self.ui.parents.analysisStack.addWidget(genSel)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(genSel)
def majDicoValues(self):
self.dico_values["choNumberOfsimData"] = str(self.ui.cnosdEdit.text())
self.dico_values["de"] = str(self.ui.deEdit.text())
self.dico_values["linearRegression"] = str(self.ui.posteriorDistributionSampleSizeEdit.text())
self.dico_values["lr"] = str(self.ui.lrEdit.text())
self.dico_values["numReg"] = str(self.ui.numRegCombo.currentText())
self.dico_values["notds"] = str(self.ui.notdsEdit.text())
#look for posteriorDataSetNumberEdit in BiasNConfidenceScenarioSelection
for child in self.ui.parents.analysisStack.children():
try :
self.dico_values['posteriorNumDataSets'] = child.posteriorDataSetNumberEdit.text()
except AttributeError as e :
pass
try :
self.dico_values['posteriorSimNumDataSets'] = child.posteriorSimulatedDataSetNumberEdit.text()
except AttributeError as e :
pass
def exit(self):
## reactivation des onglets
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
class BiasNConfidenceScenarioSelection(formBiasScenarioSelection,baseBiasScenarioSelection):
""" Selection du scenario dans la cadre d'une analyse de type bias ou confidence
"""
def __init__(self,nb_sc,analysis,parent=None):
super(BiasNConfidenceScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.checklist = []
self.radiolist = []
self.createWidgets()
self.putChoices()
self.ui.verticalLayout_3.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_3.setAlignment(Qt.AlignTop)
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.ui.verticalLayout.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
QObject.connect(self.ui.fixedRadio,SIGNAL("clicked()"),self.checkParameterValues)
QObject.connect(self.ui.drawnPriorRadio,SIGNAL("clicked()"),self.checkParameterValues)
QObject.connect(self.ui.drawnPosteriorRadio,SIGNAL("clicked()"),self.checkParameterValues)
if self.analysis.category == "bias":
self.ui.analysisTypeLabel.setText("Bias and mean square error")
else:
self.ui.analysisTypeLabel.setText("Confidence in scenario choice")
self.ui.projectDirEdit.setText(self.parents.dir)
self.ui.analysisNameLabel.setText(self.analysis.name)
# hide posterior option
if self.analysis.category != "bias":
self.ui.drawnPosteriorRadio.hide()
self.checkParameterValues()
def restoreAnalysisValues(self):
if self.analysis.chosenSc != None:
self.radiolist[self.analysis.chosenSc - 1].setChecked(True)
if self.analysis.category == "confidence_prior_specific":
for i in range(self.nb_sc):
num = i+1
check = self.checklist[i]
check.setChecked(len(self.analysis.candidateScList) == 0 or num in self.analysis.candidateScList)
if self.analysis.drawn != None:
if self.analysis.drawn is False :
self.ui.fixedRadio.setChecked(True)
# in legacy analysis, drawn can be set to True for prior :
elif self.analysis.drawn is True :
self.ui.drawnPriorRadio.setChecked(True)
else :
self.ui.drawnPriorRadio.setChecked('prior' in self.analysis.drawn)
self.ui.drawnPosteriorRadio.setChecked('posterior' in self.analysis.drawn)
cp = self.analysis.computationParameters
posteriorDataSetNumber = ""
try:
posteriorDataSetNumber = cp.split('z:')[1].split(';')[0]
except IndexError:
pass
posteriorSimulatedDataSetNumber = ""
try:
posteriorSimulatedDataSetNumber = cp.split('a:')[1].split(';')[0]
except IndexError:
pass
self.ui.posteriorDataSetNumberEdit.setText(posteriorDataSetNumber)
self.ui.posteriorSimulatedDataSetNumberEdit.setText(posteriorSimulatedDataSetNumber)
self.checkParameterValues(reset=False)
def checkParameterValues(self, reset=True):
self.ui.posteriorDataSetNumberFrame.hide()
if self.analysis.category == "confidence_prior_specific" and self.ui.drawnPosteriorRadio.isChecked():
nbRecordsSelectedScenario = self.parents.readNbRecordsOfScenario(int(self.getSelectedScenario()))
self.ui.maxPosteriorDataSetNumberLabel.setText("max = %s"%nbRecordsSelectedScenario)
if str(self.ui.posteriorSimulatedDataSetNumberEdit.text()) is '' :
self.ui.posteriorSimulatedDataSetNumberEdit.setText(str(nbRecordsSelectedScenario))
elif int(str(self.ui.posteriorSimulatedDataSetNumberEdit.text())) > nbRecordsSelectedScenario :
self.ui.posteriorSimulatedDataSetNumberEdit.setText(str(nbRecordsSelectedScenario))
if reset or str(self.ui.posteriorDataSetNumberEdit.text()) is '' :
self.ui.posteriorDataSetNumberEdit.setText(str(nbRecordsSelectedScenario/100))
self.ui.posteriorDataSetNumberFrame.show()
def validate(self):
""" passe à l'étape suivante de la définition de l'analyse
"""
# pour confidence et bias, on a selectionné un scenario
self.analysis.chosenSc = self.getSelectedScenario()
if self.ui.fixedRadio.isChecked():
self.analysis.drawn = False
elif self.ui.drawnPriorRadio.isChecked():
self.analysis.drawn = 'prior'
elif self.ui.drawnPosteriorRadio.isChecked():
self.analysis.drawn = 'posterior'
if self.analysis.category == "confidence_prior_specific":
try :
if int(str(self.ui.posteriorSimulatedDataSetNumberEdit.text())) > self.parents.readNbRecordsOfScenario(int(self.analysis.chosenSc)) \
or int(str(self.ui.posteriorSimulatedDataSetNumberEdit.text())) <= 0 :
raise
except :
QMessageBox.information(self,"Number error","Total number of simulated data considered for local regression should be a positive number and inferior to the number of records of the scenario %s : %s" \
%(self.analysis.chosenSc, self.parents.readNbRecordsOfScenario(int(self.analysis.chosenSc)) ))
return 0
try :
if int(str(self.ui.posteriorDataSetNumberEdit.text())) > int(str(self.ui.posteriorSimulatedDataSetNumberEdit.text())) \
or int(str(self.ui.posteriorDataSetNumberEdit.text())) <= 0 :
raise
except :
QMessageBox.information(self,"Number error","Number of datasets for local linear regression (simulate data closest to observed) should be a positive number and inferior to the number of records of the scenario %s : %s" \
%(self.analysis.chosenSc, str(self.ui.posteriorSimulatedDataSetNumberEdit.text()) ))
return 0
# le cas du confidence, les sc à afficher dans le hist model sont ceux selectionnés
if self.analysis.category == "confidence_prior_specific":
if len(self.getListSelectedScenarios()) >= 2:
# pour confidence on a du selectionner au moins deux scenarios
self.analysis.candidateScList = self.getListSelectedScenarios()
if self.ui.fixedRadio.isChecked():
next_widget = HistFixed(self.analysis,self.parent)
# prior
else:
next_widget = HistDrawn(self.analysis,self.parent)
else:
QMessageBox.information(self,"Selection error","At least %s scenarios have to be selected"%2)
return 0
# le cas du bias, un sc à afficher, celui du radio button
else:
# en fonction de fixed ou drawn, l'écran suivant présente un objet différent
if self.ui.fixedRadio.isChecked():
next_widget = HistFixed(self.analysis,self.parent)
elif self.ui.drawnPosteriorRadio.isChecked():
next_widget = SetupEstimationBias(self.analysis,self.parent)
else:
next_widget = HistDrawn(self.analysis,self.parent)
self.ui.parents.analysisStack.addWidget(next_widget)
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentWidget(next_widget)
# skip group loci selection for microsat and seqs analysis
# if self.ui.drawnPosteriorRadio.isChecked() and not self.parents.isSnp() :
# next_widget.validate()
self.parents.updateDoc(next_widget)
def getSelectedScenario(self):
""" retourne le numero du scenario choisi
"""
for i,r in enumerate(self.radiolist):
if r.isChecked():
return i+1
def getListSelectedScenarios(self):
""" retourne la liste des scenarios choisis
"""
res = []
for i,ch in enumerate(self.checklist):
if ch.isChecked():
res.append(i+1)
return res
def putChoices(self):
""" met les choix de scenario en place
"""
for i in range(self.nb_sc):
num = i+1
radio = QRadioButton("Scenario %s"%num,self)
self.radiolist.append(radio)
self.ui.verticalLayout_4.addWidget(radio)
QObject.connect(radio,SIGNAL("clicked()"),self.checkParameterValues)
self.radiolist[0].setChecked(True)
if self.analysis.category == "confidence_prior_specific":
for i in range(self.nb_sc):
num = i+1
check = QCheckBox("Scenario %s"%num,self)
self.checklist.append(check)
self.ui.verticalLayout_6.addWidget(check)
else:
self.ui.candidateScenariosLabel.hide()
self.ui.candidateScenariosTipLabel.hide()
self.ui.frame_3.hide()
def exit(self):
## reactivation des onglets
self.ui.parents.analysisStack.removeWidget(self)
self.ui.parents.analysisStack.setCurrentIndex(0)
class ViewAnalysisParameters(formViewAnalysisParameters,baseViewAnalysisParameters):
def __init__(self,parent,analysis):
super(ViewAnalysisParameters,self).__init__(parent)
self.parent = parent
self.analysis = analysis
self.parents = Parents(self.parent)
self.createWidgets()
def createWidgets(self):
#self.ui = Ui_Frame()
self.ui = self
self.setupUi(self)
self.ui.tableWidget.setColumnWidth(0,250)
self.ui.tableWidget.setColumnWidth(1,600)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.exit)
self.addRow("name",self.analysis.name,editable=True)
tab={"pre-ev":"Pre-evaluate scenario-prior combinations",
"estimate":"Estimate posterior distributions of parameters",
"bias":"Compute bias and precision on parameter estimations",
"compare":"Compute posterior probabilities of scenarios",
"confidence":"Evaluate confidence in scenario choice",
"confidence_posterior_global":"Evaluate confidence in scenario choice, posterior based error, global",
"confidence_prior_global":"Evaluate confidence in scenario choice, prior based error, global",
"confidence_prior_specific":"Evaluate confidence in scenario choice, prior based error, scenario specific",
"modelChecking":"Perform model checking"}
self.addRow("type",tab[self.analysis.category])
#if self.analysis.chosenSc != None:
# self.addRow("Selected scenario",self.analysis.chosenSc)
#if self.analysis.candidateScList != [] and self.analysis.candidateScList != None:
# self.addRow("Selected scenarios",self.analysis.candidateScList)
tabCompParams = self.analysis.computationParameters.split(';')
transDico = {'1':"no",'2':"log",'3':"logit",'4':"logtg"}
execRowSize = 75
if self.analysis.category == "estimate" or self.analysis.category == "modelChecking" or self.analysis.category == "bias":
if self.analysis.category == "bias":
execRowSize = 200
for e in tabCompParams:
if e.split(':')[0] == 'n':
self.addRow("Chosen number of simulated data",e.split(':')[1])
elif e.split(':')[0] == 'm':
self.addRow("Number of selected data",e.split(':')[1])
elif e.split(':')[0] == 'd':
self.addRow("Number of test data sets",e.split(':')[1])
elif e.split(':')[0] == 't':
self.addRow("Transformation applied to parameters",transDico[e.split(':')[1]])
elif e.split(':')[0] == 'p':
self.addRow("Choice of parameters",e.split(':')[1].replace('c',"COMPOSITE ").replace('o',"ORIGINAL ").lower())
elif self.analysis.category == "compare":
for e in tabCompParams:
if e.split(':')[0] == 's':
self.addRow("Chosen scenarios",e.split(':')[1])
elif e.split(':')[0] == 'd':
self.addRow("Direct estimate",e.split(':')[1])
elif e.split(':')[0] == 'n':
self.addRow("Chosen number of simulated data",e.split(':')[1])
elif e.split(':')[0] == 'l':
self.addRow("Logistic regression",e.split(':')[1])
elif e.split(':')[0] == 'm':
self.addRow("Regression number",e.split(':')[1])
elif "confidence" in self.analysis.category : # == "confidence":
execRowSize = 200
for e in tabCompParams:
if e.split(':')[0] == 's' and self.analysis.category == "confidence_prior_specific" :
self.addRow("Candidate scenarios",e.split(':')[1])
elif e.split(':')[0] == 'r' and self.analysis.category == "confidence_prior_specific" :
self.addRow("Chosen scenario",e.split(':')[1])
elif e.split(':')[0] == 'd':
self.addRow("Direct estimate",e.split(':')[1])
elif e.split(':')[0] == 'n':
self.addRow("Chosen number of simulated data",e.split(':')[1])
elif e.split(':')[0] == 'l':
self.addRow("Logistic regression",e.split(':')[1])
elif e.split(':')[0] == 'z':
self.addRow("Logistic regression, posterior global, zzzzz",e.split(':')[1])
elif e.split(':')[0] == 'm':
self.addRow("Regression number",e.split(':')[1])
elif e.split(':')[0] == 't':
self.addRow("Number of requested test data sets",e.split(':')[1])
elif e.split(':')[0] == 'c':
self.addRow("Number of requested test data sets",e.split(':')[1])
elif e.split(':')[0] == 'b':
self.addRow("Number of requested test data sets, posterior global, bbb",e.split(':')[1])
# executablePath = self.parent.parent.preferences_win.getExecutablePath()
# nbMaxThread = self.parent.parent.preferences_win.getMaxThreadNumber()
# particleLoopSize = str(self.parent.parent.preferences_win.particleLoopSizeEdit.text())
# params = self.analysis.computationParameters
#
# #self.addRow("computation parameters",self.analysis.computationParameters)
# c = self.analysis.category
# if c == "estimate":
# option = "-e"
# elif c == "modelChecking":
# option = "-j"
# elif c == "bias":
# option = "-b"
# particleLoopSize = int(params.split('d:')[1].split(';')[0])
# elif c == "compare":
# option = "-c"
# elif "confidence" in c : #== "confidence":
# option = "-f"
# suboption = "t"
# if c == "confidence_posterior_global" :
# suboption = "c"
# elif c == "confidence_prior_global" :
# suboption = "b"
# particleLoopSize = int(params.split('%s:'%suboption)[1].split(';')[0])
# elif c == "pre-ev":
# option = "-d"
#
# #cmd_args_list = [executablePath,"-p", "%s/"%self.parent.dir, option, '"%s"'%params, "-i", '%s'%self.analysis.name, "-m", "-t", "%s"%nbMaxThread]
# cmd_args_list = ['"'+executablePath+'"',"-p", '"%s/"'%self.parent.dir, "%s"%option, '"%s"'%params, "-i", '%s'%self.analysis.name,"-g" ,"%s"%particleLoopSize , "-m", "-t", "%s"%nbMaxThread]
#
cmd_args_list_quoted = self.parents.getAnalysisCmdArgsList(self.analysis, quoted=True)
command_line = " ".join(cmd_args_list_quoted)
self.addRow("executed command line",command_line,editable=True)
self.ui.tableWidget.setRowHeight(self.ui.tableWidget.rowCount()-1,execRowSize)
QObject.connect(self.ui.tableWidget,SIGNAL("cellChanged(int,int)"),self.cellChanged)
def cellChanged(self,row,col):
if row == 0 and col == 1:
val = str(self.ui.tableWidget.item(0,1).text())
self.parent.changeAnalysisName(self.analysis,val)
def addRow(self,name,value,editable=False):
self.ui.tableWidget.insertRow(self.ui.tableWidget.rowCount())
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,0,QTableWidgetItem("%s"%name))
self.ui.tableWidget.setItem(self.ui.tableWidget.rowCount()-1,1,QTableWidgetItem("%s"%value))
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,0).flags() & ~Qt.ItemIsEditable & ~Qt.ItemIsSelectable)
if not editable:
self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).setFlags(self.ui.tableWidget.item(self.ui.tableWidget.rowCount()-1,1).flags() & ~Qt.ItemIsEditable & ~Qt.ItemIsSelectable)
def exit(self):
self.parent.ui.analysisStack.removeWidget(self)
self.parent.ui.analysisStack.setCurrentIndex(0)