def reportSolution(self, output):#w#for genome-scale analysis
sampletabs = swing.JTabbedPane()
samples, monitors = QSSPN.Table.output2table(output)
outputtable=[]
for i in range(len(samples)):
sample = samples[i]
table = QSSPNTable(); table.write_output(sample, monitors, 'Output')
tab = swing.JScrollPane(table)
sampletabs.addTab('Sample'+str(i+1), tab)
outputtable+=[table]
TabCloser('Output').put(sampletabs, self)
for table in outputtable: table.setColWidths_gsa(self.getWidth())
if self.listener: self.listener()
def showQSSPN(self, model):#w# open graph building tabs
table_node = QSSPNTable(); table_node.write(model, 'Node')
tab_node = swing.JScrollPane(table_node)
table_int = QSSPNTable(); table_int.write(model, 'Intact')
tab_int = swing.JScrollPane(table_int)
table_sub = QSSPNTable(); table_sub.write(model, 'Sub')
tab_sub = swing.JScrollPane(table_sub)
table_actS = QSSPNTable(); table_actS.write(model, 'ActS')
tab_actS = swing.JScrollPane(table_actS)
table_met = QSSPNTable(); table_met.write(model, 'Met')
tab_met = swing.JScrollPane(table_met)
table_actM = QSSPNTable(); table_actM.write(model, 'ActM')
tab_actM = swing.JScrollPane(table_actM)
table_enz = QSSPNTable(); table_enz.write(model, 'Enz')
tab_enz = swing.JScrollPane(table_enz)
table_actE = QSSPNTable(); table_actE.write(model, 'ActE')
tab_actE = swing.JScrollPane(table_actE)
table_list = QSSPNTable(); table_list.write(model, 'List')
tab_list = swing.JScrollPane(table_list)
splitPane_int = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
splitPane_sub = swing.JSplitPane(swing.JSplitPane.VERTICAL_SPLIT)
panel_int = swing.JPanel().add(tab_int)
splitPane_int.setLeftComponent(panel_int)
panel_sub = swing.JPanel().add(tab_sub)
panel_actS = swing.JPanel().add(tab_actS)
splitPane_sub.setTopComponent(panel_sub)
splitPane_sub.setBottomComponent(panel_actS)
splitPane_int.setRightComponent(splitPane_sub)
splitPane_int.setDividerLocation(520)
splitPane_sub.setDividerLocation(300)
# splitPane_int.setResizeWeight(1)
# splitPane_sub.setResizeWeight(0.5)
splitPane_met = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
panel_met = swing.JPanel().add(tab_met)
splitPane_met.setLeftComponent(panel_met)
panel_actM = swing.JPanel().add(tab_actM)
splitPane_met.setRightComponent(panel_actM)
splitPane_met.setDividerLocation(500)
splitPane_enz = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
splitPane_actList = swing.JSplitPane(swing.JSplitPane.VERTICAL_SPLIT)
panel_enz = swing.JPanel().add(tab_enz)
splitPane_enz.setLeftComponent(panel_enz)
panel_actE = swing.JPanel().add(tab_actE)
panel_list = swing.JPanel().add(tab_list)
splitPane_actList.setTopComponent(panel_actE)
splitPane_actList.setBottomComponent(panel_list)
splitPane_enz.setRightComponent(splitPane_actList)
splitPane_enz.setDividerLocation(500)
splitPane_actList.setDividerLocation(250)
self.addTab('PN nodes', tab_node)
self.addTab('Interactions', splitPane_int)
self.addTab('Metabolites', splitPane_met)
self.addTab('Enzymes', splitPane_enz)
# tabs.setToolTipTextAt(tabs.indexOfTab('PN nodes'), 'define reactions into graph-groups ')
# tabs.setToolTipTextAt(tabs.indexOfTab('Interactions'), 'list of graph-groups')
# tabs.setToolTipTextAt(tabs.indexOfTab('Metabolites'), 'reactions and related metabolites for a group')
# tabs.setToolTipTextAt(tabs.indexOfTab('Enzymes'), 'map between name and tag')
# TabCloser('QSSPN').put(tabs, self)
table_actS.setRowSorter(None)
table_actM.setRowSorter(None)
table_actE.setRowSorter(None)
table_node.setColWidths_gsa(self.getWidth())
table_int.setColWidths_gsa(self.getWidth())
table_sub.setColWidths_gsa(self.getWidth())
table_actS.setColWidths_gsa(self.getWidth())
table_met.setColWidths_gsa(self.getWidth())
table_actM.setColWidths_gsa(self.getWidth())
table_enz.setColWidths_gsa(self.getWidth())
table_actE.setColWidths_gsa(self.getWidth())
table_list.setColWidths_gsa(self.getWidth())
#add listeners
SeModel = table_int.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerInt(table_int, table_sub, table_actS, self.qsspn, self.curtable))
SeModel = table_sub.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerSub(table_sub, table_actS, self.curtable))
SeModel = table_actS.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActS(table_actS, self.curtable))
SeModel = table_met.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerMet(table_met, table_actM, self.curtable))
SeModel = table_actM.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActM(table_actM, self.curtable))
SeModel = table_enz.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerEnz(table_enz, table_actE, table_list, self.curtable))
SeModel = table_actE.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActE(table_actE, self.curtable))
SeModel = table_list.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerList(table_list, self.curtable))
class QSSPNTabs(GUI.BaseTabs.BaseTabs):
def __init__(self, model, listener = False):
GUI.BaseTabs.BaseTabs.__init__(self, listener)
self.qsspn = model
self.showQSSPN(self.qsspn)
def showQSSPN(self, model):#w# open graph building tabs
table_node = QSSPNTable(); table_node.write(model, 'Node')
tab_node = swing.JScrollPane(table_node)
table_int = QSSPNTable(); table_int.write(model, 'Intact')
tab_int = swing.JScrollPane(table_int)
table_sub = QSSPNTable(); table_sub.write(model, 'Sub')
tab_sub = swing.JScrollPane(table_sub)
table_actS = QSSPNTable(); table_actS.write(model, 'ActS')
tab_actS = swing.JScrollPane(table_actS)
table_met = QSSPNTable(); table_met.write(model, 'Met')
tab_met = swing.JScrollPane(table_met)
table_actM = QSSPNTable(); table_actM.write(model, 'ActM')
tab_actM = swing.JScrollPane(table_actM)
table_enz = QSSPNTable(); table_enz.write(model, 'Enz')
tab_enz = swing.JScrollPane(table_enz)
table_actE = QSSPNTable(); table_actE.write(model, 'ActE')
tab_actE = swing.JScrollPane(table_actE)
table_list = QSSPNTable(); table_list.write(model, 'List')
tab_list = swing.JScrollPane(table_list)
splitPane_int = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
splitPane_sub = swing.JSplitPane(swing.JSplitPane.VERTICAL_SPLIT)
panel_int = swing.JPanel().add(tab_int)
splitPane_int.setLeftComponent(panel_int)
panel_sub = swing.JPanel().add(tab_sub)
panel_actS = swing.JPanel().add(tab_actS)
splitPane_sub.setTopComponent(panel_sub)
splitPane_sub.setBottomComponent(panel_actS)
splitPane_int.setRightComponent(splitPane_sub)
splitPane_int.setDividerLocation(520)
splitPane_sub.setDividerLocation(300)
# splitPane_int.setResizeWeight(1)
# splitPane_sub.setResizeWeight(0.5)
splitPane_met = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
panel_met = swing.JPanel().add(tab_met)
splitPane_met.setLeftComponent(panel_met)
panel_actM = swing.JPanel().add(tab_actM)
splitPane_met.setRightComponent(panel_actM)
splitPane_met.setDividerLocation(500)
splitPane_enz = swing.JSplitPane(swing.JSplitPane.HORIZONTAL_SPLIT)
splitPane_actList = swing.JSplitPane(swing.JSplitPane.VERTICAL_SPLIT)
panel_enz = swing.JPanel().add(tab_enz)
splitPane_enz.setLeftComponent(panel_enz)
panel_actE = swing.JPanel().add(tab_actE)
panel_list = swing.JPanel().add(tab_list)
splitPane_actList.setTopComponent(panel_actE)
splitPane_actList.setBottomComponent(panel_list)
splitPane_enz.setRightComponent(splitPane_actList)
splitPane_enz.setDividerLocation(500)
splitPane_actList.setDividerLocation(250)
self.addTab('PN nodes', tab_node)
self.addTab('Interactions', splitPane_int)
self.addTab('Metabolites', splitPane_met)
self.addTab('Enzymes', splitPane_enz)
# tabs.setToolTipTextAt(tabs.indexOfTab('PN nodes'), 'define reactions into graph-groups ')
# tabs.setToolTipTextAt(tabs.indexOfTab('Interactions'), 'list of graph-groups')
# tabs.setToolTipTextAt(tabs.indexOfTab('Metabolites'), 'reactions and related metabolites for a group')
# tabs.setToolTipTextAt(tabs.indexOfTab('Enzymes'), 'map between name and tag')
# TabCloser('QSSPN').put(tabs, self)
table_actS.setRowSorter(None)
table_actM.setRowSorter(None)
table_actE.setRowSorter(None)
table_node.setColWidths_gsa(self.getWidth())
table_int.setColWidths_gsa(self.getWidth())
table_sub.setColWidths_gsa(self.getWidth())
table_actS.setColWidths_gsa(self.getWidth())
table_met.setColWidths_gsa(self.getWidth())
table_actM.setColWidths_gsa(self.getWidth())
table_enz.setColWidths_gsa(self.getWidth())
table_actE.setColWidths_gsa(self.getWidth())
table_list.setColWidths_gsa(self.getWidth())
#add listeners
SeModel = table_int.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerInt(table_int, table_sub, table_actS, self.qsspn, self.curtable))
SeModel = table_sub.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerSub(table_sub, table_actS, self.curtable))
SeModel = table_actS.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActS(table_actS, self.curtable))
SeModel = table_met.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerMet(table_met, table_actM, self.curtable))
SeModel = table_actM.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActM(table_actM, self.curtable))
SeModel = table_enz.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerEnz(table_enz, table_actE, table_list, self.curtable))
SeModel = table_actE.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerActE(table_actE, self.curtable))
SeModel = table_list.getSelectionModel()
SeModel.addListSelectionListener(QSSPN.Table.SelectionListenerList(table_list, self.curtable))
def showControlTable(self):
self.contabs = swing.JTabbedPane()
#lines_para, lines_monitor, lines_state, lines_func = loadControl()
self.table_para = QSSPNTable(); self.table_para.write_control('ConPara', self.qsspn);tab_para = swing.JScrollPane(self.table_para)
self.table_init = QSSPNTable(); self.table_init.write_control('ConInit', self.qsspn);tab_init = swing.JScrollPane(self.table_init)
self.table_func = QSSPNTable(); self.table_func.write_control('ConFunc', self.qsspn);tab_func = swing.JScrollPane(self.table_func)
self.table_flux = QSSPNTable(); self.table_flux.write_control('ConFlux', self.qsspn);tab_flux = swing.JScrollPane(self.table_flux)
self.contabs.addTab('Parameters', tab_para)
self.contabs.addTab('InitialStates', tab_init)
self.contabs.addTab('Functions', tab_func)
self.contabs.addTab('FluxMap', tab_flux)
# scrollpane = swing.JScrollPane(table_control)
self.addTab("Control", self.contabs)
# TabCloser("Control").put(scrollpane, self)
self.table_para.setColWidths_gsa(self.getWidth())
self.table_init.setColWidths_gsa(self.getWidth())
self.table_func.setColWidths_gsa(self.getWidth())
self.table_flux.setColWidths_gsa(self.getWidth())
def readControlTable(self, path):
lines_para, lines_init, lines_func = QSSPN.Table.loadControl(path, self.qsspn)
self.table_para.getModel().loadData(lines_para)
self.table_init.getModel().loadData(lines_init)
self.table_func.getModel().loadData(lines_func)
# self.contabs.getComponentAt(self.contabs.indexOfTab("Parameters")).getViewport().getView().getModel().loadData(lines_para)
# self.contabs.getComponentAt(self.contabs.indexOfTab("InitialStates")).getViewport().getView().getModel().loadData(lines_state)
# self.contabs.getComponentAt(self.contabs.indexOfTab("Functions")).getViewport().getView().getModel().loadData(lines_func)
# self.contabs.getComponentAt(self.contabs.indexOfTab("Parameters")).getViewport().getView().write_control('ConPara', self.qsspn, lines_para)
# self.contabs.getComponentAt(self.contabs.indexOfTab("InitialStates")).getViewport().getView().write_control('ConInit', self.qsspn, lines_state)
# self.contabs.getComponentAt(self.contabs.indexOfTab("Functions")).getViewport().getView().write_control('ConFunc', self.qsspn, lines_func)
self.getTableAt("PN nodes").getModel().updateNode()
def getModelScript(self):
script = '\nSUBSTANCES\n'
for x in self.qsspn.nodes:
if x:
node = self.qsspn.Node[x]
script += ' '*3 + ' '.join([node.ID, node.ini, node.max, node.type]) + '\n'
script += 'END\n'
script += '\nREACTIONS\n'
for x in self.qsspn.interactions:
if x:
intact = self.qsspn.Int[x]
prod = []
cons = []
script_int = ' '*2 + ' '.join(['INTERACTION', intact.ID.split('__')[0], intact.rate, intact.type, intact.delay]) + '\n'
for x in intact.subs:
if x:
sub = intact[x]
script_sub = ' '*6 + 'SUBSTRATE ' + sub.ID + '\n'
if sub.actr>=0:
script_sub += ' '*9 + 'ACTIVITY ' + str(sub.actr) + '\n'
for act in sub.act:
if act.t and act.a:
script_sub += ' '*11 + ' '.join([act.t, act.a]) + '\n'
script_sub += ' '*9 + 'END\n' + ' '*6 + 'END\n'
script_int += script_sub
if bool(sub.prod) == True: prod += [sub.ID]
if bool(sub.cons) == True: cons += [sub.ID]
for x in prod:
sub = intact[x]
if sub.sto: script_int += ' '*6 + 'PRODUCT_STOICHIOMETRY ' + x + ' '+ sub.sto + '\n'
else: script_int += ' '*6 + 'PRODUCT ' + x + '\n'
for x in cons: script_int += ' '*6 + 'CONSUMED ' + x + '\n'
script_int += ' '*2 + 'END\n'
script += script_int
script += 'END\n'
script += '\nGSMN\n'
script += ' '*3 + 'MODEL ' + self.qsspn.gsmn.ID + '\n'
script += ' '*3 + 'EXT_TAG ' + self.qsspn.gsmn.extag + '\n'
for flux in self.qsspn.gsmn.flux:
script += ' '*3 + ' '.join(['FLUX']+flux) + '\n'
for x in self.qsspn.metabolites:
if x:
met = self.qsspn.Met[x]
Nactm = 0
script_met = ' '*3 + ' '.join(['METABOLITE', met.ID, met.obj]) + '\n'
script_met += ' '*6 + 'ACTIVITY ' + str(len(met.act)) + '\n'
for act in met.act:
if act.t and act.a:
script_met += ' '*9 + ' '.join([act.t, act.a]) + '\n'
Nactm += 1
script_met += ' '*6 + 'END\n' + ' '*3 + 'END\n'
if Nactm > 0: script += script_met
for x in self.qsspn.enzymes:
if x:
enz = self.qsspn.Enz[x]
Nacte = 0
Nrxn = 0
script_enz = ' '*3 + ' '.join(['ENZYME', enz.ID, enz.rxn]) + '\n'
script_enz_act = ' '*6 + 'ACTIVITY ' + str(len(enz.act)) + '\n'
for act in enz.act:
if act.t and act.lb and act.ub:
script_enz_act += ' '*9 + ' '.join([act.t, act.lb, act.ub]) + '\n'
Nacte += 1
script_enz_act += ' '*6 + 'END\n'
script_enz_lst = ' '*6 + 'LIST ' + str(len(enz.list)) + '\n'
for rxn in enz.list:
if rxn.ID and rxn.wei:
script_enz_lst += ' '*9 + ' '.join([rxn.ID, rxn.wei]) + '\n'
Nrxn += 1
script_enz_lst += ' '*6 + 'END\n'
if Nacte > 0:
script_enz += script_enz_act
if Nrxn > 0: script_enz += script_enz_lst
script_enz += ' '*3 + 'END\n'
script += script_enz
script += 'END\n'
return script
# def getControlScript(self, para, monitors):
# script = ''
# for x in ['MODEL', 'NUMBER_OF_SAMPLES', 'SEED', 'TIME_MAX', 'MAXIMAL_TIMESTEP']: script += x + ' ' + para[x] + '\n'
# script += '\n'
# for x in ['OUTPUT', 'LOG', 'MONITOR']: script += x + ' ' + para[x] + '\n'
# script += '\n'
# script += 'TARGET ' + para['TARGET'] + '\n\n'
# script += 'PETRI_NET_MONITORS\n'
# for x in monitors: script += x + '\n'
# script += 'END\n\n'
# script += para['QSSPN_ALGORITHM'] + '\n'
# return script
def getControlScript(self):
script = ''
lines_para = self.table_para.getModel().getData()
lines_init = self.table_init.getModel().getData()
lines_func = self.table_func.getModel().getData()
self.para = dict(lines_para)
for x in lines_para:
if x[0] not in ['GSMN_MODEL', 'GSMN_EXT_TAG', 'QSSPN_ALGORITHM']:
if x[0] == 'MODEL': script += ' '.join([x[0], 'gsmn.tmp']) + '\n'
else: script += ' '.join(x) + '\n'
script += '\n'+'INITIAL_STATE'+'\n'
for x in lines_init: script += ' '.join(x) + '\n'
script += 'END\n\n'
for x in lines_func: script += ' '.join(x[0:2]) + '\n' + x[2] +'\nEND\n\n'
script += 'PETRI_NET_MONITORS\n'
for ID in self.qsspn.Node.keys():
if self.qsspn.Node[ID].moni==1: script += ID+'\n'
script += 'END\n\n'
script += self.para['QSSPN_ALGORITHM'] + '\n'
return script
def writeModel(self, path):
script_model = self.getModelScript()
Data.Problem.writeTmp(path, script_model)
def writeControl(self, path):
script_control = self.getControlScript()
Data.Problem.writeTmp(path, script_control)
def solve(self):
self.writeModel(Util.MODELTMP)
self.table_para.getModel().setValueAt('gsmn.tmp', 0, 1)
self.writeControl(Util.CONTROLTMP)
cmdarray = Data.Problem.getCmdArrayQSSPN(sep = io.File.separator)
self.solver = GUI.Solver.Solver(self, cmdarray)
self.solver.start()
def reportSolution(self, output):#w#for genome-scale analysis
sampletabs = swing.JTabbedPane()
samples, monitors = QSSPN.Table.output2table(output)
outputtable=[]
for i in range(len(samples)):
sample = samples[i]
table = QSSPNTable(); table.write_output(sample, monitors, 'Output')
tab = swing.JScrollPane(table)
sampletabs.addTab('Sample'+str(i+1), tab)
outputtable+=[table]
TabCloser('Output').put(sampletabs, self)
for table in outputtable: table.setColWidths_gsa(self.getWidth())
if self.listener: self.listener()
def showTrajectory(self):
table = self.getTableAt(self.getSelectedIndex())
# colinds=[0,2]
colinds = [0]+list(table.getSelectedColumns())#w#
if 2 in colinds: colinds.remove(2)
model = table.getModel()
lists =[[model.fields.getOrder()[i] for i in colinds]]#w# get column names
lists += table.getSelectedLists(colinds)
xy = GUI.PlotPanel.XYPanelTrajectory(lists)
scrollpane = swing.JScrollPane(xy)
TabCloser("Plot trajectory").put(scrollpane, self)