def __init__(self, module, controller, parent=None):
        """ MplPlotConfigurationWidget(module: Module,
                                       controller: VistrailController,
                                       parent: QWidget)
                                       -> MplPlotConfigurationWidget                                       
        Let StandardModuleConfigurationWidget constructor store the
        controller/module object from the builder and set up the
        configuration widget.        
        After StandardModuleConfigurationWidget constructor, all of
        these will be available:
        self.module : the Module object int the pipeline        
        self.module_descriptor: the descriptor for the type registered in the registry,
                          i.e. Tuple
        self.controller: the current vistrail controller
                                       
        """
        StandardModuleConfigurationWidget.__init__(self, module,
                                                   controller, parent)

        # Give it a nice window title
        self.setWindowTitle('Tuple Configuration')

        # Add an empty vertical layout
        centralLayout = QtGui.QVBoxLayout()
        centralLayout.setMargin(0)
        centralLayout.setSpacing(0)
        self.setLayout(centralLayout)
        
        # Then add a PortTable to our configuration widget
        self.portTable = PortTable(self)
        self.portTable.setHorizontalHeaderLabels(
            QtCore.QStringList() << 'Input Port Name' << 'Type')
        
        # We know that the Tuple module initially doesn't have any
        # input port, we just use the local registry to see what ports
        # it has at the time of configuration.
        if self.module.registry:
            iPorts = self.module.registry.destination_ports_from_descriptor(self.module_descriptor)
            self.portTable.initializePorts(iPorts)
        else:
            self.portTable.fixGeometry()
        centralLayout.addWidget(self.portTable)

        # We need a padded widget to take all vertical white space away
        paddedWidget = QtGui.QWidget(self)
        paddedWidget.setSizePolicy(QtGui.QSizePolicy.Ignored,
                                   QtGui.QSizePolicy.Expanding)
        centralLayout.addWidget(paddedWidget, 1)

        # Then we definitely need an Ok & Cancel button
        self.createButtons()
class TupleConfigurationWidget(StandardModuleConfigurationWidget):
    """
    TupleConfigurationWidget is the configuration widget for Tuple
    module, we want to build an interface for specifying a number of
    input ports and the type of each port. Then compose a tuple of
    those input as a result.

    When subclassing StandardModuleConfigurationWidget, there are
    only two things we need to care about:
    
    1) The builder will provide the VistrailController (through the
       constructor) associated with the pipeline the module is in. The
       configuration widget can use the controller to change the
       current vistrail such as delete connections, add/delete module
       port...

    2) The builder also provide the current Module object (through the
       constructor) of the module. This is the instance of the module
       in the pipeline. Changes to this Module object usually will not
       result a new version in the current Vistrail. Such changes are
       change the visibility of input/output ports on the builder,
       change module color.

       Each module has a local registry which is exactly like the
       global modules.module_registry.registry. However, it holds
       module information (ports) changing in time. The same module
       can have different types of input ports at two different time
       in the same vistrail.

    That's it, the rest of the widget will be just like a regular Qt
    widget.
    
    """
    def __init__(self, module, controller, parent=None):
        """ MplPlotConfigurationWidget(module: Module,
                                       controller: VistrailController,
                                       parent: QWidget)
                                       -> MplPlotConfigurationWidget                                       
        Let StandardModuleConfigurationWidget constructor store the
        controller/module object from the builder and set up the
        configuration widget.        
        After StandardModuleConfigurationWidget constructor, all of
        these will be available:
        self.module : the Module object int the pipeline        
        self.module_descriptor: the descriptor for the type registered in the registry,
                          i.e. Tuple
        self.controller: the current vistrail controller
                                       
        """
        StandardModuleConfigurationWidget.__init__(self, module,
                                                   controller, parent)

        # Give it a nice window title
        self.setWindowTitle('Tuple Configuration')

        # Add an empty vertical layout
        centralLayout = QtGui.QVBoxLayout()
        centralLayout.setMargin(0)
        centralLayout.setSpacing(0)
        self.setLayout(centralLayout)
        
        # Then add a PortTable to our configuration widget
        self.portTable = PortTable(self)
        self.portTable.setHorizontalHeaderLabels(
            QtCore.QStringList() << 'Input Port Name' << 'Type')
        
        # We know that the Tuple module initially doesn't have any
        # input port, we just use the local registry to see what ports
        # it has at the time of configuration.
        if self.module.registry:
            iPorts = self.module.registry.destination_ports_from_descriptor(self.module_descriptor)
            self.portTable.initializePorts(iPorts)
        else:
            self.portTable.fixGeometry()
        centralLayout.addWidget(self.portTable)

        # We need a padded widget to take all vertical white space away
        paddedWidget = QtGui.QWidget(self)
        paddedWidget.setSizePolicy(QtGui.QSizePolicy.Ignored,
                                   QtGui.QSizePolicy.Expanding)
        centralLayout.addWidget(paddedWidget, 1)

        # Then we definitely need an Ok & Cancel button
        self.createButtons()

    def createButtons(self):
        """ createButtons() -> None
        Create and connect signals to Ok & Cancel button
        
        """
        self.buttonLayout = QtGui.QHBoxLayout()
        self.buttonLayout.setMargin(5)
        self.okButton = QtGui.QPushButton('&OK', self)
        self.okButton.setAutoDefault(False)
        self.okButton.setFixedWidth(100)
        self.buttonLayout.addWidget(self.okButton)
        self.cancelButton = QtGui.QPushButton('&Cancel', self)
        self.cancelButton.setAutoDefault(False)
        self.cancelButton.setShortcut('Esc')
        self.cancelButton.setFixedWidth(100)
        self.buttonLayout.addWidget(self.cancelButton)
        self.layout().addLayout(self.buttonLayout)
        self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'),
                     self.okTriggered)
        self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'),
                     self.close)        

    def sizeHint(self):
        """ sizeHint() -> QSize
        Return the recommended size of the configuration window
        
        """
        return QtCore.QSize(384, 256)

    def okTriggered(self, checked = False):
        """ okTriggered(checked: bool) -> None
        Update vistrail controller and module when the user click Ok
        
        """
        self.updateVistrail()
        self.close()

    def newInputPorts(self):
        """ newInputPorts() -> [port]        
        Return the set of ports specify in the port table
        
        """
        ports = []
        for i in range(self.portTable.rowCount()):
            model = self.portTable.model()
            name = str(model.data(model.index(i, 0),
                                  QtCore.Qt.DisplayRole).toString())
            typeName = str(model.data(model.index(i, 1),
                                      QtCore.Qt.DisplayRole).toString())
            if name!='' and typeName!='':
                ports.append(('input', name, '('+typeName+')'))
        return ports

    def specsFromPorts(self, portType, ports):
        return [(portType,
                 p.name,
                 '('+registry.get_descriptor(p.spec.signature[0][0]).name+')')
                for p in ports[0][1]]

    def registryChanges(self, oldRegistry, newPorts):
        if oldRegistry:
            oldIn = self.specsFromPorts('input',
                                        oldRegistry.all_destination_ports(self.module_descriptor))
            oldOut = self.specsFromPorts('output',
                                         oldRegistry.all_source_ports(self.module_descriptor))
        else:
            oldIn = []
            oldOut = []
        deletePorts = [p for p in oldIn if not p in newPorts]
        deletePorts += [p for p in oldOut if not p in newPorts]
        addPorts = [p for p in newPorts if ((not p in oldIn) and (not p in oldOut))]
        return (deletePorts, addPorts)
    
    def updateVistrail(self):
        """ updateVistrail() -> None
        Update Vistrail to contain changes in the port table
        
        """
        old_registry = self.module.registry
        newPorts = self.newInputPorts()
        (deletePorts, addPorts) = self.registryChanges(old_registry, newPorts)

        # Remove any connections or functions related to delete ports
        for (cid, c) in self.controller.current_pipeline.connections.items():
            if ((c.sourceId==self.module.id and
                 any([c.source.name==p[1] for p in deletePorts])) or
                (c.destinationId==self.module.id and
                 any([c.destination.name==p[1] for p in deletePorts]))):
                self.controller.delete_connection(cid)
        for p in deletePorts:
            module = self.controller.current_pipeline.modules[self.module.id]
            ids = []
            for fid in range(module.getNumFunctions()):
                if module.functions[fid].name==p[1]:
                    ids.append(fid)
            for i in ids:
                self.controller.delete_method(i, self.module.id)
        for p in deletePorts:
            self.controller.delete_module_port(self.module.id, p)

        # Add all addPorts
        for p in addPorts:
            self.controller.add_module_port(self.module.id, p)

        # If output spec change, remove all connections
        spec = [p[2][1:-1] for p in newPorts]
        if len(deletePorts)+len(addPorts)>0:
            for (cid, c) in self.controller.current_pipeline.connections.items():
                if (c.sourceId==self.module.id and c.source.name=='value'):
                    self.controller.delete_connection(cid)

        tpl = ('output', 'value')
        if self.controller.has_module_port(self.module.id, tpl):
            # Remove the current output port and add a new one                    
            self.controller.delete_module_port(self.module.id, tpl)
        spec = '('+','.join(spec)+')'
        self.controller.add_module_port(self.module.id,
                                        ('output', 'value', spec))

    def lcs(self, l1, l2):
        """ lcs(l1: list, l2: list) -> (keep, delete, add list)        
        Given 2 lists, we want to find our which part of l1 is the
        same as l2 and which should be deleted or added. This is very
        small in our case, we just use memoization.
        
        """
        res = {}
        def rec(i1, i2):
            if (i1<0 or i2<0):
                return 0
            cached = res.get(i1*len(l2)+i2, -1)
            if cached!=-1:
                return cached
            if l1[i1]==l2[i2]:
                r = rec(i1-1, i2-1) + 1
            else:
                r = max(rec(i1, i2-1), rec(i1-1, i2))
            res[i1*len(l2)+i2] = r
            return r
        same = []
        delete = copy.copy(l1)
        add = copy.copy(l2)
        def trace(i1, i2):
            if i1>=0 and i2>=0:
                if l1[i1]==l2[i2]:
                    same.append(l1[i1])
                    del delete[i1]
                    del add[i2]
                    trace(i1-1, i2-1)
                else:
                    if rec(i1, i2)==rec(i1, i2-1):
                        trace(i1, i2-1)
                    else:
                        trace(i1-1, i2)
        rec(len(l1)-1, len(l2)-1)
        trace(len(l1)-1, len(l2)-1)
        same.reverse()
        return (same, delete, add)