def __init__(self, nodeIndex, itsHMM):
self.itsHMM = itsHMM
self.index = nodeIndex # The node index in the underlying graph
self.id = ValidatingString("%s" % nodeIndex)
self.state_class = PopupableInt()
self.state_class.setPopup(itsHMM.hmmClass.name,
itsHMM.hmmClass.name2code, 10)
self.label = ValidatingString("<none>")
self.order = DefaultedInt()
self.order.setDefault(1, 0)
self.emissions = []
self.initial = Probability("0.0")
self.tiedto = DefaultedString()
self.tiedto.setDefault(1, '')
self.desc = self.id
self.reading_frame = PopupableInt(-1)
code2name = {-1: 'None', 0: '0', 1: '1', 2: '2'}
name2code = {'None': -1, '0': 0, '1': 1, '2': 2}
self.reading_frame.setPopup(code2name, name2code, 4)
self.duration = DefaultedInt()
self.duration.setDefault(1, 0)
self.background = PopupableInt(-1)
self.background.setPopup(self.itsHMM.backgroundDistributions.code2name,
self.itsHMM.backgroundDistributions.name2code,
10)
def symbolsFromDom(self, XMLNode):
symbols = XMLNode.getElementsByTagName("symbol")
for symbol in symbols:
symbolCode = ValidatingInt(int(symbol.getAttribute("code")))
symbolName = ValidatingString(symbol.firstChild.nodeValue)
symbolDesc = symbol.getAttribute("desc")
if symbolDesc != None:
self.addCode(symbolCode, symbolName,
ValidatingString(symbolDesc))
else:
self.addCode(symbolCode, symbolName)
def __init__(self, XMLFileName=None, G=None):
# self.itsEditor = itsEditor
if (G is None):
self.G = Graph()
else:
self.G = G
self.G.directed = 1
self.G.euclidian = 0
self.G.simple = 0
self.Pi = {}
self.id2index = {}
# self.hmmAlphabet = DiscreteHMMAlphabet()
self.hmmClass = HMMClass()
# in the case of pair HMMs we have several
self.hmmAlphabets = {}
self.transitionFunctions = {}
self.editableAttr = {}
self.editableAttr['HMM'] = ['desc']
self.desc = ValidatingString()
self.state = {}
self.modelType = 0
self.name = "NoName"
self.backgroundDistributions = NamedDistributions(self)
self.DocumentName = "graphml"
if XMLFileName != None:
self.OpenXML(XMLFileName)
def Clear(self):
self.G.Clear()
self.Pi = {}
self.id2index = {}
# self.hmmAlphabet = DiscreteHMMAlphabet()
self.hmmAlphabets = {}
self.hmmClass = HMMClass()
self.backgroundDistributions = NamedDistributions(self)
self.editableAttr = {}
self.editableAttr['HMM'] = ['desc']
self.desc = ValidatingString()
self.state = {}
self.DocumentName = "graphml"
def __init__(self, nodeIndex, itsHMM):
self.initial = Probability("0.0")
self.label = ValidatingString("None")
self.itsHMM = itsHMM
# print type(self.label)
self.index = nodeIndex # The node index in the underlying graph
self.id = DefaultedInt(
) # identification by the canvas, not always the same
self.state_class = PopupableInt(-1)
self.state_class.setPopup(itsHMM.hmmClass.code2name,
itsHMM.hmmClass.name2code, 10)
# XXX self.state_class.setPopup(itsHMM.hmmClass.name, itsHMM.hmmClass.name2code, 10)
self.order = DefaultedInt()
self.order.setDefault(1, 0) # the default state order is 0
self.emissions = []
self.tiedto = DefaultedString()
self.tiedto.setDefault(1, '')
self.desc = self.id
self.reading_frame = PopupableInt(-1)
code2name = {-1: 'None', 0: '0', 1: '1', 2: '2'}
name2code = {'None': -1, '0': 0, '1': 1, '2': 2}
self.reading_frame.setPopup(code2name, name2code, 4)
self.duration = DefaultedInt()
self.duration.setDefault(1, 0)
self.background = PopupableInt(-1)
self.background.setPopup(self.itsHMM.backgroundDistributions.code2name,
self.itsHMM.backgroundDistributions.name2code,
10)
self.editableAttr = [
'label', 'state_class', 'initial', 'order', 'background',
'offsetX', 'offsetY', 'alphabet_id'
]
self.xmlAttr = self.editableAttr + ['ngeom', 'emissions']
# pair HMM stuff
self.alphabet_id = ValidatingInt(0)
self.offsetX = ValidatingInt(1)
self.offsetY = ValidatingInt(0)
self.kclasses = ValidatingInt(1)
self.transitionFunction = ValidatingInt(-1)
def EditPropertiesUp(self, event):
if event.widget.find_withtag(CURRENT):
widget = event.widget.find_withtag(CURRENT)[0]
tags = self.canvas.gettags(widget)
if not "edges" in tags:
v = self.FindVertex(event)
# print "Found Vertex " + "%s" % v
#XXX if self.HMM.state[v].state_class != -1: # we have attribute state_class
#d = EditObjectAttributesDialog(self, self.HMM.state[v], HMMState.editableAttr + ['state_class'])
#else:
d = EditObjectAttributesDialog(
self, self.HMM.state[v],
HMMState.editableAttr + ['state_class'])
# We only show the label out of the editable items
self.HMM.G.labeling[v] = ValidatingString(
"%s" % (self.HMM.state[v].label)) # XXX Hack Aaaargh!
self.UpdateVertexLabel(v, 0)
def __init__(self, XMLFileName=None):
self.G = Graph()
self.G.directed = 1
self.G.euclidian = 0
self.Pi = {}
self.id2index = {}
self.hmmAlphabet = DiscreteHMMAlphabet()
self.hmmClass = HMMClass()
self.editableAttr = {}
self.editableAttr['HMM'] = ['desc']
self.desc = ValidatingString()
self.state = {}
self.backgroundDistributions = NamedDistributions(self)
if XMLFileName != None:
self.OpenXML(XMLFileName)
def set_value(self, value):
editor.Editor.set_value(self, ValidatingString(value))
def fromDOM(self, XMLNode):
self.id = ValidatingString(XMLNode.attributes['id'].nodeValue.encode(
'ascii', 'replace'))
self.index = self.itsHMM.G.AddVertex()
datas = XMLNode.getElementsByTagName("data")
for data in datas:
dataKey = data.attributes['key'].nodeValue
dataValue = data.firstChild.nodeValue
if dataKey == 'class':
self.state_class = typed_assign(self.state_class,
int(dataValue))
elif dataKey == 'label':
self.label = type(self.label)(dataValue.encode(
'ascii', 'replace'))
elif dataKey == 'order':
if dataValue == None: # Use default value
self.order = typed_assign(self.order,
self.order.defaultValue)
self.order.useDefault = 1
else:
self.order = typed_assign(self.order, int(dataValue))
self.order.useDefault = 0
elif dataKey == 'initial':
self.initial = typed_assign(self.initial, float(dataValue))
elif dataKey == 'tiedto':
if dataValue == None: # Use default value
self.tiedto = typed_assign(self.tiedto,
self.tiedto.defaultValue)
self.tiedto.useDefault = 1
else:
self.tiedto = typed_assign(
self.tiedto, dataValue.encode('ascii', 'replace'))
self.tiedto.useDefault = 0
elif dataKey == 'reading-frame':
self.reading_frame = typed_assign(self.reading_frame,
int(dataValue))
elif dataKey == 'background':
self.background = typed_assign(
self.background,
self.itsHMM.backgroundDistributions.name2code[dataValue])
elif dataKey == 'duration':
self.duration = typed_assign(self.duration, int(dataValue))
self.duration.useDefault = 0
elif dataKey == 'ngeom':
# We only use pos
pos = XMLNode.getElementsByTagName('pos')[
0] # Just one pos ...
self.pos = Point2D(float(pos.attributes['x'].nodeValue),
float(pos.attributes['y'].nodeValue))
elif dataKey == 'emissions':
# collect all strings from childnodes
dataValue = ""
for child in data.childNodes:
dataValue += child.nodeValue
self.emissions = listFromCSV(dataValue, types.FloatType)
#print self.emissions
else:
print "HMMState.fromDOM: unknown key %s of value %s" % (
dataKey, dataValue)