class GenomeModel(Observable):
"""contains data of genome-view"""
genome = Genome()
featureListContainer = FeatureListContainer()
position = 0
startRange = 0
endRange = 0
layout = Layout()
def __init__(self, genome=Genome(), flc=FeatureListContainer(), initial_position=3520, initial_startRange=0, initial_endRange=5000):
self.genome=genome
self.featureListContainer=flc
self.position=initial_position
self.startRange=initial_startRange
self.endRange=initial_endRange
self.layout=Layout()
def getGenome(self):
return self.genome
def setGenome(self, genome):
self.genome=genome
self.setChanged()
def getFeatureListContainer(self):
return self.featureListContainer
def setFeatureListContainer(self, flc):
self.featureListContainer=flc
self.setChanged()
def getCharsPerLine(self):
return self.layout.getCharsPerLine()
def setCharsPerLine(self, n):
self.layout.setCharsPerLine(n)
def getPosition(self):
return self.position
def setPosition(self, n):
self.position=n
self.setChanged()
def getStartRange(self):
return self.startRange
def setStartRange(self, n):
self.startRange=n
self.setChanged()
def getEndRange(self):
return self.endRange
def setEndRange(self, n):
self.endRange=n
self.setChanged()
def setRanges(self, start ,end):
self.startRange = start
self.endRange = end
self.setChanged()
def resetLayout(self):
new = Layout()
self.layout = Layout()
self.setChanged()
def getTypeDict(self):
return self.layout.getTypeDict()
def getNumSize(self):
return self.layout.getNumSize()
def incNumSize(self, int):
numsize=self.layout.getNumSize()
self.layout.setNumSize(numsize+int)
def decNumSize(self, int):
numsize=self.layout.getNumSize()
if (numsize-int >=0):
self.layout.setNumSize(numsize-int)
else:
self.layout.setNumSize(0)
def getSeqSize(self):
return self.layout.getSeqSize();
def incSeqSize(self, int):
seqsize=self.layout.getSeqSize()
self.layout.setSeqSize(seqsize+int)
def decSeqSize(self, int):
seqsize=self.layout.getSeqSize()
if (seqsize-int >=0):
self.layout.setSeqSize(seqsize-int)
else:
self.layout.setSeqSize(0)
def isItalic(self):
return self.layout.getSeqStyle() == wx.ITALIC
def isBold(self):
return self.layout.getSeqWeight() == wx.BOLD
def changeSeqWeight(self):
if self.layout.getSeqWeight()== wx.NORMAL:
self.layout.setSeqWeight(wx.BOLD)
else:
self.layout.setSeqWeight(wx.NORMAL)
def changeSeqStyle(self):
if self.layout.getSeqStyle()== wx.NORMAL:
self.layout.setSeqStyle(wx.ITALIC)
else:
self.layout.setSeqStyle(wx.NORMAL)
def increaseLineSp(self, int):
lp=self.layout.getLineSpacing()
self.layout.setLineSpacing(lp+int)
def decreaseLineSp(self, int):
lp=self.layout.getLineSpacing()
if lp-int >= 0:
self.layout.setLineSpacing(lp-int)
else:
self.layout.setLineSpacing(0)
def indentMore(self, int):
indent=self.layout.getLeftIndent()
self.layout.setLeftIndent(indent+int)
def indentLess(self, int):
indent=self.layout.getLeftIndent()
if indent-int>=0:
self.layout.setLeftIndent(indent-int)
else:
self.layout.setLeftIndent(0)
def setSeqColor(self, color):
self.layout.setSeqColor(color)
def getSeqColor(self):
return self.layout.getSeqColor()
def setNumColor(self, color):
self.layout.setNumColor(color)
def getNumColor(self):
return self.layout.getNumColor()
def isUpperCase(self):
return self.layout.getUpperCase()
def changeUpperCase(self):
if self.layout.getUpperCase():
self.layout.setUpperCase(False)
else:
self.layout.setUpperCase(True)
def getCharWidth(self):
self.layout.getCharWidth()
def writeSequence(self, txtctrl):
#print self.genome.getSequence()[0:50]
#print "UpperCase: " + str(self.layout.getUpperCase())
if self.layout.getUpperCase():
sequence=self.genome.getSequence()[self.startRange:self.endRange].upper()
else:
sequence=self.genome.getSequence()[self.startRange:self.endRange].lower()
seqLen=len(sequence)
numeration=self.startRange
i=0
while i+self.layout.getCharsPerLine() <= seqLen:
txtctrl.BeginStyle(self.layout.getSeqTextAttrEx())
# print str(len(sequence[i:i+self.charsPerLine]))
txtctrl.WriteText(sequence[i:i+self.layout.getCharsPerLine()])
txtctrl.Newline()
txtctrl.EndStyle()
txtctrl.BeginStyle(self.layout.getNumTextAttrEx())
txtctrl.WriteText(self.writeNum(len(str(self.endRange-1)), str(numeration), str(numeration+txtctrl.GetLineLength(txtctrl.GetNumberOfLines()-2)-1)))
# letzte Zeile ohne Newline()
if i+self.layout.getCharsPerLine() < seqLen:
# print "charsPerLine" + str(i+self.charsPerLine) + "=" + str(seqLen)
txtctrl.Newline()
txtctrl.EndStyle()
i+=self.layout.getCharsPerLine()
numeration+=txtctrl.GetLineLength(txtctrl.GetNumberOfLines()-3)
if seqLen-i>0:
txtctrl.BeginStyle(self.layout.getSeqTextAttrEx())
txtctrl.WriteText(sequence[i:])
txtctrl.Newline()
txtctrl.EndStyle()
txtctrl.BeginStyle(self.layout.getNumTextAttrEx())
txtctrl.WriteText(self.writeNum(len(str(self.endRange)), str(numeration), str(numeration+txtctrl.GetLineLength(txtctrl.GetNumberOfLines()-2))))
txtctrl.EndStyle()
# gibt Nummerierung als gleichlange Strings zurueck
def writeNum(self, strLen, str1, str2):
while len(str1) < strLen:
str1= "0" + str1
while len(str2) < strLen:
str2= "0" + str2
return str1 + "-" + str2
# durchsucht den Container nach allen aktiven Features und uebergibt deren Parameter an writeFeaturesHelper
def writeFeatures(self, txtctrl):
for iFlist in range(self.featureListContainer.getContainerLength()):
# print iFlist
# print self.featureListContainer.getContainerLength()
if self.featureListContainer.getFlistActive(iFlist):
for iFeature in range(self.featureListContainer.getFlistLength(iFlist)):
# print iFeature
# print self.featureListContainer.getFlistLength(iFlist)
if self.featureListContainer.getFeatureActive(iFlist, iFeature):
start=self.featureListContainer.getStartPos(iFlist, iFeature)
end=self.featureListContainer.getEndPos(iFlist, iFeature)
if start >= self.startRange and end <= self.endRange:
type=self.featureListContainer.getType(iFlist, iFeature)
description=self.featureListContainer.getDescription(iFlist, iFeature)
self.writeFeaturesHelper(txtctrl, start, end, type, description)
# faerbt Bereiche und ueberspringt Nummerierung
def writeFeaturesHelper(self, txtctrl, start, end, type, description):
#print "start1: " + str(start)
#print "end1: " + str(end)
rta = rt.RichTextAttr()
#Farbgebung
self.layout.addTypeColDict(type)
rta.SetTextColour(self.layout.getTypeColDict(type))
description=description+";"+str(start)+";"+str(end)+";"+type
rta.SetURL(description)
txtctrl.Bind(wx.EVT_TEXT_URL, self.onUrl)
#txtctrl.SetStyle((246, 306), rta)
calc1=start%self.layout.getCharsPerLine()
calc2=self.layout.getCharsPerLine()-calc1
calc3=self.startRange%self.layout.getCharsPerLine()
calc4=(calc2+calc3)%self.layout.getCharsPerLine()
modStart=self.modifyStartPos(start,txtctrl)
modEnd=self.modifyEndPos(end, txtctrl)
#print "calc1: " + str(calc1)
#print "calc2: " + str(calc2)
#print "calc3: " + str(calc3)
#print "calc4: " + str(calc4)
#print "start2: " + str(modStart)
#print "end2: " + str(modEnd)
# Anfang: wenn Einfaerbung nicht am Zeilenanfang beginnt
if calc4!=0:
if end-start<=calc4:
txtctrl.SetStyle((modStart,modEnd), rta)
modStart+=modEnd
#print "if"
else:
txtctrl.SetStyle((modStart,modStart+calc4), rta)
modStart+=calc4+txtctrl.GetLineLength(1)+2
#print "else"
# Mitte: faerbt ganze Zeilen
while modStart+self.layout.getCharsPerLine()<=modEnd:
txtctrl.SetStyle((modStart,modStart+self.layout.getCharsPerLine()), rta)
#print str(modStart+self.charsPerLine+txtctrl.GetLineLength(1)+1)
modStart+=self.layout.getCharsPerLine()+txtctrl.GetLineLength(1)+2
#print "middle"
# Ende: faerbt letzte Zeile nicht ganz
if modEnd-modStart>0:
txtctrl.SetStyle((modStart,modEnd), rta)
#print "end"
# wandelt Positionen auf dem Genom in Positionen im Genomtextfeld um
def modifyStartPos(self, n, txtctrl):
newN=n-self.startRange
quot=newN/self.layout.getCharsPerLine()*2
numCount=0
i=1
while i <= quot:
numCount+=txtctrl.GetLineLength(i)
i+=2
#print newN+quot+numCount
return newN+quot+numCount
def modifyEndPos(self, n, txtctrl):
newN=n-self.startRange
quot=newN/self.layout.getCharsPerLine()*2
numCount=0
i=1
while i < quot:
numCount+=txtctrl.GetLineLength(i)
i+=2
#print str(newN+quot+numCount+1)
return newN+quot+numCount+1
def onUrl(self, evt):
info = Information(None, -1, evt.GetString(), 'Information')
info.ShowModal()
info.Destroy()
#wx.MessageBox(evt.GetString(), "Description")
# rechnet Position im Genom in Position im Textfeld um und scrollt im Textfeld an richtige Stelle
def showPos(self, txtctrl):
if self.position>=self.startRange and self.position<=self.endRange:
realPos=self.modifyStartPos(self.position, txtctrl)
txtctrl.ShowPosition(realPos)
txtctrl.SelectWord(realPos)
# rechnet Position des Features in Position im Textfeld um und scrollt im Textfeld an richtige Stelle
def showFeature(self, start, end, txtctrl):
realStart=self.modifyStartPos(start, txtctrl)
realEnd=self.modifyEndPos(end, txtctrl)
txtctrl.ShowPosition(realStart)
txtctrl.SetSelection(realStart, realEnd)
