def addRow(self, name):
"""Add row to end"""
ek = self.ek
i = ek.length()
TableModel.addRow(self, i)
ek.add()
return
def __init__(self, dataset=None, fitmodel=None):
"""create a model dict from ekin dataset and allow simple add/remove rows"""
ek = self.ek = dataset
modeldata = self.createData(ek)
TableModel.__init__(self, modeldata)
return
def addRow(self, name):
"""Add row to end"""
ek=self.ek
i = ek.length()
TableModel.addRow(self, i)
ek.add()
return
def __init__(self, dictdata=None):
self.dict = dictdata
TableModel.__init__(self)
if dictdata == None:
return
for key in dictdata:
#assumes D is dict with some text fields
D = dictdata[key]
if D.has_key('name'):
del D['name']
self.addRecord(name=key, **D)
return
def __init__(self, dictdata=None):
self.dict = dictdata
TableModel.__init__(self)
if dictdata == None:
return
for key in dictdata:
#assumes D is dict with some text fields
D = dictdata[key]
if D.has_key('name'):
del D['name']
self.addRecord(name=key, **D)
return
def viewAll(self, parent=None):
"""Display all meta data in a table"""
from PEATDB.Tables import TableCanvas
from PEATDB.TableModels import TableModel
tp = Toplevel(master=parent)
tframe = Frame(tp)
tframe.pack()
m = TableModel()
m.importDict(self.data)
table = TableCanvas(tframe, model=m)
table.createTableFrame()
return
def viewAll(self, parent=None):
"""Display all meta data in a table"""
from PEATDB.Tables import TableCanvas
from PEATDB.TableModels import TableModel
tp = Toplevel(master=parent)
tframe = Frame(tp)
tframe.pack()
m = TableModel()
m.importDict(self.data)
table = TableCanvas(tframe, model=m)
table.createTableFrame()
return
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f=open('jobstates.log','r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,state=jl[jobid]['State'],date=jl[jobid]['Date'])
except:
M.addRecord(j,state='Not in DB')
self.jobstable = TableCanvas(self.tf, model=M, height=100, editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def matrix2Table(self, matrix):
"""Creates a table model from a peatsa matrix"""
M = TableModel()
M.addColumn('Mutations')
fields = matrix.columnHeaders()
for f in fields:
M.addColumn(f)
i = matrix.indexOfColumnWithHeader('Mutations')
for row in matrix:
mutationSet = Core.Data.MutationSet(row[i])
code = '+'.join(mutationSet.mutationCodes(reduced=True))
M.addRow(code)
for f in fields:
j = matrix.indexOfColumnWithHeader(f)
if f == 'Mutations':
M.data[code]['Mutations'] = code
else:
M.data[code][f] = str(row[j])
return M
def setValueAt(self, value, rowIndex, columnIndex):
"""Overridden for ekin updates"""
TableModel.setValueAt(self, value, rowIndex, columnIndex)
ek = self.ek
i = self.reclist[rowIndex]
col = columnIndex
if value == '':
value = None
else:
value = float(value)
if col == 0:
ek.x[i] = value
elif col == 1:
ek.y[i] = value
else:
ek.errors[col - 2][i] = value
if hasattr(self, 'callback'):
self.callback()
return
def setValueAt(self, value, rowIndex, columnIndex):
"""Overridden for ekin updates"""
TableModel.setValueAt(self,value,rowIndex,columnIndex)
ek = self.ek
i = self.reclist[rowIndex]
col=columnIndex
if value=='':
value=None
else:
value=float(value)
if col==0:
ek.x[i]=value
elif col==1:
ek.y[i]=value
else:
ek.errors[col-2][i] = value
if hasattr(self, 'callback'):
self.callback()
return
def __init__(self, E):
self.E = E
TableModel.__init__(self)
self.addColumn('name'); self.addColumn('model')
for d in E.datasets:
fdata = E.getFitData(d)
M = E.getMetaData(d)
if E.currentmode == 'NMR titration':
try:
edata = E.getDataset(d)
M['residue'] = edata['residue']
M['resnum'] = edata['res_num']
M['atom'] = edata['atom_type']
except:
pass
if fdata != {} and fdata!= None:
model = fdata['model']
else:
model=''
self.checkDict(M)
self.addRecord(name=d, **M)
return
def __init__(self, E):
self.E = E
TableModel.__init__(self)
self.addColumn('name')
self.addColumn('model')
for d in E.datasets:
fdata = E.getFitData(d)
M = E.getMetaData(d)
if E.currentmode == 'NMR titration':
try:
edata = E.getDataset(d)
M['residue'] = edata['residue']
M['resnum'] = edata['res_num']
M['atom'] = edata['atom_type']
except:
pass
if fdata != {} and fdata != None:
model = fdata['model']
else:
model = ''
self.checkDict(M)
self.addRecord(name=d, **M)
return
def matrix2Table(self, matrix):
"""Creates a table model from a peatsa matrix"""
M = TableModel()
M.addColumn('Mutations')
fields = matrix.columnHeaders()
for f in fields:
M.addColumn(f)
i = matrix.indexOfColumnWithHeader('Mutations')
for row in matrix:
mutationSet = Core.Data.MutationSet(row[i])
code = '+'.join(mutationSet.mutationCodes(reduced=True))
M.addRow(code)
for f in fields:
j = matrix.indexOfColumnWithHeader(f)
if f == 'Mutations':
M.data[code]['Mutations'] = code
else:
M.data[code][f] = str(row[j])
return M
def sendDB2Labbook(self, DB, recs=None, cols=None, name='main'):
"""Send copy of selected DB cols to a labbook table
convenience method to allow quick duplication of main DB data"""
from PEATDB.TableModels import TableModel
if cols == None:
cols = DB.meta.userfields.keys()
if recs == None:
recs = DB.getRecs()
cols.append('name')
M = TableModel()
#M.addColumn('name')
for rec in recs:
M.addRow(rec)
for c in cols:
M.addColumn(c)
if DB[rec].has_key(c):
M.data[rec][c] = DB[rec][c]
DB.createLabbookSheet(name, M)
return M
def updateColsMenu(self, evt=None):
"""create drop menus of available cols in chosen sheet"""
sheet = self.smenu.getcurselection()
S = self.DB.meta.labbook[sheet]
model = TableModel(S)
names = model.columnNames
if hasattr(self, 'xcolsmenu'):
self.xcolsmenu.destroy()
self.ycolsmenu.destroy()
self.filterbymenu.destroy()
self.filtervalentry.destroy()
self.bf.destroy()
self.xcolsmenu = Pmw.OptionMenu(self.mainwin,
labelpos='w',
label_text='X-Col:',
items=names,
menubutton_width=10)
self.xcolsmenu.pack(side=TOP, fill=BOTH)
self.ycolsmenu = Pmw.OptionMenu(self.mainwin,
labelpos='w',
label_text='Y-Col:',
items=names,
menubutton_width=10)
self.ycolsmenu.pack(side=TOP, fill=BOTH)
self.bf = Frame(self.mainwin)
self.bf.pack(side=TOP, fill=BOTH)
names.extend('-')
self.filterbymenu = Pmw.OptionMenu(self.bf,
labelpos='w',
label_text='Filter by:',
items=names,
initialitem='-',
menubutton_width=5)
self.filterbymenu.pack(side=LEFT, fill=BOTH)
self.filtervalentry = Pmw.EntryField(self.bf,
labelpos='w',
label_text='Value:')
self.filtervalentry.pack(side=LEFT, fill=BOTH)
return
def sendDB2Labbook(self, DB, recs=None, cols=None, name='main'):
"""Send copy of selected DB cols to a labbook table
convenience method to allow quick duplication of main DB data"""
from PEATDB.TableModels import TableModel
if cols == None:
cols = DB.meta.userfields.keys()
if recs == None:
recs = DB.getRecs()
cols.append('name')
M = TableModel()
#M.addColumn('name')
for rec in recs:
M.addRow(rec)
for c in cols:
M.addColumn(c)
if DB[rec].has_key(c):
M.data[rec][c] = DB[rec][c]
DB.createLabbookSheet(name, M)
return M
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f = open('jobstates.log', 'r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,
state=jl[jobid]['State'],
date=jl[jobid]['Date'])
except:
M.addRecord(j, state='Not in DB')
self.jobstable = TableCanvas(self.tf,
model=M,
height=100,
editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def __init__(self, dataset=None, fitmodel=None):
"""create a model dict from ekin dataset and allow simple add/remove rows"""
ek = self.ek = dataset
modeldata = self.createData(ek)
TableModel.__init__(self, modeldata)
return
