def viewDnaOrderFile(self, openFileInEditor=True):
"""
Writes a DNA Order file in comma-separated values (CSV) format
and opens it in a text editor.
The user must save the file to a permanent location using the
text editor.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format='CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile, self.assy,
self.getNumberOfBases(),
self.getNumberOfBases(unassignedOnly=True),
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
return
def viewDnaOrderFile(self, openFileInEditor = True):
"""
Opens a text editor and loads a temporary text file containing all the
DNA strand names and their sequences in the current DNA object. It will
look something like this:
Strand1,ATCAGCTACGCATCGCT
Strand2,TAGTCGATGCGTAGCGA
...
Strandn, ...
The user can then save the file to a permanent location using the
text editor the file is loaded (and displayed) in.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format = 'CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile,
self.assy,
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
def viewDnaOrderFile(self, openFileInEditor = True):
"""
Writes a DNA Order file in comma-separated values (CSV) format
and opens it in a text editor.
The user must save the file to a permanent location using the
text editor.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format = 'CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile,
self.assy,
self.getNumberOfBases(),
self.getNumberOfBases(unassignedOnly = True),
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
return
def open_tmp_inputfile(self):
'''Writes a temporary GAMESS inputfile of the current Gamess jig and opens the
file in an editor.
'''
# Make tmp_inputfile filename (i.e. ~/Nanorex/temp/jigname_parms_info.inp)
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
tmpdir = find_or_make_Nanorex_subdir('temp')
basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info('_')
tmp_inputfile = os.path.join(tmpdir, "%s.inp" % basename)
# Write INP file (in ~/Nanorex/temp subdirectory)
from analysis.GAMESS.files_gms import writegms_inpfile
writegms_inpfile(tmp_inputfile, self.gamessJig)
from platform_dependent.PlatformDependent import open_file_in_editor
open_file_in_editor(tmp_inputfile)
def openGNUplotFile(self):
"""Opens the current GNUplot file in an editor.
"""
open_file_in_editor(self.plotFile)
def openTraceFile(self):
"""Opens the current tracefile in an editor.
"""
open_file_in_editor(self.traceFile)
def openGNUplotFile(self):
"""Opens the current GNUplot file in an editor.
"""
open_file_in_editor(self.plotFile)
def openTraceFile(self):
"""Opens the current tracefile in an editor.
"""
open_file_in_editor(self.traceFile)
