def __init__(self, path, *args):
fileInfo = QFileInfo(path)
QgsRasterLayer.__init__(self, path, *args)
GLayer.__init__(self, baseName=fileInfo.baseName(), name="rLayer<" + fileInfo.baseName() + ">")
if not self.isValid():
GPrint(self._name + " failed to load.", "!!")
else:
GPrint(self._name + " successfully loaded.")
def load_icon(self, fileinfo):
key = 'default'
icons = self.icons
if fileinfo.isSymLink():
if not fileinfo.exists():
return icons['zero']
fileinfo = QFileInfo(fileinfo.readLink())
if fileinfo.isDir():
key = 'dir'
else:
ext = unicode(fileinfo.completeSuffix()).lower()
key = self.key_from_ext(ext)
return self.cached_icon(key)
def __init__(self, postGISDatabase=None, baseName=None, table=None, subset=None, schema="public",
geoColumn="geom", path=None, fileType="ogr", loadDefaultStyleFlag=True):
# Parameters
self._name = ""
self._baseName = ""
self._symbols = None
self._color = QColor()
# Query data from PostGIS database
if postGISDatabase:
if baseName:
name = "vLayer<" + baseName + ">"
else:
baseName = table
name = "vLayer<" + table + ">"
GLayer.__init__(self, name=name, baseName=baseName)
postGISDatabase.uri.setDataSource(schema, table, geoColumn, subset)
QgsVectorLayer.__init__(self, postGISDatabase.uri.uri(), self._name, postGISDatabase.user)
# Query data from file
else:
fileInfo = QFileInfo(path)
name = "vLayer<" + fileInfo.baseName() + ">"
baseName = fileInfo.baseName()
GLayer.__init__(self, name=name, baseName=baseName)
QgsVectorLayer.__init__(self, path=path, baseName=fileInfo.baseName(), providerLib=fileType,
loadDefaultStyleFlag=loadDefaultStyleFlag)
if not self.isValid():
GPrint(self._name + " failed to load.", "!!")
else:
GPrint(self._name + " successfully loaded.")
# Deal with color param
self._symbols = self.rendererV2().symbols()
self._color = self._symbols[0].color()
def run_using_old_movie_obj_to_hold_sim_params(self, movie, args):
self._movie = movie
assert args >= 1
#for now args has number of simulations
self.numSim = args[0][0]
#set the program path, database path and write the paths.txt in here
self.errcode = self.set_options_errQ( )
if self.errcode: # used to be a local var 'r'
return
self.sim_input_file = self.sim_input_filename(self.part)
if self.sim_input_file is None:
return
self.set_waitcursor(True)
progressBar = self.win.statusBar().progressBar
# Disable some QActions (menu items/toolbar buttons) while the sim is running.
self.win.disable_QActions_for_sim(True)
try: #bruce 050325 added this try/except wrapper, to always restore cursor
self.simProcess = None #bruce 051231
self.setup_sim_args(args)
progressBar.setRange(0, 0)
progressBar.reset()
progressBar.show()
env.history.statusbar_msg("Running Rosetta")
rosettaFullBaseFileName = self.tmp_file_prefix
rosettaFullBaseFileInfo = QFileInfo(rosettaFullBaseFileName)
rosettaWorkingDir = rosettaFullBaseFileInfo.dir().absolutePath()
rosettaBaseFileName = rosettaFullBaseFileInfo.fileName()
rosettaProcess = Process()
rosettaProcess.setProcessName("rosetta")
rosettaProcess.redirect_stdout_to_file("%s-rosetta-stdout.txt" %
rosettaFullBaseFileName)
rosettaProcess.redirect_stderr_to_file("%s-rosetta-stderr.txt" %
rosettaFullBaseFileName)
rosettaStdOut = rosettaFullBaseFileName + "-rosetta-stdout.txt"
rosettaProcess.setWorkingDirectory(rosettaWorkingDir)
environmentVariables = rosettaProcess.environment()
rosettaProcess.setEnvironment(environmentVariables)
msg = greenmsg("Starting Rosetta sequence design")
env.history.message(self.cmdname + ": " + msg)
env.history.message("%s: Rosetta files at %s%s%s.*" %
(self.cmdname, rosettaWorkingDir, os.sep,
rosettaFullBaseFileInfo.completeBaseName()))
abortHandler = AbortHandler(self.win.statusBar(), "rosetta")
errorCode = rosettaProcess.run(self.program, self._arguments, False, abortHandler)
abortHandler = None
if (errorCode != 0):
if errorCode == -2: # User pressed Abort button in progress dialog.
msg = redmsg("Aborted.")
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
if self.simProcess: #bruce 051231 added condition (since won't be there when use_dylib)
self.simProcess.kill()
else:
msg = redmsg("Rosetta sequence design failed. For details check" + rosettaStdOut)
env.history.message(self.cmdname + ": " + msg)
self.errcode = 2;
env.history.statusbar_msg("")
else:
#run has been successful
#open pdb file
env.history.statusbar_msg("")
errorInStdOut = self.checkErrorInStdOut(rosettaStdOut)
if errorInStdOut:
msg = redmsg("Rosetta sequence design failed, Rosetta returned %d" % errorCode)
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
else:
#env.history.message(self.cmdname + ": " + msg)
outputFile = self.outfile + '_0001.pdb'
outPath = os.path.join(os.path.dirname(self.tmp_file_prefix), outputFile)
if os.path.exists(outPath):
msg = greenmsg("Rosetta sequence design succeeded")
env.history.message(self.cmdname + ": " + msg)
#find out best score from all the generated outputs
score, bestSimOutFileName = getScoreFromOutputFile(self.tmp_file_prefix, self.outfile, self.numSim)
chosenOutPath = os.path.join(os.path.dirname(self.tmp_file_prefix), bestSimOutFileName)
insertpdb(self.assy, str(chosenOutPath), None)
env.history.statusbar_msg("")
fastaFile = self.outfile + "_design.fasta"
fastaFilePath = os.path.join(os.path.dirname(self.tmp_file_prefix), fastaFile)
proteinSeqList = processFastaFile(fastaFilePath, bestSimOutFileName, self.sim_input_file[0:len(self.sim_input_file)-4])
#score = getScoreFromOutputFile(outPath)
if score is not None and proteinSeqList is not []:
self.showResults(score, proteinSeqList)
else:
msg1 = redmsg("Rosetta sequence design failed. ")
msg2 = redmsg(" %s file was never created by Rosetta." % outputFile)
msg = msg1 + msg2
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
except:
print_compact_traceback("bug in simulator-calling code: ")
self.errcode = -11111
self.set_waitcursor(False)
self.win.disable_QActions_for_sim(False)
env.history.statusbar_msg("")
if not self.errcode:
return # success
return # caller should look at self.errcode
