def _getBasicTrackFormat(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
genome = GeneralGuiTool._getGenomeChoice(choices, genomeChoiceIndex)[0]
tn = GeneralGuiTool._getTrackChoice(choices, tnChoiceIndex)[0]
from quick.application.GalaxyInterface import GalaxyInterface
from gold.description.TrackInfo import TrackInfo
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.track.TrackFormat import TrackFormat
if ExternalTrackManager.isGalaxyTrack(tn):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
tn, genome)
try:
tf = GeneralGuiTool._convertToBasicTrackFormat(
TrackFormat.createInstanceFromGeSource(
geSource).getFormatName())
except Warning:
return genome, tn, ''
else:
if GalaxyInterface.isNmerTrackName(genome, tn):
tfName = 'Points'
else:
tfName = TrackInfo(genome, tn).trackFormatName
tf = GeneralGuiTool._convertToBasicTrackFormat(tfName)
return genome, tn, tf
def _isValidTrack(prevChoices, tnChoiceIndex=1):
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.ProcTrackOptions import ProcTrackOptions
genome = prevChoices[0]
tn = prevChoices[tnChoiceIndex].split(':')
return ProcTrackOptions.isValidTrack(genome, tn, True) or \
GalaxyInterface.isNmerTrackName(genome, tn)
def _isValidTrack(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.ProcTrackOptions import ProcTrackOptions
genome, errorStr = GeneralGuiTool._getGenomeChoice(
choices, genomeChoiceIndex)
if errorStr or genome is None:
return False
trackName, errorStr = GeneralGuiTool._getTrackChoice(
choices, tnChoiceIndex)
if errorStr:
return False
return ProcTrackOptions.isValidTrack(genome, trackName, True) or \
GalaxyInterface.isNmerTrackName(genome, trackName)
def _getValueTypeName(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
genome = GeneralGuiTool._getGenomeChoice(choices, genomeChoiceIndex)[0]
tn = GeneralGuiTool._getTrackChoice(choices, tnChoiceIndex)[0]
from quick.application.GalaxyInterface import GalaxyInterface
from gold.description.TrackInfo import TrackInfo
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.track.TrackFormat import TrackFormat
if ExternalTrackManager.isGalaxyTrack(tn):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
tn, genome)
valTypeName = TrackFormat.createInstanceFromGeSource(
geSource).getValTypeName()
else:
if GalaxyInterface.isNmerTrackName(genome, tn):
valTypeName = ''
else:
valTypeName = TrackInfo(genome, tn).markType
return valTypeName.lower()
def _getBasicTrackFormat(choices, tnChoiceIndex=1):
from quick.application.GalaxyInterface import GalaxyInterface
from gold.description.TrackInfo import TrackInfo
genome = choices[0]
tn = choices[tnChoiceIndex].split(':')
if GalaxyInterface.isNmerTrackName(genome, tn):
tfName = 'Points'
else:
tfName = TrackInfo(genome, tn).trackFormatName
tfName = tfName.lower()
if tfName.startswith('linked '):
tfName = tfName[7:]
tfName = tfName.replace('unmarked ','')
tfName = tfName.replace('marked','valued')
return genome, tn, tfName
