def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "whatsNewDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["whatsNewDialog"])
self.dlg = self.wTree.get_object("whatsNewDialog")
self.textView = self.wTree.get_object('whatsNewDialogTextView')
buffer = gtk.TextBuffer()
self.textView.set_buffer(buffer)
try:
from bzrlib.branch import Branch
my_branch = Branch.open(
os.path.join(os.path.dirname(__file__), '../..'))
rev_ids = my_branch.revision_history()
rev_ids.reverse()
repo = my_branch.repository
for rev_id in rev_ids:
revision = repo.get_revision(rev_id)
buffer.insert_at_cursor('revision ')
buffer.insert_at_cursor(
str(my_branch.revision_id_to_revno(rev_id)))
buffer.insert_at_cursor(' :: ')
buffer.insert_at_cursor(revision.message)
buffer.insert_at_cursor('\n\n')
except:
pass
self.result = self.dlg.run()
self.dlg.destroy()
def run(self):
"""This function will show the addPhageDialog"""
#load the dialog from the glade file
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "AddPhageDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["AddPhageDialog"])
#Get the actual dialog widget
self.dlg = self.wTree.get_object("AddPhageDialog")
#Get all of the Entry Widgets and set their text
self.enName = self.wTree.get_object("AddPhage_EnterName")
self.allowRefSeqsCheckBox = self.wTree.get_object(
"allowRefSeqsCheckBox")
#run the dialog and store the response
self.result = self.dlg.run()
#get the value of the entry fields
self.phage.name = self.enName.get_text()
#we are done with the dialog, destroy it
self.dlg.destroy()
if self.result == gtk.RESPONSE_CANCEL: return None
self.logger.log('destroying AddPhageDialog')
#return the result and the phage
return (self.result, self.phage,
self.allowRefSeqsCheckBox.get_active())
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "whatsNewDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["whatsNewDialog"])
self.dlg = self.wTree.get_object("whatsNewDialog")
self.textView = self.wTree.get_object('whatsNewDialogTextView')
buffer = gtk.TextBuffer()
self.textView.set_buffer(buffer)
try:
from bzrlib.branch import Branch
my_branch = Branch.open(os.path.join(os.path.dirname(__file__), '../..'))
rev_ids = my_branch.revision_history()
rev_ids.reverse()
repo = my_branch.repository
for rev_id in rev_ids:
revision=repo.get_revision(rev_id)
buffer.insert_at_cursor('revision ')
buffer.insert_at_cursor(str(my_branch.revision_id_to_revno(rev_id)))
buffer.insert_at_cursor(' :: ')
buffer.insert_at_cursor(revision.message)
buffer.insert_at_cursor('\n\n')
except:
pass
self.result = self.dlg.run()
self.dlg.destroy()
def __init__(self):
self.gladefile = gladeFile().filename
import gconf
self.client = gconf.client_get_default()
self.client.add_dir('/apps/phamerator', gconf.CLIENT_PRELOAD_NONE)
hideDialog = self.client.get_bool(
'/apps/phamerator/hide_BLAST_warning_dialog')
def __init__(self, dbname):
print 'open database setup dialog'
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "databaseSetupWarningDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["databaseSetupWarningDialog"])
self.dbname = self.wTree.get_object("databaseSetupWarningDbname")
self.dbname.set_text(dbname)
def __init__(self, name): print 'creating saveDialog' #Dialog.__init__(self) self.gladefile = gladeFile().filename self.wTree = gtk.Builder() self.wTree.add_objects_from_file(self.gladefile, [name]) self.current_folder = os.path.join(os.environ['HOME'], 'Desktop') if name is not None: self.wTree.get_object(name).set_current_folder(self.current_folder)
def run(self):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["newDatabaseAvailableDialog"])
self.dlg = self.wTree.get_object("newDatabaseAvailableDialog")
self.result = self.dlg.run()
self.dlg.destroy()
return self.result
def __init__(self, pM):
SaveDialog.__init__(self, "batchFileSaveAsDialog")
self.gladefile = gladeFile().filename
dic = {"on_appendDateCheckButton_toggled" : self.on_appendDateCheckButton_toggled}
self.wTree.connect_signals(dic)
self.chooser = self.wTree.get_object("batchFileSaveAsDialog")
#self.chooser.set_current_name('pham####')
self.pM = pM
def __init__(self,showPopUp=True,filePath=None):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
dic = {"on_specifyButton_activate" : self.on_specifyButton_activate,"on_downloadSpecificPathButton_activate":self.on_downloadSpecificPathButton_activate, "on_okbutton_activate":self.on_okbutton_activate}
self.wTree.add_objects_from_file(self.gladefile, ["blastDownloadDialog"])
self.wTree.connect_signals(dic)
self.dlg = self.wTree.get_object("blastDownloadDialog")
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "OpenGenBankFileDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["OpenGenBankFileDialog"])
self.dlg = self.wTree.get_object("OpenGenBankFileDialog")
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def run(self):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["blastCustomLocationDialog"])
self.dlg = self.wTree.get_object("blastCustomLocationDialog")
self.dlg.set_current_folder(os.environ['HOME'])
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def __init__(self, name):
print 'creating saveDialog'
#Dialog.__init__(self)
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, [name])
self.current_folder = os.path.join(os.environ['HOME'], 'Desktop')
if name is not None:
self.wTree.get_object(name).set_current_folder(self.current_folder)
def run(self):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["newDatabaseAvailableDialog"])
self.dlg = self.wTree.get_object("newDatabaseAvailableDialog")
self.result = self.dlg.run()
self.dlg.destroy()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "InvalidConfigurationDialog")
#self.dlg = self.wTree.get_object("InvalidConfigurationDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["InvalidConfigurationDialog"])
self.dlg = self.wTree.get_object("InvalidConfigurationDialog")
self.result = self.dlg.run()
self.dlg.destroy()
def __init__(self, dbname):
print 'open database setup dialog'
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "databaseSetupWarningDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["databaseSetupWarningDialog"])
self.dbname = self.wTree.get_object("databaseSetupWarningDbname")
self.dbname.set_text(dbname)
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "OpenGenBankFileDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["OpenGenBankFileDialog"])
self.dlg = self.wTree.get_object("OpenGenBankFileDialog")
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "InvalidConfigurationDialog")
#self.dlg = self.wTree.get_object("InvalidConfigurationDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["InvalidConfigurationDialog"])
self.dlg = self.wTree.get_object("InvalidConfigurationDialog")
self.result = self.dlg.run()
self.dlg.destroy()
def __init__(self, error):
print error
errno, errmsg = error
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "databaseConnectionErrorDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["databaseConnectionErrorDialog"])
label = self.wTree.get_object("databaseConnectionErrorLabel")
label.set_text('%s: %s' % (errno, errmsg))
def run(self):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["blastCustomLocationDialog"])
self.dlg = self.wTree.get_object("blastCustomLocationDialog")
self.dlg.set_current_folder(os.environ['HOME'])
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "openBlastFolderDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["openBlastFolderDialog"])
self.dlg = self.wTree.get_object("openBlastFolderDialog")
self.dlg.set_current_folder(os.environ['HOME'])
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def __init__(self, error):
print error
errno, errmsg = error
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "databaseConnectionErrorDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["databaseConnectionErrorDialog"])
label = self.wTree.get_object("databaseConnectionErrorLabel")
label.set_text('%s: %s' % (errno, errmsg))
def __init__(self, pM):
SaveDialog.__init__(self, "batchFileSaveAsDialog")
self.gladefile = gladeFile().filename
dic = {
"on_appendDateCheckButton_toggled":
self.on_appendDateCheckButton_toggled
}
self.wTree.connect_signals(dic)
self.chooser = self.wTree.get_object("batchFileSaveAsDialog")
#self.chooser.set_current_name('pham####')
self.pM = pM
def __init__(self, name=None):
#setup the glade file
self.gladefile = gladeFile().filename
self.client = gconf.client_get_default()
self.conf = config.PhameratorConfiguration()
self.current_folder = self.conf.get('/apps/phamerator/default_folder')
if not self.current_folder: self.current_folder = os.path.join(os.environ['HOME'], 'Desktop')
#self.wTree = gtk.glade.XML(self.gladefile, name)
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, [name])
if name is not None: self.wTree.get_object(name).set_current_folder(self.current_folder)
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "openBlastFolderDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["openBlastFolderDialog"])
self.dlg = self.wTree.get_object("openBlastFolderDialog")
self.dlg.set_current_folder(os.environ['HOME'])
self.result = self.dlg.run()
self.dlg.hide()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "ErrorAddingPhageDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["ErrorAddingPhageDialog"])
self.dlg = self.wTree.get_object("ErrorAddingPhageDialog")
errTextView = self.wTree.get_object("errorAddingPhageTextView") # errorAddingPhageTextView
errText = gtk.TextBuffer(table=None)
errText.set_text(self.msg)
errTextView.set_buffer(errText)
self.result = self.dlg.run()
self.dlg.destroy()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "addDatabaseDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["addDatabaseDialog"])
self.dlg = self.wTree.get_object("addDatabaseDialog")
self.result = self.dlg.run()
text = self.wTree.get_object("addDatabaseEntry").get_text()
self.dlg.destroy()
if not self.result:
return None
else:
return text
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "addDatabaseDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["addDatabaseDialog"])
self.dlg = self.wTree.get_object("addDatabaseDialog")
self.result = self.dlg.run()
text = self.wTree.get_object("addDatabaseEntry").get_text()
self.dlg.destroy()
if not self.result:
return None
else:
return text
def __init__(self, name=None):
#setup the glade file
self.gladefile = gladeFile().filename
self.client = gconf.client_get_default()
self.conf = config.PhameratorConfiguration()
self.current_folder = self.conf.get('/apps/phamerator/default_folder')
if not self.current_folder:
self.current_folder = os.path.join(os.environ['HOME'], 'Desktop')
#self.wTree = gtk.glade.XML(self.gladefile, name)
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, [name])
if name is not None:
self.wTree.get_object(name).set_current_folder(self.current_folder)
def __init__(self, showPopUp=True, filePath=None):
self.gladefile = gladeFile().filename
self.wTree = gtk.Builder()
dic = {
"on_specifyButton_activate": self.on_specifyButton_activate,
"on_downloadSpecificPathButton_activate":
self.on_downloadSpecificPathButton_activate,
"on_okbutton_activate": self.on_okbutton_activate
}
self.wTree.add_objects_from_file(self.gladefile,
["blastDownloadDialog"])
self.wTree.connect_signals(dic)
self.dlg = self.wTree.get_object("blastDownloadDialog")
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "ErrorAddingPhageDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile,
["ErrorAddingPhageDialog"])
self.dlg = self.wTree.get_object("ErrorAddingPhageDialog")
errTextView = self.wTree.get_object(
"errorAddingPhageTextView") # errorAddingPhageTextView
errText = gtk.TextBuffer(table=None)
errText.set_text(self.msg)
errTextView.set_buffer(errText)
self.result = self.dlg.run()
self.dlg.destroy()
return self.result
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "AboutDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["AboutDialog"])
self.dlg = self.wTree.get_object("AboutDialog")
try:
from bzrlib.branch import Branch
my_branch = Branch.open(os.path.join(os.path.dirname(__file__), '../..'))
version = my_branch.last_revision_info()[0]
self.dlg.set_comments('you are using a development version')
except:
self.dlg.set_comments('')
version = open(os.path.join(os.path.dirname(__file__), '../..', 'README.txt')).readlines()[0].split(' ')[-1]
self.dlg.set_version('%s' % version)
self.result = self.dlg.run()
self.dlg.destroy()
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "AboutDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["AboutDialog"])
self.dlg = self.wTree.get_object("AboutDialog")
try:
from bzrlib.branch import Branch
my_branch = Branch.open(
os.path.join(os.path.dirname(__file__), '../..'))
version = my_branch.last_revision_info()[0]
self.dlg.set_comments('you are using a development version')
except:
self.dlg.set_comments('')
version = open(
os.path.join(os.path.dirname(__file__), '../..',
'README.txt')).readlines()[0].split(' ')[-1]
self.dlg.set_version('%s' % version)
self.result = self.dlg.run()
self.dlg.destroy()
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "dbStatsDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["dbStatsDialog"])
self.show_number_of_genes()
self.show_number_of_genomes()
self.show_number_of_phamilies()
self.show_genome_length_min()
self.show_genome_length_max()
self.show_genome_length_mean()
self.show_gene_length_min()
self.show_gene_length_max()
self.show_gene_length_mean()
self.show_phamily_size_min()
self.show_phamily_size_max()
self.show_phamily_size_mean()
self.dlg = self.wTree.get_object("dbStatsDialog")
self.result = self.dlg.run()
self.dlg.destroy()
def run(self):
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "dbStatsDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["dbStatsDialog"])
self.show_number_of_genes()
self.show_number_of_genomes()
self.show_number_of_phamilies()
self.show_genome_length_min()
self.show_genome_length_max()
self.show_genome_length_mean()
self.show_gene_length_min()
self.show_gene_length_max()
self.show_gene_length_mean()
self.show_phamily_size_min()
self.show_phamily_size_max()
self.show_phamily_size_mean()
self.dlg = self.wTree.get_object("dbStatsDialog")
self.result = self.dlg.run()
self.dlg.destroy()
def run(self):
"""This function will show the addPhageDialog"""
#load the dialog from the glade file
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "AddPhageDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["AddPhageDialog"])
#Get the actual dialog widget
self.dlg = self.wTree.get_object("AddPhageDialog")
#Get all of the Entry Widgets and set their text
self.enName = self.wTree.get_object("AddPhage_EnterName")
self.allowRefSeqsCheckBox = self.wTree.get_object("allowRefSeqsCheckBox")
#run the dialog and store the response
self.result = self.dlg.run()
#get the value of the entry fields
self.phage.name = self.enName.get_text()
#we are done with the dialog, destroy it
self.dlg.destroy()
if self.result == gtk.RESPONSE_CANCEL: return None
self.logger.log('destroying AddPhageDialog')
#return the result and the phage
return (self.result,self.phage,self.allowRefSeqsCheckBox.get_active())
def __init__(self, results):
self.gi_list = results
self.gladefile = gladeFile().filename
self.active = None
def __init__(self):
self.gladefile = gladeFile().filename
import gconf
self.client = gconf.client_get_default()
self.client.add_dir('/apps/phamerator', gconf.CLIENT_PRELOAD_NONE)
hideDialog = self.client.get_bool('/apps/phamerator/hide_BLAST_warning_dialog')
def __init__(self, results): self.gi_list = results self.gladefile = gladeFile().filename self.active = None
def __init__(self,pManager):
self.PManager = pManager
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "preferencesDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["preferencesDialog"])
dic = {"preferencesChangedSignalHandler" : self.preferencesChangedSignalHandler,
"radioChangedSignalHandler":self.radioChangedSignalHandler,
"on_preferencesServerComboBox_changed": self.on_preferencesServerComboBox_changed,
"on_preferencesDatabaseComboBox_changed": self.on_preferencesDatabaseComboBox_changed,
"on_updateDatabaseButton_clicked": self.on_updateDatabaseButton_clicked,
"on_addServerButton_clicked": self.on_addServerButton_clicked,
"on_removeServerButton_clicked": self.on_removeServerButton_clicked,
"on_addDatabaseButton_clicked": self.on_addDatabaseButton_clicked,
"on_removeDatabaseButton_clicked": self.on_removeDatabaseButton_clicked,
}
self.dlg = self.wTree.get_object("preferencesDialog")
spinner = self.wTree.get_object("preferencesDialogSpinner")
spinner.start()
conf = config.PhameratorConfiguration()
if conf.get('/apps/phamerator/pham_circle_color_scheme') == 'alignmentType':
self.wTree.get_object("alignmentTypeRadioButton").set_active(True)
self.wTree.get_object("phamColorRadioButton").set_active(False)
if conf.get('/apps/phamerator/pham_circle_color_scheme') == 'phamColor':
self.wTree.get_object("alignmentTypeRadioButton").set_active(False)
self.wTree.get_object("phamColorRadioButton").set_active(True)
adj = self.wTree.get_object("transparency_slider").get_adjustment()
adj.configure(conf.get_float('/apps/phamerator/transparency_adjustment'), 0.0, 100.0, 1.0, 10.0, 0)
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.phamerator', 'phamerator.conf'))
if cfg.get('Phamerator','draw_blast_alignments') == 'False':
self.wTree.get_object("eValuesCheckBox").set_sensitive(False)
self.wTree.get_object("blastAlignmentCheckBox").set_sensitive(False)
#self.wTree.signal_autoconnect(dic)
self.wTree.connect_signals(dic)
try:
self.database = cfg.get('Phamerator','defaultDatabase')
print "self.database = " + self.database
except: self.database = 'SEA'
try: self.remote_server = cfg.get('Phamerator','defaultServer')
except:
pass
self.remote_server = 'http://localhost'
comboBoxes = [('server', 'preferencesServerComboBox'), ('database', 'preferencesDatabaseComboBox')]
for box in comboBoxes:
boxType, boxName = box[0], box[1]
cbe = self.wTree.get_object(boxName)
listStore = gtk.ListStore(str)
cbe.set_model(listStore)
cell = gtk.CellRendererText()
cbe.pack_start(cell, True)
cbe.add_attribute(cell, "text", 0)
#cbe.set_text_column(0)
if boxType == 'server':
others = cfg.get('Phamerator','otherServers')
elif boxType == 'database':
others = cfg.get('Phamerator','otherDatabases')
otherList = others.split(',')
otherListNew = []
for n,o in enumerate(otherList):
if o != "":
otherListNew.append(o.strip())
otherListNew.sort()
for o in otherListNew:
print o
listStore.append(row=(o,))
if boxType == 'server' and self.remote_server:
print 'POPULATING SERVER COMBOX BOX with %s' % self.remote_server
#listStore.prepend(row=(self.remote_server,))
cbe.prepend_text(self.remote_server)
elif boxType == 'database':
cbe.prepend_text(self.database)
cbe.set_active(0)
def __init__(self, pManager):
self.PManager = pManager
self.gladefile = gladeFile().filename
#self.wTree = gtk.glade.XML(self.gladefile, "preferencesDialog")
self.wTree = gtk.Builder()
self.wTree.add_objects_from_file(self.gladefile, ["preferencesDialog"])
dic = {
"preferencesChangedSignalHandler":
self.preferencesChangedSignalHandler,
"radioChangedSignalHandler":
self.radioChangedSignalHandler,
"on_preferencesServerComboBox_changed":
self.on_preferencesServerComboBox_changed,
"on_preferencesDatabaseComboBox_changed":
self.on_preferencesDatabaseComboBox_changed,
"on_updateDatabaseButton_clicked":
self.on_updateDatabaseButton_clicked,
"on_addServerButton_clicked":
self.on_addServerButton_clicked,
"on_removeServerButton_clicked":
self.on_removeServerButton_clicked,
"on_addDatabaseButton_clicked":
self.on_addDatabaseButton_clicked,
"on_removeDatabaseButton_clicked":
self.on_removeDatabaseButton_clicked,
}
self.dlg = self.wTree.get_object("preferencesDialog")
spinner = self.wTree.get_object("preferencesDialogSpinner")
spinner.start()
conf = config.PhameratorConfiguration()
if conf.get('/apps/phamerator/pham_circle_color_scheme'
) == 'alignmentType':
self.wTree.get_object("alignmentTypeRadioButton").set_active(True)
self.wTree.get_object("phamColorRadioButton").set_active(False)
if conf.get(
'/apps/phamerator/pham_circle_color_scheme') == 'phamColor':
self.wTree.get_object("alignmentTypeRadioButton").set_active(False)
self.wTree.get_object("phamColorRadioButton").set_active(True)
adj = self.wTree.get_object("transparency_slider").get_adjustment()
adj.configure(
conf.get_float('/apps/phamerator/transparency_adjustment'), 0.0,
100.0, 1.0, 10.0, 0)
cfg = ConfigParser.RawConfigParser()
cfg.read(
os.path.join(os.environ['HOME'], '.phamerator', 'phamerator.conf'))
if cfg.get('Phamerator', 'draw_blast_alignments') == 'False':
self.wTree.get_object("eValuesCheckBox").set_sensitive(False)
self.wTree.get_object("blastAlignmentCheckBox").set_sensitive(
False)
#self.wTree.signal_autoconnect(dic)
self.wTree.connect_signals(dic)
try:
self.database = cfg.get('Phamerator', 'defaultDatabase')
print "self.database = " + self.database
except:
self.database = 'SEA'
try:
self.remote_server = cfg.get('Phamerator', 'defaultServer')
except:
pass
self.remote_server = 'http://localhost'
comboBoxes = [('server', 'preferencesServerComboBox'),
('database', 'preferencesDatabaseComboBox')]
for box in comboBoxes:
boxType, boxName = box[0], box[1]
cbe = self.wTree.get_object(boxName)
listStore = gtk.ListStore(str)
cbe.set_model(listStore)
cell = gtk.CellRendererText()
cbe.pack_start(cell, True)
cbe.add_attribute(cell, "text", 0)
#cbe.set_text_column(0)
if boxType == 'server':
others = cfg.get('Phamerator', 'otherServers')
elif boxType == 'database':
others = cfg.get('Phamerator', 'otherDatabases')
otherList = others.split(',')
otherListNew = []
for n, o in enumerate(otherList):
if o != "":
otherListNew.append(o.strip())
otherListNew.sort()
for o in otherListNew:
print o
listStore.append(row=(o, ))
if boxType == 'server' and self.remote_server:
print 'POPULATING SERVER COMBOX BOX with %s' % self.remote_server
#listStore.prepend(row=(self.remote_server,))
cbe.prepend_text(self.remote_server)
elif boxType == 'database':
cbe.prepend_text(self.database)
cbe.set_active(0)