def addComponents( self, container ) :
container.setLayout( GridBagLayout() )
c = GridBagConstraints()
c.gridx = 0 # first column
c.gridy = 0 # first row
container.add( JButton( '1' ), c )
c = GridBagConstraints()
c.gridx = 1 # second column
c.gridy = 1 # second row
container.add( JButton( '2' ), c )
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.gridx = 2 # third column
c.gridy = 2 # third row
# c.ipadx = 64 # specify (don't default) width
c.weightx = 0.0
c.gridwidth = 3
container.add( JButton( '3 being the third number' ), c )
c = GridBagConstraints()
c.gridx = 1 # second column
c.gridy = 3 # forth row
c.ipady = 32 # make this one taller
container.add( JButton( 'Four shalt thou not count' ), c )
c = GridBagConstraints()
c.gridx = 1 # second column
c.gridy = 4 # fifth row
c.gridwidth = 3 # make this one 3 columns wide
container.add( JButton( 'Five is right out' ), c )
def __init__(self):
self.running = True
menuBar = JMenuBar()
menu = JMenu("File")
menu.add(OpenAction(self))
menu.add(CloseAction(self))
menu.addSeparator()
menu.add(QuitAction(self))
self.addWindowListener(ProfelisWindowAdapter(self))
menuBar.add(menu)
self.setJMenuBar(menuBar)
self.contentPane = JPanel()
self.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
self.blastLocation = JTextField(
System.getProperty("user.home") + "/blast")
self.databaseLocation = JTextField(
System.getProperty("user.home") + "/blast/db")
self.projects = JTabbedPane()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridx, constraints.gridy = 1, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.blastLocation, constraints)
constraints.gridx, constraints.gridy = 2, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(BlastAction(self)), constraints)
constraints.gridx, constraints.gridy = 3, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Database Location"), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.databaseLocation, constraints)
constraints.gridx, constraints.gridy = 5, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(DatabaseAction(self)), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.gridwidth, constraints.gridheight = 6, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.contentPane.add(self.projects, constraints)
def __init__(self):
self.running = True
menuBar = JMenuBar()
menu = JMenu("File")
menu.add(OpenAction(self))
menu.add(CloseAction(self))
menu.addSeparator()
menu.add(QuitAction(self))
self.addWindowListener(ProfelisWindowAdapter(self))
menuBar.add(menu)
self.setJMenuBar(menuBar)
self.contentPane = JPanel()
self.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
self.blastLocation = JTextField(System.getProperty("user.home") + "/blast")
self.databaseLocation = JTextField(System.getProperty("user.home") + "/blast/db")
self.projects = JTabbedPane()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridx, constraints.gridy = 1, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.blastLocation, constraints)
constraints.gridx, constraints.gridy = 2, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(BlastAction(self)), constraints)
constraints.gridx, constraints.gridy = 3, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JLabel("Database Location"), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx, constraints.weighty = 1, 0
self.contentPane.add(self.databaseLocation, constraints)
constraints.gridx, constraints.gridy = 5, 0
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.contentPane.add(JButton(DatabaseAction(self)), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.gridwidth, constraints.gridheight = 6, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.contentPane.add(self.projects, constraints)
def __init__(self, plugin):
super(EmulatorComponentProvider,
self).__init__(plugin.getTool(), "Emulator", "emulate_function")
self.plugin = plugin
self.panel = JPanel(GridBagLayout())
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.gridy = 0
c.gridx = 0
c.weightx = 0.8
self.panel_label = JLabel("")
self.panel.add(self.panel_label, c)
c.gridx = 1
c.weightx = 0.2
self.panel_btn = JButton("Start")
self.panel_btn.addActionListener(EmulatorBtnAction(self))
self.panel.add(self.panel_btn, c)
c.gridy = 1
c.gridx = 0
c.gridwidth = 2
self.panel_input = JTextField()
self.panel_input.addActionListener(EmulatorInputAction(self))
self.panel.add(self.panel_input, c)
self.setStatus("Stopped")
def add(parent,
child,
gridx=0,
gridy=0,
anchor=GC.NORTHWEST,
fill=GC.NONE,
weightx=0.0,
weighty=0.0,
gridwidth=1):
c = GC()
c.gridx = gridx
c.gridy = gridy
c.anchor = anchor
c.fill = fill
c.weightx = weightx
c.weighty = weighty
c.gridwidth = gridwidth
"""
# Same, more flexible, less verbose: BUT FAILS at parent, child args
kv = locals() # dict of local variables including the function arguments
c = GC()
for key, value in kv.iteritems():
setattr(c, key, value)
"""
#
parent.getLayout().setConstraints(child, c)
parent.add(child)
def __createDropDownConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.HORIZONTAL
constr.weighty = 1
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 0
return constr
def create_gui():
global dropdown, current_file
frame = JFrame('',
defaultCloseOperation = JFrame.DISPOSE_ON_CLOSE,
size = (400, 150));
frame.setBounds(350,350,400,150);
container_panel = JPanel(GridBagLayout());
c = GridBagConstraints();
dropdown = JComboBox(list(img_paths.keys()));
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = 0;
c.weightx = 0.5;
c.gridwidth = 3;
container_panel.add(dropdown, c);
add_file_button = JButton('<html>Add Image/File</html>', actionPerformed=select_file);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 3;
c.gridy = 0;
c.weightx = 0.5;
c.gridwidth = 1;
container_panel.add(add_file_button, c);
process_file_button = JButton('<html>Process Selected Image</html>', actionPerformed=process_current_img);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = 1;
c.weightx = 0.5;
c.gridwidth = 2;
container_panel.add(process_file_button, c);
process_all_button = JButton('<html>Process Entire Stack</html>', actionPerformed=process_stack);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 2;
c.gridy = 1;
c.weightx = 0.5;
c.gridwidth = 2;
container_panel.add(process_all_button, c);
current_file = dropdown.getSelectedItem();
frame.add(container_panel);
frame.visible = True;
def cachedBPROM(genome, fileName, frame):
"""
genome: Genome as a string.
fileName: File to save the BPROM results in.
swing: A JFrame or None. If this is None then messages will be printed, if it isn't then
they will also be put in a dialog box.
return: Results of the BPROM prediction stored in a list of Promoter objects.
If the file Specified by fileName already exists then this function simply parses the file
already there. Also, if a request is made to BPROM and nothing is returned, no file is
created, the user is warned, and an empty list is returned.
"""
offset = 25 if ".forward.bprom" in fileName else 50
direction = "forward" if offset == 50 else "reverse"
def getPromoters():
input = open(fileName, "r")
results = parseBPROM(input.read())
input.close()
return results
if not os.path.isfile(fileName):
results = urllib.urlopen("http://linux1.softberry.com/cgi-bin/programs/gfindb/bprom.pl",
urllib.urlencode({"DATA" : genome}))
resultString = results.read()
results.close()
resultString = resultString[resultString.find("<pre>"):resultString.find("</pre>")]
resultString = re.sub("<+.+>+", "", resultString).strip()
if resultString:
output = open(fileName, "w")
output.write(resultString)
output.close()
return getPromoters()
else:
if frame:
messageFrame = JFrame("BPROM Error",
defaultCloseOperation = WindowConstants.DISPOSE_ON_CLOSE)
messageFrame.setLocation(frame.location().x + offset, frame.location().y + offset)
messageFrame.contentPane.layout = GridBagLayout()
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
messageFrame.contentPane.add(JLabel("<html>The pipeline will continue to run but BPROM<br/>did not process the request for promoters on the<br/>" + direction + " strand. Try again tomorrow.</html>"), constraints)
constraints.gridx, constraints.gridy = 0, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 1, 1
constraints.anchor = GridBagConstraints.LINE_END
messageFrame.contentPane.add(JButton("Ok", actionPerformed = lambda e: messageFrame.dispose()), constraints)
messageFrame.pack()
messageFrame.visible = True
print "BPROM Error:", "The pipeline will continue to run but BPROM did not process the request for promoters on the " + direction + " strand. Try again tomorrow"
return []
else:
return getPromoters()
def __createTableConstraints(self):
constr = GridBagConstraints()
constr.fill = GridBagConstraints.BOTH
constr.weighty = 1000
constr.weightx = 2
constr.gridwidth = 4
constr.gridx = 0
constr.gridy = 2
return constr
def _new_grid_bag(gridx, gridy, gridwidth=1):
"""Creates a new GridBagConstraints"""
g = GridBagConstraints()
g.gridx = gridx
g.gridy = gridy
g.gridwidth = gridwidth
g.fill = GridBagConstraints.BOTH
g.insets = Insets(2, 2, 5, 5)
return g
def _new_grid_bag(gridx, gridy, gridwidth=1):
"""Creates a new GridBagConstraints"""
g = GridBagConstraints()
g.gridx = gridx
g.gridy = gridy
g.gridwidth = gridwidth
g.fill = GridBagConstraints.BOTH
g.insets = Insets(2,2,5,5)
return g
def compose_ui(self, components):
panel = JPanel()
panel.setLayout(GridBagLayout())
constraints= GridBagConstraints()
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.insets = Insets(2, 1, 2, 1)
for i in components:
for j in components[i]:
constraints.gridy, constraints.gridx = i, j
constraints.gridwidth = components[i][j]['width'] if type(components[i][j]) == dict and 'width' in components[i][j] else 1
constraints.gridheight = components[i][j]['height'] if type(components[i][j]) == dict and 'height' in components[i][j] else 1
item = components[i][j]['item'] if type(components[i][j]) == dict and 'item' in components[i][j] else components[i][j]
panel.add(item, constraints)
return panel
def initializeDisplay(self, queries, swing):
"""
queries: A list of the fasts files to be processed.
swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout.
Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the
number of queries the pipeline will process and to size the swing display(if it is used) so that text
isn't cutoff at the edge of the window. The swing display is setup if swing is true.
"""
self.numJobs = len(queries)
if swing:
self.frame = JFrame("Neofelis")
self.frame.addWindowListener(PipelineWindowAdapter(self))
contentPane = JPanel(GridBagLayout())
self.frame.setContentPane(contentPane)
self.globalLabel = JLabel(max(queries, key=len))
self.globalProgress = JProgressBar(0, self.numJobs)
self.currentLabel = JLabel(max(self.messages, key=len))
self.currentProgress = JProgressBar(0, len(self.messages))
self.doneButton = JButton(DoneAction(self.frame))
self.doneButton.setEnabled(False)
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.weightx = 1
constraints.fill = GridBagConstraints.HORIZONTAL
contentPane.add(self.globalLabel, constraints)
constraints.gridy = 1
contentPane.add(self.globalProgress, constraints)
constraints.gridy = 2
contentPane.add(self.currentLabel, constraints)
constraints.gridy = 3
contentPane.add(self.currentProgress, constraints)
constraints.gridy = 4
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(self.doneButton, constraints)
self.frame.pack()
self.frame.setResizable(False)
self.globalLabel.setText(" ")
self.currentLabel.setText(" ")
self.frame.setLocationRelativeTo(None)
self.frame.setVisible(True)
def initializeDisplay(self, queries, swing):
"""
queries: A list of the fasts files to be processed.
swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout.
Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the
number of queries the pipeline will process and to size the swing display(if it is used) so that text
isn't cutoff at the edge of the window. The swing display is setup if swing is true.
"""
self.numJobs = len(queries)
if swing:
self.frame = JFrame("Neofelis")
self.frame.addWindowListener(PipelineWindowAdapter(self))
contentPane = JPanel(GridBagLayout())
self.frame.setContentPane(contentPane)
self.globalLabel = JLabel(max(queries, key = len))
self.globalProgress = JProgressBar(0, self.numJobs)
self.currentLabel = JLabel(max(self.messages, key = len))
self.currentProgress = JProgressBar(0, len(self.messages))
self.doneButton = JButton(DoneAction(self.frame))
self.doneButton.setEnabled(False)
constraints = GridBagConstraints()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.weightx = 1
constraints.fill = GridBagConstraints.HORIZONTAL
contentPane.add(self.globalLabel, constraints)
constraints.gridy = 1
contentPane.add(self.globalProgress, constraints)
constraints.gridy = 2
contentPane.add(self.currentLabel, constraints)
constraints.gridy = 3
contentPane.add(self.currentProgress, constraints)
constraints.gridy = 4
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(self.doneButton, constraints)
self.frame.pack()
self.frame.setResizable(False)
self.globalLabel.setText(" ")
self.currentLabel.setText(" ")
self.frame.setLocationRelativeTo(None)
self.frame.setVisible(True)
def addComponents( self, container ) :
container.setLayout( GridBagLayout() )
names = '1,2,3 being the third number'.split( ',' )
for col in range( len( names ) ) :
c = GridBagConstraints()
c.gridx = col # gridx is the grid column
c.gridy = col # gridy is the grid row #
container.add( JButton( names[ col ] ), c )
c = GridBagConstraints()
c.gridx = 1
c.gridy = 3 # put on a new row
c.ipady = 32 # make this one taller
container.add( JButton( 'Four shalt thou not count' ), c )
c = GridBagConstraints()
c.gridx = 1 # middle column
c.gridy = 4 # put on a new row
c.gridwidth = 3 # make this one 3 columns wide
container.add( JButton( 'Five is right out' ), c )
def getGridBagConstraints(game,node):
c = GridBagConstraints()
for str in node.getAttribute("constraints").split(","):
a = str.split(":")
if a[0]=="fill":
c.fill = int(a[1])
elif a[0]=="gridwidth":
c.gridwidth = int(a[1])
elif a[0]=="gridheight":
c.gridheight = int(a[1])
elif a[0]=="gridx":
c.gridx = int(a[1])
elif a[0]=="gridy":
c.gridy = int(a[1])
elif a[0]=="weightx":
c.weightx = int(a[1])
elif a[0]=="weighty":
c.weighty = int(a[1])
else:
print a[0]+"was not found"
return c
def __init__(self):
''' Configuration Panel '''
# pconfig = JPanel(GridBagLayout())
# pconfig.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Configuration panel')
c1 = GridBagConstraints()
c1.fill = GridBagConstraints.HORIZONTAL
c1.weightx = 0.5
c1.gridwidth = 4
c1.gridx = 0
c1.gridy = 0
self.add(label, c1)
''' fila 2 '''
self.radioBtnOMC = JRadioButton('OpenModelica')
c2 = GridBagConstraints()
c2.fill = GridBagConstraints.HORIZONTAL
c2.weightx = 0.5
c2.gridx = 0
c2.gridy = 1
self.add(self.radioBtnOMC, c2)
self.radioBtnJM = JRadioButton('JModelica')
c3 = GridBagConstraints()
c3.fill = GridBagConstraints.HORIZONTAL
c3.weightx = 0.5
c3.gridx = 1
c3.gridy = 1
self.add(self.radioBtnJM, c3)
self.radioBtnDY = JRadioButton('Dymola')
c4 = GridBagConstraints()
c4.fill = GridBagConstraints.HORIZONTAL
c4.weightx = 0.5
c4.gridx = 2
c4.gridy = 1
self.add(self.radioBtnDY, c4)
rbBtnGroup = ButtonGroup()
rbBtnGroup.add(self.radioBtnOMC)
rbBtnGroup.add(self.radioBtnJM)
rbBtnGroup.add(self.radioBtnDY)
''' fila 2 '''
label = JLabel('Start time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 2
self.add(label, c)
self.txtstart= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 2
self.add(self.txtstart, c)
label = JLabel('Stop time')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 2
self.add(label, c)
self.txtstop= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 2
self.add(self.txtstop, c)
''' fila 3 '''
label = JLabel('Solver')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 3
self.add(label, c)
self.cbsolver= JComboBox(['dassl','rkfix2'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 3
self.add(self.cbsolver, c)
label = JLabel('Algorithm (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 3
self.add(label, c)
self.cbalgorithm= JComboBox(['AssimuloAlg'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 3
self.add(self.cbalgorithm, c)
''' fila 4 '''
label = JLabel('Interval')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 4
self.add(label, c)
self.txtinterval= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 4
self.add(self.txtinterval, c)
''' fila 5 '''
label = JLabel('Tolerance')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 5
self.add(label, c)
self.txttolerance= JTextField('0')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 5
self.add(self.txttolerance, c)
''' fila 6 '''
label = JLabel('Output format')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 0
c.gridy = 6
self.add(label, c)
self.cboutformat= JComboBox(['.mat','.h5','.csv'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 1
c.gridy = 6
self.add(self.cboutformat, c)
label = JLabel('Initialize (JM)')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 2
c.gridy = 6
self.add(label, c)
self.cbinitialize= JComboBox(['True','False'])
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridx = 3
c.gridy = 6
self.add(self.cbinitialize, c)
''' fila 7 '''
bSaveCfg= JButton('Save Configuration', actionPerformed= self.saveConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 7
self.add(bSaveCfg, c)
self.bSimulation= JButton('Load Configuration', actionPerformed= self.loadConfiguration)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 7
self.add(self.bSimulation, c)
''' fila 8 '''
self.bSimulation= JButton('Simulate', actionPerformed= self.startSimlation)
self.bSimulation.enabled= 0
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 8
self.add(self.bSimulation, c)
''' file 9 '''
simProgress= JProgressBar(0, self.getWidth(), value=0, stringPainted=True)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 9
self.add(simProgress, c)
''' fila 10 '''
self.lblResult= JLabel('Simulation information')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 10
self.add(self.lblResult, c)
def build_gui(self):
component = JPanel(GridBagLayout())
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.gridwidth = 2
# 1st line
c.gridy = 0
c.gridx = 0
component.add(
JLabel(
'Don\'t forget to create a Session handling rule invoking this Burp extension under Project options > Sessions and to configure the tool and URL scopes.'
), c)
c.gridwidth = 1
# 2nd line
c.gridy = 1
c.gridx = 0
component.add(JLabel(' '), c)
# 3rd line
c.gridy = 2
c.gridx = 0
component.add(
JLabel(
'Name of the anti-CSRF token, can also be a substring of the name of the anti-CSRF token:'
), c)
self._csrf_name_contains_field = JTextField('csrf', 40)
c.gridx = 1
component.add(self._csrf_name_contains_field, c)
# 4th line
c.gridy = 3
c.gridx = 0
component.add(
JLabel(
'Start marker of the anti-CSRF token in the response, #csrf_name# is replaced by the name of the anti-CSRF token:'
), c)
self._csrf_start_marker_field = JTextField(
'name="' + CSRF_NAME_PLACEHOLDER + '" value="', 40)
c.gridx = 1
component.add(self._csrf_start_marker_field, c)
# 5th line
c.gridy = 4
c.gridx = 0
component.add(
JLabel(
'End marker of the anti-CSRF token in the response, #csrf_name# is replaced by the name of the anti-CSRF token:'
), c)
self._csrf_end_marker_field = JTextField('"', 40)
c.gridx = 1
component.add(self._csrf_end_marker_field, c)
# 6th line
c.gridy = 5
c.gridx = 0
component.add(JLabel(' '), c)
# 7th line
c.gridy = 6
c.gridx = 0
component.add(JLabel('HTML decode the anti-CSRF token:'), c)
self._do_html_decode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_html_decode, c)
# 8th line
c.gridy = 7
c.gridx = 0
component.add(JLabel('URL decode the anti-CSRF token:'), c)
self._do_url_decode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_url_decode, c)
# 9th line
c.gridy = 8
c.gridx = 0
component.add(JLabel('URL encode the anti-CSRF token:'), c)
self._do_url_encode = JCheckBox("", True)
c.gridx = 1
component.add(self._do_url_encode, c)
# 10th line
c.gridy = 9
c.gridx = 0
component.add(JLabel(' '), c)
self._callbacks.customizeUiComponent(component)
self._ui_component = component
def registerExtenderCallbacks(self, this_callbacks): ### IBurpExtender
global callbacks, helpers
global extension_enable
global remove_csrf_headers, remove_csrf_params, change_method_to_post
global change_ct_to_json, change_ct_to_plain, change_to_get
callbacks = this_callbacks
helpers = callbacks.getHelpers()
callbacks.setExtensionName(NAME)
self.settings = JPanel(GridBagLayout())
c = GridBagConstraints()
self.extension_enable_box = JCheckBox('Enable extension',
extension_enable)
self.extension_enable_box.setFont(Font("Serif", Font.BOLD, 20))
self.extension_enable_box.setForeground(Color(0, 0, 153))
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 0
c.gridwidth = 1
c.weightx = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.WEST
self.settings.add(self.extension_enable_box, c)
self.remove_csrf_headers_box = JCheckBox('Remove CSRF headers',
remove_csrf_params)
self.remove_csrf_headers_box.setFont(Font("Serif", Font.BOLD, 20))
self.remove_csrf_headers_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 1
self.settings.add(self.remove_csrf_headers_box, c)
remove_csrf_headers_box_lbl = JLabel(
'Check to remove headers with CSRF tokens from all requests.')
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 2
self.settings.add(remove_csrf_headers_box_lbl, c)
self.remove_csrf_params_box = JCheckBox('Remove CSRF parameters',
remove_csrf_params)
self.remove_csrf_params_box.setFont(Font("Serif", Font.BOLD, 20))
self.remove_csrf_params_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 3
self.settings.add(self.remove_csrf_params_box, c)
remove_csrf_params_box_lbl = JLabel(
'Check to remove URL/body parameters with CSRF tokens from all requests. URL-encoded, multipart, JSON parameters are supported.'
)
c.gridx = 0
c.gridy = 4
self.settings.add(remove_csrf_params_box_lbl, c)
self.change_method_to_post_box = JCheckBox(
'Change HTTP method to POST', change_method_to_post)
self.change_method_to_post_box.setFont(Font("Serif", Font.BOLD, 20))
self.change_method_to_post_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 5
self.settings.add(self.change_method_to_post_box, c)
change_method_to_post_lbl = JLabel(
'Check to convert PUT/DELETE/PATCH method to POST in all requests.'
)
c.gridx = 0
c.gridy = 6
self.settings.add(change_method_to_post_lbl, c)
self.change_ct_to_json_box = JCheckBox('Change media type to json',
change_ct_to_json)
self.change_ct_to_json_box.setFont(Font("Serif", Font.BOLD, 20))
self.change_ct_to_json_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 7
self.settings.add(self.change_ct_to_json_box, c)
change_ct_to_json_lbl = JLabel(
'Check to convert body to json and set Content-Type to application/json in url-encoded requests.'
)
c.gridx = 0
c.gridy = 8
self.settings.add(change_ct_to_json_lbl, c)
self.change_ct_to_plain_box = JCheckBox(
'Change Content-Type to text/plain', change_ct_to_plain)
self.change_ct_to_plain_box.setFont(Font("Serif", Font.BOLD, 20))
self.change_ct_to_plain_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 9
self.settings.add(self.change_ct_to_plain_box, c)
change_ct_to_plain_lbl = JLabel(
'Check to set Content-Type to text/plain in request with non-simple media type. Simple media types - application/application/x-www-form-urlencoded, text/plain, multipart/form-data.'
)
c.gridx = 0
c.gridy = 10
self.settings.add(change_ct_to_plain_lbl, c)
self.change_to_get_box = JCheckBox('Change to GET', change_to_get)
self.change_to_get_box.setFont(Font("Serif", Font.BOLD, 20))
self.change_to_get_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 11
self.settings.add(self.change_to_get_box, c)
change_to_get_lbl = JLabel(
'Check to convert POST/PUT/DELETE/PATCH url-encoded requests to GET.'
)
c.gridx = 0
c.gridy = 12
self.settings.add(change_to_get_lbl, c)
callbacks.customizeUiComponent(self.settings)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
print "Successfully loaded %s v%s" % (NAME, VERSION)
all.add(jsp)
# Convert from row index in the view (could e.g. be sorted)
# to the index in the underlying table model
def getSelectedRowIndex():
viewIndex = table.getSelectionModel().getLeadSelectionIndex()
modelIndex = table.convertRowIndexToModel(viewIndex)
return modelIndex
# Top component: a text area showing the full file path to the image in the selected table row
c.gridx = 1
c.gridy = 0
c.gridheight = 1
c.gridwidth = 2
path = JTextArea("")
path.setEditable(False)
path.setMargin(Insets(4, 4, 4, 4))
path.setLineWrap(True)
path.setWrapStyleWord(True)
gb.setConstraints(path, c)
all.add(path)
# Function for the button to open the folder containing the image file path in the selected table row
def openAtFolder(event):
if 0 == path.getText().find("http"):
IJ.showMessage("Can't open folder: it's an URL")
return
directory = os.path.dirname(path.getText())
def generateDeconvolutionScriptUI(srcDir,
tgtDir,
calibration,
preCropAffines,
ROI,
postCropAffines):
"""
Open an UI to automatically generate a script to:
1. Register the views of each time point TM folder, and deconvolve them.
2. Register deconvolved time points to each other, for a range of consecutive time points.
Will ask for the file path to the kernel file,
and also for the range of time points to process,
and for the deconvolution iterations for CM00-CM01, and CM02-CM03.
"""
template = """
# AUTOMATICALLY GENERATED - %s
import sys, os
sys.path.append("%s")
from lib.isoview import deconvolveTimePoints
from mpicbg.models import RigidModel3D, TranslationModel3D
from net.imglib2.img.display.imagej import ImageJFunctions as IL
# The folder with the sequence of TM\d+ folders, one per time point in the 4D series.
# Each folder should contain 4 KLB files, one per camera view of the IsoView microscope.
srcDir = "%s"
# A folder to save deconvolved images in, and CSV files describing features, point matches and transformations
targetDir = "%s"
# Path to the volume describing the point spread function (PSF)
kernelPath = "%s"
calibration = [%s] # An array with 3 floats (identity--all 1.0--because the coarse affines, that is,
# the camera transformations, already include the scaling to isotropy computed using the original calibration.
# The transformations of each timepoint onto the camera at index zero.
def cameraTransformations(dims0, dims1, dims2, dims3, calibration):
return {
0: [%s],
1: [%s],
2: [%s],
3: [%s]
}
# Deconvolution parameters
paramsDeconvolution = {
"blockSizes": None, # None means the image size + kernel size. Otherwise specify like e.g. [[128, 128, 128]] for img in images]
"CM_0_1_n_iterations": %i,
"CM_2_3_n_iterations": %i,
}
# Joint dictionary of parameters
params = {}
params.update(paramsDeconvolution)
# A region of interest for each camera view, for cropping after registration but prior to deconvolution
roi = ([%s], # array of 3 integers, top-left coordinates
[%s]) # array of 3 integers, bottom-right coordinates
# All 4 cameras relative to CM00
fineTransformsPostROICrop = \
[[1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0],
[%s],
[%s],
[%s]]
deconvolveTimePoints(srcDir, targetDir, kernelPath, calibration,
cameraTransformations, fineTransformsPostROICrop,
params, roi, fine_fwd=True, subrange=range(%i, %i))
"""
od = OpenDialog("Choose kernel file", srcDir)
kernel_path = od.getPath()
if not kernel_path:
JOptionPane.showMessageDialog(None, "Can't proceed without a filepath to the kernel", "Alert", JOptionPane.ERROR_MESSAGE)
return
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
msg = ["Edit parameters, then push the button",
"to generate a script that, when run,",
"will execute the deconvolution for each time point",
"saving two 3D stacks per time point as ZIP files",
"in the target directory under subfolder 'deconvolved'.",
"Find the script in a new Script Editor window.",
" "]
gc.gridy = -1 # init
for line in msg:
label = JLabel(line)
gc.anchor = GBC.WEST
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gc.gridheight = 1
gb.setConstraints(label, gc)
panel.add(label)
strings = [["Deconvolution iterations",
"CM_0_1_n_iterations", "CM_2_3_n_iterations"],
["Range",
"First time point", "Last time point"]]
params = {"CM_0_1_n_iterations": 5,
"CM_2_3_n_iterations": 7,
"First time point": 0,
"Last time point": -1} # -1 means last
insertFloatFields(panel, gb, gc, params, strings)
def asString(affine):
matrix = zeros(12, 'd')
affine.toArray(matrix)
return ",".join(imap(str, matrix))
def generateScript(event):
script = template % (str(datetime.now()),
filter(lambda path: path.endswith("IsoView-GCaMP"), sys.path)[-1],
srcDir,
tgtDir,
kernel_path,
", ".join(imap(str, calibration)),
asString(preCropAffines[0]),
asString(preCropAffines[1]),
asString(preCropAffines[2]),
asString(preCropAffines[3]),
params["CM_0_1_n_iterations"],
params["CM_2_3_n_iterations"],
", ".join(imap(str, ROI[0])),
", ".join(imap(str, ROI[1])),
asString(postCropAffines[1]),
asString(postCropAffines[2]),
asString(postCropAffines[3]),
params["First time point"],
params["Last time point"])
tab = None
for frame in JFrame.getFrames():
if str(frame).startswith("org.scijava.ui.swing.script.TextEditor["):
try:
tab = frame.newTab(script, "python")
break
except:
print sys.exc_info()
if not tab:
try:
now = datetime.now()
with open(os.path.join(System.getProperty("java.io.tmpdir"),
"script-%i-%i-%i_%i:%i.py" % (now.year, now.month, now.day,
now.hour, now.minute)), 'w') as f:
f.write(script)
except:
print sys.exc_info()
print script
gen = JButton("Generate script")
gen.addActionListener(generateScript)
gc.anchor = GBC.CENTER
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gb.setConstraints(gen, gc)
panel.add(gen)
frame = JFrame("Generate deconvolution script")
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(True)
def makeCropUI(imp, images, tgtDir, panel=None, cropContinuationFn=None):
""" imp: the ImagePlus to work on.
images: the list of ImgLib2 images, one per frame, not original but already isotropic.
(These are views that use a nearest neighbor interpolation using the calibration to scale to isotropy.)
tgtDir: the target directory where e.g. CSV files will be stored, for ROI, features, pointmatches.
panel: optional, a JPanel controlled by a GridBagLayout.
cropContinuationFn: optional, a function to execute after cropping,
which is given as arguments the original images,
minC, maxC (both define a ROI), and the cropped images. """
independent = None == panel
if not panel:
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
gc = GBC()
else:
gb = panel.getLayout()
# Constraints of the last component
gc = gb.getConstraints(panel.getComponent(panel.getComponentCount() - 1))
# Horizontal line to separate prior UI components from crop UI
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
gc.fill = GBC.HORIZONTAL
sep = JSeparator()
sep.setMinimumSize(Dimension(200, 10))
gb.setConstraints(sep, gc)
panel.add(sep)
# ROI UI header
title = JLabel("ROI controls:")
gc.gridy +=1
gc.anchor = GBC.WEST
gc.gridwidth = 4
gb.setConstraints(title, gc)
panel.add(title)
# Column labels for the min and max coordinates
gc.gridy += 1
gc.gridwidth = 1
for i, title in enumerate(["", "X", "Y", "Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
textfields = []
rms = []
# Load stored ROI if any
roi_path = path = os.path.join(tgtDir, "crop-roi.csv")
if os.path.exists(roi_path):
with open(roi_path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
minC = map(int, reader.next()[1:])
maxC = map(int, reader.next()[1:])
# Place the ROI over the ImagePlus
imp.setRoi(Roi(minC[0], minC[1], maxC[0] + 1 - minC[0], maxC[1] + 1 - minC[1]))
else:
# Use whole image dimensions
minC = [0, 0, 0]
maxC = [v -1 for v in Intervals.dimensionsAsLongArray(images[0])]
# Text fields for the min and max coordinates
for rowLabel, coords in izip(["min coords: ", "max coords: "],
[minC, maxC]):
gc.gridx = 0
gc.gridy += 1
label = JLabel(rowLabel)
gb.setConstraints(label, gc)
panel.add(label)
for i in xrange(3):
gc.gridx += 1
tf = JTextField(str(coords[i]), 10)
gb.setConstraints(tf, gc)
panel.add(tf)
textfields.append(tf)
listener = RoiMaker(imp, textfields, len(textfields) -1)
rms.append(listener)
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
# Listen to changes in the ROI of imp
rfl = RoiFieldListener(imp, textfields)
Roi.addRoiListener(rfl)
# ... and enable cleanup
ImagePlus.addImageListener(FieldDisabler(rfl, rms))
# Functions for cropping images
cropped = None
cropped_imp = None
def storeRoi(minC, maxC):
if os.path.exists(roi_path):
# Load ROI
with open(path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
same = True
for a, b in izip(minC + maxC, map(int, reader.next()[1:] + reader.next()[1:])):
if a != b:
same = False
# Invalidate any CSV files for features and pointmatches: different cropping
for filename in os.listdir(tgtDir):
if filename.endswith("features.csv") or filename.endswith("pointmatches.csv"):
os.remove(os.path.join(tgtDir, filename))
break
if same:
return
# Store the ROI as crop-roi.csv
with open(roi_path, 'w') as csvfile:
w = csv.writer(csvfile, delimiter=',', quotechar="\"", quoting=csv.QUOTE_NONNUMERIC)
w.writerow(["coords", "x", "y", "z"])
w.writerow(["min"] + map(int, minC))
w.writerow(["max"] + map(int, maxC))
def crop(event):
global cropped, cropped_imp
coords = [int(float(tf.getText())) for tf in textfields]
minC = [max(0, c) for c in coords[0:3]]
maxC = [min(d -1, c) for d, c in izip(Intervals.dimensionsAsLongArray(images[0]), coords[3:6])]
storeRoi(minC, maxC)
print "ROI min and max coordinates"
print minC
print maxC
cropped = [Views.zeroMin(Views.interval(img, minC, maxC)) for img in images]
cropped_imp = showAsStack(cropped, title="cropped")
cropped_imp.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax())
if cropContinuationFn:
cropContinuationFn(images, minC, maxC, cropped, cropped_imp)
# Buttons to create a ROI and to crop to ROI,
# which when activated enables the fine registration buttons
crop_button = JButton("Crop to ROI")
crop_button.addActionListener(crop)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
buttons_panel = JPanel()
buttons_panel.add(crop_button)
gb.setConstraints(buttons_panel, gc)
panel.add(buttons_panel)
if independent:
frame = JFrame("Crop by ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
else:
# Re-pack the JFrame
parent = panel.getParent()
while not isinstance(parent, JFrame) and parent is not None:
parent = parent.getParent()
if parent:
frame = parent
frame.pack()
found = False
for wl in frame.getWindowListeners():
if isinstance(wl, CloseControl):
wl.addDestroyables(rms + [rfl])
found = True
break
if not found:
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
return panel
def create(self):
# Estilo general para todas las sub-tab.
gBC = GridBagConstraints()
gBC.fill = GridBagConstraints.BOTH
gBC.ipadx = 5
gBC.ipady = 5
gBC.insets = Insets(0, 5, 5, 5)
gBC.weightx = 0.5
#gBC.weighty = 0.7
#######################################
### Creamos la primera sub-tab. (MASHUP)
#######################################
tab_1 = JPanel(GridBagLayout())
tab_1_jlabelAyuda = JLabel(
'<html><i>•Tip: This Mashup receive one or more keywords in order to generate a list of possible passwords</i></html>'
)
tab_1_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_1.add(
JLabel('<html><font color=green><i>Income:</i></font></html>'),
gBC)
gBC.gridy = 1
tab_1.add(JLabel('<html><b>• Name:</b></html>'), gBC)
gBC.gridy = 2
tab_1.add(self._tab1_nombre, gBC)
gBC.gridy = 3
tab_1.add(JLabel('<html><b>• Surname:</b></html>'), gBC)
gBC.gridy = 4
tab_1.add(self._tab1_apellido, gBC)
gBC.gridy = 5
tab_1.add(JLabel('<html><b>• Birthdate: (DDMMYYYY)</b></html>'),
gBC)
gBC.gridy = 6
tab_1.add(self._tab1_FNacimiento, gBC)
gBC.gridy = 7
tab_1.add(JLabel('<html><b>• Pet:</b></html>'), gBC)
gBC.gridy = 8
tab_1.add(self._tab1_mascota, gBC)
gBC.gridy = 9
tab_1.add(JLabel('<html><b>• Anyother:</b></html>'), gBC)
gBC.gridy = 10
tab_1.add(self._tab1_otro, gBC)
gBC.gridy = 11
tab_1.add(JLabel('<html><b>• Passwd Min Size:</b></html>'), gBC)
gBC.gridy = 12
tab_1.add(self._tab1_minsize, gBC)
gBC.gridy = 13
tab_1.add(JLabel('<html><b>• Passwd Max Size:</b></html>'), gBC)
gBC.gridy = 14
tab_1.add(self._tab1_maxsize, gBC)
gBC.gridy = 15
tab_1.add(
JLabel(
'<html><b>• Especial Chars: (comma separated)</b></html>'
), gBC)
gBC.gridy = 16
tab_1.add(self._tab1_specialchars, gBC)
gBC.gridy = 17
tab_1.add(self._tab1_transformations, gBC)
gBC.gridy = 18
tab_1.add(self._tab1_firstcapital, gBC)
gBC.gridy = 19
tab_1.add(JButton('Mashup!', actionPerformed=self.mashup), gBC)
gBC.gridy = 20
gBC.gridwidth = 3
tab_1.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.gridy = 21
gBC.gridwidth = 3
tab_1.add(tab_1_jlabelAyuda, gBC)
gBC.gridwidth = 1
gBC.gridx = 1
gBC.gridy = 0
gBC.gridheight = 20
gBC.weightx = 0
tab_1.add(JSeparator(SwingConstants.VERTICAL), gBC)
gBC.gridheight = 1
gBC.weightx = 0.5
gBC.gridx = 2
gBC.gridy = 0
tab_1.add(
JLabel('<html><font color=green><i>Outcome:</i></font></html>'),
gBC)
gBC.gridy = 1
gBC.gridwidth = 2
gBC.gridheight = 18
tab_1.add(self._tab1_feedback_sp, gBC)
gBC.gridwidth = 1
gBC.gridheight = 1
gBC.gridy = 19
tab_1.add(
JButton('Copy to clipboard!', actionPerformed=self.cpy_clipboard),
gBC)
#######################################
### Creamos la segunda sub-tab. (REDIRECT)
#######################################
tab_2 = JPanel(GridBagLayout())
tab_2_jlabelAyuda = JLabel(
'<html><i>•Tip: This Redirect receive a pair of hosts x,y in order to redirect from x to y.</i></html>'
)
tab_2_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_2.add(
JLabel('<html><b>• From: (i.e. www.facebook.com)</b></html>'),
gBC)
gBC.gridx = 1
gBC.gridy = 0
tab_2.add(self._tab2_JTFa, gBC)
gBC.gridx = 2
gBC.gridy = 0
tab_2.add(
JLabel('<html><b>• To: (i.e. www.myhomepage.es)</b></html>'),
gBC)
gBC.gridx = 3
gBC.gridy = 0
tab_2.add(self._tab2_JTFaa, gBC)
gBC.gridx = 0
gBC.gridy = 1
gBC.gridwidth = 4
tab_2.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.gridx = 0
gBC.gridy = 2
tab_2.add(JLabel('<html><b>• From:</b></html>'), gBC)
gBC.gridx = 1
gBC.gridy = 2
tab_2.add(self._tab2_JTFb, gBC)
gBC.gridx = 2
gBC.gridy = 2
tab_2.add(JLabel('<html><b>• To:</b></html>'), gBC)
gBC.gridx = 3
gBC.gridy = 2
tab_2.add(self._tab2_JTFbb, gBC)
gBC.gridx = 0
gBC.gridy = 3
gBC.gridwidth = 4
tab_2.add(self._tab2_boton, gBC)
gBC.gridwidth = 1
gBC.gridx = 0
gBC.gridy = 4
gBC.gridwidth = 4
gBC.insets = Insets(100, 10, 5, 10)
tab_2.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridx = 0
gBC.gridy = 5
gBC.gridwidth = 4
tab_2.add(tab_2_jlabelAyuda, gBC)
gBC.gridwidth = 1
#######################################
### Creamos la tercera sub-tab. (LOADER)
#######################################
tab_3 = JPanel(GridBagLayout())
tab_3_jlabelAyuda = JLabel(
'<html><i>•Tip: This Loader receive a list of Hosts or IPs that will be added to the Burp Scope.</i></html>'
)
tab_3_jlabelAyuda.setFont(Font("Serif", 0, 12))
gBC.gridx = 0
gBC.gridy = 0
tab_3.add(
JLabel(
'<html><font color=green><i>List of targets: (i.e. http://www.mytargetweb.com)</i></font></html>'
), gBC)
gBC.gridy = 1
gBC.gridheight = 10
gBC.weighty = 0.5
tab_3.add(self._tab3_urls_sp, gBC)
gBC.gridheight = 1
gBC.weighty = 0
gBC.gridy = 11
tab_3.add(
JButton('Load Into Target => Scope!', actionPerformed=self.loader),
gBC)
gBC.gridy = 12
gBC.gridwidth = 5
gBC.insets = Insets(100, 10, 5, 10)
tab_3.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridy = 13
tab_3.add(tab_3_jlabelAyuda, gBC)
#######################################
### Creamos la cuarta sub-tab. (HEADERS)
#######################################
tab_4_jlabelAyuda = JLabel(
"<html><i>•Tip: This Headers records all unique headers that appear in every host, check out the security headers.</i></html>"
)
tab_4_jlabelAyuda.setFont(Font("Serif", 0, 12))
tab_4_jLabelRecomendacion = JLabel(
"<html>•<b>Server</b>: Don't give away much information.<br> •<b>Content-Security-Policy</b>: Protect your site from XSS attacks by whitelisting sources of approved content.<br> •<b>Strict-Transport-Security</b>: Enforce the browser to use HTTPS.<br> •<b>Public-Key-Pins</b>: Protect your site from MITM attacks.<br> •<b>X-Content-Type-Options</b>: the valid value is -> nosniff .<br> •<b>X-Frame-Options</b>: tells the browser whether you want to allow your site to be framed or not.<br> •<b>X-XSS-Protection</b>: the best value is -> 1; mode=block .</html>"
)
tab_4_jLabelRecomendacion.setFont(Font("Dialog", 0, 13))
tab_4 = JPanel(GridBagLayout())
splitpane = JSplitPane(JSplitPane.VERTICAL_SPLIT)
tab_4_top = JPanel(GridBagLayout())
tab_4_bottom = JPanel(GridBagLayout())
gBC_table = GridBagConstraints()
gBC_table.fill = GridBagConstraints.BOTH
gBC_table.ipadx = 5
gBC_table.ipady = 5
gBC_table.insets = Insets(5, 10, 5, 10)
gBC_table.weightx = 1
gBC_table.weighty = 1
tabla_datos = []
tabla_headers = ('Severity', 'Header', 'Value', 'Host')
self._tab4_tabla_model = DefaultTableModel(tabla_datos, tabla_headers)
tabla_ej = JTable(self._tab4_tabla_model)
tabla_example = JScrollPane(tabla_ej,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
gBC_table.gridx = 0
gBC_table.gridy = 0
gBC_table.gridheight = 5
tab_4_top.add(tabla_example, gBC_table)
gBC_table.gridheight = 1
gBC_table.weightx = 0.5
gBC_table.weighty = 0
gBC_table.gridwidth = 2
gBC_table.gridx = 0
gBC_table.gridy = 0
tab_4_bottom.add(JSeparator(), gBC_table)
gBC_table.gridy = 1
tab_4_bottom.add(tab_4_jlabelAyuda, gBC_table)
gBC_table.gridy = 2
tab_4_bottom.add(tab_4_jLabelRecomendacion, gBC_table)
splitpane.setTopComponent(tab_4_top)
splitpane.setBottomComponent(tab_4_bottom)
gBC_table.weightx = 1
gBC_table.weighty = 1
gBC_table.gridx = 0
gBC_table.gridy = 0
tab_4.add(splitpane, gBC_table)
#######################################
### Creamos la quinta sub-tab. (ACTIVE SCAN)
#######################################
tab_5 = JPanel(GridBagLayout())
tab_5_jlabelAyuda = JLabel(
'<html><i>•Tip: This Quick Scan receive a list of targets and launch an active scan.</i></html>'
)
tab_5_jlabelAyuda.setFont(Font("Serif", 0, 12))
tab_5_jlabelWarning = JLabel(
'<html><font color=red><i>•Warning: Active scanning generates large numbers of requests which are malicious in form and which may result in compromise of the application. You should use this scanning mode with caution, only with the explicit permission of the application owner. For more information, read the documentation of active scan, Burp Suite.</font></i></html>'
)
tab_5_jlabelWarning.setFont(Font("Dialog", 0, 13))
gBC.gridx = 0
gBC.gridy = 0
tab_5.add(
JLabel(
'<html><font color=green><i>List of targets: (i.e. http://192.168.1.1/index.html)</i></font></html>'
), gBC)
gBC.gridy = 1
gBC.gridheight = 8
gBC.weighty = 0.5
tab_5.add(self._tab5_target_sp, gBC)
gBC.gridheight = 1
gBC.weighty = 0
gBC.gridy = 9
tab_5.add(JButton('Launch Scan!', actionPerformed=self.do_active_scan),
gBC)
gBC.gridy = 10
gBC.gridwidth = 5
gBC.insets = Insets(100, 10, 5, 10)
tab_5.add(JSeparator(), gBC)
gBC.gridwidth = 1
gBC.insets = Insets(5, 10, 5, 10)
gBC.gridy = 11
tab_5.add(tab_5_jlabelAyuda, gBC)
gBC.gridy = 12
tab_5.add(tab_5_jlabelWarning, gBC)
#######################################
### Creamos la ultima sub-tab.
#######################################
tab_about = JPanel(GridBagLayout())
gBC_about = GridBagConstraints()
gBC_about.fill = GridBagConstraints.HORIZONTAL
gBC_about.ipadx = 5
gBC_about.ipady = 5
gBC_about.insets = Insets(5, 10, 5, 10)
gBC_about.weightx = 1
gBC_about.weighty = 1
Jlabel1 = JLabel('<html><b>Plug-in L-Tools</b></html>')
Jlabel1.setFont(Font("Dialog", 1, 18))
jlabel2 = JLabel(
'<html>This Plug-in provides utilities for pentesters, researchers and developers, in order to support their work.</html>'
)
jlabel3 = JLabel('<html><b>CC-BY 4.0, 2017. Gino Angles</b></html>')
jlabel3.setFont(Font("Dialog", 1, 14))
jlabel4 = JLabel('<html><b>License</b></html>')
jlabel4.setFont(Font("Dialog", 1, 14))
jlabel5 = JLabel(
'<html><img alt="Licensed under a Creative Commons BY" style="border-width:0" src="https://licensebuttons.net/l/by/4.0/88x31.png"></html>'
)
jlabel6 = JLabel(
'<html>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</html>'
)
jlabel7 = JLabel('<html><b>Dependencies</b></html>')
jlabel7.setFont(Font("Dialog", 1, 14))
jlabel8 = JLabel('Jython +2.7')
jlabel9 = JLabel('http://www.jython.org')
gBC_about.gridx = 0
gBC_about.gridy = 0
tab_about.add(Jlabel1, gBC_about)
gBC_about.gridy = 1
tab_about.add(jlabel2, gBC_about)
gBC_about.gridy = 2
tab_about.add(jlabel3, gBC_about)
gBC_about.gridy = 3
gBC_about.gridwidth = 5
tab_about.add(JSeparator(), gBC_about)
gBC_about.gridwidth = 1
gBC_about.gridy = 4
tab_about.add(jlabel4, gBC_about)
gBC_about.gridy = 5
tab_about.add(jlabel5, gBC_about)
gBC_about.gridy = 6
tab_about.add(jlabel6, gBC_about)
gBC_about.gridy = 7
gBC_about.gridwidth = 5
tab_about.add(JSeparator(), gBC_about)
gBC_about.gridwidth = 1
gBC_about.gridy = 8
tab_about.add(jlabel7, gBC_about)
gBC_about.gridy = 9
tab_about.add(jlabel8, gBC_about)
gBC_about.gridy = 10
tab_about.add(jlabel9, gBC_about)
# Añadimos los sub-tab al contenedor y lo devolvemos.
self.contenedor.addTab('Mashup', tab_1)
self.contenedor.addTab('Redirect', tab_2)
self.contenedor.addTab('Loader', tab_3)
self.contenedor.addTab('Headers', tab_4)
self.contenedor.addTab('Quick Scan', tab_5)
self.contenedor.addTab('About', tab_about)
return self.contenedor
def registerExtenderCallbacks(self, callbacks):
self._callbacks = callbacks
self._helpers = callbacks.getHelpers()
callbacks.setExtensionName("Module Importer")
self.out = callbacks.getStdout()
self.tab = JPanel(GridBagLayout())
self.tableData = []
colNames = ('Enabled', 'Module')
self.dataModel = MyTableModel(self.tableData, colNames)
self.table = JTable(self.dataModel)
self.tablecont = JScrollPane(self.table)
c = GridBagConstraints()
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 4
c.gridheight = 6
c.gridwidth = 6
c.weightx = 0.6
c.weighty = 0.5
self.tab.add(self.tablecont, c)
self.fc = JFileChooser()
self.fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY)
label_for_openDirectory = JLabel("Module Importer")
c = GridBagConstraints()
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 0
self.tab.add(label_for_openDirectory, c)
label_plugin_desc = JLabel(
"This module makes your development of Burp Suite Plugin easier.")
label_plugin_desc.setPreferredSize(Dimension(400, 50))
c = GridBagConstraints()
c.gridx = 0
c.gridy = 1
self.tab.add(label_plugin_desc, c)
label_for_openDirectory = JLabel("Module Path:")
c = GridBagConstraints()
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 2
self.tab.add(label_for_openDirectory, c)
c = GridBagConstraints()
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 0
c.gridy = 3
self.input_id = JTextField(40)
self.input_id.setEditable(java.lang.Boolean.FALSE)
self.tab.add(self.input_id, c)
c = GridBagConstraints()
c.anchor = GridBagConstraints.FIRST_LINE_START
c.gridx = 1
c.gridy = 3
self.openButton = JButton("Open Directory",
actionPerformed=self.openDialog)
self.tab.add(self.openButton, c)
if M_PATH:
self.set_fixed_module_path()
#callbacks.customizeUiComponent(self.tab)
#callbacks.customizeUiComponent(self.table)
#callbacks.customizeUiComponent(self.tablecont)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
return
def createAndShowGUI(self):
'''
Create and display the gui.
'''
layout = GridBagLayout()
c = GridBagConstraints()
self.setLayout(layout)
projectLabel = Label("Project: ")
c.gridx = 0
c.gridy = 0
c.ipady = 5
c.ipadx = 5
c.anchor = GridBagConstraints.EAST
layout.setConstraints(projectLabel, c)
self.projectChoice = Choice()
for name in self.projectNames:
self.projectChoice.add(name)
c.gridx = 1
c.gridy = 0
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.projectChoice, c)
storageLabel = Label("Storage: ")
c.gridx = 0
c.gridy = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(storageLabel, c)
self.storageChoice = Choice()
for name in self.storageNames:
self.storageChoice.add(name)
c.gridx = 1
c.gridy = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.storageChoice, c)
self.convertToOMETIFCheckBox = Checkbox("convert to OME-TIF", True)
c.gridx = 1
c.gridy = 2
layout.setConstraints(self.convertToOMETIFCheckBox, c)
self.uploadAsGroundTruthCheckBox = Checkbox("upload as ground-truth images")
c.gridx = 1
c.gridy = 3
layout.setConstraints(self.uploadAsGroundTruthCheckBox, c)
self.folderTextField = TextField("", 15)
self.folderTextField.setText("<Image-Folder>")
c.gridx = 0
c.gridy = 4
layout.setConstraints(self.folderTextField, c)
self.folderTextField.setEditable(False)
browseButton = Button('Browse...')
browseButton.addActionListener(self)
c.gridx = 1
c.gridy = 4
layout.setConstraints(browseButton, c)
statusLabel = Label("Status:")
c.gridy = 5
c.gridx = 0
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(statusLabel, c)
self.statusTextField = TextField("Select a folder!", 20)
c.gridy = 5
c.gridx = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.statusTextField, c)
self.statusTextField.setEditable(False)
self.uploadButton = Button("Upload Images")
self.uploadButton.addActionListener(self)
c.gridwidth = 2
c.gridheight = 2
c.gridy = 6
c.gridx = 0
c.weighty = 1.0
layout.setConstraints(self.uploadButton, c)
self.add(projectLabel)
self.add(self.projectChoice)
self.add(storageLabel)
self.add(self.storageChoice)
self.add(self.convertToOMETIFCheckBox)
self.add(self.uploadAsGroundTruthCheckBox)
self.add(self.folderTextField)
self.add(browseButton)
self.add(statusLabel)
self.add(self.statusTextField)
self.add(self.uploadButton)
self.setSize(400,300)
self.setVisible(True)
def show_detectable_objects_dialog(self, e):
parentComponent = SwingUtilities.windowForComponent(self.panel0)
self.detectable_obejcts_dialog = JDialog(
parentComponent, "List of Objects to Detect",
ModalityType.APPLICATION_MODAL)
panel = JPanel()
self.detectable_obejcts_dialog.add(panel)
gbPanel = GridBagLayout()
gbcPanel = GridBagConstraints()
panel.setLayout(gbPanel)
y = 0
x = 0
for line in self.local_settings.getClassesOfInterest():
if y > 15:
y = 0
x = x + 1
class_check_box = JCheckBox(line['name'])
self.classes_of_interest_checkboxes.append(class_check_box)
class_check_box.setEnabled(True)
class_check_box.setSelected(line['enabled'])
class_check_box.addItemListener(self.on_class_checkbox_clicked)
gbcPanel.gridx = x
gbcPanel.gridy = y
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(class_check_box, gbcPanel)
panel.add(class_check_box)
y = y + 1
blank_1_L = JLabel(" ")
blank_1_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 1
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_1_L, gbcPanel)
panel.add(blank_1_L)
deselect_all_button = JButton("Deselect all")
deselect_all_button.setEnabled(True)
deselect_all_button.addActionListener(self.on_deselect_all_clicked)
gbcPanel.gridx = 1
gbcPanel.gridy = y + 2
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(deselect_all_button, gbcPanel)
panel.add(deselect_all_button)
select_all_button = JButton("Select all")
select_all_button.setEnabled(True)
select_all_button.addActionListener(self.on_select_all_clicked)
gbcPanel.gridx = 3
gbcPanel.gridy = y + 2
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(select_all_button, gbcPanel)
panel.add(select_all_button)
blank_2_L = JLabel(" ")
blank_2_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 3
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_2_L, gbcPanel)
panel.add(blank_2_L)
cancel_button = JButton("Cancel")
cancel_button.setEnabled(True)
cancel_button.addActionListener(
self.on_cancel_classes_of_interest_click)
gbcPanel.gridx = 1
gbcPanel.gridy = y + 4
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(cancel_button, gbcPanel)
panel.add(cancel_button)
save_button = JButton("Save")
save_button.setEnabled(True)
save_button.addActionListener(self.on_save_classes_of_interest_click)
gbcPanel.gridx = 3
gbcPanel.gridy = y + 4
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 2
gbcPanel.weighty = 1
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(save_button, gbcPanel)
panel.add(save_button)
blank_3_L = JLabel(" ")
blank_3_L.setEnabled(True)
gbcPanel.gridx = 0
gbcPanel.gridy = y + 5
gbcPanel.gridwidth = 1
gbcPanel.gridheight = 1
gbcPanel.fill = GridBagConstraints.BOTH
gbcPanel.weightx = 1
gbcPanel.weighty = 0
gbcPanel.anchor = GridBagConstraints.NORTH
gbPanel.setConstraints(blank_3_L, gbcPanel)
panel.add(blank_3_L)
self.detectable_obejcts_dialog.pack()
screenSize = Toolkit.getDefaultToolkit().getScreenSize()
self.detectable_obejcts_dialog.setLocation(
int((screenSize.getWidth() / 2) -
(self.detectable_obejcts_dialog.getWidth() / 2)),
int((screenSize.getHeight() / 2) -
(self.detectable_obejcts_dialog.getHeight() / 2)))
self.detectable_obejcts_dialog.setVisible(True)
def getArguments(self):
"""
This function brings up a window to retreive any required arguments. It uses a window with fields for each argument, filled with any arguments already given.
While this window is visible the program will wait, once it is no longer visible all the arguments will be filled with the entries in the fields.
"""
class LocationAction(AbstractAction):
"""
Action to set the text of a text field to a folder or directory.
"""
def __init__(self, field):
AbstractAction.__init__(self, "...")
self.field = field
def actionPerformed(self, event):
fileChooser = JFileChooser()
fileChooser.fileSelectionMode = JFileChooser.FILES_AND_DIRECTORIES
if fileChooser.showOpenDialog(None) == JFileChooser.APPROVE_OPTION:
self.field.text = fileChooser.selectedFile.absolutePath
class HelpAction(AbstractAction):
"""
Displays a help page in a web browser.
"""
def __init__(self):
AbstractAction.__init__(self, "Help")
def actionPerformed(self, event):
browsers = ["google-chrome", "firefox", "opera", "epiphany", "konqueror", "conkeror", "midori", "kazehakase", "mozilla"]
osName = System.getProperty("os.name")
helpHTML = ClassLoader.getSystemResource("help.html").toString()
if osName.find("Mac OS") == 0:
Class.forName("com.apple.eio.FileManager").getDeclaredMethod( "openURL", [String().getClass()]).invoke(None, [helpHTML])
elif osName.find("Windows") == 0:
Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + helpHTML)
else:
browser = None
for b in browsers:
if browser == None and Runtime.getRuntime().exec(["which", b]).getInputStream().read() != -1:
browser = b
Runtime.getRuntime().exec([browser, helpHTML])
class OKAction(AbstractAction):
"""
Action for starting the pipeline. This action will simply make the window invisible.
"""
def __init__(self):
AbstractAction.__init__(self, "Ok")
def actionPerformed(self, event):
frame.setVisible(False)
class CancelAction(AbstractAction):
"""
Action for canceling the pipeline. Exits the program.
"""
def __init__(self):
AbstractAction.__init__(self, "Cancel")
def actionPerformed(self, event):
sys.exit(0)
frame = JFrame("Neofelis")
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
constraints = GridBagConstraints()
contentPane = JPanel(GridBagLayout())
frame.setContentPane(contentPane)
blastField = JTextField(self.blastLocation)
genemarkField = JTextField(self.genemarkLocation)
transtermField = JTextField(self.transtermLocation)
tRNAscanField = JTextField(self.tRNAscanLocation)
databaseLocationField = JTextField(os.path.split(self.database)[0])
databaseField = JTextField(os.path.split(self.database)[1])
matrixField = JTextField(str(self.matrix))
eValueField = JTextField(str(self.eValue))
minLengthField = JTextField(str(self.minLength))
scaffoldingDistanceField = JTextField(str(self.scaffoldingDistance))
promoterScoreField = JTextField(str(self.promoterScoreCutoff))
queryField = JTextField(self.sources[0])
constraints.gridx = 0
constraints.gridy = 0
constraints.gridwidth = 1
constraints.gridheight = 1
constraints.fill = GridBagConstraints.HORIZONTAL
constraints.weightx = 0
constraints.weighty = 0
contentPane.add(JLabel("Blast Location"), constraints)
constraints.gridy = 1
contentPane.add(JLabel("Genemark Location"), constraints)
constraints.gridy = 2
contentPane.add(JLabel("Transterm Location"), constraints)
constraints.gridy = 3
contentPane.add(JLabel("tRNAscan Location"), constraints)
constraints.gridy = 4
contentPane.add(JLabel("Databases Location"), constraints)
constraints.gridy = 5
contentPane.add(JLabel("Database"), constraints)
constraints.gridy = 6
contentPane.add(JLabel("Matrix(Leave blank to use heuristic matrix)"), constraints)
constraints.gridy = 7
contentPane.add(JLabel("E Value"), constraints)
constraints.gridy = 8
contentPane.add(JLabel("Minimum Intergenic Length"), constraints)
constraints.gridy = 9
contentPane.add(JLabel("Scaffold Distance"), constraints)
constraints.gridy = 10
contentPane.add(JLabel("Promoter Score Cutoff"), constraints)
constraints.gridy = 11
contentPane.add(JLabel("Query"), constraints)
constraints.gridx = 1
constraints.gridy = 0
constraints.weightx = 1
contentPane.add(blastField, constraints)
constraints.gridy = 1
contentPane.add(genemarkField, constraints)
constraints.gridy = 2
contentPane.add(transtermField, constraints)
constraints.gridy = 3
contentPane.add(tRNAscanField, constraints)
constraints.gridy = 4
contentPane.add(databaseLocationField, constraints)
constraints.gridy = 5
contentPane.add(databaseField, constraints)
constraints.gridy = 6
contentPane.add(matrixField, constraints)
constraints.gridy = 7
contentPane.add(eValueField, constraints)
constraints.gridy = 8
contentPane.add(minLengthField, constraints)
constraints.gridy = 9
contentPane.add(scaffoldingDistanceField, constraints)
constraints.gridy = 10
contentPane.add(promoterScoreField, constraints)
constraints.gridy = 11
contentPane.add(queryField, constraints)
constraints.gridx = 2
constraints.gridy = 0
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(LocationAction(blastField)), constraints)
constraints.gridy = 1
contentPane.add(JButton(LocationAction(genemarkField)), constraints)
constraints.gridy = 2
contentPane.add(JButton(LocationAction(transtermField)), constraints)
constraints.gridy = 3
contentPane.add(JButton(LocationAction(tRNAscanField)), constraints)
constraints.gridy = 4
contentPane.add(JButton(LocationAction(databaseLocationField)), constraints)
constraints.gridy = 11
contentPane.add(JButton(LocationAction(queryField)), constraints)
constraints.gridx = 0
constraints.gridy = 12
constraints.anchor = GridBagConstraints.LINE_START
contentPane.add(JButton(HelpAction()), constraints)
constraints.gridx = 1
constraints.anchor = GridBagConstraints.LINE_END
contentPane.add(JButton(OKAction()), constraints)
constraints.gridx = 2
contentPane.add(JButton(CancelAction()), constraints)
frame.pack()
frame.setLocationRelativeTo(None)
frame.setVisible(True)
while frame.isVisible():
pass
self.blastLocation = blastField.getText()
self.genemarkLocation = genemarkField.getText()
self.transtermLocation = transtermField.getText()
self.database = databaseLocationField.getText() + "/" + databaseField.getText()
self.matrix = matrixField.getText()
self.eValue = float(eValueField.getText())
self.minLength = int(minLengthField.getText())
self.scaffoldingDistance = int(scaffoldingDistanceField.getText())
self.promoterScoreCutoff = float(promoterScoreField.getText())
self.sources = [queryField.getText()]
def registerExtenderCallbacks(self, this_callbacks): ### IBurpExtender
global callbacks, helpers
global extension_enable, in_scope_only
global remove_csrf_headers, remove_csrf_params, change_method_to_post
global change_ct_to_json, change_ct_to_plain, change_to_get
callbacks = this_callbacks
helpers = callbacks.getHelpers()
callbacks.setExtensionName(NAME)
self.settings = JPanel(GridBagLayout())
c = GridBagConstraints()
self.extension_enable_box = JCheckBox('Enable extension',
extension_enable)
self.setFontBold(self.extension_enable_box)
self.extension_enable_box.setForeground(Color(0, 0, 153))
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 0
c.gridwidth = 1
c.weightx = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.WEST
self.settings.add(self.extension_enable_box, c)
self.in_scope_only_box = JCheckBox('Modify only in-scope requests',
in_scope_only)
self.setFontBold(self.in_scope_only_box)
self.in_scope_only_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 1
self.settings.add(self.in_scope_only_box, c)
self.remove_csrf_headers_box = JCheckBox('Remove CSRF headers',
remove_csrf_params)
self.setFontBold(self.remove_csrf_headers_box)
self.remove_csrf_headers_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 2
self.settings.add(self.remove_csrf_headers_box, c)
remove_csrf_headers_box_lbl = JLabel(
'Check to remove headers with CSRF tokens from all requests.')
self.setFontItalic(remove_csrf_headers_box_lbl)
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 3
self.settings.add(remove_csrf_headers_box_lbl, c)
self.remove_csrf_params_box = JCheckBox('Remove CSRF parameters',
remove_csrf_params)
self.setFontBold(self.remove_csrf_params_box)
self.remove_csrf_params_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 4
self.settings.add(self.remove_csrf_params_box, c)
remove_csrf_params_box_lbl = JLabel(
'Check to remove URL/body parameters with CSRF tokens from all requests. URL-encoded, multipart, JSON parameters are supported.'
)
self.setFontItalic(remove_csrf_params_box_lbl)
c.gridx = 0
c.gridy = 5
self.settings.add(remove_csrf_params_box_lbl, c)
self.change_method_to_post_box = JCheckBox(
'Change HTTP method to POST', change_method_to_post)
self.setFontBold(self.change_method_to_post_box)
self.change_method_to_post_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 6
self.settings.add(self.change_method_to_post_box, c)
change_method_to_post_lbl = JLabel(
'Check to convert PUT/DELETE/PATCH method to POST in all requests.'
)
self.setFontItalic(change_method_to_post_lbl)
c.gridx = 0
c.gridy = 7
self.settings.add(change_method_to_post_lbl, c)
self.change_ct_to_json_box = JCheckBox('Change media type to json',
change_ct_to_json)
self.setFontBold(self.change_ct_to_json_box)
self.change_ct_to_json_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 8
self.settings.add(self.change_ct_to_json_box, c)
change_ct_to_json_lbl = JLabel(
'Check to convert body to json and set Content-Type to application/json in url-encoded requests.'
)
self.setFontItalic(change_ct_to_json_lbl)
c.gridx = 0
c.gridy = 9
self.settings.add(change_ct_to_json_lbl, c)
self.change_ct_to_plain_box = JCheckBox(
'Change Content-Type to text/plain', change_ct_to_plain)
self.setFontBold(self.change_ct_to_plain_box)
self.change_ct_to_plain_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 10
self.settings.add(self.change_ct_to_plain_box, c)
change_ct_to_plain_lbl = JLabel(
'Check to set Content-Type to text/plain in request with non-simple media type. Simple media types - application/application/x-www-form-urlencoded, text/plain, multipart/form-data.'
)
self.setFontItalic(change_ct_to_plain_lbl)
c.gridx = 0
c.gridy = 11
self.settings.add(change_ct_to_plain_lbl, c)
self.change_to_get_box = JCheckBox('Change to GET', change_to_get)
self.setFontBold(self.change_to_get_box)
self.change_to_get_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 12
self.settings.add(self.change_to_get_box, c)
change_to_get_lbl = JLabel(
'Check to convert POST/PUT/DELETE/PATCH url-encoded requests to GET.'
)
self.setFontItalic(change_to_get_lbl)
c.gridx = 0
c.gridy = 13
self.settings.add(change_to_get_lbl, c)
self.csrf_headers_params = JPanel(GridBagLayout())
c = GridBagConstraints()
lblParams = JLabel("CSRF parameters:")
self.setFontBold(lblParams)
lblParams.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.csrf_headers_params.add(lblParams, c)
self.csrf_param_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.csrf_headers_params.add(self.csrf_param_text_field, c)
lblParamsNote = JLabel(
"Remove parameter from request if name contains")
self.setFontItalic(lblParamsNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.csrf_headers_params.add(lblParamsNote, c)
self.csrf_params_text_area = JTextArea()
self.csrf_params_text_area.setColumns(20)
self.csrf_params_text_area.setRows(10)
self.csrf_params_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.csrf_params_mouse_listener = TextAreaMouseListener(
self.csrf_params_text_area)
self.csrf_params_text_area.addMouseListener(
self.csrf_params_mouse_listener)
for name in csrf_params_names:
self.csrf_params_text_area.append(name + os.linesep)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.csrf_params_text_area)
self.csrf_headers_params.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.csrf_param_text_field,
self.csrf_params_text_area,
self.csrf_params_mouse_listener,
csrf_params_names)
self.csrf_param_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.csrf_param_rm_button = JButton(
'Remove', actionPerformed=handlers.handler_rm)
self.csrf_param_restore_button = JButton(
'Restore', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.csrf_param_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.csrf_param_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.csrf_param_restore_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.csrf_headers_params.add(buttonsPanel, c)
lblHeaders = JLabel("CSRF headers:")
self.setFontBold(lblHeaders)
lblHeaders.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 2
c.insets = Insets(40, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.csrf_headers_params.add(lblHeaders, c)
self.csrf_header_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 2
self.csrf_headers_params.add(self.csrf_header_text_field, c)
lblHeadersNote = JLabel("Remove header from request if name equals to")
self.setFontItalic(lblHeadersNote)
c.fill = GridBagConstraints.NONE
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 3
self.csrf_headers_params.add(lblHeadersNote, c)
self.csrf_headers_text_area = JTextArea()
self.csrf_headers_text_area.setColumns(20)
self.csrf_headers_text_area.setRows(10)
self.csrf_headers_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.csrf_headers_mouse_listener = TextAreaMouseListener(
self.csrf_headers_text_area)
self.csrf_headers_text_area.addMouseListener(
self.csrf_headers_mouse_listener)
for name in csrf_headers_names:
self.csrf_headers_text_area.append(name + os.linesep)
c.gridx = 1
c.gridy = 3
sp = JScrollPane(self.csrf_headers_text_area)
self.csrf_headers_params.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.csrf_header_text_field,
self.csrf_headers_text_area,
self.csrf_headers_mouse_listener,
csrf_headers_names)
self.csrf_header_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.csrf_header_rm_button = JButton(
'Remove', actionPerformed=handlers.handler_rm)
self.csrf_header_restore_button = JButton(
'Restore', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.csrf_header_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.csrf_header_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.csrf_header_restore_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 3
c.fill = GridBagConstraints.NONE
self.csrf_headers_params.add(buttonsPanel, c)
self.whitelist = JPanel(GridBagLayout())
c = GridBagConstraints()
lblWhitelist = JLabel("URLs whitelist:")
self.setFontBold(lblWhitelist)
lblWhitelist.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.whitelist.add(lblWhitelist, c)
self.whitelist_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.whitelist.add(self.whitelist_text_field, c)
lblWhitelistNote = JLabel(
"Do not perform request modification if URL starts with")
self.setFontItalic(lblWhitelistNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.whitelist.add(lblWhitelistNote, c)
self.whitelist_text_area = JTextArea()
self.whitelist_text_area.setColumns(30)
self.whitelist_text_area.setRows(10)
self.whitelist_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.whitelist_mouse_listener = TextAreaMouseListener(
self.whitelist_text_area)
self.whitelist_text_area.addMouseListener(
self.whitelist_mouse_listener)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.whitelist_text_area)
self.whitelist.add(sp, c)
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.gridy = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.whitelist_text_field,
self.whitelist_text_area,
self.whitelist_mouse_listener, [])
self.whitelist_add_button = JButton(
'Add', actionPerformed=handlers.handler_add)
self.whitelist_rm_button = JButton('Remove',
actionPerformed=handlers.handler_rm)
self.whitelist_clear_button = JButton(
'Clear', actionPerformed=handlers.handler_restore)
buttonsPanel.add(self.whitelist_add_button, _c)
_c.gridy = 1
buttonsPanel.add(self.whitelist_rm_button, _c)
_c.gridy = 2
buttonsPanel.add(self.whitelist_clear_button, _c)
_c.gridy = 3
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.whitelist.add(buttonsPanel, c)
self.tabs = JTabbedPane()
self.tabs.addTab('Settings', self.settings)
self.tabs.addTab('CSRF params/headers to remove',
self.csrf_headers_params)
self.tabs.addTab('Requests whitelist', self.whitelist)
callbacks.customizeUiComponent(self.tabs)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
callbacks.registerContextMenuFactory(
SendToWhitelist(self.whitelist_text_area))
print "Successfully loaded %s v%s by Mikhail Egorov @0ang3el" % (
NAME, VERSION)
def registerExtenderCallbacks(self, this_callbacks): ### IBurpExtender
global callbacks, helpers
global extension_enable, in_scope_only
global change_method_to_post
callbacks = this_callbacks
helpers = callbacks.getHelpers()
callbacks.setExtensionName(NAME)
self.settings = JPanel(GridBagLayout())
c = GridBagConstraints()
self.extension_enable_box = JCheckBox('Enable extension',
extension_enable)
self.setFontBold(self.extension_enable_box)
self.extension_enable_box.setForeground(Color(0, 0, 153))
c.insets = Insets(5, 5, 5, 5)
c.gridx = 0
c.gridy = 0
c.gridwidth = 1
c.weightx = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.WEST
self.settings.add(self.extension_enable_box, c)
self.in_scope_only_box = JCheckBox('Modify only in-scope requests',
in_scope_only)
self.setFontBold(self.in_scope_only_box)
self.in_scope_only_box.setForeground(Color(0, 0, 153))
c.insets = Insets(40, 5, 5, 5)
c.gridx = 0
c.gridy = 1
self.settings.add(self.in_scope_only_box, c)
self.change_method_to_post_box = JCheckBox(
'Change HTTP method to POST', change_method_to_post)
self.setFontBold(self.change_method_to_post_box)
self.change_method_to_post_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 6
self.settings.add(self.change_method_to_post_box, c)
change_method_to_post_lbl = JLabel(
'Check to convert PUT/DELETE/PATCH method to POST in all requests.'
)
self.setFontItalic(change_method_to_post_lbl)
c.gridx = 0
c.gridy = 7
self.settings.add(change_method_to_post_lbl, c)
self.change_to_get_box = JCheckBox('Change to GET', change_to_get)
self.setFontBold(self.change_to_get_box)
self.change_to_get_box.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 12
self.settings.add(self.change_to_get_box, c)
change_to_get_lbl = JLabel(
'Check to convert POST/PUT/DELETE/PATCH url-encoded requests to GET.'
)
self.setFontItalic(change_to_get_lbl)
c.gridx = 0
c.gridy = 13
self.settings.add(change_to_get_lbl, c)
self.tabs = JTabbedPane()
self.tabs.addTab('Settings', self.settings)
callbacks.customizeUiComponent(self.tabs)
callbacks.addSuiteTab(self)
callbacks.registerProxyListener(self)
print "Successfully loaded %s v%s by Mohammed alsaggaf " % (NAME,
VERSION)
def initComponents(self):
self.setLayout(GridBagLayout())
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridx = 0
gbc.gridy = 0
descriptionLabel = JLabel("FEA - Forensics Email Analysis")
self.add(descriptionLabel, gbc)
gbc.gridy = 1
self.cbNSLookup = JCheckBox(
"Perform DNS Lookup on email domains",
actionPerformed=self.cbNSLookupActionPerformed)
self.cbNSLookup.setSelected(True)
self.add(self.cbNSLookup, gbc)
# TODO: include option to browse for text file with list of emails to exclude from analysis
numberThreadsLabel = JLabel(
"Maximum number of threads for DNS Lookup task: ")
gbc.gridy = 2
self.add(numberThreadsLabel, gbc)
self.numberThreadsSlider = JSlider(
JSlider.HORIZONTAL,
1,
16,
8,
stateChanged=self.sliderActionPerformed)
self.numberThreadsSlider.setMajorTickSpacing(1)
self.numberThreadsSlider.setPaintLabels(True)
self.numberThreadsSlider.setPaintTicks(True)
self.numberThreadsSlider.setSnapToTicks(True)
self.numberThreadsSlider.setToolTipText(
"set maximum number of concurrent threads when performing DNS lookup on email domains"
)
gbc.gridy = 5
gbc.gridwidth = 15
gbc.gridheight = 1
gbc.fill = GridBagConstraints.BOTH
gbc.weightx = 0
gbc.weighty = 0
gbc.anchor = GridBagConstraints.NORTHWEST
gbc.gridy = 3
self.add(self.numberThreadsSlider, gbc)
self.cbGenerateExcel = JCheckBox(
"Generate Excel format report (more detailed)",
actionPerformed=self.cbGenerateExcelActionPerformed)
self.cbGenerateExcel.setSelected(True)
gbc.gridy = 4
self.add(self.cbGenerateExcel, gbc)
self.cbGenerateCSV = JCheckBox(
"Generate CSV format report (plaintext)",
actionPerformed=self.cbGenerateCSVActionPerformed)
self.cbGenerateCSV.setSelected(True)
gbc.gridy = 5
self.add(self.cbGenerateCSV, gbc)
gbc.gridy = 6
self.cbWayback = JCheckBox(
"Perform Wayback Machine Lookup on email domains (WARNING: can be a slow process!)",
actionPerformed=self.cbWaybackActionPerformed)
self.cbWayback.setSelected(True)
self.add(self.cbWayback, gbc)
def makeTranslationUI(affines, imp, show=True, print_button_text="Print transforms"):
"""
A GUI to control the translation components of a list of AffineTransform3D instances.
When updated, the ImagePlus is refreshed.
affines: a list (will be read multiple times) of one affine transform per image.
imp: the ImagePlus that hosts the virtual stack with the transformed images.
show: defaults to True, whether to make the GUI visible.
print_button_text: whatever you want the print button to read like, defaults to "Print transforms".
Returns the JFrame, the main JPanel and the lower JButton panel.
"""
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
gc.anchor = GBC.WEST
gc.fill = GBC.NONE
# Column labels
gc.gridy = 0
for i, title in enumerate(["Camera", "translation X", "translation Y", "translation Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
gc.anchor = GBC.WEST
listeners = []
# One row per affine to control: skip the first
for i, affine in enumerate(affines[1:]):
gc.gridx = 0
gc.gridy += 1
label = JLabel("CM0%i: " % (i + 1))
gb.setConstraints(label, gc)
panel.add(label)
# One JTextField per dimension
for dimension, translation in enumerate(affine.getTranslation()):
tf = JTextField(str(translation), 10)
listener = MatrixTextFieldListener(affine, dimension, tf, imp)
listeners.append(listener)
imp.addImageListener(listener) # to disable the JTextField when closed
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
gc.gridx += 1
gb.setConstraints(tf, gc)
panel.add(tf)
# Documentation for the user
help_lines = ["Type a number and push enter,",
"or use the scroll wheel."]
gc.gridx = 0
gc.gridwidth = 4
for line in help_lines:
gc.gridy += 1
help = JLabel(line)
gb.setConstraints(help, gc)
panel.add(help)
# Buttons
printButton = JButton(print_button_text)
def printTransforms(event):
for i, aff in enumerate(affines): # print all, including the first
matrix = zeros(12, 'd')
aff.toArray(matrix)
msg = "# Coarse affine matrix " + str(i) + ": \n" + \
"affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist())
# Print everywhere
print msg
IJ.log(msg)
System.out.println(msg)
printButton.addActionListener(printTransforms)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
button_panel = JPanel()
button_panel.add(printButton)
gb.setConstraints(button_panel, gc)
panel.add(button_panel)
frame = JFrame("Translation control")
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=listeners))
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(show)
return frame, panel, button_panel
def __init__(self, extender=None, *rows):
self.extender = extender
self.table = table = JTable(ParameterProcessingRulesTableModel(*rows))
table.setPreferredScrollableViewportSize(Dimension(500, 70))
table.setRowSorter(TableRowSorter(table.getModel()))
table.setFillsViewportHeight(True)
gridBagLayout = GridBagLayout()
gridBagLayout.columnWidths = [0, 0, 25, 0 ]
gridBagLayout.rowHeights = [0, 0, 0, 0]
gridBagLayout.columnWeights = [0.0, 1.0, 1.0, Double.MIN_VALUE]
gridBagLayout.rowWeights = [0.0, 0.0, 0.0, Double.MIN_VALUE]
self.setLayout(gridBagLayout)
addButton = JButton("Add")
addButton.addActionListener(AddRemoveParameterListener(table))
addButtonConstraints = GridBagConstraints()
addButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addButtonConstraints.insets = Insets(0, 0, 5, 5)
addButtonConstraints.gridx = 0
addButtonConstraints.gridy = 0
self.add(addButton, addButtonConstraints)
removeButton = JButton("Remove")
removeButton.addActionListener(AddRemoveParameterListener(table))
removeButtonConstraints = GridBagConstraints()
removeButtonConstraints.fill = GridBagConstraints.HORIZONTAL
removeButtonConstraints.insets = Insets(0, 0, 5, 5)
removeButtonConstraints.gridx = 0
removeButtonConstraints.gridy = 1
self.add(removeButton, removeButtonConstraints)
upButton = JButton("Up")
upButton.addActionListener(AddRemoveParameterListener(table))
upButtonConstraints = GridBagConstraints()
upButtonConstraints.fill = GridBagConstraints.HORIZONTAL
upButtonConstraints.insets = Insets(0, 0, 5, 5)
upButtonConstraints.gridx = 0
upButtonConstraints.gridy = 2
self.add(upButton, upButtonConstraints)
downButton = JButton("Down")
downButton.addActionListener(AddRemoveParameterListener(table))
downButtonConstraints = GridBagConstraints()
downButtonConstraints.fill = GridBagConstraints.HORIZONTAL
downButtonConstraints.anchor = GridBagConstraints.NORTH
downButtonConstraints.insets = Insets(0, 0, 5, 5)
downButtonConstraints.gridx = 0
downButtonConstraints.gridy = 3
self.add(downButton, downButtonConstraints)
scrollPane = JScrollPane(table)
scrollPaneConstraints = GridBagConstraints()
scrollPaneConstraints.gridwidth = 2
scrollPaneConstraints.gridheight = 5
scrollPaneConstraints.insets = Insets(0, 0, 5, 5)
scrollPaneConstraints.anchor = GridBagConstraints.NORTHWEST
scrollPaneConstraints.gridx = 1
scrollPaneConstraints.gridy = 0
self.add(scrollPane, scrollPaneConstraints)
self.initParameterColumn(table)
self.initColumnSizes(table)
def makeRegistrationUI(original_images, original_calibration, coarse_affines, params, images, minC, maxC, cropped, cropped_imp):
"""
Register cropped images either all to all or all to the first one,
and print out a config file with the coarse affines,
the ROI for cropping, and the refined affines post-crop.
original_images: the original, raw images, with original dimensions.
original_calibration: the calibration of the images as they are on disk.
coarse_affines: list of AffineTransform3D, one per image, that specify the translation between images
as manually set using the makeTranslationUI.
params: dictionary with parameters for registering the given cropped images.
This includes a calibration that is likely [1.0, 1.0, 1.0] as the cropped images
are expected to have been scaled to isotropy.
images: the list of near-original images but scaled (by calibration) to isotropy.
(These are really views of the original images, using nearest neighbor interpolation
to scale them to isotropy.)
minC, maxC: the minimum and maximum coordinates of a ROI with which the cropped images were made.
cropped: the list of images that have been scaled to isotropy, translated and cropped by the ROI.
(These are really interval views of the images, the latter using nearest neighbor interpolation.)
cropped_imp: the ImagePlus holding the virtual stack of cropped image views.
The computed registration will merge the scaling to isotropy + first transform (a translation)
+ roi cropping translation + the params["modelclass"] registration transform, to read directly
from the original images using a nearest interpolation, for best performance (piling two nearest
interpolations over one another would result in very slow access to pixel data).
"""
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
calibration = params["calibration"]
params["cal X"] = calibration[0]
params["cal Y"] = calibration[1]
params["cal Z"] = calibration[2]
# Add a label and a text field for every parameter, with titles for every block
strings = [["Calibration",
"cal X", "cal Y", "cal Z"],
["Difference of Gaussian",
"minPeakValue", "sigmaSmaller", "sigmaLarger"],
["Feature extraction",
"radius", "min_angle", "max_per_peak",
"angle_epsilon", "len_epsilon_sq",
"pointmatches_nearby", "pointmatches_search_radius"],
["RANSAC parameters for the model",
"maxEpsilon", "minInlierRatio", "minNumInliers",
"n_iterations", "maxTrust"],
["All to all registration",
"maxAllowedError", "maxPlateauwidth", "maxIterations", "damp"]]
# Insert all as fields, with values populated from the params dictionary
# and updating dynamically the params dictionary
params = dict(params) # copy, will be updated
insertFloatFields(panel, gb, gc, params, strings)
# Identity transforms prior to registration
affines = [affine3D([1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0]) for img in cropped]
def run():
exe = newFixedThreadPool(min(len(cropped), numCPUs()))
try:
# Dummy for in-RAM reading of isotropic images
img_filenames = [str(i) for i in xrange(len(cropped))]
loader = InRAMLoader(dict(zip(img_filenames, cropped)))
getCalibration = params.get("getCalibration", None)
if not getCalibration:
getCalibration = lambda img: [1.0] * cropped[0].numDimensions()
csv_dir = params["csv_dir"]
modelclass = params["modelclass"]
# Matrices describing the registration on the basis of the cropped images
matrices = computeOptimizedTransforms(img_filenames, loader, getCalibration,
csv_dir, exe, modelclass, params)
# Store outside, so they can be e.g. printed, and used beyond here
for matrix, affine in zip(matrices, affines):
affine.set(*matrix)
# Combine the transforms: scaling (by calibration)
# + the coarse registration (i.e. manual translations)
# + the translation introduced by the ROI cropping
# + the affine matrices computed above over the cropped images.
coarse_matrices = []
for coarse_affine in coarse_affines:
matrix = zeros(12, 'd')
coarse_affine.toArray(matrix)
coarse_matrices.append(matrix)
# NOTE: both coarse_matrices and matrices are from the camera X to camera 0. No need to invert them.
# NOTE: uses identity calibration because the coarse_matrices already include the calibration scaling to isotropy
transforms = mergeTransforms([1.0, 1.0, 1.0], coarse_matrices, [minC, maxC], matrices, invert2=False)
print "calibration:", [1.0, 1.0, 1.0]
print "cmTransforms:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in coarse_matrices)
print "ROI", [minC, maxC]
print "fineTransformsPostROICrop:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in matrices)
print "invert2:", False
# Show registered images
registered = [transformedView(img, transform, interval=cropped[0])
for img, transform in izip(original_images, transforms)]
registered_imp = showAsStack(registered, title="Registered with %s" % params["modelclass"].getSimpleName())
registered_imp.setDisplayRange(cropped_imp.getDisplayRangeMin(), cropped_imp.getDisplayRangeMax())
"""
# TEST: same as above, but without merging the transforms. WORKS, same result
# Copy into ArrayImg, otherwise they are rather slow to browse
def copy(img1, affine):
# Copy in two steps. Otherwise the nearest neighbor interpolation on top of another
# nearest neighbor interpolation takes a huge amount of time
dimensions = Intervals.dimensionsAsLongArray(img1)
aimg1 = ArrayImgs.unsignedShorts(dimensions)
ImgUtil.copy(ImgView.wrap(img1, aimg1.factory()), aimg1)
img2 = transformedView(aimg1, affine)
aimg2 = ArrayImgs.unsignedShorts(dimensions)
ImgUtil.copy(ImgView.wrap(img2, aimg2.factory()), aimg2)
return aimg2
futures = [exe.submit(Task(copy, img, affine)) for img, affine in izip(cropped, affines)]
aimgs = [f.get() for f in futures]
showAsStack(aimgs, title="DEBUG Registered with %s" % params["modelclass"].getSimpleName())
"""
except:
print sys.exc_info()
finally:
exe.shutdown()
SwingUtilities.invokeLater(lambda: run_button.setEnabled(True))
def launchRun(event):
# Runs on the event dispatch thread
run_button.setEnabled(False) # will be re-enabled at the end of run()
# Fork:
Thread(run).start()
def printAffines(event):
for i, affine in enumerate(affines):
matrix = zeros(12, 'd')
affine.toArray(matrix)
msg = "# Refined post-crop affine matrix " + str(i) + ": \n" + \
"affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist())
# Print everywhere
print msg
IJ.log(msg)
System.out.println(msg)
def prepareDeconvolutionScriptUI(event):
"""
# DEBUG generateDeconvolutionScriptUI: generate params as a loadable serialized file
with open("/tmp/parameters.pickle", 'w') as f:
import pickle
def asArrays(affines):
arrays = []
for affine in affines:
matrix = zeros(12, 'd')
affine.toArray(matrix)
arrays.append(matrix)
return arrays
pickle.dump([params["srcDir"], params["tgtDir"], calibration,
asArrays(coarse_affines), [minC, maxC], asArrays(affines)], f)
"""
generateDeconvolutionScriptUI(params["srcDir"], params["tgtDir"], calibration,
coarse_affines, [minC, maxC], affines)
# Buttons
panel_buttons = JPanel()
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 2
gb.setConstraints(panel_buttons, gc)
panel.add(panel_buttons)
run_button = JButton("Run")
run_button.addActionListener(launchRun)
gb.setConstraints(run_button, gc)
panel_buttons.add(run_button)
print_button = JButton("Print affines")
print_button.addActionListener(printAffines)
panel_buttons.add(print_button)
prepare_button = JButton("Prepare deconvolution script")
prepare_button.addActionListener(prepareDeconvolutionScriptUI)
panel_buttons.add(prepare_button)
frame = JFrame("Registration")
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl())
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(True)
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(
MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
def __init__(self):
''' Resources Panel '''
# psimures= JPanel(GridBagLayout())
# psimures.setSize(Dimension(500,300))
self.setLayout(GridBagLayout())
# super(self,GridBagLayout())
self.setSize(Dimension(500,300))
''' fila 1 '''
label = JLabel('Resources panel')
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 1
c.gridwidth = 4
c.gridx = 0
c.gridy = 0
self.add(label, c)
''' fila 2 '''
self.dModelFile = []
self.cbMoFile = JComboBox(self.dModelFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 1
self.add(self.cbMoFile, c)
bloadmodel= JButton('Load Model',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 1
self.add(bloadmodel, c)
''' fila 3 '''
self.dLibFile = []
self.cbMoLib = JComboBox(self.dLibFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 2
self.add(self.cbMoLib, c)
bloadlib= JButton('Load Library',actionPerformed=self.onOpenFile)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 2
self.add(bloadlib, c)
''' fila 4 '''
self.dModel = []
self.cbModel = JComboBox(self.dModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 3
self.add(self.cbModel, c)
bselectmodel= JButton('Select Model',actionPerformed=self.onOpenModel)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 3
self.add(bselectmodel, c)
''' fila 5 '''
self.dOutPath = []
self.cbOutDir = JComboBox(self.dOutPath)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.75
c.gridwidth = 3
c.gridx = 0
c.gridy = 4
self.add(self.cbOutDir, c)
bloadoutpath= JButton('Output Path',actionPerformed=self.onOpenFolder)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.25
# c.gridwidth = 1
c.gridx = 3
c.gridy = 4
self.add(bloadoutpath, c)
''' fila 6 '''
bsaveSource= JButton('Save Resources',actionPerformed=self.saveResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 0
c.gridy = 5
self.add(bsaveSource, c)
bloadSource= JButton('Load Resources',actionPerformed=self.loadResources)
c = GridBagConstraints()
c.fill = GridBagConstraints.HORIZONTAL
c.weightx = 0.5
c.gridwidth = 2
c.gridx = 2
c.gridy = 5
self.add(bloadSource, c)
def tag_3_1(self, c):
# 输入框-标题
lblParams = JLabel(u'请填写域名:')
self.setFontBold(lblParams)
lblParams.setForeground(Color(0, 0, 153))
c.gridx = 0
c.gridy = 0
c.insets = Insets(5, 5, 5, 5)
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.FIRST_LINE_END
self.white_list_domain_settings.add(lblParams, c)
# 输入框
self.white_list_text_field = JTextField()
c.fill = GridBagConstraints.BOTH
c.gridx = 1
c.gridy = 0
self.white_list_domain_settings.add(self.white_list_text_field, c)
lblParamsNote = JLabel(u"白名单域名列表")
self.setFontItalic(lblParamsNote)
c.fill = GridBagConstraints.NONE
c.gridx = 0
c.gridy = 1
self.white_list_domain_settings.add(lblParamsNote, c)
# 添加 文本框
self.white_list_text_area = JTextArea()
self.white_list_text_area.setColumns(20)
self.white_list_text_area.setRows(10)
self.white_list_text_area.setEditable(False)
c.fill = GridBagConstraints.BOTH
self.white_list_mouse_listener = TextAreaMouseListener(
self.white_list_text_area)
self.white_list_text_area.addMouseListener(
self.white_list_mouse_listener)
# 向文本框添加数据
for name in white_list_names:
self.white_list_text_area.append(name + '\n' + os.linesep)
c.gridx = 1
c.gridy = 1
sp = JScrollPane(self.white_list_text_area)
self.white_list_domain_settings.add(sp, c)
# 添加 删除 重置
buttonsPanel = JPanel(GridBagLayout())
_c = GridBagConstraints()
_c.insets = Insets(3, 3, 3, 3)
_c.gridx = 0
_c.fill = GridBagConstraints.BOTH
_c.weightx = 1
_c.gridwidth = 1
handlers = ButtonHandlers(self.white_list_text_field,
self.white_list_text_area,
self.white_list_mouse_listener,
white_list_names)
# 添加按钮
self.white_list_add_button = JButton(
u'添加', actionPerformed=handlers.handler_add)
_c.gridy = 1
buttonsPanel.add(self.white_list_add_button, _c)
# 删除按钮
self.white_list_rm_button = JButton(
u'删除', actionPerformed=handlers.handler_rm)
_c.gridy = 2
buttonsPanel.add(self.white_list_rm_button, _c)
# 重置按钮
self.white_list_restore_button = JButton(
u'重置', actionPerformed=handlers.handler_restore)
_c.gridy = 3
buttonsPanel.add(self.white_list_restore_button, _c)
c.gridx = 2
c.gridy = 1
c.fill = GridBagConstraints.NONE
self.white_list_domain_settings.add(buttonsPanel, c)
def specifyRoiUI(roi=Roi(0, 0, 0, 0)):
# A panel in which to place UI elements
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
bounds = roi.getBounds() if roi else Rectangle()
textfields = []
roimakers = []
# Basic properties of most UI elements, will edit when needed
gc.gridx = 0 # can be any natural number
gc.gridy = 0 # idem.
gc.gridwidth = 1 # when e.g. 2, the UI element will occupy two horizontally adjacent grid cells
gc.gridheight = 1 # same but vertically
gc.fill = GBC.NONE # can also be BOTH, VERTICAL and HORIZONTAL
for title in ["x", "y", "width", "height"]:
# label
gc.gridx = 0
gc.anchor = GBC.EAST
label = JLabel(title + ": ")
gb.setConstraints(label, gc) # copies the given constraints 'gc',
# so we can modify and reuse gc later.
panel.add(label)
# text field, below the title
gc.gridx = 1
gc.anchor = GBC.WEST
text = str(getattr(bounds,
title)) # same as e.g. bounds.x, bounds.width, ...
textfield = JTextField(text,
10) # 10 is the size of the field, in digits
gb.setConstraints(textfield, gc)
panel.add(textfield)
textfields.append(
textfield) # collect all 4 created textfields for the listeners
# setup ROI and text field listeners
listener = RoiMaker(textfields,
len(textfields) -
1) # second argument is the index of textfield
# in the list of textfields.
roimakers.append(listener)
textfield.addKeyListener(listener)
textfield.addMouseWheelListener(listener)
# Position next ROI property in a new row by increasing the Y coordinate of the layout grid
gc.gridy += 1
# User documentation (uses HTML to define line breaks)
doc = JLabel(
"<html><body><br />Click on a field to activate it, then:<br />" +
"Type in integer numbers<br />" +
"or use arrow keys to increase by 1<br />" +
"or use the scroll wheel on a field.</body></html>")
gc.gridx = 0 # start at the first column
gc.gridwidth = 2 # Spans both columns
gb.setConstraints(doc, gc)
panel.add(doc)
# Listen to changes in the ROI of imp
roilistener = TextFieldUpdater(textfields)
Roi.addRoiListener(roilistener)
# Show window
frame = JFrame("Specify rectangular ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setDefaultCloseOperation(
JFrame.DO_NOTHING_ON_CLOSE) # prevent closing the window
frame.addWindowListener(
CloseControl(roilistener)) # handles closing the window
frame.setVisible(True)
def __init__(self, extender):
super(BeautifierOptionsPanel, self).__init__()
self._extender = extender
self.contentWrapper = JPanel(GridBagLayout())
self.setViewportView(self.contentWrapper)
self.getVerticalScrollBar().setUnitIncrement(16)
self.addMouseListener(self.RequestFocusListener(
self)) # Let textArea lose focus when click empty area
innerContainer = JPanel(GridBagLayout())
innerContainer.setFocusable(
True
) # make sure the maxSizeText TextField is not focused when BeautifierOptionsPanel display
# generalOptionPanel and it's inner component
maxSizeLabel = JLabel("Max Size: ")
self.maxSizeText = JTextField(5)
self.maxSizeText.setHorizontalAlignment(SwingConstants.RIGHT)
self.maxSizeText.addFocusListener(self.MaxSizeTextListener(self))
sizeUnitLabel = JLabel("KB")
generalOptionPanel = JPanel(GridBagLayout())
generalOptionPanel.setBorder(
BorderFactory.createTitledBorder("General Options"))
gbc = GridBagConstraints()
gbc.anchor = GridBagConstraints.WEST
gbc.gridx = 0
gbc.gridy = 0
generalOptionPanel.add(maxSizeLabel, gbc)
gbc.fill = GridBagConstraints.HORIZONTAL
gbc.gridx = 1
gbc.gridy = 0
generalOptionPanel.add(self.maxSizeText, gbc)
gbc.fill = GridBagConstraints.NONE
gbc.gridx = 2
gbc.gridy = 0
gbc.weightx = 1.0
generalOptionPanel.add(sizeUnitLabel, gbc)
gbc = GridBagConstraints()
gbc.fill = GridBagConstraints.BOTH
gbc.gridx = 1
gbc.gridy = 0
gbc.gridheight = 2
innerContainer.add(generalOptionPanel, gbc)
# messageTabOptionPanel and it's inner component
self.messageTabFormatCheckBoxs = []
for f in supportedFormats:
ckb = JCheckBox(f)
ckb.addItemListener(self.messageTabFormatListener)
self.messageTabFormatCheckBoxs.append(ckb)
messageTabOptionPanel = JPanel()
messageTabOptionPanel.setLayout(
BoxLayout(messageTabOptionPanel, BoxLayout.Y_AXIS))
messageTabOptionPanel.setBorder(
BorderFactory.createTitledBorder("Enable in MessageEditorTab"))
for b in self.messageTabFormatCheckBoxs:
messageTabOptionPanel.add(b)
gbc.gridx = 1
gbc.gridy = 2
gbc.gridheight = 9
innerContainer.add(messageTabOptionPanel, gbc)
# replaceResponsePanel and it's inner component
self.chkEnableReplace = JCheckBox("Enable")
self.chkEnableReplace.addItemListener(self.repalceResponseBoxListener)
replaceResponseFormatLabel = JLabel("Format")
self.replaceResponseFormatCheckBoxs = []
for f in supportedFormats:
ckb = JCheckBox(f)
ckb.addItemListener(self.replaceResponseFormatListener)
self.replaceResponseFormatCheckBoxs.append(ckb)
replaceResponseIncludeLabel = JLabel(
"Include URL that matches below(one item one line)")
self.URLIncludeTextArea = JTextArea(6, 32)
self.URLIncludeTextArea.addFocusListener(
self.URLIncludeFocusListener(self))
URLIncludeScrollPane = JScrollPane(self.URLIncludeTextArea)
URLIncludeScrollPane.setAlignmentX(Component.LEFT_ALIGNMENT)
replaceResponseExcludeLabel = JLabel(
"Exclude URL that matches below(one item one line)")
self.URLExcludeTextArea = JTextArea(5, 32)
self.URLExcludeTextArea.addFocusListener(
self.URLExcludeFocusListener(self))
URLExcludeScrollPane = JScrollPane(self.URLExcludeTextArea)
URLExcludeScrollPane.setAlignmentX(Component.LEFT_ALIGNMENT)
replaceResponsePanel = JPanel()
replaceResponsePanel.setLayout(
BoxLayout(replaceResponsePanel, BoxLayout.Y_AXIS))
replaceResponsePanel.setBorder(
BorderFactory.createTitledBorder("Replace PROXY Response"))
replaceResponsePanel.add(self.chkEnableReplace)
replaceResponsePanel.add(Box.createVerticalStrut(10))
replaceResponsePanel.add(replaceResponseFormatLabel)
for b in self.replaceResponseFormatCheckBoxs:
replaceResponsePanel.add(b)
replaceResponsePanel.add(Box.createVerticalStrut(10))
replaceResponsePanel.add(replaceResponseIncludeLabel)
replaceResponsePanel.add(URLIncludeScrollPane)
replaceResponsePanel.add(Box.createVerticalStrut(10))
replaceResponsePanel.add(replaceResponseExcludeLabel)
replaceResponsePanel.add(URLExcludeScrollPane)
gbc.gridy = 11
innerContainer.add(replaceResponsePanel, gbc)
# let innerContainer keep away from left and up
gbc = GridBagConstraints()
gbc.gridx = 1
gbc.gridy = 1
self.contentWrapper.add(Box.createHorizontalStrut(15), gbc)
# gbc.ipadx = gbc.ipady = 25
gbc.gridx = 2
self.contentWrapper.add(innerContainer, gbc)
# let innerContainer stay left side
gbc = GridBagConstraints()
gbc.gridx = 3
gbc.gridy = 2
gbc.gridwidth = 1
gbc.weightx = gbc.weighty = 1
paddingPanel = JPanel()
self.contentWrapper.add(paddingPanel, gbc)
self.setDefaultOptionDisplay()
def _constructAttackPanel(self, insets, messageEditorComponent):
attackPanel = JPanel(GridBagLayout())
targetHeadingLabel = JLabel("<html><b>Target</b></html>")
targetHeadingLabelConstraints = GridBagConstraints()
targetHeadingLabelConstraints.gridx = 0
targetHeadingLabelConstraints.gridy = 0
targetHeadingLabelConstraints.gridwidth = 4
targetHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
targetHeadingLabelConstraints.insets = insets
attackPanel.add(targetHeadingLabel, targetHeadingLabelConstraints)
startAttackButton = JButton("<html><b>Start Attack</b></html>",
actionPerformed=self._startAttack)
startAttackButtonConstraints = GridBagConstraints()
startAttackButtonConstraints.gridx = 4
startAttackButtonConstraints.gridy = 0
startAttackButtonConstraints.insets = insets
attackPanel.add(startAttackButton, startAttackButtonConstraints)
hostLabel = JLabel("Host:")
hostLabelConstraints = GridBagConstraints()
hostLabelConstraints.gridx = 0
hostLabelConstraints.gridy = 1
hostLabelConstraints.anchor = GridBagConstraints.LINE_START
hostLabelConstraints.insets = insets
attackPanel.add(hostLabel, hostLabelConstraints)
self._hostTextField = JTextField(25)
self._hostTextField.setMinimumSize(
self._hostTextField.getPreferredSize())
hostTextFieldConstraints = GridBagConstraints()
hostTextFieldConstraints.gridx = 1
hostTextFieldConstraints.gridy = 1
hostTextFieldConstraints.weightx = 1
hostTextFieldConstraints.gridwidth = 2
hostTextFieldConstraints.anchor = GridBagConstraints.LINE_START
hostTextFieldConstraints.insets = insets
attackPanel.add(self._hostTextField, hostTextFieldConstraints)
portLabel = JLabel("Port:")
portLabelConstraints = GridBagConstraints()
portLabelConstraints.gridx = 0
portLabelConstraints.gridy = 2
portLabelConstraints.anchor = GridBagConstraints.LINE_START
portLabelConstraints.insets = insets
attackPanel.add(portLabel, portLabelConstraints)
self._portTextField = JTextField(5)
self._portTextField.setMinimumSize(
self._portTextField.getPreferredSize())
portTextFieldConstraints = GridBagConstraints()
portTextFieldConstraints.gridx = 1
portTextFieldConstraints.gridy = 2
portTextFieldConstraints.gridwidth = 2
portTextFieldConstraints.anchor = GridBagConstraints.LINE_START
portTextFieldConstraints.insets = insets
attackPanel.add(self._portTextField, portTextFieldConstraints)
self._protocolCheckBox = JCheckBox("Use HTTPS")
protocolCheckBoxConstraints = GridBagConstraints()
protocolCheckBoxConstraints.gridx = 0
protocolCheckBoxConstraints.gridy = 3
protocolCheckBoxConstraints.gridwidth = 3
protocolCheckBoxConstraints.anchor = GridBagConstraints.LINE_START
protocolCheckBoxConstraints.insets = insets
attackPanel.add(self._protocolCheckBox, protocolCheckBoxConstraints)
requestHeadingLabel = JLabel("<html><b>Request</b></html>")
requestHeadingLabelConstraints = GridBagConstraints()
requestHeadingLabelConstraints.gridx = 0
requestHeadingLabelConstraints.gridy = 4
requestHeadingLabelConstraints.gridwidth = 4
requestHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
requestHeadingLabelConstraints.insets = insets
attackPanel.add(requestHeadingLabel, requestHeadingLabelConstraints)
messageEditorComponentConstraints = GridBagConstraints()
messageEditorComponentConstraints.gridx = 0
messageEditorComponentConstraints.gridy = 5
messageEditorComponentConstraints.weightx = 1
messageEditorComponentConstraints.weighty = .75
messageEditorComponentConstraints.gridwidth = 4
messageEditorComponentConstraints.gridheight = 2
messageEditorComponentConstraints.fill = GridBagConstraints.BOTH
messageEditorComponentConstraints.insets = insets
attackPanel.add(
messageEditorComponent, messageEditorComponentConstraints)
addPayloadButton = JButton(
"Add \xa7", actionPerformed=self._addPayload)
addPayloadButtonConstraints = GridBagConstraints()
addPayloadButtonConstraints.gridx = 4
addPayloadButtonConstraints.gridy = 5
addPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
addPayloadButtonConstraints.insets = insets
attackPanel.add(addPayloadButton, addPayloadButtonConstraints)
clearPayloadButton = JButton(
"Clear \xa7", actionPerformed=self._clearPayloads)
clearPayloadButtonConstraints = GridBagConstraints()
clearPayloadButtonConstraints.gridx = 4
clearPayloadButtonConstraints.gridy = 6
clearPayloadButtonConstraints.anchor = GridBagConstraints.PAGE_START
clearPayloadButtonConstraints.fill = GridBagConstraints.HORIZONTAL
clearPayloadButtonConstraints.insets = insets
attackPanel.add(clearPayloadButton, clearPayloadButtonConstraints)
payloadHeadingLabel = JLabel("<html><b>Payloads<b></html>")
payloadHeadingLabelConstraints = GridBagConstraints()
payloadHeadingLabelConstraints.gridx = 0
payloadHeadingLabelConstraints.gridy = 7
payloadHeadingLabelConstraints.gridwidth = 4
payloadHeadingLabelConstraints.anchor = GridBagConstraints.LINE_START
payloadHeadingLabelConstraints.insets = insets
attackPanel.add(payloadHeadingLabel, payloadHeadingLabelConstraints)
self._payloadTextArea = JTextArea()
payloadScrollPane = JScrollPane(self._payloadTextArea)
payloadScrollPaneConstraints = GridBagConstraints()
payloadScrollPaneConstraints.gridx = 0
payloadScrollPaneConstraints.gridy = 8
payloadScrollPaneConstraints.weighty = .25
payloadScrollPaneConstraints.gridwidth = 3
payloadScrollPaneConstraints.fill = GridBagConstraints.BOTH
payloadScrollPaneConstraints.insets = insets
attackPanel.add(payloadScrollPane, payloadScrollPaneConstraints)
requestsNumLabel = JLabel("Number of requests for each payload:")
requestsNumLabelConstraints = GridBagConstraints()
requestsNumLabelConstraints.gridx = 0
requestsNumLabelConstraints.gridy = 9
requestsNumLabelConstraints.gridwidth = 2
requestsNumLabelConstraints.anchor = GridBagConstraints.LINE_START
requestsNumLabelConstraints.insets = insets
attackPanel.add(requestsNumLabel, requestsNumLabelConstraints)
self._requestsNumTextField = JTextField("100", 4)
self._requestsNumTextField.setMinimumSize(
self._requestsNumTextField.getPreferredSize())
requestsNumTextFieldConstraints = GridBagConstraints()
requestsNumTextFieldConstraints.gridx = 2
requestsNumTextFieldConstraints.gridy = 9
requestsNumTextFieldConstraints.anchor = GridBagConstraints.LINE_START
requestsNumTextFieldConstraints.insets = insets
attackPanel.add(
self._requestsNumTextField, requestsNumTextFieldConstraints)
return attackPanel
def __init__(self, frame, name):
self.frame = frame
self.exception = None
self.name = name
self.searchTerm = None
self.searchIndex = -1
self.searchField = JTextField("")
self.searchField.addActionListener(SearchListener(self))
self.newGeneFrom = JTextField("")
self.newGeneTo = JTextField("")
self.newGeneButton = JButton("New Gene")
newGeneActionListener = NewGeneActionListener(self)
self.newGeneFrom.addActionListener(newGeneActionListener)
self.newGeneTo.addActionListener(newGeneActionListener)
self.newGeneButton.addActionListener(newGeneActionListener)
self.markForRemovalButton = JButton("Mark For Removal")
self.markForRemovalButton.addActionListener(MarkForRemovalListener(self))
self.inGenes = JList(DefaultListModel())
self.inGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.inGenes.cellRenderer = ProfelisCellRenderer()
self.markButtonLabelerTimer = Timer(100, MarkButtonLabeler(self))
self.markButtonLabelerTimer.start()
self.loadFile()
self.outGenes = JList(DefaultListModel())
self.outGenes.selectionMode = ListSelectionModel.SINGLE_SELECTION
self.outGenes.cellRenderer = ProfelisCellRenderer()
constraints = GridBagConstraints()
self.layout = GridBagLayout()
constraints.gridx, constraints.gridy = 0, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes In Artemis File"), constraints)
constraints.gridx, constraints.gridy = 0, 1
self.add(JButton(RemoveAction(self)), constraints)
constraints.gridx, constraints.gridy = 1, 1
self.add(self.markForRemovalButton, constraints)
constraints.gridx, constraints.gridy = 2, 1
self.add(JLabel("Search"), constraints)
constraints.gridx, constraints.gridy = 3, 1
constraints.fill = GridBagConstraints.HORIZONTAL
self.add(self.searchField, constraints)
constraints.gridx, constraints.gridy = 0, 2
constraints.gridwidth, constraints.gridheight = 4, 2
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.inGenes), constraints)
constraints.gridx, constraints.gridy = 4, 0
constraints.gridwidth, constraints.gridheight = 1, 1
constraints.fill = GridBagConstraints.NONE
constraints.weightx, constraints.weighty = 0, 0
self.add(JLabel("Genes To Add To Artemis File"), constraints)
constraints.gridx, constraints.gridy = 4, 1
self.add(self.newGeneButton, constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 5, 1
self.add(self.newGeneFrom, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 6, 1
self.add(JLabel("To"), constraints)
constraints.weightx = 1
constraints.fill = GridBagConstraints.BOTH
constraints.gridx, constraints.gridy = 7, 1
self.add(self.newGeneTo, constraints)
constraints.weightx = 0
constraints.fill = GridBagConstraints.NONE
constraints.gridx, constraints.gridy = 4, 2
self.add(JButton(AddGenesAction(self)), constraints)
constraints.gridx, constraints.gridy = 4, 3
constraints.gridwidth, constraints.gridheight = 4, 1
constraints.fill = GridBagConstraints.BOTH
constraints.weightx, constraints.weighty = 1, 1
self.add(JScrollPane(self.outGenes), constraints)
