def complex_console():
global frame
#generates frame
frame = JFrame("[BETA] Game Master\'s Bot - Console Log")
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
frame.setResizable(False)
frame.setAlwaysOnTop(True)
frame.setBounds(8,545,600,130)
frame.contentPane.layout = FlowLayout()
#add QUIT button
quitButton = JButton("QUIT", actionPerformed = closeFrame)
quitButton.setForeground(Color.RED)
quitButton.setPreferredSize(Dimension(100,100))
frame.contentPane.add(quitButton)
#add text message
global textArea
textArea = JTextArea(6,38)
textArea.setEditable(False)
frame.contentPane.add(textArea)
scrollPane = JScrollPane(textArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
frame.contentPane.add(scrollPane)
#show frame
frame.pack()
frame.setVisible(True)
log("Welcome to Game Master\'s Bot!")
def onInfo(self, e):
info = JFrame()
info.setTitle("Info")
info.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE)
info.setSize(410, 400)
info.setLocationRelativeTo(None)
info.setResizable(False)
info.setVisible(True)
panel = JPanel()
#panel.setBackground(Color(46, 64, 96))
#panel.setLayout(GridLayout(0, 2))
logo = JLabel(ImageIcon("/icons/logo.jpg"))
panel.add(logo)
f = Font("", Font.ITALIC, 40)
title = JLabel("Stylus OS 1.0 beta")
title.setFont(f)
panel.add(title)
f = Font("", Font.ITALIC, 14)
copyright = JLabel(
"Copyright (c) 2016 Niccolo' Ciavarella. All rights reserved.")
copyright.setFont(f)
panel.add(copyright)
info.getContentPane().add(panel)
info.add(panel)
def bg(self, panel2, e):
bground = JFrame()
bground.setTitle("Change Background")
bground.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE)
bground.setSize(350, 100)
bground.setLocationRelativeTo(None)
bground.setVisible(True)
bground.setResizable(False)
panel = JPanel()
#panel.setBackground(Color(46, 64, 96))
bground.getContentPane().add(panel)
path = JLabel("File:")
panel.add(path)
path2 = JTextField()
path2.setPreferredSize(Dimension(180, 20))
panel.add(path2)
browse = JButton("Browse file",
actionPerformed=lambda e: self.browse(path2, e))
panel.add(browse)
change = JButton(
"Change",
actionPerformed=lambda e: self.change(path2.getText(), panel2, e))
panel.add(change)
bground.add(panel)
def createFrame():
global isDominant
manager = doAction()
if isTemporal:
frame = JFrame("LosiTemp - LOoking for Selection In TEMPoral datasets")
elif isDominant:
frame = JFrame("Mcheza - Dominant Selection Workbench")
else:
frame = JFrame("LOSITAN - Selection Workbench")
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
doPrettyType(frame, manager)
frame.setVisible(1)
frame.setResizable(0)
return frame
def show_pannel(self):
# BP_STDOUT.println("Event code: %s" % self.contextMenuInvocation.getInputEvent())
# self.scannerInstance.show_pannel.show()
window = JFrame()
window.setLayout(None)
window.setTitle("Xcrpter")
window.setSize(720, 540)
window.setLocationRelativeTo(None)
window.setResizable(True)
window.setContentPane(self.scannerInstance.xpannel)
window.setVisible(True)
self.scannerInstance.xpannel.setPlain("")
self.scannerInstance.xpannel.setVisible(True)
def onExit(self, e):
exit = JFrame()
exit.setTitle("Exit Stylus")
exit.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE)
exit.setSize(250, 225)
exit.setLocationRelativeTo(None)
exit.setVisible(True)
exit.setResizable(False)
panel = JPanel()
panel.setBorder(BorderFactory.createEtchedBorder())
panel.setLayout(GridLayout(0, 1))
exit.getContentPane().add(panel)
icon1 = ImageIcon("/icons/shutdown.png")
poweroff = JButton("Shutdown", icon1, actionPerformed=self.shutdown)
panel.add(poweroff)
icon2 = ImageIcon("/icons/reboot.png")
reboot = JButton(" Reboot ", icon2, actionPerformed=self.reboot)
panel.add(reboot)
exit.add(panel)
def main(args):
_WIDTH = 300
_HEIGHT = 300
fps = 20#frames per second
bgColor = Color.white
frame = JFrame("Graphics!")
frame.setBackground(bgColor);
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE)
drawgraphics = DrawGraphics()
content = Animator(drawgraphics, _WIDTH, _HEIGHT, fps)
content.setBackground(bgColor)
content.setSize(_WIDTH, _HEIGHT)
content.setMinimumSize(Dimension(_WIDTH, _HEIGHT))
content.setPreferredSize(Dimension(_WIDTH, _HEIGHT))
frame.setSize(_WIDTH, _HEIGHT)
frame.setContentPane(content)
frame.setResizable(True)
frame.pack()
Thread(content).start()
frame.setVisible(True)
class Pipeline():
def __init__(self):
#If a swing interface is asked for this will be the JFrame.
self.frame = None
#Keeps track of the number of queries processed.
self.jobCount = 0
#Keeps track of the query currently being processed.
self.currentJob = ""
#Keeps track of the massage to be displayed.
self.message = 0
#Messages to be displayed at each stage in the processing of a single query.
self.messages = ["Searching for genes via genemark",
"Extending genes found via genemark",
"Searching for intergenic genes",
"Removing overlapping genes",
"Searching for promoters",
"Using transterm to find terminators",
"Removing transcription signals which conflict with genes",
"Using tRNAscan to find transfer RNAs",
"Writing Artemis file",
"Writing summary .xml, .html, and .xls files"]
self.exception = None
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 updateProgress(self, job):
"""
query: Name of the query currently being processed.
This function use used for updating the progress shown in the interface. If job is not equal to currentJob then
global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob
then the globalProgress does not change and currentProgress is increased.
"""
if self.exception:
raise self.exception
if self.frame:
if job != self.currentJob:
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.globalLabel.setText(job)
self.globalProgress.setValue(self.jobCount)
print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages))
self.currentProgress.setValue(self.message)
self.currentLabel.setText(self.messages[self.message])
else:
if job != self.currentJob:
print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages))
def finished(self):
"""
This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished
and if a swing interface is being used the Done button is enabled.
"""
print "Processing 100.00% done"
if self.frame:
self.globalLabel.setText("Finished")
self.globalProgress.setValue(self.globalProgress.getMaximum())
self.currentLabel.setText(" ")
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.doneButton.setEnabled(True)
while self.frame.isVisible():
pass
def run(self, blastLocation, genemarkLocation, transtermLocation, tRNAscanLocation, database, eValue, matrix, minLength, scaffoldingDistance, promoterScoreCutoff, queries, swing = False, email = ""):
"""
blastLocation: Directory blast was installed in.
genemarkLocation: Directory genemark was installed in.
transtermLocation: Directory transterm was installed in.
tRNAscanLocation: Directory tRNAscan was installed in.
database: Name of the blast database to use.
eValue: The e value used whenever a blast search is done.
matrix: The matrix to use when running genemark. If None then genemark is run heuristically.
minLength: Minimum length of any genes included in the resulting annotation.
scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified
promoterScoreCutoff: Minimum score allowed for any promoters included in the resulting annotation
queries: A list of faster files to process.
swing: If true a swing window will be used to updated the user about the pipeline's progress.
email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. This will be attempted with the sendmail command on the local computer.
The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches
for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove
any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any
signals which are inside or too far away from any genes. Next, tRNAscan is used to find any transfer RNAs in the genome. Finally, all the remaining genes,
promoters, and terminators are written to an artemis file in the directory of the query with the same name but with a .art extension, and .xml, .html, and
.xls files will be generating describing the blast results of the final genes.
"""
self.initializeDisplay(queries, swing)
try:
for query in queries:
name = os.path.splitext(query)[0]
queryDirectory, name = os.path.split(name)
genome = utils.loadGenome(query)
swapFileName = "query" + str(id(self)) + ".fas"
queryFile = open(swapFileName, "w")
queryFile.write(">" + name + "\n")
for i in range(0, len(genome), 50):
queryFile.write(genome[i:min(i+50, len(genome))] + "\n")
queryFile.close()
self.updateProgress(query)
initialGenes = genemark.findGenes(swapFileName, name, blastLocation, database, eValue, genemarkLocation, matrix, self)
self.updateProgress(query)
extendedGenes = extend.extendGenes(swapFileName, initialGenes, name, blastLocation, database, eValue, self)
self.updateProgress(query)
intergenicGenes = intergenic.findIntergenics(swapFileName, extendedGenes, name, minLength, blastLocation, database, eValue, self)
genes = {}
for k, v in extendedGenes.items() + intergenicGenes.items():
genes[k] = v
self.updateProgress(query)
scaffolded = scaffolds.refineScaffolds(genes, scaffoldingDistance)
self.updateProgress(query)
initialPromoters = promoters.findPromoters(swapFileName, name, promoterScoreCutoff, self.frame)
self.updateProgress(query)
initialTerminators = terminators.findTerminators(swapFileName, name, genes.values(), transtermLocation)
self.updateProgress(query)
filteredSignals = signals.filterSignals(scaffolded.values(), initialPromoters + initialTerminators)
filteredPromoters = filter(lambda x: isinstance(x, promoters.Promoter), filteredSignals)
filteredTerminators = filter(lambda x: isinstance(x, terminators.Terminator), filteredSignals)
self.updateProgress(query)
transferRNAs = rna.findtRNAs(tRNAscanLocation, swapFileName)
os.remove(swapFileName)
self.updateProgress(query)
artemis.writeArtemisFile(os.path.splitext(query)[0] + ".art", genome, scaffolded.values(), filteredPromoters, filteredTerminators, transferRNAs)
self.updateProgress(query)
report.report(name, scaffolded, os.path.splitext(query)[0])
if email:
if not os.path.isfile("EMAIL_MESSAGE"):
message = open("EMAIL_MESSAGE", "w")
message.write("Subject: Annotation Complete\nYour genome has been annotated.\n")
message.close()
sent = False
while not sent:
message = open("EMAIL_MESSAGE", "r")
sendmailProcess = subprocess.Popen(["/usr/sbin/sendmail", "-F", "Neofelis", "-f", "*****@*****.**", email],
stdin = message,
stdout = subprocess.PIPE)
result = ""
nextRead = sendmailProcess.stdout.read()
while nextRead:
result += nextRead
nextRead = sendmailProcess.stdout.read()
sent = not result.strip()
message.close()
self.finished()
except PipelineException:
return
class FilamentGame_ModelEditor(EditorExtension, JPanel, MouseListener, MouseMotionListener):
def getExtensionName(self):
return "Filament Model Tool"
def initializeExtension(self, manager):
self.manager = manager
self.frame = JFrame(self.getExtensionName())
self.frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
# instance setup
self.state = State.NOTHING
self.entity = Entity()
# Setupgui
self.setupGui()
self.addMouseListener(self)
self.addMouseMotionListener(self)
self.setPreferredSize(Dimension(500, 500))
self.frame.pack()
self.frame.setResizable(False)
self.frame.setVisible(True)
self.cameraPos = [0, 0]
def setupGui(self):
cPanel = JPanel()
# Draw Shape Button
self.drawShapeButton = JButton("Draw", actionPerformed=self.drawShapeButtonAction)
cPanel.add(self.drawShapeButton)
drawShapeButton = JButton("Clear", actionPerformed=self.clearShapeButtonAction)
cPanel.add(drawShapeButton)
# Label
self.infoLabel = JLabel("Shape Editor")
cPanel.add(self.infoLabel)
self.frame.add(BorderLayout.NORTH, cPanel)
self.frame.add(BorderLayout.CENTER, self)
def entitySelected(self, entity):
self.entity = entity
self.repaint()
def sceneChanged(self, scene):
self.scene = scene
self.entity = Entity()
self.repaint()
# BUTTONS
def drawShapeButtonAction(self, e):
if self.state == State.NOTHING:
self.state = State.DRAW_SHAPE
self.infoLabel.setText("Click to Draw Shape")
self.drawShapeButton.setText("Stop Drawing")
elif self.state != State.NOTHING:
self.state = State.NOTHING
self.infoLabel.setText("")
self.drawShapeButton.setText("Draw")
self.revalidate()
def clearShapeButtonAction(self, e):
if self.state != State.NOTHING:
self.drawShapeButtonAction(e)
self.state = State.NOTHING
polygon = self.entity.getModel().pol
polygon.reset()
self.repaint()
# DRAWING
def paintComponent(self, g):
self.super__paintComponent(g)
g.scale(1, -1)
g.translate(-self.cameraPos[0] + self.getWidth() / 2, -self.cameraPos[1] - self.getHeight() / 2)
self.drawGrid(g)
polygon = self.entity.getModel().pol
x = []
y = []
g.setColor(Color.BLACK)
for i in range(polygon.npoints):
x = x + [int(polygon.xpoints[i])]
y = y + [int(polygon.ypoints[i])]
g.drawRect(int(polygon.xpoints[i]) - 2, int(polygon.ypoints[i]) - 2, 4, 4)
g.fillPolygon(x, y, polygon.npoints)
def drawGrid(self, g):
g.setColor(Color.RED)
g.drawLine(50, 0, -50, 0)
g.drawLine(0, 50, 0, -50)
# MOUSE LISTENER
def mouseCicked(self, e):
return
def mouseEntered(self, e):
return
def mouseExited(self, e):
return
def mousePressed(self, e):
self.anchor = e.getPoint()
self.oldCamPos = self.cameraPos
def findMousePos(self, p):
w = self.getWidth()
h = self.getHeight()
cX = self.cameraPos[0]
cY = self.cameraPos[1]
y = h - p.y
x = p.x - w / 2 + cX
y = y - h / 2 + cY
return [x, y]
def mouseReleased(self, e):
if self.state == State.DRAW_SHAPE:
try:
p = self.findMousePos(e.getPoint())
self.entity.getModel().pol.addPoint(p[0], p[1])
except IllegalPathStateException:
print "Error Building Polygon path!"
self.repaint()
def mouseMoved(self, e):
return
def mouseDragged(self, e):
if self.state == State.NOTHING:
self.cameraPos = [
self.oldCamPos[0] + self.anchor.x - e.getX(),
self.oldCamPos[1] - self.anchor.y + e.getY(),
]
print str(self.cameraPos)
self.repaint()
def update(self, delta):
return
class Image:
"""Holds an image of RGB pixels accessed by column and row indices (col, row).
Origin (0, 0) is at upper left."""
# QUESTION: For efficiency, should we also extract and save self.pixels (at image reading time)?
# Also make setPixel(), getPixel(), setPixels() and getPixels() work on/with self.pixels.
# And when writing, use code in current setPixels() to update image buffer, before writing it out?
# This is something to try.
def __init__(self, filename, width=None, height=None):
"""Create an image from a file, or an empty (black) image with specified dimensions."""
# Since Python does not allow constructors with different signatures,
# the trick is to reuse the first argument as a filename or a width.
# If it is a string, we assume they want is to open a file.
# If it is an int, we assume they want us to create a blank image.
if type(filename) == type(""): # is it a string?
self.filename = filename # treat is a filename
self.image = BufferedImage(
1, 1, BufferedImage.TYPE_INT_RGB) # create a dummy image
self.read(filename) # and read external image into ti
elif type(filename) == type(1): # is it a int?
# create blank image with specified dimensions
self.filename = "Untitled"
self.width = filename # holds image width (shift arguments)
self.height = width # holds image height
self.image = BufferedImage(
self.width, self.height,
BufferedImage.TYPE_INT_RGB) # holds image buffer (pixels)
else:
raise TypeError(
"Image(): first argument must a filename (string) or an blank image width (int)."
)
# display image
self.display = JFrame() # create frame window to hold image
icon = ImageIcon(
self.image) # wrap image appropriately for displaying in a frame
container = JLabel(icon)
self.display.setContentPane(container) # and place it
self.display.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.display.setTitle(self.filename)
self.display.setResizable(False)
self.display.pack()
self.display.setVisible(True)
# remember that this image has been created and is active (so that it can be stopped/terminated by JEM, if desired)
_ActiveImages_.append(self)
def getWidth(self):
"""Returns the width of the image."""
return self.width
def getHeight(self):
"""Returns the height of the image."""
return self.height
def getPixel(self, col, row):
"""Returns a list of the RGB values for this pixel, e.g., [255, 0, 0]."""
# Obsolete - convert the row so that row zero refers to the bottom row of pixels.
#row = self.height - row - 1
color = Color(self.image.getRGB(col, row)) # get pixel's color
return [color.getRed(),
color.getGreen(),
color.getBlue()] # create list of RGB values (0-255)
def setPixel(self, col, row, RGBlist):
"""Sets this pixel's RGB values, e.g., [255, 0, 0]."""
# Obsolete - convert the row so that row zero refers to the bottom row of pixels.
#row = self.height - row - 1
color = Color(RGBlist[0], RGBlist[1],
RGBlist[2]) # create color from RGB values
self.image.setRGB(col, row, color.getRGB())
def getPixels(self):
"""Returns a 2D list of pixels (col, row) - each pixel is a list of RGB values, e.g., [255, 0, 0]."""
pixels = [] # initialize list of pixels
#for row in range(self.height-1, 0, -1): # load pixels from image
for row in range(0, self.height): # load pixels from image
pixels.append([]) # add another empty row
for col in range(self.width): # populate row with pixels
# RGBlist = self.getPixel(col, row) # this works also (but slower)
color = Color(self.image.getRGB(col, row)) # get pixel's color
RGBlist = [color.getRed(),
color.getGreen(),
color.getBlue()
] # create list of RGB values (0-255)
pixels[-1].append(
RGBlist) # add a pixel as (R, G, B) values (0-255, each)
# now, 2D list of pixels has been created, so return it
return pixels
def setPixels(self, pixels):
"""Sets image to the provided 2D list of pixels (col, row) - each pixel is a list of RGB values, e.g., [255, 0, 0]."""
self.height = len(pixels) # get number of rows
self.width = len(
pixels[0]
) # get number of columns (assume all columns have same length
#for row in range(self.height-1, 0, -1): # iterate through all rows
for row in range(0, self.height): # iterate through all rows
for col in range(
self.width): # iterate through every column on this row
RGBlist = pixels[row][col]
#self.setPixel(col, row, RGBlist) # this works also (but slower)
color = Color(RGBlist[0], RGBlist[1],
RGBlist[2]) # create color from RGB values
self.image.setRGB(col, row, color.getRGB())
def read(self, filename):
"""Read an image from a .png, .gif, or .jpg file. as 2D list of RGB pixels."""
# JEM working directory fix (see above)
filename = fixWorkingDirForJEM(filename) # does nothing if not in JEM
# ***
#print "fixWorkingDirForJEM( filename ) =", filename
file = File(filename) # read file from current directory
self.image = ImageIO.read(file)
self.width = self.image.getWidth(None)
self.height = self.image.getHeight(None)
pixels = [] # initialize list of pixels
# load pixels from image
for row in range(self.height):
pixels.append([]) # add another empty row
for col in range(self.width): # now, populate row with pixels
color = Color(self.image.getRGB(col, row)) # get pixel's color
RGBlist = [color.getRed(),
color.getGreen(),
color.getBlue()
] # create list of RGB values (0-255)
pixels[-1].append(
RGBlist) # add a pixel as (R, G, B) values (0-255, each)
# now, pixels have been loaded from image file, so create an image
self.setPixels(pixels)
def write(self, filename):
"""Saves the pixels to a file (.png or .jpg)."""
# JEM working directory fix (see above)
filename = fixWorkingDirForJEM(filename) # does nothing if not in JEM
# ***
#print "fixWorkingDirForJEM( filename ) =", filename
# get suffix
suffix = filename[-3:]
suffix = suffix.lower()
if suffix == "jpg" or suffix == "png":
ImageIO.write(self.image, suffix, File(filename)) # save, and also
self.filename = filename # update image filename
self.display.setTitle(self.filename) # update display title
else:
print "Filename must end in .jpg or .png"
def show(self):
"""It displays the image."""
self.display.setVisible(True)
#self.display.repaint() # draw it
def hide(self):
"""It hides the image."""
self.display.setVisible(False)
def guiFrame(self):
frame = JFrame("PyNews")
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
frame.setLocationRelativeTo(None)
frame.setSize(600, 200)
frame.setResizable(False)
frame.setLayout(GridLayout(5, 3, 10, 10))
# logo
self.logo = JLabel(" PyNews")
# query input
self.input_field = JTextField(30)
# search button
self.src_button = JButton("Search!", actionPerformed=self.pyNewsSearch)
# expand button
self.exp_button = JButton("Expand!", actionPerformed=self.expandNews)
self.exp_button.setEnabled(False)
# open button
self.opn_button = JButton("Open!", actionPerformed=self.openNews)
self.opn_button.setEnabled(False)
# open html button
self.htm_button = JButton("HTML-Open!", actionPerformed=self.openHTML)
self.htm_button.setEnabled(False)
# write to file button
self.wrt_button = JButton("CSV-Write!",
actionPerformed=self.writeToCSV)
self.wrt_button.setEnabled(False)
# checkboxes
self.categories = [
"authors", "publish_date", "top_image", "movies", "text",
"article_html", "summary", "keywords"
]
self.checkboxes = []
for cat in self.categories:
self.checkboxes.append(JCheckBox(cat))
# add to frame
frame.add(self.logo)
frame.add(self.input_field)
frame.add(self.src_button)
frame.add(self.exp_button)
for cb in self.checkboxes[:2]:
frame.add(cb)
frame.add(self.opn_button)
for cb in self.checkboxes[2:4]:
frame.add(cb)
frame.add(self.htm_button)
for cb in self.checkboxes[4:6]:
frame.add(cb)
frame.add(self.wrt_button)
for cb in self.checkboxes[6:8]:
frame.add(cb)
print("got to end ")
frame.setVisible(True)
while results.next():
i += 1
#logger.debug("%s" % results)
logger.debug("%s : %s" % (results.getString("TABLE_NAME"), results.getString("TABLE_TEXT")))
#logger.debug("%s : %s [%s]" % (results.getString("COLUMN_NAME"), results.getString("COLUMN_TEXT"), results.getString("TYPE_NAME")))
if i == 1000:
exit()
logger.debug("Success!")
def exit_all(event):
exit
if __name__ == "__main__":
f = JFrame('Hello, Jython!', defaultCloseOperation = JFrame.EXIT_ON_CLOSE, size = (550, 200))
f.setResizable(True)
b = JButton('Connect!', actionPerformed=change_text)
#d = JButton('Exit!!', actionPerformed=exit_all)
c = f.getContentPane()
c.setBackground(Color.DARK_GRAY)
c.add(b)
#c.add(d)
f.setVisible(True)
class Pipeline():
def __init__(self):
#If a swing interface is asked for this will be the JFrame.
self.frame = None
#Keeps track of the number of queries processed.
self.jobCount = 0
#Keeps track of the query currently being processed.
self.currentJob = ""
#Keeps track of the massage to be displayed.
self.message = 0
#Messages to be displayed at each stage in the processing of a single query.
self.messages = [
"Searching for genes via genemark",
"Extending genes found via genemark",
"Searching for intergenic genes", "Removing overlapping genes",
"Searching for promoters", "Using transterm to find terminators",
"Removing transcription signals which conflict with genes",
"Writing Artemis file", "Writing summary file"
]
self.exception = None
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 updateProgress(self, job):
"""
query: Name of the query currently being processed.
This function use used for updating the progress shown in the interface. If job is not equal to currentJob then
global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob
then the globalProgress does not change and currentProgress is incremented.
"""
if self.exception:
raise self.exception
if self.frame:
if job != self.currentJob:
self.currentProgress.setValue(
self.currentProgress.getMaximum())
self.globalLabel.setText(job)
self.globalProgress.setValue(self.jobCount)
print "Processing %s, %.2f%% done" % (
job, 100.0 * self.jobCount / self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0 *
self.message / len(self.messages))
self.currentProgress.setValue(self.message)
self.currentLabel.setText(self.messages[self.message])
else:
if job != self.currentJob:
print "Processing %s, %.2f%% done" % (
job, 100.0 * self.jobCount / self.numJobs)
self.jobCount += 1
self.currentJob = job
self.message = -1
self.message += 1
print " %s, %.2f%% done" % (self.messages[self.message], 100.0 *
self.message / len(self.messages))
def finished(self):
"""
This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished
and if a swing interface is being used the Done button is enabled.
"""
print "Processing 100.00% done"
if self.frame:
self.globalLabel.setText("Finished")
self.globalProgress.setValue(self.globalProgress.getMaximum())
self.currentLabel.setText(" ")
self.currentProgress.setValue(self.currentProgress.getMaximum())
self.doneButton.setEnabled(True)
while self.frame.isVisible():
pass
def run(self,
blastLocation,
genemarkLocation,
transtermLocation,
database,
eValue,
matrix,
minLength,
scaffoldingDistance,
ldfCutoff,
queries,
swing=False,
email=""):
"""
blastLocation: Directory blast was installed in.
genemarkLocation: Directory genemark was installed in.
transtermLocation: Directory transterm was installed in.
database: Name of the blast database to use.
eValue: The e value used whenever a blast search is done.
matrix: The matrix to use when running genemark. If None then genemark is run heuristically.
minLength: Minimum length of any genes included in the resulting annotation.
scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified
ldfCutoff: Minimum LDF allowed for any promoters included in the resulting annotation
queries: A list of faster files to process.
swing: If true a swing window will be used to updated the user about the pipeline's progress.
email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. The local machine will be used as
an SMTP server and this will not work if it isn't.
The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches
for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove
any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any
signals which are inside or too far away from any genes. Finally, all the remaining genes, promoters, and terminators ar written to an artemis file in the directory
of the query with the same name but with a .art extension, and .dat and .xls files will be generating describing the blast results of the final genes.
"""
self.initializeDisplay(queries, swing)
try:
for query in queries:
name = os.path.splitext(query)[0]
queryDirectory, name = os.path.split(name)
genome = utils.loadGenome(query)
swapFileName = "query" + str(id(self)) + ".fas"
queryFile = open(swapFileName, "w")
queryFile.write(">" + name + "\n")
for i in range(0, len(genome), 50):
queryFile.write(genome[i:min(i + 50, len(genome))] + "\n")
queryFile.close()
self.updateProgress(query)
initialGenes = genemark.findGenes(swapFileName, name,
blastLocation, database,
eValue, genemarkLocation,
matrix, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".genemark.art", genome, initialGenes.values())
self.updateProgress(query)
extendedGenes = extend.extendGenes(swapFileName, initialGenes,
name, blastLocation,
database, eValue, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".extended.art", genome, extendedGenes.values())
self.updateProgress(query)
intergenicGenes = intergenic.findIntergenics(
swapFileName, extendedGenes, name, minLength,
blastLocation, database, eValue, self)
#artemis.writeArtemisFile(os.path.splitext(query)[0] + ".intergenic.art", genome, intergenicGenes.values())
genes = {}
for k, v in extendedGenes.items() + intergenicGenes.items():
genes[k] = v
self.updateProgress(query)
scaffolded = scaffolds.refineScaffolds(genes,
scaffoldingDistance)
self.updateProgress(query)
initialPromoters = promoters.findPromoters(swapFileName, name)
self.updateProgress(query)
initialTerminators = terminators.findTerminators(
swapFileName, name, genes.values(), transtermLocation)
self.updateProgress(query)
filteredSignals = signals.filterSignals(
scaffolded.values(), initialPromoters + initialTerminators)
filteredPromoters = filter(
lambda x: isinstance(x, promoters.Promoter),
filteredSignals)
filteredTerminators = filter(
lambda x: isinstance(x, terminators.Terminator),
filteredSignals)
self.updateProgress(query)
artemis.writeArtemisFile(
os.path.splitext(query)[0] + ".art", genome,
scaffolded.values(), filteredPromoters,
filteredTerminators)
self.updateProgress(query)
report.report(name, scaffolded, os.path.splitext(query)[0])
if email:
message = MIMEText("Your genome has been annotated.")
message["Subject"] = "Annotation complete"
message["From"] = "Neofelis"
message["To"] = email
smtp = smtplib.SMTP("tmpl.arizona.edu", 587)
smtp.ehlo()
smtp.starttls()
smtp.ehlo
smtp.sendmail("Neofelis", [email], message.as_string())
smtp.close()
self.finished()
except PipelineException:
return
class Image:
"""Holds an image of RGB pixels accessed by column and row indices (col, row).
Origin (0, 0) is at upper left."""
# QUESTION: For efficiency, should we also extract and save self.pixels (at image reading time)?
# Also make setPixel(), getPixel(), setPixels() and getPixels() work on/with self.pixels.
# And when writing, use code in current setPixels() to update image buffer, before writing it out?
# This is something to try.
def __init__(self, filename, width=None, height=None):
"""Create an image from a file, or an empty (black) image with specified dimensions."""
# Since Python does not allow constructors with different signatures,
# the trick is to reuse the first argument as a filename or a width.
# If it is a string, we assume they want is to open a file.
# If it is an int, we assume they want us to create a blank image.
if type(filename) == type(""): # is it a string?
self.filename = filename # treat is a filename
self.image = BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB) # create a dummy image
self.read(filename) # and read external image into ti
elif type(filename) == type(1): # is it a int?
# create blank image with specified dimensions
self.filename = "Untitled"
self.width = filename # holds image width (shift arguments)
self.height = width # holds image height
self.image = BufferedImage(self.width, self.height, BufferedImage.TYPE_INT_RGB) # holds image buffer (pixels)
else:
raise TypeError("Image(): first argument must a filename (string) or an blank image width (int).")
# display image
self.display = JFrame() # create frame window to hold image
icon = ImageIcon(self.image) # wrap image appropriately for displaying in a frame
container = JLabel(icon)
self.display.setContentPane(container) # and place it
self.display.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.display.setTitle(self.filename)
self.display.setResizable(False)
self.display.pack()
self.display.setVisible(True)
def getWidth(self):
"""Returns the width of the image."""
return self.width
def getHeight(self):
"""Returns the height of the image."""
return self.height
def getPixel(self, col, row):
"""Returns a list of the RGB values for this pixel, e.g., [255, 0, 0]."""
# Obsolete - convert the row so that row zero refers to the bottom row of pixels.
#row = self.height - row - 1
color = Color(self.image.getRGB(col, row)) # get pixel's color
return [color.getRed(), color.getGreen(), color.getBlue()] # create list of RGB values (0-255)
def setPixel(self, col, row, RGBlist):
"""Sets this pixel's RGB values, e.g., [255, 0, 0]."""
# Obsolete - convert the row so that row zero refers to the bottom row of pixels.
#row = self.height - row - 1
color = Color(RGBlist[0], RGBlist[1], RGBlist[2]) # create color from RGB values
self.image.setRGB(col, row, color.getRGB())
def getPixels(self):
"""Returns a 2D list of pixels (col, row) - each pixel is a list of RGB values, e.g., [255, 0, 0]."""
pixels = [] # initialize list of pixels
#for row in range(self.height-1, 0, -1): # load pixels from image
for row in range(0, self.height): # load pixels from image
pixels.append( [] ) # add another empty row
for col in range(self.width): # populate row with pixels
# RGBlist = self.getPixel(col, row) # this works also (but slower)
color = Color(self.image.getRGB(col, row)) # get pixel's color
RGBlist = [color.getRed(), color.getGreen(), color.getBlue()] # create list of RGB values (0-255)
pixels[-1].append( RGBlist ) # add a pixel as (R, G, B) values (0-255, each)
# now, 2D list of pixels has been created, so return it
return pixels
def setPixels(self, pixels):
"""Sets image to the provided 2D list of pixels (col, row) - each pixel is a list of RGB values, e.g., [255, 0, 0]."""
self.height = len(pixels) # get number of rows
self.width = len(pixels[0]) # get number of columns (assume all columns have same length
#for row in range(self.height-1, 0, -1): # iterate through all rows
for row in range(0, self.height): # iterate through all rows
for col in range(self.width): # iterate through every column on this row
RGBlist = pixels[row][col]
#self.setPixel(col, row, RGBlist) # this works also (but slower)
color = Color(RGBlist[0], RGBlist[1], RGBlist[2]) # create color from RGB values
self.image.setRGB(col, row, color.getRGB())
def read(self, filename):
"""Read an image from a .png, .gif, or .jpg file. as 2D list of RGB pixels."""
# JEM working directory fix (see above)
filename = fixWorkingDirForJEM( filename ) # does nothing if not in JEM
# ***
#print "fixWorkingDirForJEM( filename ) =", filename
file = File(filename) # read file from current directory
self.image = ImageIO.read(file)
self.width = self.image.getWidth(None)
self.height = self.image.getHeight(None)
pixels = [] # initialize list of pixels
# load pixels from image
for row in range(self.height):
pixels.append( [] ) # add another empty row
for col in range(self.width): # now, populate row with pixels
color = Color(self.image.getRGB(col, row)) # get pixel's color
RGBlist = [color.getRed(), color.getGreen(), color.getBlue()] # create list of RGB values (0-255)
pixels[-1].append( RGBlist ) # add a pixel as (R, G, B) values (0-255, each)
# now, pixels have been loaded from image file, so create an image
self.setPixels(pixels)
def write(self, filename):
"""Saves the pixels to a file (.png or .jpg)."""
# JEM working directory fix (see above)
filename = fixWorkingDirForJEM( filename ) # does nothing if not in JEM
# ***
#print "fixWorkingDirForJEM( filename ) =", filename
# get suffix
suffix = filename[-3:]
suffix = suffix.lower()
if suffix == "jpg" or suffix =="png":
ImageIO.write(self.image, suffix, File(filename)) # save, and also
self.filename = filename # update image filename
self.display.setTitle(self.filename) # update display title
else:
print "Filename must end in .jpg or .png"
def show(self):
"""It displays the image."""
self.display.setVisible(True)
#self.display.repaint() # draw it
def hide(self):
"""It hides the image."""
self.display.setVisible(False)
# Ensure we have an APIKEY
elif APIKEY == "":
show_error_message("VirusTotal API key must be set.")
# Initial checks good, lets run the script
else:
global cancelled
cancelled = False
# Do some UI setup here to keep the main() method a little easier to read
jframe = JFrame("VirusTotal Integration",
defaultCloseOperation=JFrame.DISPOSE_ON_CLOSE,
size=(300, 100),
locationRelativeTo=None)
jframe.setUndecorated(True)
statusLabel = JLabel("", JLabel.CENTER)
jframe.setResizable(False)
jframe.setLayout(GridLayout(3, 1))
statusLabel.setSize(300, 50)
jframe.getContentPane().add(statusLabel)
jbutton = JButton('Cancel')
jbutton.addActionListener(cancel)
# Run the main code function
result = main()
# Clean up jframe and show the result message
jframe.setVisible(False)
jframe.dispose()
if result:
JOptionPane.showMessageDialog(None, result)
