def createGui (self):
panel = JPanel ()
panel.setLayout (BorderLayout ())
chooserPanel = JPanel (); # JScrollPane (conditionsList)
chooserPanel.setLayout (BorderLayout ())
root = DefaultMutableTreeNode ('Experiments')
assert (len (self.dataDirectories) >= 1)
self.experimentNavigator = MetaDataNavigator (self.dataDirectories [0])
experimentsTree = self.experimentNavigator.getTree ()
#print 'experimentTree: %s' % experimentsTree
self.createTreeNodes (root, experimentsTree)
self.treeWidget = JTree (root)
#tree.setRootVisible (0)
self.treeWidget.getSelectionModel().setSelectionMode (
TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION)
self.treeWidget.addTreeSelectionListener (self)
treePane = JScrollPane (self.treeWidget)
treePanel = JPanel ()
treePanel.setLayout (BorderLayout ())
treePanel.add (treePane, BorderLayout.CENTER)
self.resultsPanel = JPanel ()
self.resultsPanel.setLayout (BorderLayout ())
self.outerSplitPane = JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
treePanel,
self.resultsPanel)
self.outerSplitPane.setDividerLocation (200)
self.outerSplitPane.setOneTouchExpandable (1)
self.dataBrowserHasEntireWindow = 0
panel.add (self.outerSplitPane, BorderLayout.CENTER)
dismissButton = JButton (actions.IconFactory.getDismissIcon(), actionPerformed=self.dismiss)
dismissButton.setBackground(Color.WHITE)
dismissButton.setToolTipText('Close This Window')
buttonAndReadoutPanel = JPanel ()
buttonAndReadoutPanel.setLayout (GridBagLayout ())
gbc = GridBagConstraints ()
gbc.gridx = 0
gbc.gridy = 0
gbc.weightx = 1.0
gbc.anchor = GridBagConstraints.LINE_START
gbc.insets = Insets (5,20,5,0)
selectionPanel = JPanel ()
buttonAndReadoutPanel.add (selectionPanel, gbc)
label = JLabel ('Explicit Selection Count: ')
selectionPanel.add (label)
self.conditionCounterTextField = JTextField (5)
selectionPanel.add (self.conditionCounterTextField)
gbc.weightx = 0.5
gbc.gridx = 3
gbc.anchor = GridBagConstraints.LINE_END
gbc.insets = Insets (5,0,5,20)
buttonAndReadoutPanel.add (dismissButton, gbc)
panel.add (buttonAndReadoutPanel, BorderLayout.SOUTH)
toolbar = JToolBar ()
panel.add (toolbar, BorderLayout.NORTH)
#toolbar.add (JButton ('Add Data Source', actionPerformed=self.addSource))
self.loadSelectedConditionsButton = JButton (actions.IconFactory.getLoadSelectedConditionsIcon(),
actionPerformed=self.loadSelectedConditions)
self.loadSelectedConditionsButton.setBackground(Color.WHITE)
self.loadSelectedConditionsButton.setToolTipText('Load Selected Conditions')
self.loadSelectedConditionsButton.setEnabled (0)
toolbar.add (self.loadSelectedConditionsButton)
expandButton = JButton(actions.IconFactory.getExpandAndContractIcon(),
actionPerformed=self.expandContractDataBrowser)
expandButton.setToolTipText('Expand/Contract')
expandButton.setBackground(Color.WHITE)
toolbar.add (expandButton)
# Volcano plot button
volcanoPlotButton = JButton(actions.IconFactory.getVolcanoPlotterIcon(), actionPerformed=self.plot)
volcanoPlotButton.setToolTipText("Scatter Plotter")
volcanoPlotButton.setBackground(Color.WHITE)
toolbar.add (volcanoPlotButton)
return panel
class TreeDataBrowser (AbstractPlugin, TreeSelectionListener, WindowListener):
def __init__ (self, cytoscapeWindow=None):
self. dataDirectories = []
self.currentTreeSelection = []
self.dataMatrixBrowser = None
self.treeWidget = None
self.experimentNavigator = None
self.currentlySelectedExperiments = []
#repository = '/users/pshannon/data/halo/microarrayXml/sampleData/small'
#repository = 'file:///users/pshannon/cy/csplugins/isb/pshannon/experimentNavigator/sampleData/bat'
#repository = '/users/pshannon/data/halo/microarrayXml/FeSO4-2004.07.07'
#repository = 'file:///home/pshannon/data/halo/microarray/'
#repository = 'file://c:\halo\metals'
#repository = 'http://www.sewardpark.net/isb'
#repository = 'http://db:8060/halo/data/xmlv2'
#repository = 'http://db:8060/halo/data/test'
#repository = 'http://db.systemsbiology.net/cytoscape/projects/static/mjohnson/2004.oct'
#repository = 'file:///users/pshannon/data/halo/microarrayXml/tbpTfbKnockout'
#repository = 'http://db.systemsbiology.net:8060/halo/data/'
repository = 'httpIndirect://db.systemsbiology.net:8080/halo/DataFetcher.py'
self.dataDirectories.append (repository)
self.cytoscapeWindow = cytoscapeWindow
if (self.cytoscapeWindow):
menuItem = JMenuItem ('Data Browser & Chooser', actionPerformed=self.createFrame)
self.cytoscapeWindow.getOperationsMenu().add (menuItem)
else:
self.createFrame ()
#-------------------------------------------------------------------------------
def menuItemCreateFrame (self, event):
self.createFrame ()
#-------------------------------------------------------------------------------
def createFrameTitle (self):
id = '$Revision: 18 $'
signature = 'Revision: '
start = id.find (signature)
start += len (signature)
end = id.find (' $', start)
versionNumber = id [start:end]
return 'Data Matrix Browser %s' % versionNumber
#-------------------------------------------------------------------------------
def createFrame (self, event=None):
self.jframe = JFrame (title='%s' % self.createFrameTitle (), size = (800, 600))
self.jframe.setDefaultCloseOperation (JFrame.DISPOSE_ON_CLOSE)
self.jframe.addWindowListener (self)
self.currentDirectory = File (os.getcwd ())
self.experiments = {}
self.SEPARATOR = ': ' # used in listbox names, e.g., copper: concentration: 10
self.jframe.getContentPane().add (self.createGui ())
self.jframe.show ()
#------------------------------------------------------------------------------------------
def windowClosing (self, event):
self.dismiss (None)
#------------------------------------------------------------------------------------------
def windowClosed (self, event):
pass
def windowOpened (self, event):
pass
def windowIconified (self, event):
pass
def windowDeiconified (self, event):
pass
def windowActivated (self, event):
pass
def windowDeactivated (self, event):
pass
def windowGainedFocus (self, event):
pass
def windowLostFocus (self, event):
pass
#------------------------------------------------------------------------------------------
def createTreeNodes (self, root, hash):
kids = [x for x in hash.keySet().toArray ()]
if (isArrayOfNumbers (kids)):
kids.sort (lambda x, y: float(x) > float (y))
else:
kids.sort ()
for kid in kids:
newNode = DefaultMutableTreeNode (kid)
root.add (newNode)
self.createTreeNodes (newNode, hash [kid])
#-----------------------------------------------------------------------------------
def __updateCurrentTreeSelection (self, treeSelectionEvent):
"""
update class member variable 'currentTreeSelection' which holds a list
of TreePath's (a TreePath is an array of Objects (here, Strings)
specifying the tree branch. paths are either added or removed
"""
for p in treeSelectionEvent.getPaths ():
added = treeSelectionEvent.isAddedPath (p)
if (added):
self.currentTreeSelection.append (p)
else:
if (p in self.currentTreeSelection):
self.currentTreeSelection.remove (p)
#-----------------------------------------------------------------------------------
def __convertTreePathsToHash (self, treePaths):
# translate from, eg,
#
# [[Experiments, environmental, metals, FeSO4, time, -1],
# [Experiments, environmental, metals, FeSO4, time, 20]]
#
# to
#
# {'environmental:metals:FeSO4': ['time:-1', 'time:20']}
#
result = {}
for path in self.currentTreeSelection:
stringList = ['%s' % element for element in path.getPath ()]
if (len (stringList) <= 1):
return # the selection is simply the root of the tree, and
# we don't support selection of just the root
trimmedList = stringList [1:]
experimentKeys = \
self.experimentNavigator.findExperimentKeyForPerturbation (trimmedList)
for element in experimentKeys:
[experimentKey, condition] = element
#print 'experimentKey: %s condition: %s' % (experimentKey, condition)
if (not experimentKey in result.keys ()):
result [experimentKey] = []
list = result [experimentKey]
if (not condition in list):
list.append (condition)
result [experimentKey] = list
return result
#-----------------------------------------------------------------------------------
def valueChanged (self, treeSelectionEvent):
# respond to a change in the selection state of the treeWidget.
# the goal is to translate the current selection state of the JTree widget
# into selected conditions in all of the relevant experiements -- which are
# here actually MetaData objects. these MetaData objects originally supplied
# the JTree hierarchy. they also carry information about every observed condition
# in the experiment (typically a dosage level, or a point in a time course);
# any of these conditions may be selected, and that's the result we seek here:
# that all JTree selections are mirrored by selections in the MetaData objects
# these MetaData objects can then be used to create matrices that consist only
# of the selected columns (data columns are, in effect, experimental conditions)
self.__updateCurrentTreeSelection (treeSelectionEvent)
if (len (self.currentTreeSelection) == 0):
self.loadSelectedConditionsButton.setEnabled (0)
self.conditionCounterTextField.setText ('%s' % 0)
self.currentTreeSelection = []
for experiment in self.currentlySelectedExperiments:
experiment.clearSelectionCriteria ()
return
# there is at least one selection. translate the TreePath's
# into a hash.
self.loadSelectedConditionsButton.setEnabled (1)
selectedConditions = self.__convertTreePathsToHash (self.currentTreeSelection)
if (selectedConditions == None or len (selectedConditions) == 0):
self.loadSelectedConditionsButton.setEnabled (0)
self.conditionCounterTextField.setText ('%s' % 0)
self.currentTreeSelection = []
for experiment in self.currentlySelectedExperiments:
experiment.clearSelectionCriteria ()
return
self.currentlySelectedExperiments = []
selectedConditionCount = 0
for experimentKey in selectedConditions.keys ():
# the experiment key is just a convenenient form of the tree paths selected in
# the jtree. it might be an explicit, single experiment
# 'environmental:metals:FeSO4'
# or implicitly, a whole group of experiments
# 'environmental:metals'
# which implies FeSO4, cobalt, copper, iron, manganese, ...
experimentList = self.experimentNavigator.getExperimentByPerturbationList (experimentKey)
# now select conditions in each experiment
for experiment in experimentList:
experiment.clearSelectionCriteria ()
if (not experiment in self.currentlySelectedExperiments):
self.currentlySelectedExperiments.append (experiment)
conditions = selectedConditions [experimentKey]
experiment = self.__makeSelections (experiment, conditions)
selectedConditionCount += len (experiment.getSelectedConditionsAsAliases ())
self.conditionCounterTextField.setText ('%s' % selectedConditionCount)
#---------------------------------------------------------------------------------
def __makeSelections (self, experiment, conditions):
# selected conditions for the current experiment take several forms,
# directly reflecting how deeply into the JTree the user clicked
# treePath experimentKey conditions
# -------------------------- ------------------------- ----------
# environmental:metals:FeSO4 environmental:metals:FeSO4 null
# environmental:metals:FeSO4:time environmental:metals:FeSO4 time
# environmental:metals:FeSO4:time:-1 environmental:metals:FeSO4 time:-1
if (conditions == [None]):
experiment.selectAllConditions ()
else:
for conditionPairRaw in conditions:
conditionPair = conditionPairRaw.split (':')
if (len (conditionPair) == 1): # select all values for this condition
experiment.selectConditionByName (conditionPair [0])
elif (len (conditionPair) == 2):
name = conditionPair [0]
value = conditionPair [1]
experiment.addSelectionCriterion (name, value)
return experiment
#---------------------------------------------------------------------------------
def expandTree (self):
done = 0
while (not done):
rowCount = self.treeWidget.getRowCount ()
for r in range (rowCount, 0, -1):
self.treeWidget.expandRow (r)
if (rowCount == self.treeWidget.getRowCount ()):
done = 1
#---------------------------------------------------------------------------------
def createGui (self):
panel = JPanel ()
panel.setLayout (BorderLayout ())
chooserPanel = JPanel (); # JScrollPane (conditionsList)
chooserPanel.setLayout (BorderLayout ())
root = DefaultMutableTreeNode ('Experiments')
assert (len (self.dataDirectories) >= 1)
self.experimentNavigator = MetaDataNavigator (self.dataDirectories [0])
experimentsTree = self.experimentNavigator.getTree ()
#print 'experimentTree: %s' % experimentsTree
self.createTreeNodes (root, experimentsTree)
self.treeWidget = JTree (root)
#tree.setRootVisible (0)
self.treeWidget.getSelectionModel().setSelectionMode (
TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION)
self.treeWidget.addTreeSelectionListener (self)
treePane = JScrollPane (self.treeWidget)
treePanel = JPanel ()
treePanel.setLayout (BorderLayout ())
treePanel.add (treePane, BorderLayout.CENTER)
self.resultsPanel = JPanel ()
self.resultsPanel.setLayout (BorderLayout ())
self.outerSplitPane = JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
treePanel,
self.resultsPanel)
self.outerSplitPane.setDividerLocation (200)
self.outerSplitPane.setOneTouchExpandable (1)
self.dataBrowserHasEntireWindow = 0
panel.add (self.outerSplitPane, BorderLayout.CENTER)
dismissButton = JButton (actions.IconFactory.getDismissIcon(), actionPerformed=self.dismiss)
dismissButton.setBackground(Color.WHITE)
dismissButton.setToolTipText('Close This Window')
buttonAndReadoutPanel = JPanel ()
buttonAndReadoutPanel.setLayout (GridBagLayout ())
gbc = GridBagConstraints ()
gbc.gridx = 0
gbc.gridy = 0
gbc.weightx = 1.0
gbc.anchor = GridBagConstraints.LINE_START
gbc.insets = Insets (5,20,5,0)
selectionPanel = JPanel ()
buttonAndReadoutPanel.add (selectionPanel, gbc)
label = JLabel ('Explicit Selection Count: ')
selectionPanel.add (label)
self.conditionCounterTextField = JTextField (5)
selectionPanel.add (self.conditionCounterTextField)
gbc.weightx = 0.5
gbc.gridx = 3
gbc.anchor = GridBagConstraints.LINE_END
gbc.insets = Insets (5,0,5,20)
buttonAndReadoutPanel.add (dismissButton, gbc)
panel.add (buttonAndReadoutPanel, BorderLayout.SOUTH)
toolbar = JToolBar ()
panel.add (toolbar, BorderLayout.NORTH)
#toolbar.add (JButton ('Add Data Source', actionPerformed=self.addSource))
self.loadSelectedConditionsButton = JButton (actions.IconFactory.getLoadSelectedConditionsIcon(),
actionPerformed=self.loadSelectedConditions)
self.loadSelectedConditionsButton.setBackground(Color.WHITE)
self.loadSelectedConditionsButton.setToolTipText('Load Selected Conditions')
self.loadSelectedConditionsButton.setEnabled (0)
toolbar.add (self.loadSelectedConditionsButton)
expandButton = JButton(actions.IconFactory.getExpandAndContractIcon(),
actionPerformed=self.expandContractDataBrowser)
expandButton.setToolTipText('Expand/Contract')
expandButton.setBackground(Color.WHITE)
toolbar.add (expandButton)
# Volcano plot button
volcanoPlotButton = JButton(actions.IconFactory.getVolcanoPlotterIcon(), actionPerformed=self.plot)
volcanoPlotButton.setToolTipText("Scatter Plotter")
volcanoPlotButton.setBackground(Color.WHITE)
toolbar.add (volcanoPlotButton)
return panel
#---------------------------------------------------------------------------------
def combineSelectedConditions (self):
"""
create a single matrix from all of the selected columns in
all selected experiments
"""
if (len (self.currentlySelectedExperiments) == 0):
return
allSelectedMatrices = {}
for experiment in self.currentlySelectedExperiments:
name = experiment.getTitle ()
#print ' checking experiment with name %s' % name
columnNames = experiment.getSelectedConditionsAsAliases ()
#print '%s: columnNames: %s' % (name, columnNames)
if (len (columnNames) > 0):
slicer = datamatrix.MatrixSlicer (experiment)
slicedMatrices = slicer.slice () # there may be one, two, or more...
#print 'slicer returned %d matrices: ' % len (slicedMatrices)
matrixTypes = [x for x in slicedMatrices.keySet().toArray ()]
for type in matrixTypes:
m = slicedMatrices [type]
#print 'matrix shape: %d x %d' % (m.getColumnCount (), m.getRowCount ())
#print 'colum names: %s' % m.getColumnTitles ()
if (not allSelectedMatrices.has_key (type)):
allSelectedMatrices [type] = []
allSelectedMatrices [type].append (m)
finalMatrices = []
for type in allSelectedMatrices.keys ():
combiner = datamatrix.MatrixCombiner (allSelectedMatrices [type])
combinedMatrix = combiner.combine ()
combinedMatrix.setShortName (type)
finalMatrices.append (combinedMatrix)
return finalMatrices
#---------------------------------------------------------------------------------
def expandContractDataBrowser (self, event):
if (self.dataBrowserHasEntireWindow):
lastLocation = self.outerSplitPane.getLastDividerLocation ()
self.outerSplitPane.setDividerLocation (lastLocation)
self.dataBrowserHasEntireWindow = 0
else:
self.outerSplitPane.setDividerLocation (0)
self.dataBrowserHasEntireWindow = 1
#---------------------------------------------------------------------------------
def plot (self, event):
if (self.dataMatrixBrowser == None):
return
matrices = self.dataMatrixBrowser.getMatrices ()
if (not len (matrices) == 2):
return
plotController = PlotControllerListBox (matrices)
#---------------------------------------------------------------------------------
def loadSelectedConditions (self, event):
matrices = self.combineSelectedConditions ()
if (matrices == None or len (matrices) == 0):
return
if (self.dataMatrixBrowser):
for matrix in matrices:
#print 'adding matrix to *PRE-EXISTING* dataMatrixBrowser'
self.dataMatrixBrowser.addMatrixToGui (matrix)
else:
#print 'creating *NEW* dataMatrixBrowser'
self.dataMatrixBrowser = gui.DataMatrixBrowser (self.cytoscapeWindow, matrices)
self.resultsPanel.add (self.dataMatrixBrowser, BorderLayout.CENTER)
self.resultsPanel.paintAll (self.resultsPanel.getGraphics ())
#---------------------------------------------------------------------------------
def dismiss (self, event):
self.dataMatrixBrowser = None
self.jframe.dispose ()
#---------------------------------------------------------------------------------
def addSource (self, event):
chooser = JFileChooser (self.currentDirectory)
chooser.setFileSelectionMode (JFileChooser.DIRECTORIES_ONLY)
status = chooser.showOpenDialog (JFrame ())
if (status == JFileChooser.APPROVE_OPTION):
self.sourceDirectory = chooser.getSelectedFile()
directory = self.sourceDirectory.getPath ()
#self.sourcesList.getModel ().addElement (directory)
self.currentDirectory = chooser.getCurrentDirectory()
self.loadXmlFiles (directory)
#---------------------------------------------------------------------------------
def loadXmlFiles (self, source):
if (source.find ('http://') == 0):
fetcher = PasswordProtectedMetaDataFetcher (source)
fileHash = fetcher.getXmlFilesList ()
xmlFiles = fileHash.keys ()
else:
candidates = os.listdir (source)
#print 'candidates: %s' % candidates
xmlFiles = [f for f in candidates if f.count ('.xml') > 0]
if (len (xmlFiles) == 0):
return
xmlFiles.sort ()
for file in xmlFiles:
#print 'xmlFile: %s' % file
pathAsString = '%s/%s' % (source, file)
parser = ExperimentXmlParser (pathAsString)
self.experiments [parser.experiment.name] = parser.experiment
#print 'experiment count: %d' % len (self.experiments)
newExperimentNames = self.experiments.keys ()
newExperimentNames.sort ()
#existingExperimentNames = [n for n in self.sourcesList.getSelectedValues ()]
#print 'existing: %s' % existingExperimentNames
for experimentName in newExperimentNames:
if (experimentName in existingExperimentNames):
continue
self.chooserList1.getModel ().addElement (experimentName)
#print '----------------- %s' % experimentName
experiment = self.experiments [experimentName]
