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SpectraViewer.py
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SpectraViewer.py
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#!/usr/bin/env python
"""
Author: Chris Mitchell (chris.mit7@gmail.com)
Copyright (C) 2012 Chris Mitchell
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import operator, os, re, xml.etree.cElementTree as etree, random, figureIons, sys, masses, itertools, time, math
from collections import OrderedDict
import pythomics.proteomics.parsers as fileIterators
from pythomics.proteomics.structures import ScanObject, PeptideObject
from PyQt4.QtCore import *
from PyQt4.QtGui import *
import pyqtgraph as pg
import SpecView, SettingsPanel
import numpy as np
import six
try:
range = xrange
except NameError:
range = range
#some globals for us
fileNames = {}
titleParse = re.compile('(.+?)\.\d+\.\d+\.\d+|\w+')
SCAN_MAP = {}
FILE_MAP = {}
def loadConfig():
try:
config = etree.ElementTree(file='spectraConf.xml')
except IOError:#doesn't exist
return
root = config.getroot()
losses = root.find('LossMasses')
for child in losses:
loss = []
for mass, frags, display in zip(child.findall('Mass'),child.findall('Fragments'), child.findall('Display')):
if mass.text and frags.text and display.text:
loss.append((float(mass.text),tuple(frags.text.split(',')),display.text))
loss = tuple(loss)
masses.lossMasses[child.text] = loss
def saveConfig():
root = etree.Element('SpectraViewerConfig')
losses = etree.SubElement(root,'LossMasses')
for aa in masses.lossMasses:
info = masses.lossMasses[aa]
nl = etree.SubElement(losses,'AminoAcid')
nl.text = aa
for mass,fragments,display in info:
nm = etree.SubElement(nl,'Mass')
nm.text = str(mass)
nf = etree.SubElement(nl,'Fragments')
nf.text = ','.join(fragments)
nd = etree.SubElement(nl,'Display')
nd.text = display
elTree = etree.ElementTree(root)
elTree.write('spectraConf.xml', xml_declaration=True)
def toFloat(v):
try:
return float(y)
except Exception:
return False
SORT_FUNCS = {
str: lambda x,y: float(x)<float(y) if toFloat(x) and toFloat(y) else x<y,
float: lambda x,y: float(x) < float(y),
int: lambda x,y: int(x) < int(y),
}
class SortableTreeWidgetItem(QTreeWidgetItem):
def __lt__(self, other):
tree = self.treeWidget()
column = tree.sortColumn()
return SORT_FUNCS[tree.sort_funcs[column]](self.text(column).lower(), other.text(column).lower())
class FileObject(object):
def __init__(self, path):
self.path = path
self.scanMap = {}
self.titleRegex = None
pepSpecType = ('pep.xml', 'xml', 'msf', 'dat')
specType = ('mgf', 'mzml')
self.groupBy = 1
self.idColumn = 0
fileTypes = [i for i in pepSpecType if path.lower().endswith(i)]
if any(fileTypes):
fileType = fileTypes[0]#this changes based on the file input somewhat
self.colnames = OrderedDict([("Scan Title",(str,'id',1)), ("Peptide",(str,'peptide',1)), ("Modifications",(str,'getModifications',0)), ("Charge",(int,'charge',1)), ("Accession",(str, 'acc',1))])
if fileType == 'pep.xml':
self.iObj = fileIterators.PepXMLIterator(path)
self.colnames['Expect'] = (float,'expect',1)
elif fileType == 'xml':
self.iObj = fileIterators.XTandemXMLIterator(path)
self.colnames['Expect'] = (float,'expect',1)
elif fileType == 'dat':
self.iObj = fileIterators.MascotDATIterator(path)
self.colnames['Hit Id'] = (int,'hit',1)
self.colnames['Rank'] = (int,'rank',1)
elif fileType == 'msf':
self.iObj = fileIterators.ThermoMSFIterator(path)
self.colnames['Spectrum ID'] = (int, 'spectrumId',1)
self.idColumn = 5
self.colnames['Confidence Level'] = (int, 'confidence',1)
self.colnames['Search Engine Rank'] = (int, 'rank',1)
self.colnames["RT"] = (float,'rt',1)
elif [i for i in specType if path.lower().endswith(i)]:
fileType = [i for i in specType if path.lower().endswith(i)][0]
if fileType == 'mzml':
self.colnames = OrderedDict([("Scan Title",(str,'title',1)), ("MS Level",(int,'ms_level',1)), ("Charge",(int,'charge',1)), ("RT",(float,'rt',1)), ("Precursor Mass",(str,'mass',1))])
self.iObj = fileIterators.MZMLIterator(path)
else:
self.colnames = OrderedDict([("Scan Title",(str,'title',1)), ("Charge",(int,'charge',1)), ("RT",(float,'rt',1)), ("Precursor Mass",(str,'mass',1))])
self.iObj = fileIterators.MGFIterator(path, random=True)
self.groupBy = 0
else:
self.colnames = ["none"]
def getChromatogram(self):
return self.iObj.getChromatogram()
def getBaseTrace(self):
return self.iObj.getChromatogram()
def getScan(self, treeItem):
try:
scan = self.scanMap[id(treeItem)]
except Exception:
scanTitle = treeItem.data[self.idColumn]
if self.titleRegex:
title = self.titleRegex.search(scanTitle)
if title:
scanTitle = title.group(1)
peptide = treeItem.data[1]
# print scanTitle, peptide, type(self.iObj)
scan = self.iObj.getScan(scanTitle, peptide=peptide)
# convert the scans to numpy arrays
scan.scans = np.array(scan.scans)
# try:
# scan.ms1_scan.scans = np.array(scan.ms1_scan.scans)
# except:
# pass
self.scanMap[id(treeItem)] = scan
# print scan
return scan
class LoaderThread(QThread):
"""
thread to load files
"""
def __init__(self, parent, files):
QThread.__init__(self, parent)
self.parent = parent
self.files = files
self.data = {}
self.objMap = {}
self.connect(self, SIGNAL('finished()'), self.parent.threadReturn)
def run(self):
self.its = []
for fileindex,path in enumerate(self.files):
iterObj = FileObject(path)
if path not in FILE_MAP:
FILE_MAP[path] = iterObj
self.its.append(iterObj)
self.colnames = iterObj.colnames
if not self.colnames:
self.emit(SIGNAL('fileDone'),fileindex,len(self.files))
return
self.groupBy = iterObj.groupBy
added = set([])
for i in iterObj.iObj:
if not i or i in added:
continue
added.add(i)
try:
self.emit(SIGNAL('updateProgress'), iterObj.iObj.getProgress())
except AttributeError:
pass
toAdd = tuple(getattr(i,j[1]) if j[2] else getattr(i,j[1])() for j in self.colnames.values())
if toAdd in added:
continue
added.add(toAdd)
nid = toAdd[self.groupBy]#group on peptide by default
node = self.objMap.get(nid)
if node is None:
newNode = SortableTreeWidgetItem()
[newNode.setText(k,str(v)) for k,v in enumerate(toAdd)]
newNode.fileName = path
newNode.data = toAdd
newNode.subnodes = []
self.data[id(newNode)] = newNode
self.objMap[nid] = newNode
else:
newNode = SortableTreeWidgetItem(node)
[newNode.setText(k,str(v)) for k,v in enumerate(toAdd)]
newNode.fileName = path
newNode.data = toAdd
self.data[id(node)].subnodes.append(newNode)
self.emit(SIGNAL('fileDone'),fileindex,len(self.files))
class PeptidePanel(QDockWidget):
def __init__(self, parent):
super(PeptidePanel, self).__init__()
self.setWindowTitle("Peptide")
self.parent = parent
self.peptide = ""
self.sLen = len(self.peptide)
self.ions = []
self.errors = []
self.errorboxes = []
self.setMouseTracking(True)
def mouseMoveEvent(self, event):
x,y = int(event.x()),int(event.y())
for i in self.errorboxes:
if i.contains(x,y):
QToolTip.showText(self.mapToGlobal(i.center().toPoint()), i.ion)
def sizeHint(self):
return QSize(self.width(), 100)
def plotPeptide(self, pep, ions):
self.peptide = pep
self.sLen = len(pep)
self.revTypes = set([])
self.ions = [i[0] for i in ions]
self.errors = [i[1] for i in ions]
self.update()
def paintEvent(self, event):
"""
3/4 of left side is devoted to peptide, 1/4 of right is error measurement
"""
if not self.peptide:
return
qp = QPainter()
w,h = self.width()*9/10, self.height()
qp.begin(self)
qp.setPen(QColor(255,0,0))
font = QFont()
fm = QFontMetrics(font)
tpos=0
lx=0
ly=0
tw=0
th=0
fsize = 1
for i in self.peptide:
tsize = fm.size(Qt.TextSingleLine,i)
pw = tsize.width()
ph = tsize.height()
if pw > tw:
tw = pw
pp = i
if ph > th:
th = pw
pp = i
isize=1
font.setPointSize(isize)
fm = QFontMetrics(font)
tsize = fm.size(Qt.TextSingleLine,"10")
tw, th = tsize.width(),tsize.height()
while th < h*1/10:
isize+=1
font.setPointSize(isize)
fm = QFontMetrics(font)
tsize = fm.size(Qt.TextSingleLine,"10")
tw,th = tsize.width(),tsize.height()
ih=th
fsize=1
while (th*1.25+ih*2 <= h*1/2) and (tw*len(self.peptide) < w*1/2):
font.setPointSize(fsize)
fm = QFontMetrics(font)
try:
tsize = fm.size(Qt.TextSingleLine,pp)
tw,th = tsize.width(),tsize.height()
except IndexError:
break
fsize+=1
totalw = len(self.peptide)*tw
font.setPointSize(isize)
fm = QFontMetrics(font)
tsize = fm.size(Qt.TextSingleLine,"x")
ixw,ixh = tsize.width(),tsize.height()
tsize = fm.size(Qt.TextSingleLine,"y")
iyw,iyh = tsize.width(),tsize.height()
tsize = fm.size(Qt.TextSingleLine,"z")
izw,izh = tsize.width(),tsize.height()
tsize = fm.size(Qt.TextSingleLine,"a")
iaw,iah = tsize.width(),tsize.height()
tsize = fm.size(Qt.TextSingleLine,"b")
ibw,ibh = tsize.width(),tsize.height()
tsize = fm.size(Qt.TextSingleLine,"c")
icw,ich = tsize.width(),tsize.height()
cy = h/2
lx = w/2-totalw/2
toDraw = {}
sLen = self.sLen
for entry,error in zip(self.ions,self.errors):
fType = entry[2]
index = entry[3]
idesc = '%s%d%s'%(fType,index,entry[5]) if entry[5] else '%s%d'%(fType,index)
try:
toDraw[index].append((fType,error,idesc))
except KeyError:
toDraw[index] = [(fType,error,idesc)]
#draw our error line on the right (a black line up and down)
esize = self.width()/20
#"normalize" our error to the width so a delta of 0.0001 actually has pixels
escale = esize/self.parent.getTolerance()
elx = self.width()-2*esize
ely = (self.height()*9/10)/len(self.peptide)
qp.drawLine(QLineF(elx,0,elx,h))
#draw some axes for the top
qp.drawLine(QLineF(elx-esize,0,elx+esize,0))
font.setPointSize(isize)
qp.setFont(font)
tsize = fm.size(Qt.TextSingleLine,str(self.parent.getTolerance()))
tw,th = tsize.width(),tsize.height()
qp.drawText(QPointF(elx-esize-tw,th),str(self.parent.getTolerance()))
qp.drawText(QPointF(elx+esize,th),str(self.parent.getTolerance()))
for i,v in enumerate(self.peptide):
font.setPointSize(fsize)
qp.setFont(font)
fm = QFontMetrics(font)
tsize = fm.size(Qt.TextSingleLine,v)
tw,th = tsize.width(),tsize.height()
qp.setPen(QColor((0,0,0)))
qp.drawText(QPoint(lx-tw/2,cy), v)
if i==sLen-1:
break
font.setPointSize(isize)
qp.setFont(font)
qp.drawLine(QLineF(lx+tw/2,cy-th/2-ixh/2-iyh-izh,lx+tw/2,cy+th/2+iah+ibh+ich/2))
qp.setPen(QColor((255,0,255)))
ind = str(sLen-i-1)
fm = QFontMetrics(font)
tsize = fm.size(Qt.TextSingleLine,ind)
iw,ih = tsize.width(),tsize.height()
qp.drawText(QPoint(lx+tw/2,cy-ixh/2-iyh-izh-ih),ind)
qp.drawText(QPoint(lx+tw/2,cy+th/2+iah+ibh+ich/2),str(i+1))
try:
todraw = toDraw[i+1]
for fragType,error,errortype in todraw:
esize = error*escale
if fragType == 'a':
qp.setPen(QColor((255,0,0)))
ay = cy+th/2
qp.drawLine(QLineF(lx,ay,lx+tw/2,ay))
qp.setPen(QColor(255,0,0))
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
qp.drawText(QPoint(lx-iw/2,ay),"a")
elif fragType == 'b':
by = cy+th/2+iah
qp.setPen(QColor((255,0,0)))
qp.drawLine(QLineF(lx,by,lx+tw/2,by))
qp.setPen(QColor(255,0,0))
qp.drawText(QPoint(lx-iw/2,by), "b")
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
elif fragType == 'c':
cy2 = cy+th/2+iah+ibh
qp.setPen(QColor((255,0,0)))
qp.drawLine(QLineF(lx,cy2,lx+tw/2,cy2))
qp.setPen(QColor(255,0,0))
qp.drawText(QPoint(lx-iw/2,cy2), "c")
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
except KeyError:
pass
try:
todraw = toDraw[int(ind)]
for fragType,error,errortype in todraw:
esize = error*escale
if fragType == 'x':
#we're x/y/z ions, we go in reverse
xy = cy-th/2-izh-iyh
qp.setPen(QColor((0,0,255)))
qp.drawLine(QLineF(lx+tw,xy,lx+tw/2,xy))
qp.setPen(QColor(0,0,255))
qp.drawText(QPoint(lx+tw,xy),"x")
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
elif fragType == 'y':
#we're x/y/z ions, we go in reverse
yy = cy-th/2-ixh
qp.setPen(QColor((0,0,255)))
qp.drawLine(QLineF(lx+tw,yy,lx+tw/2,yy))
qp.setPen(QColor(0,0,255))
qp.drawText(QPoint(lx+tw,yy), "y")
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
elif fragType == 'z':
#we're x/y/z ions, we go in reverse
zy = cy-th/2
qp.setPen(QColor((0,0,255)))
qp.drawLine(QLineF(lx+tw,zy,lx+tw/2,zy))
qp.setPen(QColor(0,0,255))
qp.drawText(QPoint(lx+tw,zy), "z")
errorBox = QRectF(elx-esize,ely*(i+1),3,3)
qp.drawRect(errorBox)
errorBox.ion = errortype
self.errorboxes.append(errorBox)
except KeyError:
pass
lx+=tw+5
qp.end()
class CustomClick(object):
def mouseClickEvent(self, ev):
pass
class AUCText(pg.TextItem, CustomClick):
def __init__(self, *args, **kwargs):
super(AUCText, self).__init__(*args, **kwargs)
self.setAcceptHoverEvents(True)
self.text = kwargs.get('text', '')
self.color = kwargs.get('color', [1,1,1])
self.contextMenu = [QAction("Copy Value", self)]
self.contextMenu[0].triggered.connect(self.copyText)
def copyText(self):
print('do it')
def hoverEnterEvent(self, ev):
self.setText(text=self.text, color='r')
ev.ignore()
def hoverLeaveEvent(self, ev):
self.setText(text=self.text, color=self.color)
ev.ignore()
def mouseClickEvent(self, ev):
super(AUCText, self).mouseClickEvent(ev)
if ev.double():
self.line.hide()
self.hide()
class ChromatogramPanel(pg.PlotWidget):
def __init__(self, *args, **kwargs):
super(ChromatogramPanel, self).__init__(*args, **kwargs)
self.setBackground([255, 255, 255, 255])
self.chromatogram = None
self.controlDown = False
self.startPos = False
self.appended = False
self.plot = pg.PlotDataItem()
x = self.getAxis('bottom')
x.setPen('k')
y = self.getAxis('left')
y.setPen('k')
self.vb = self.getViewBox()
self.addItem(self.plot)
self.sceneObj.sigMouseMoved.connect(self.onMouseMove)
self.sceneObj.sigMouseClicked.connect(self.onMouseClick)
def keyPressEvent(self, event):
mods = event.modifiers()
if mods == Qt.ControlModifier:
self.controlDown = True
else:
self.controlDown = False
event.ignore()
def plotChromatogram(self, **kwargs):
x = np.array(kwargs.get('x', []))
y = np.array(kwargs.pop('y', []))
append = kwargs.pop('append', False)
print('append status',append)
if x.any() and y.any():
# self.clear()
# FIXME: make a failsafe against different x values
if append:
if self.appended:
y = self.y+y
else:
y = y
self.appended = True
self.plot.setData(x, y, pen=[0,0,0])
self.x, self.y = x,y
return
self.appended = False
if self.chromatogram is None:
return
# self.clear()
self.x = self.chromatogram.times
self.y = self.chromatogram.intensities
self.plot.setData(self.x, self.y, pen=[0,0,0])
# print self.chromatogram.times
def integrate(self, y_vals, h):
"""
Integration using simpson's rule
http://stackoverflow.com/questions/13320262/calculating-the-area-under-a-curve-given-a-set-of-coordinates-without-knowing-t
"""
i=1
total=y_vals[0]+y_vals[-1]
for y in y_vals[1:-1]:
if i%2 == 0:
total+=2*y
else:
total+=4*y
i+=1
return total*(h/3.0)
def onMouseClick(self, click):
if click.double():
self.plotChromatogram()
view_click = click.pos()
vcx, vcy = view_click.x(), view_click.y()
clicks = []
for i in self.items():
if not issubclass(type(i), CustomClick):
continue
pos = i.pos()
pos = self.vb.mapFromView(pos)
br = i.boundingRect()
br_w, br_h = br.width(), br.height()
x = pos.x()
if x < vcx < x+br_w:
y = pos.y()
if y < vcy < y+br_h:
clicks.append(i)
for i in clicks:
i.mouseClickEvent(click)
if self.controlDown:
if self.startPos:
#we have a start position and clicked again, so we're ending our line
self.controlDown = False
start_xy = self.mapToView(self.startPos.scenePos())
end_xy = self.mapToView(click.scenePos())
#we don't care about y
x1,y1 = start_xy.x(), start_xy.y()
x2, y2 = end_xy.x(), end_xy.y()
if x1 > x2:
x1, x2, y1, y2 = x2, x1, y2, y1
self.startPos = False
# get the area
x = []
y = []
overlay_y = []
slope = (y2-y1)/(x2-x1)
b = y1-slope*x1
for i,j in zip(self.x, self.y):
if x1 <= i <= x2:
x.append(i)
y_pos = slope*i+b
overlay_y.append(j)
if y_pos < 0:
y_pos = 0
if j >= y_pos:
y.append(j-y_pos)
else:
y.append(0)
# average delta
deltas = [a - x[i - 1] for i, a in enumerate(x)][1:]
gap = sum(deltas)/len(deltas)
if not gap:
area = sum(y)
else:
area = self.integrate(y, gap)
txt='AUC:%s'%area
self.annotate = AUCText(text = txt, color=[1,1,1])
self.annotate.line = self.chromLine
self.addItem(self.annotate)
self.annotate.setZValue(100)
self.annotate.setPos(end_xy.x(), end_xy.y())
# fill the curve
# self.overlay = pg.PlotDataItem()
# self.overlay.setData(x, overlay_y, pen=[1,1,1])
# self.addItem(self.overlay)
# self.fill = pg.FillBetweenItem(self.overlay, self.chromLine, brush='k')
# self.fill.setZValue(100)
# self.addItem(self.fill)
else:
self.chromLine = pg.PlotDataItem()
self.startPos = click
self.addItem(self.chromLine)
def onMouseMove(self,event):
if self.controlDown and self.startPos:
# draw a line from start to here
plot_xy = self.mapToView(self.startPos.scenePos())
x = [plot_xy.x()]
y = [plot_xy.y()]
plot_xy = self.mapToView(event)
x.append(plot_xy.x())
y.append(plot_xy.y())
self.chromLine.setData(x, y, pen=[1,1,1])
class MainWindow(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
self.setWindowTitle("Spectrum Viewer")
self._form = SpecView.Ui_MainWindow()
self._form.setupUi(self)
self._form.retranslateUi(self)
self.pepFiles = {}
self.mgfFiles = {}
self.gffFiles = {}
self.tabs = []
self.resize(1000,600)
self.setAcceptDrops(True)
#our menu
menu = self.menuBar()
self.filemenu = menu.addMenu('&File')
exitAction = QAction('Exit', self)
exitAction.triggered.connect(qApp.quit)
openAction = QAction('&Open', self)
openAction.triggered.connect(self.onOpen)
settingsAction = QAction('&Settings', self)
settingsAction.triggered.connect(self.onSettings)
self.filemenu.addAction(openAction)
self.filemenu.addAction(settingsAction)
self.filemenu.addAction(exitAction)
self.validExtensions = set(['.xml', '.msf', '.mgf', '.dat', '.mzml', '.gz'])
self._form.tabWidget.setTabsClosable(True)
self._form.tabWidget.tabCloseRequested.connect(self.onTabClose)
loadConfig()
self.connect(self,SIGNAL('triggered()'),self.closeEvent)
self.show()
def closeEvent(self, event):
saveConfig()
def settingsSave(self):
global dError
txt = self.dlg.defaultError.text()
if txt:
try:
dError = int(txt)
except ValueError:
pass
def addLoss(self):
aa = str(self.dlg.aaBox.currentText())
ions = []
if self.dlg.checkBoxa.checkState() == Qt.Checked: ions.append('a')
if self.dlg.checkBoxb.checkState() == Qt.Checked: ions.append('b')
if self.dlg.checkBoxc.checkState() == Qt.Checked: ions.append('c')
if self.dlg.checkBoxx.checkState() == Qt.Checked: ions.append('x')
if self.dlg.checkBoxy.checkState() == Qt.Checked: ions.append('y')
if self.dlg.checkBoxz.checkState() == Qt.Checked: ions.append('z')
loss = float(self.dlg.massLoss.text())
display = str(self.dlg.displayName.text())
if masses.lossMasses.has_key(aa):
closses = list(masses.lossMasses[aa])
else:
closses = set([])
if not closses.count((loss,tuple(ions),display)):
closses.append((loss,tuple(ions),display))
masses.lossMasses[aa] = tuple(closses)
# print masses.lossMasses[aa]
def onSettings(self, args):
self.dtmp = QDialog()
self.dlg = SettingsPanel.Ui_Dialog()
self.dlg.setupUi(self.dtmp)
self.connect(self.dlg.buttonBox, SIGNAL('accepted()'),self.settingsSave)
self.dlg.addLoss.pressed.connect(self.addLoss)
self.dtmp.show()
def isValidFile(self,name):
if os.path.splitext(str(name))[1].lower() in self.validExtensions:
return True
return False
def onOpen(self):
fileNames = list(QFileDialog.getOpenFileNames(self, 'Select File(s) To Open'))
files = [str(fileName) for fileName in fileNames if self.isValidFile(fileName)]
self.addPage(files)
def dragEnterEvent(self, event):
if event.mimeData().hasUrls:
event.accept()
else:
event.ignore()
def dropEvent(self, event):
if event.mimeData().hasUrls:
event.setDropAction(Qt.CopyAction)
event.accept()
files = [str(fileName.toLocalFile()) for fileName in event.mimeData().urls() if self.isValidFile(str(fileName.toLocalFile()))]
if (event.keyboardModifiers()&Qt.ControlModifier):
self.appendPage(files)
else:
self.addPage(files)
else:
event.ignore()
def appendPage(self, files):
#get current tab
self._form.tabWidget.currentWidget().appendFiles(files)
def addPage(self, files):
if not self._form.instructions.isHidden():
self._form.instructions.setHidden(True)
vt = ViewerTab(self, files)
self.tabs.append(vt)
if len(files)>1:
self._form.tabWidget.addTab(vt, '%d Merged Files'%len(files))
elif files:
self._form.tabWidget.addTab(vt, os.path.split(files[0])[1])
self._form.tabWidget.setCurrentWidget(vt)
vt.threadPage()
def onTabClose(self, tab):
self.tabs[tab].prepareDestruct()
self._form.tabWidget.removeTab(tab)
self.tabs.pop(tab)
if not self._form.tabWidget.count():
self._form.instructions.setHidden(False)
class LossPanel(QWidget):
"""
a panel to add neutral losses
"""
def __init__(self, parent):
pass
class ViewerTab(QMainWindow):
def __init__(self, parent, files):
super(ViewerTab, self).__init__()
self.parent = parent
self.data = {}
self.objMap = {}
self.skipLosses = {}
self.fileType = ""
self.files = files
def prepareDestruct(self):
del self.data
del self.objMap
# self.deleteLater()
def onClick(self, item, *args):
self.item = item
self.loadScan(FILE_MAP[item.fileName].getScan(item))
def onHeaderRC(self, pos):
gpos = self.mapToGlobal(pos)
menu = QMenu()
menu.addAction("Group By Column")
ty = self.tree.pos().y()
gpos.setY(gpos.y()+ty+self.tree.parent().pos().y())
selected = menu.exec_(gpos)#self.mapToParent(gpos))
if selected:
self.Group(self.tree.header().logicalIndexAt(pos))
def appendFiles(self, files):
self.LoadThread = LoaderThread(self, files)
self.files+=files
self.LoadThread.data = self.data
self.LoadThread.objMap = self.objMap
self.progress.show()
self.progressText.show()
self.onFileText.show()
self.connect(self.LoadThread, SIGNAL('updateProgress'), self.updateProgress)
self.connect(self.LoadThread, SIGNAL('fileDone'), self.fileDone)
self.LoadThread.start()
def threadPage(self):
self.progress = QProgressBar()
self.vl = QVBoxLayout(self.parent._form.tabWidget.currentWidget())
self.vl.setObjectName('vl')
self.progressText = QLabel()
self.progressText.setText("Loading Spectra File...MSF & DAT Files may take longer to start showing load status")
self.onFileText = QLabel()
self.onFileText.setText("Loading file 1 of %d"%len(self.files))
self.vl.addWidget(self.progressText, 0, Qt.AlignTop)
self.vl.addWidget(self.onFileText, 0, Qt.AlignTop)
self.vl.addWidget(self.progress, 15)
self.LoadThread = LoaderThread(self, self.files)
self.connect(self.LoadThread, SIGNAL('updateProgress'), self.updateProgress)
self.connect(self.LoadThread, SIGNAL('fileDone'), self.fileDone)
self.LoadThread.start()
def updateProgress(self, perc):
self.progress.setValue(perc)
def fileDone(self, i,j):
self.onFileText.setText('Loading file %d of %d'%(i+1,j))
def threadReturn(self):
#set up our page layout
# if hasattr(self, 'splitter'):
# iterObjects = self.LoadThread.its
# self.data = self.LoadThread.data
# self.objMap = self.LoadThread.objMap
# for it in iterObjects:
# if it.fileType == 'gff':
# self.parent.gffFiles[it.path] = it.iObj
# elif it.dataType == 'pepspectra' or it.fileType == 'xml' or it.fileType == 'msf' or it.fileType == 'dat':
# self.parent.pepFiles[it.path] = it.iObj
# elif it.fileType == 'spectra':
# self.parent.mgfFiles[it.path] = it.iObj
# if self.data:
# for i in self.data.keys():
# if not i.treeWidget():
# self.tree.addTopLevelItem(i)
# i.addChildren(self.data[i].subnodes)
# self.tree.setSortingEnabled(True)
# self.onFileText.hide()
# self.progress.hide()
# self.progressText.hide()
# return
# self.splitter = QSplitter()
# self.splitter.setChildrenCollapsible(True)
self.vl.removeWidget(self.progress)
self.vl.removeWidget(self.progressText)
# self.vl.addWidget(self.splitter)
self.progress.hide()
self.progressText.hide()
self.onFileText.hide()
self.vl.addWidget(self.onFileText)
self.vl.addWidget(self.progressText)
self.vl.addWidget(self.progress)
# self.splitter.setOrientation(Qt.Vertical)
# self.splitter.setParent(self)
# self.peptidePanelDock = QDockWidget()
self.peptidePanel = PeptidePanel(self)
# self.peptidePanelDock.setWidget(self.peptidePanel)
self.chromaPanel = ChromatogramPanel(self)
self.baseTracePanel = ChromatogramPanel(self)
self.ms2_draw = DrawFrame(self)
self.ms1_draw = DrawFrame(self)
self.searchBox = QLineEdit()
self.searchBox.editingFinished.connect(self.onSearch)
#search button
self.sbutton = QToolButton(self.searchBox)
self.sicon = QPixmap('icons/search.ico')
self.sbutton.setIcon(QIcon(self.sicon))
self.sbutton.setIconSize(self.sicon.size())
self.sbutton.setCursor(Qt.ArrowCursor)
self.sbutton.setStyleSheet("border: none; padding: 0px; ")
self.searchBox.setStyleSheet("padding-left: %dpx;"%(int(self.sicon.width())))
self.searchCols = QComboBox()
self.searchGroup = QWidget()
#filter box
self.filterBox = QLineEdit()
self.filterBox.editingFinished.connect(self.onFilter)
self.filterList = OrderedDict()
self.filterBoxes = []
#filter button
self.fbutton = QToolButton(self.filterBox)
self.ficon = QPixmap('icons/filter.ico').scaled(self.sicon.width(), self.sicon.height())
self.fbutton.setIcon(QIcon(self.ficon))
self.fbutton.setIconSize(self.ficon.size())
self.fbutton.setCursor(Qt.ArrowCursor)
self.fbutton.setStyleSheet("border: none; padding: 0px;")
self.filterBox.setStyleSheet("padding-left: %dpx;"%(int(self.ficon.width())))
#our close icon for filters
self.cicon = QPixmap('icons/close.ico')
self.searchGroupLayout = QGridLayout()
self.searchGroupLayout.addWidget(self.searchBox,0,1)
self.searchGroupLayout.addWidget(self.filterBox,0,2)
self.searchGroupLayout.addWidget(self.searchCols,0,3)
self.filterBoxLayout = QHBoxLayout()
self.searchGroupLayout.addLayout(self.filterBoxLayout,1,1,1,4,Qt.AlignLeft)
self.searchGroup.setLayout(self.searchGroupLayout)
dock = QDockWidget("Chromatography")
dock.setWidget(self.chromaPanel)
self.addDockWidget(Qt.RightDockWidgetArea, dock)
self.addDockWidget(Qt.RightDockWidgetArea, self.peptidePanel)
self.tabifyDockWidget(self.peptidePanel, dock)
base_dock = QDockWidget("Base Trace")
base_dock.setWidget(self.baseTracePanel)
self.addDockWidget(Qt.RightDockWidgetArea, base_dock)
self.tabifyDockWidget(dock, base_dock)
dock = QDockWidget("MS2")
dock.setWidget(self.ms2_draw)
self.ms2_draw.dock = dock
ms1dock = QDockWidget("MS1")
ms1dock.setWidget(self.ms1_draw)
self.ms1_draw.dock = ms1dock
self.addDockWidget(Qt.RightDockWidgetArea, dock)
self.addDockWidget(Qt.RightDockWidgetArea, ms1dock)
self.tabifyDockWidget(dock, ms1dock)
dock = QDockWidget("Searching and Filtering")
dock.setWidget(self.searchGroup)
self.addDockWidget(Qt.RightDockWidgetArea, dock)
# self.splitter.addWidget(self.chromaPanel)
# self.splitter.addWidget(self.peptidePanelDock)
# self.splitter.addWidget(self.draw)
# self.splitter.addWidget(self.searchGroup)#search box
self.tree = QTreeWidget()
dock = QDockWidget("Mass Spectra Table")
dock.setWidget(self.tree)
self.addDockWidget(Qt.RightDockWidgetArea, dock)
# self.splitter.addWidget(self.tree)
self.tree.header().setContextMenuPolicy(Qt.CustomContextMenu)
self.tree.header().customContextMenuRequested.connect(self.onHeaderRC)
self.tree.itemDoubleClicked.connect(self.onClick)
self.tree.currentItemChanged.connect(self.onClick)
self.groupBy = self.LoadThread.groupBy
self.colnames = self.LoadThread.colnames
self.tree.sort_funcs = [v[0] for i,v in six.iteritems(self.colnames)]
self.searchCols.addItems(list(self.colnames.keys()))
if self.chromaPanel.chromatogram is None:
for iterObj in self.LoadThread.its:
chroma = iterObj.getChromatogram()
if chroma:
self.chromaPanel.chromatogram = chroma
self.chromaPanel.plotChromatogram()
break
bt = iterObj.getBaseTrace()
if bt:
self.baseTracePanel.chromatogram = bt
self.baseTracePanel.plotChromatogram()
break
self.searchCols.setCurrentIndex(self.groupBy)
self.objMap = self.LoadThread.objMap
self.data = self.LoadThread.data
self.tree.setColumnCount(len(self.colnames))
self.tree.setHeaderLabels(list(self.colnames.keys()))
if self.data:
self.tree.addTopLevelItems(list(self.data.values()))
for node in self.data.values():
node.addChildren(node.subnodes)
self.tree.setSortingEnabled(True)
def recurseTree(self, itemList, item):
itemList[id(item)] = item
for i in range(item.childCount()):
self.recurseTree(itemList, item.child(i))
def onFilter(self):
"""
the stored filter list contains items that were filtered out
"""
filterTerm = self.filterBox.text()
if not filterTerm:
return
col = self.searchCols.currentIndex()
items = {id(i): i for i in self.tree.findItems(filterTerm,Qt.MatchRecursive|Qt.MatchContains,column=col)}
allItems = {}
for i in range(self.tree.topLevelItemCount()):
self.recurseTree(allItems, self.tree.topLevelItem(i))
#we have all items, and we want to remove those matching our filter -- the resulting list is who to hide
toHide = set(allItems.keys())-set(items.keys())
if (filterTerm,col) in self.filterList:
return
self.filterList[(filterTerm,col)] = {i: allItems[i] for i in toHide}
if toHide:
for i, v in six.iteritems(self.data):
v.subnodes.insert(0, v)
for subnode in v.subnodes:
if not subnode.isHidden() and id(subnode) in toHide:
subnode.setHidden(True)
v.subnodes.pop(0)
newFilter = QPushButton()
newFilter.setText('%s on %s'%(filterTerm, self.searchCols.itemText(col)))
newFilter.setIcon(QIcon(self.cicon))
newFilter.setStyleSheet("image-position: right")
newFilter.setLayoutDirection(Qt.RightToLeft)
newFilter.connect(newFilter, SIGNAL("clicked()"), lambda fbutton=newFilter,fterm=filterTerm,fcol=col: self.onFilterClick(fbutton,fterm,fcol))
spol = QSizePolicy(QSizePolicy.Fixed,QSizePolicy.Fixed)
newFilter.setSizePolicy(spol)
self.filterBoxes.append(newFilter)
self.filterBoxLayout.addWidget(newFilter)
def onFilterClick(self, fbut,fterm,fcol):
fbut.deleteLater()
filterKey = (fterm,fcol)
# items filtered out by the current selection