This file is indexed.

/usr/lib/python2.7/dist-packages/pymzml/plot.py is in python-pymzml 0.7.6-dfsg-4.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
# -*- coding: utf-8 -*-
# encoding: utf-8
"""
Plotting functions for pymzML
"""

# pymzml
#
# Copyright (C) 2010-2011 T. Bald, J. Barth, A. Niehues, C. Fufezan
#
#    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/>.

from __future__ import print_function
import math
import sys
import collections


class Factory(object):
    """
    Class to plot pymzml.spec.Spectrum as svg/xhtml.

    :param filename: Name for the output file. Default = "spectra.xhtml"
    :type filename: string

    Example:

    >>> import pymzml, get_example_file
    >>> mzMLFile = 'profile-mass-spectrum.mzml'
    >>> example_file = get_example_file.open_example(mzMLFile)
    >>> run = pymzml.run.Run("../mzML_example_files/"+mzMLFile, precisionMSn = 250e-6)
    >>> p = pymzml.plot.Factory()
    >>> for spec in run:
    >>>     p.newPlot()
    >>>     p.add(spec.peaks, color=(200,00,00), style='circles')
    >>>     p.add(spec.centroidedPeaks, color=(00,00,00), style='sticks')
    >>>     p.add(spec.reprofiledPeaks, color=(00,255,00), style='circles')
    >>>     p.save( filename="output/plotAspect.xhtml" , mzRange = [745.2,745.6] )

    """

    def __init__(self, filename = None):
        self.filename = filename if filename != None else "spectra.xhtml"
        self.plots = [  ]     # list of plots, where each plot hold a list of mz-i lists that should be plotted in the same plot
        self.styles = [  ]
        self.colors = [  ]
        self.opacities = [  ]
        self.header = [  ]
        self.labelPos = [  ]
        self.mzRanges = [  ]
        self.normalizations = [ ]
        self.additionalLegend = None
        self.imax = None
        pass

    def newPlot(self, header = None , mzRange = [None,None] , normalize = False):
        """
        Add new plot to the plotFactory.

        :param header: an optional title that will be printed above the plot
        :type header: string
        :param mzRange: Boundaries of the new plot
        :type mzRange: tuple of minMZ,maxMZ
        :param normalize: whether or not the individal data sets are normalized in the plot
        :type boolean:


        """
        self.plots.append( [] )
        self.styles.append( [] )
        self.colors.append( [] )
        self.opacities.append([])
        self.labelPos.append( set() )
        self.mzRanges.append( mzRange )
        self.normalizations.append( normalize )
        if header == None:
            self.header.append( '' )
        else:
            self.header.append( header )
        return

    def setAdditionalLegend( self, listOfStrings = None):
        """
        Add Legend to the plot.

        :param listOfStrings: Extra Legend to the plot
        :type listOfStrings: list of string

        """
        self.additionalLegend = listOfStrings
        return


    def add(self,data, color=(00,00,00) , style = 'sticks', mzRange = [None,None], opacity = 0.4 ):
        """
        Add data to the graph.

        :param data: The data added to the graph
        :type data: list of tuples (mz,i)
        :param color: color encoded in RGB. Default = (0,0,0)
        :type color: tuple (R,G,B)
        :param style: plotting style. Default = "circles".
        :type style: string
        :param mzRange: Boundaries that should be added to the current plot
        :type mzRange: tuple of minMZ,maxMZ

        Currently supported styles are:
            *   'emptycircles'
            *   'circles'
            *   'sticks'
            *   'squares'
            *   'area'
            *   'triangle'
            *   'label'

        NOTE: The data format for label style is [( mz1, 'label1' ), ( mz2, 'label2' ), ( mz3, 'label3' ) ].
        """
        if len(self.plots) == 0:
            self.newPlot()
        self.styles[-1].append(style)
        self.colors[-1].append(color)
        self.opacities[-1].append(opacity)
        selective = True
        if mzRange == [None,None]:
            if self.mzRanges[-1] == [None,None]:
                selective = False
                self.plots[-1].append(data)
            else:
                mzRange = self.mzRanges[-1]
        else:
            self.mzRanges[-1] = mzRange
            # NOTE this allows us to define the mzRange in the call of the add function, otherwise it has to be in the call of the new function
            # NOTE Problem can be: mzRanges[-1] can be overwritten ... don't know what is best here
        if selective:
            self.plots[-1].append([(mz,i) for mz,i in data if mzRange[0] <= mz <=mzRange[1]])
        #print("Added {0} data points".format(len(self.plots[-1][-1])))
        return

    def info(self):
        """
        Returns summary about the plotting factory, i.e.how many plots and how many datasets per plot.
        """
        print("""
        Factory holds {0} unique plots""".format(len(self.plots)))
        for i,plot in enumerate(self.plots):
            print("                Plot {0} holds {1} unique datasets".format(i,len(plot)))
            for j,dataset in enumerate(plot):
                print("                  Dataset {0} holds {1} datapoints".format(j,len(dataset)))

        print()
        return

    def save(self, filename = None, mzRange = [None,None], pureSvg = False):
        """
        Saves all plots and their data points that have been added to the plotFactory.

        :param filename: Name for the output file. Default = "spectra.xhtml"
        :type filename: string
        :param mzRange: m/z range which should be considered [start, end]. Default = [ ``None`` , ``None`` ]
        :type mzRange: list
        """
        if filename == None:
            filename = self.filename

        io = open("{0}".format(filename), 'w' )
        # NOTE: we need to check if file exists and/or if file can be written ...
        if pureSvg == False:
            print("""<html xmlns="http://www.w3.org/1999/xhtml">
            <head>
            <title>pymzml spectrum visualisation</title>
            <style>
            </style>
            </head>
            <body style="position:relative; z-index:0; width:100%; height:100%;">

            """, file = io)
        for plotNumber,plot in enumerate(self.plots):
            w = 1200
            h = 2100
            heada = self.header[plotNumber]
            resolved_mzRange = [ None, None ]

            if mzRange != [ None, None ]:
                resolved_mzRange = mzRange

            else:
                if self.mzRanges[plotNumber] == [None,None]:
                    # we have to determine ranges ...
                    for dataset in plot:
                        # print("Determing mzRanges ...")
                        if len(dataset) == 0:
                            continue

                        if resolved_mzRange[0] == None:
                            resolved_mzRange[0] = min(dataset)[0]
                        else:
                            if resolved_mzRange[0] > min(dataset)[0]:
                                resolved_mzRange[0] = min(dataset)[0]

                        if resolved_mzRange[1] == None:
                            resolved_mzRange[1] = max(dataset)[0]
                        else:
                            if resolved_mzRange[1] < max(dataset)[0]:
                                resolved_mzRange[1] = max(dataset)[0]
                else:
                    # Ranges have been defined by newPlot()
                    # i.e we want to plot no matter what ...
                    resolved_mzRange = self.mzRanges[plotNumber]

            if resolved_mzRange == [None,None]:
                print("Skipping empty plot, plotNumber {0} , header :{1} ...".format(plotNumber,heada))
                continue

            i_max = 0
            i_min = 0
            for dataset in plot:
                for mz,i in dataset:
                    if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
                        try:
                            i = float(i)
                        except:
                            continue
                        if i >= i_max:
                            i_max = i
            if i_max == 0:
                i_max = 0.1
            if self.imax != None:
                i_max = self.imax

            if self.normalizations[plotNumber] == True:
                resolved_i_max = 1.05
            else:
                resolved_i_max = i_max * 1.05
            print("""
            <svg xmlns="http://www.w3.org/2000/svg" version="1.1"
            width="{w}" height="{h}"
            style="position:relative; top:0; left:0; z-index:-1;">
            """.format(w = w + 300, h = h ), file = io)
            PADDING = (300,250,1400,50) # css style convention
            baseline = h-PADDING[2]

            # Drawing Frame ...
            for x1,y1,x2,y2 in [    (PADDING[3],PADDING[0],w-PADDING[1],PADDING[0]),
                                    (w-PADDING[1],PADDING[0],w-PADDING[1],h-PADDING[2]),
                                    (PADDING[3],h-PADDING[2],w-PADDING[1],h-PADDING[2]),
                                    (PADDING[3],PADDING[0],PADDING[3],h-PADDING[2]),
            ]:
                print("""<line x1="{0}" y1="{1}" x2="{2}" y2="{3}"
                style="stroke:rgb(00,00,00);stroke-width:1"/>""".format(x1,y1,x2,y2),file=io)

            if heada != '':
                heada_y = 30
                for subheada in heada.split("\n"):
                    print("""<text x="{x}" y="{y}" font-family="Courier" text-anchor="start" font-size="{fontsize}" fill="black" >{0}</text>
                        """.format(subheada, x = 0, y = heada_y, fontsize = 24), file = io)
                    heada_y += 30
            pixelpermz = float( w - PADDING[1] - PADDING[3] ) / float(resolved_mzRange[1]-resolved_mzRange[0]) # NOTE this returns ZeroDivisionError if the range to plot contains only one peak
            pixelper_i = float( h - PADDING[0] - PADDING[2] ) / float(resolved_i_max-i_min)
            delta = resolved_mzRange[1]-resolved_mzRange[0]
            sep = round(math.log(delta,10))
            factor = 10**(-1*(sep-1))

            # grid
            # Drawing ticks and x labels
            for _ in range(int(round(resolved_mzRange[0]*factor)),int(round(resolved_mzRange[1]*factor))+1 ):
                x = int(round(PADDING[3]  +   (float(_)/float(factor) - resolved_mzRange[0] ) * pixelpermz   ))
                y = baseline
                color = 77 #if _ % 10 == 0 else 125
                # Dashed lines
                # print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
                # style="stroke-dasharray: 9, 5;stroke:rgb({3},{3},{3});stroke-width:0.5"/>""".format(x,PADDING[0],baseline,color),file=io)
                print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
                style="stroke:rgb(00,00,00);stroke-width:0.5;"/>""".format(x,baseline,baseline+10),file=io)
                print("""<text x="{x}" y="{y}" transform="rotate(90 {x},{y})" font-family="Courier" text-anchor="start" font-size="{fontsize}" fill="black" >{0:7.3f}</text>
                    """.format(float(_)/float(factor), x = x, y = y + 30, fontsize = 12), file = io)

            # Drawing data points .. labels first
            LabelsNotToBePlottedTwice = set()
            for datasetnumber,dataset in enumerate(plot):
                r,g,b = self.colors[plotNumber][datasetnumber]
                style = self.styles[plotNumber][datasetnumber]
                opacity = self.opacities[plotNumber][datasetnumber]

                if style[:5] == 'label':
                    for pos,(mz,i) in enumerate(dataset):
                        if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
                            x = int(round(PADDING[3]  +   (mz - resolved_mzRange[0] ) * pixelpermz   ))
                            y = baseline
                            y2 = baseline - (resolved_i_max * pixelper_i)

                            x3 = round(x,-1)
                            if style.upper().endswith('X1'):
                                y3 = round(y+10)
                                sign = 1
                                stroke_width = 0.50
                            else:
                                y3 = round(y2)
                                sign = -1
                                stroke_width = 0.30
                            layers = 15
                            while (x3,y3) in self.labelPos[plotNumber]:
                                y3 = y3 + sign * 15
                                layers -= 1
                                if layers <= 0:
                                    break

                            if (mz, i) in LabelsNotToBePlottedTwice:
                                continue

                            print('''
                                    <g id="Label{0}">
                                        <title>{1} {2}</title>
                            '''.format( pos, mz, i ), file = io)
                            LabelsNotToBePlottedTwice.add( (mz,i) )
                            print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
                            style="stroke-opacity: 0.6;stroke:rgb({r},{g},{b});stroke-width:{o};" />""".format(x, y, y2, o=stroke_width, r=r,g=g,b=b),file=io)

                            self.labelPos[plotNumber].add((x3,y3))
                            self.labelPos[plotNumber].add((x3+10,y3 + sign * 15))

                            print("""<text x="{x}" y="{y}" transform="rotate({angle} {x},{y})" font-family="Courier" text-anchor="start" font-size="{fontsize}" style="fill:rgb({r},{g},{b});" >{0}</text>
                                """.format(i, x = x, y = y3, fontsize = 10, angle = sign * 45 , r = r, g = g, b = b), file = io)
                            print('</g>', file = io)
                    # print( LabelsNotToBePlottedTwice )
                elif style[:5] == 'area':
                    if self.normalizations[plotNumber] == True:
                        maxI = max([ i for mz,i in dataset ])
                    else:
                        maxI = None

                    first = True
                    for pos,(mz,i) in enumerate(sorted(dataset)):
                        if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
                            x = int(round(PADDING[3]  +   (mz - resolved_mzRange[0] ) * pixelpermz   ))
                            if self.normalizations[plotNumber] == True:
                                y = baseline - ((float(i)/float(maxI)) * pixelper_i)
                            else:
                                y = baseline - (i * pixelper_i)

                            if first:
                                print('<path d="M{0} {2} L{0} {1}'.format(x,y,baseline), end=" ", file = io)
                                first = False
                            else:
                                print('L{0} {1}'.format(x,y ), end=" ", file = io)
                    if first == False:
                        # aka we have seen some points ;)
                        print(' L{0} {1} Z" style="fill:rgb({r},{g},{b}); fill-opacity:{opacity}; stroke:rgb({r},{g},{b}); stroke-width:1" />'.format(x,baseline,r=r,g=g,b=b, opacity=opacity), file = io)

                elif style[:8] == 'triangle':

                    if self.normalizations[plotNumber] == True:
                        maxI = max([ i for mz,i in dataset ])
                    else:
                        maxI = None

                    #first = True
                    for pos,(mz,i) in enumerate(sorted(dataset)):
                        if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
                            x = int(round(PADDING[3]  +   (mz - resolved_mzRange[0] ) * pixelpermz   ))
                            xl = int(round(PADDING[3]  +   (mz-0.175 - resolved_mzRange[0] ) * pixelpermz   ))
                            xr = int(round(PADDING[3]  +   (mz+0.175 - resolved_mzRange[0] ) * pixelpermz   ))
                            if self.normalizations[plotNumber] == True:
                                y = baseline - ((float(i)/float(maxI)) * pixelper_i)
                            else:
                                y = baseline - (i * pixelper_i)

                            print('<path d="M{0} {4} L{2} {3} L{1} {4} Z" style="fill:rgb({r},{g},{b}); fill-opacity:{opacity}"/>'.format(xl,xr,x,y,baseline,r=r,g=g,b=b, opacity=opacity), file = io)
                            #print('<line x1="{0}" y1="{1}" x2="{0}" y2="{2}" style="stroke:rgb({r},{g},{b});stroke-width:1"/>'.format(x,y,baseline,r=r,g=g,b=b), file = io)

            # Drawing data ...
            for datasetnumber,dataset in enumerate(plot):
                r,g,b = self.colors[plotNumber][datasetnumber]
                style = self.styles[plotNumber][datasetnumber]
                if style[:5] not in ['label', 'area', 'trian']:
                    if len(dataset) == 0:
                        continue
                    if self.normalizations[plotNumber] == True:
                        maxI = max([ i for mz,i in dataset ])
                    else:
                        maxI = None

                    for pos,(mz,i) in enumerate(dataset):
                        if resolved_mzRange[0] <= mz <= resolved_mzRange[1]:
                            x = int(round(PADDING[3]  +   (mz - resolved_mzRange[0] ) * pixelpermz   ))
                            if self.normalizations[plotNumber] == True:
                                y = baseline - ((float(i)/float(maxI)) * pixelper_i)
                            else:
                                y = baseline - (i * pixelper_i)
                            print('''
                                    <g id="Label{0}{1}{2}">
                                        <title>{1} {2}</title>
                            '''.format( pos, mz, i ), file = io)

                            if style == 'circles':
                                print("""<circle cx="{x}" cy="{y}" r="2" style="fill:rgb({r},{g},{b});" />""".format( x = x, y = y , r = r, g = g, b = b),file=io)

                            elif style == 'emptycircles':
                                print("""<circle cx="{x}" cy="{y}" r="4" style="stroke:rgb({r},{g},{b}); stroke-width:2; fill:none" />""".format( x = x, y = y , r = r, g = g, b = b),file=io)

                            elif style == 'sticks':
                                print("""<line x1="{0}" y1="{1}" x2="{0}" y2="{2}"
                                style="stroke:rgb({r},{g},{b});stroke-width:1."/>""".format(x,y,baseline,r=r,g=g,b=b),file=io)

                            elif style == 'squares':
                                # this is experimental, the squares are not centred
                                print("""<rect x="{0}" y="{1}" width="4" height="4" style="fill:rgb({r},{g},{b});
                                fill-opacity:0.8;" />
                                """.format(x-2,y-2,r=r,g=g,b=b),file=io)
                            else:
                                print("Style {0} not support yet ...".format(style),file=sys.stderr)
                                exit(1)
                            print('</g>', file = io)

            if self.additionalLegend != None:
                for pos, text in enumerate( self.additionalLegend ):
                    print("""<text x="{x}" y="{y}" font-family="Courier" text-anchor="start" font-size="{fontsize}" fill="black" >{0}</text>
                                """.format( text, x = w-PADDING[1]+30, y = PADDING[0] + pos * 9 , fontsize = 8), file = io)
            print("</svg>", file = io)

        if pureSvg == False:
            print("""
            </body>
            </html>
            """, file = io)
        return

if __name__ == '__main__':
    print(__doc__)