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
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
|
<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>core.PlotData</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
>ARDEN</th>
</tr></table></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="core-module.html">Package core</a> ::
Module PlotData
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="core.PlotData-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="core.PlotData-module.html">Module core.PlotData</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">'''
</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">Created 2012
</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">@author: GieseS
</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">Little plotting script which is called in the analysis of different mappings to an artificial reference genome.
</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">It produces the following plots:
</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">1) ROC Curve
</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">2) Overview histograms for FP / TP.
</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line">
</tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">pyplot</tt> <tt class="py-keyword">as</tt> <tt class="py-name">plt</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">mpl_toolkits</tt><tt class="py-op">.</tt><tt class="py-name">mplot3d</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Axes3D</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">p</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line">
</tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment">##### HELP FUNCTIONS ####</tt>
</tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line">
</tt>
<a name="trapezoidal_rule"></a><div id="trapezoidal_rule-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="trapezoidal_rule-toggle" onclick="return toggle('trapezoidal_rule');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#trapezoidal_rule">trapezoidal_rule</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="trapezoidal_rule-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="trapezoidal_rule-expanded"><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-docstring">"""Approximates the integral through the points a,b"""</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">xdiff</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">ysum</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">dot</tt><tt class="py-op">(</tt><tt class="py-name">xdiff</tt><tt class="py-op">,</tt><tt class="py-name">ysum</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line">
</tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line">
</tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment">#### HELP FUNCTIONS END ############</tt>
</tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line">
</tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line">
</tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-string">"""
</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-string">abbreviations:
</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-string">tp = True positives
</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-string">fp = false positives
</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-string">NM = number of mismtaches
</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-string">mq = mapping quality
</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-string">rq = readquality
</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-string">subs = substitutions in artifical reference genome (ARG)
</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line">
</tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line">
</tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line">
</tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment">############################################################################### </tt>
</tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line">
</tt>
<a name="CalculateRoc2"></a><div id="CalculateRoc2-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="CalculateRoc2-toggle" onclick="return toggle('CalculateRoc2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#CalculateRoc2">CalculateRoc2</a><tt class="py-op">(</tt><tt class="py-param">dataArray</tt><tt class="py-op">,</tt><tt class="py-param">prefix</tt><tt class="py-op">,</tt><tt class="py-param">readsize</tt><tt class="py-op">,</tt><tt class="py-param">uniquehits</tt><tt class="py-op">,</tt><tt class="py-param">mappedreads</tt><tt class="py-op">,</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CalculateRoc2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CalculateRoc2-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""
</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the adjusted ROC curve as well as the AUC value derived from the adjusted points
</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> and writes the ROC tables to .txt files.
</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">starttime</tt><tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">uniquehits</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">readsize</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">readsize</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line">
</tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line">
</tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line">
</tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line">
</tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">resultmatrix</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">entries</tt><tt class="py-op">*</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">resultmatrix</tt> <tt class="py-op">=</tt> <tt class="py-name">resultmatrix</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line">
</tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">maxrq</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">maxnm</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">maxGaps</tt><tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">maxMism</tt><tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line">
</tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line">
</tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">minrq</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">minnm</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">minmq</tt><tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">minGaps</tt><tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">minMism</tt><tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line">
</tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line">
</tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-comment"># adjust stepsize for rq since the score behaves the other way</tt>
</tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">quants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">tempa</tt> <tt class="py-op">=</tt> <tt class="py-name">maxrq</tt><tt class="py-op">-</tt><tt class="py-name">minrq</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">stepsize</tt> <tt class="py-op">=</tt> <tt class="py-name">tempa</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line">
</tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">rqQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">minrq</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">stepsize</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">rqQuants</tt><tt class="py-op">.</tt><tt class="py-name">reverse</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment"># last entry is rounded bigger than the smallest in the dataset</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line">
</tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">nmQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxnm</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">GapsQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxGaps</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">MismQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxMism</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line">
</tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">rocvector</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line">
</tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-comment"># i = NM,l = RQ, k = MQ</tt>
</tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># RQ</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># GAPS</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># MISMATCH</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">temparray</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">m</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><=</tt> <tt class="py-name">GapsQuants</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><=</tt> <tt class="py-name">MismQuants</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-op">>=</tt><tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line">
</tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line">
</tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">tempids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">temparray</tt><tt class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">uniquereads</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tempids</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">uniquereads</tt><tt class="py-op">[</tt><tt class="py-name">tempids</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line">
</tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">mappedreads</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">uniquereads</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line">
</tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line">
</tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line">
</tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">templength</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">temparray</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line">
</tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">templength</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">tempTP</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">temparray</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">tempFP</tt> <tt class="py-op">=</tt><tt class="py-name">templength</tt><tt class="py-op">-</tt><tt class="py-name">tempTP</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">F</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">mappedreads</tt><tt class="py-op">)</tt><tt class="py-op">/</tt> <tt class="py-name">readsize</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">sens</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">tempTP</tt><tt class="py-op">/</tt> <tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">F</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tempFP</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">spec</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">spec</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">tempFP</tt> <tt class="py-op">/</tt> <tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">F</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line">
</tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">rocvector</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">GapsQuants</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">MismQuants</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">tempTP</tt><tt class="py-op">,</tt><tt class="py-name">tempFP</tt><tt class="py-op">,</tt><tt class="py-name">templength</tt><tt class="py-op">,</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spec</tt><tt class="py-op">,</tt><tt class="py-name">F</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line">
</tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-comment">#print ("%d\t%d\t%d\t" % (templength,tempTP,tempFP))</tt>
</tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line">
</tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment">#0 = NM 4 = TP 7 = sens</tt>
</tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-comment">#1 = RQ 5 = FP 8 = 1-spec</tt>
</tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-comment">#2 = GAPS 6 = P 9 = F</tt>
</tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-comment">#append needed for last entry in AUC calculation</tt>
</tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">rocvector</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">nproc</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">rocvector</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line">
</tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment">#write the sens and specificity values from nproc according to the enumeration in line 149. </tt>
</tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment">#specificity is in cell -2</tt>
</tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment"># sensitivity is in cell -3</tt>
</tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">sens</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nproc</tt><tt class="py-op">]</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">spez</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nproc</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line">
</tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment"># adjust ROC curve. It is necessary that it the 1-specificity ends in 1.</tt>
</tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-comment"># for the last record copy the predecessor in sens to it</tt>
</tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># and write 1 to specificity </tt>
</tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">spez</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">sens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">sens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line">
</tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line">
</tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">rocarray1</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spez</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">rocarray1</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-string">'F'</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">rocarray1</tt><tt class="py-op">=</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">spez</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line">
</tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spez</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-string">'F'</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">spez</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-string">'float,float'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f0'</tt><tt class="py-op">,</tt><tt class="py-string">'f1'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line">
</tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">rocarrayCorrected</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line">
</tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-comment">#print rocarrayCorrected</tt>
</tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment"># project points where...</tt>
</tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">>=</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line">
</tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line">
</tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-comment">#print rocarrayCorrected </tt>
</tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">hold</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-comment">#plt.scatter(spez, sens, c='b', marker='o', facecolor='red')</tt>
</tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-comment">#plt.plot(rocarray[:,1], rocarray[:,0]</tt>
</tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">=</tt><tt class="py-string">'o'</tt><tt class="py-op">,</tt> <tt class="py-name">markersize</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-name">linestyle</tt><tt class="py-op">=</tt><tt class="py-string">'--'</tt><tt class="py-op">,</tt> <tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">'projected'</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">rocarray1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">linestyle</tt><tt class="py-op">=</tt><tt class="py-string">"None"</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">'real'</tt><tt class="py-op">,</tt><tt class="py-name">marker</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'g'</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'1-specificity'</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'sensitivity'</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">r'ROC:'</tt><tt class="py-op">+</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-string">'lower right'</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt> <tt class="py-op">+</tt> <tt class="py-string">"_ROC.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line">
</tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line">
</tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">AUC</tt> <tt class="py-op">=</tt> <tt id="link-0" class="py-name" targets="Function core.PlotData.trapezoidal_rule()=core.PlotData-module.html#trapezoidal_rule"><a title="core.PlotData.trapezoidal_rule" class="py-name" href="#" onclick="return doclink('link-0', 'trapezoidal_rule', 'link-0');">trapezoidal_rule</a></tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line">
</tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt><tt class="py-op">+</tt><tt class="py-string">"_roctable.txt"</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"RQ\tGAPS\tMM\tPTP\tFP\tP\tSn\t1-Sp\tF\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rocvector</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">temp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rocvector</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">tempstr</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">temp</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">tempstr</tt><tt class="py-op">+</tt><tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line">
</tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">endtime</tt><tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"X"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">AUC</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line">
</tt>
<a name="plotOverviewHist"></a><div id="plotOverviewHist-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="plotOverviewHist-toggle" onclick="return toggle('plotOverviewHist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#plotOverviewHist">plotOverviewHist</a><tt class="py-op">(</tt><tt class="py-param">fp</tt><tt class="py-op">,</tt><tt class="py-param">tp</tt><tt class="py-op">,</tt><tt class="py-param">label</tt><tt class="py-op">,</tt><tt class="py-param">prefix</tt><tt class="py-op">,</tt><tt class="py-param">mappernames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plotOverviewHist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plotOverviewHist-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""Plots true positives and false positives into 2 different histogram subplots. """</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">prefix2</tt> <tt class="py-op">=</tt> <tt class="py-string">"/"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"/"</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt><tt class="py-op">+</tt><tt class="py-string">"indexMappingTools.txt"</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"%s - %s\r\n"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">mappernames</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line">
</tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">xmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">ymaxTP</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">tp</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.1</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">ymaxFP</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.1</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line">
</tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment">##### SUBPLOT NUMBER OF MISMATCHES ####</tt>
</tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">tp</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt><tt class="py-name">x</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-name">fp</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line">
</tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line">
</tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-comment"># only plot every 2nd label</tt>
</tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">widthp</tt> <tt class="py-op">=</tt> <tt class="py-number">0.7</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-name">label</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">widthp</tt> <tt class="py-op">=</tt> <tt class="py-number">0.3</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">else</tt> <tt class="py-string">""</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">label</tt><tt class="py-op">]</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-comment"># Here we're adding 2 subplots. The grid is set</tt>
</tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment"># up as one row, two columns.</tt>
</tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">ax1</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkgreen'</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'#TP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison #TP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ymaxTP</tt><tt class="py-op">+</tt><tt class="py-name">ymaxTP</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">/</tt><tt class="py-number">100</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line">
</tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment"># on the second axis, make the width smaller (default is 0.8)</tt>
</tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">ax2</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkred'</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'#FP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison #FP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ymaxFP</tt><tt class="py-op">+</tt><tt class="py-name">ymaxFP</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">/</tt><tt class="py-number">100</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt> <tt class="py-op">+</tt> <tt class="py-string">"Overall_histabs.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line">
</tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line">
</tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">tpsum</tt> <tt class="py-op">=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">tp</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">fpsum</tt> <tt class="py-op">=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tpsum</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tp</tt><tt class="py-op">]</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt><tt class="py-name">x</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">fpsum</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fp</tt><tt class="py-op">]</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">ymax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.2</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line">
</tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment"># only plot every 2nd labelare provided</tt>
</tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-name">label</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">else</tt> <tt class="py-string">""</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">label</tt><tt class="py-op">]</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-comment"># Here we're adding 2 subplots. The grid is set</tt>
</tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-comment"># up as one row, two columns.</tt>
</tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">ax1</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line">
</tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line">
</tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkgreen'</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'%TP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison %TP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line">
</tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-comment"># on the second axis, make the width smaller (default is 0.8)</tt>
</tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">ax2</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkred'</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'%FP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison %FP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt> <tt class="py-op">+</tt> <tt class="py-string">"Overall_histper.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line">
</tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"X"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
</div><a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
>ARDEN</th>
</tr></table></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Fri Mar 15 09:41:18 2013
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
|
