-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathcaferror_8py.html
264 lines (262 loc) · 37.8 KB
/
caferror_8py.html
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
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.12"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>CAFE: /mnt/c/Users/befulton/Documents/GIT/CAFE/cafe/caferror.py File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">CAFE
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.12 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_815ec9b478b15e8b47eb45d0c766f1f4.html">cafe</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#namespaces">Namespaces</a> |
<a href="#func-members">Functions</a> |
<a href="#var-members">Variables</a> </div>
<div class="headertitle">
<div class="title">caferror.py File Reference</div> </div>
</div><!--header-->
<div class="contents">
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespacecaferror"><td class="memItemLeft" align="right" valign="top">  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html">caferror</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ad123a25b4c5554a7c45ad8038dbb5ac1"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ad123a25b4c5554a7c45ad8038dbb5ac1">caferror.errorOut</a> (errnum, errmsg)</td></tr>
<tr class="memdesc:ad123a25b4c5554a7c45ad8038dbb5ac1"><td class="mdescLeft"> </td><td class="mdescRight">Function Definitions. <a href="namespacecaferror.html#ad123a25b4c5554a7c45ad8038dbb5ac1">More...</a><br /></td></tr>
<tr class="separator:ad123a25b4c5554a7c45ad8038dbb5ac1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5dac7321713eced91e607988ce0088a1"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5dac7321713eced91e607988ce0088a1">caferror.optParse</a> (errorflag)</td></tr>
<tr class="separator:a5dac7321713eced91e607988ce0088a1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a18d5960b17750770fc935ba21f2946e0"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a18d5960b17750770fc935ba21f2946e0">caferror.printWrite</a> (o_name, v, o_line1, o_line2="", pad=0)</td></tr>
<tr class="separator:a18d5960b17750770fc935ba21f2946e0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a840d071f77e0313c6ea53ad46176aa"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a4a840d071f77e0313c6ea53ad46176aa">caferror.cafeRun</a> (families, newick, lamb, path, tempDir, cafLog, specDict, spectomin, logrm, fflag, nr, vb)</td></tr>
<tr class="separator:a4a840d071f77e0313c6ea53ad46176aa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a15a2f4fbeee2a2bb920e0b0baf8f98af"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a15a2f4fbeee2a2bb920e0b0baf8f98af">caferror.errFileCheck</a> (errspec_check, errstring_check, specdict_check, thedir, cafLog)</td></tr>
<tr class="separator:a15a2f4fbeee2a2bb920e0b0baf8f98af"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af8331881d620f38f8e91c91b881d08eb"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#af8331881d620f38f8e91c91b881d08eb">caferror.getScore</a> (error, spectomin, tempDir, wout, cafLog)</td></tr>
<tr class="separator:af8331881d620f38f8e91c91b881d08eb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67f01dd2a6b938ffdfc2ab8901d05357"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a67f01dd2a6b938ffdfc2ab8901d05357">caferror.maxfamsize</a> (inFilename, totError, errFilename)</td></tr>
<tr class="separator:a67f01dd2a6b938ffdfc2ab8901d05357"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="var-members"></a>
Variables</h2></td></tr>
<tr class="memitem:a502368f9ca1c05bd070da8ae90f3bfd2"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a502368f9ca1c05bd070da8ae90f3bfd2">caferror.startsec</a> = time.time();</td></tr>
<tr class="memdesc:a502368f9ca1c05bd070da8ae90f3bfd2"><td class="mdescLeft"> </td><td class="mdescRight">Main Block. <a href="namespacecaferror.html#a502368f9ca1c05bd070da8ae90f3bfd2">More...</a><br /></td></tr>
<tr class="separator:a502368f9ca1c05bd070da8ae90f3bfd2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae81a37caf49cfa11e1ae7dd11ae96802"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ae81a37caf49cfa11e1ae7dd11ae96802">caferror.start</a> = datetime.datetime.now().strftime("%m.%d.%Y | %I:%M:%S");</td></tr>
<tr class="separator:ae81a37caf49cfa11e1ae7dd11ae96802"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1ef6d8bb7026f74066fb533376ab055d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a1ef6d8bb7026f74066fb533376ab055d">caferror.inFilename</a></td></tr>
<tr class="separator:a1ef6d8bb7026f74066fb533376ab055d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a019b0f1c67551f5ef2f7be91ad97aa88"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a019b0f1c67551f5ef2f7be91ad97aa88">caferror.outFilename</a> = tmpDir + outFilename;</td></tr>
<tr class="separator:a019b0f1c67551f5ef2f7be91ad97aa88"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aca2deaabe7c3b4f75136a2a445c216d7"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aca2deaabe7c3b4f75136a2a445c216d7">caferror.initError</a></td></tr>
<tr class="separator:aca2deaabe7c3b4f75136a2a445c216d7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afbf4c147a4911ef9bfe249abd4a17ce8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#afbf4c147a4911ef9bfe249abd4a17ce8">caferror.tmpDir</a> = os.getcwd() + "/" + dirName + "/";</td></tr>
<tr class="separator:afbf4c147a4911ef9bfe249abd4a17ce8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8f9c08aa30abddd10ff3baba241dd9d0"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a8f9c08aa30abddd10ff3baba241dd9d0">caferror.wholeCurveOpt</a></td></tr>
<tr class="separator:a8f9c08aa30abddd10ff3baba241dd9d0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5b737fecae7c3c132d6e7f7be6f942d5"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5b737fecae7c3c132d6e7f7be6f942d5">caferror.errTries</a></td></tr>
<tr class="separator:a5b737fecae7c3c132d6e7f7be6f942d5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afa6aa43ec33d9d6a1a7fde0a43bcb91e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#afa6aa43ec33d9d6a1a7fde0a43bcb91e">caferror.caferrorLog</a> = tmpDir + caferrorLog;</td></tr>
<tr class="separator:afa6aa43ec33d9d6a1a7fde0a43bcb91e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adf3c6d6516e0ae89e05d5346d1463839"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#adf3c6d6516e0ae89e05d5346d1463839">caferror.indSpecMin</a></td></tr>
<tr class="separator:adf3c6d6516e0ae89e05d5346d1463839"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5903323966a5f0ae3ef9490a44df4ca4"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5903323966a5f0ae3ef9490a44df4ca4">caferror.Mode</a></td></tr>
<tr class="separator:a5903323966a5f0ae3ef9490a44df4ca4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa6560f026b6441fa57f5e1a4ed596890"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aa6560f026b6441fa57f5e1a4ed596890">caferror.vOpt</a></td></tr>
<tr class="separator:aa6560f026b6441fa57f5e1a4ed596890"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae75a039749cc52f056a8fb3d1c169547"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ae75a039749cc52f056a8fb3d1c169547">caferror.firstRun</a></td></tr>
<tr class="separator:ae75a039749cc52f056a8fb3d1c169547"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abf9ccc003b04c8b03c95ee787294bb78"><td class="memItemLeft" align="right" valign="top">string </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#abf9ccc003b04c8b03c95ee787294bb78">caferror.initCheck</a> = "";</td></tr>
<tr class="separator:abf9ccc003b04c8b03c95ee787294bb78"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a24f218dcf317c181537192847614ed53"><td class="memItemLeft" align="right" valign="top">list </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a24f218dcf317c181537192847614ed53">caferror.spec_to_min</a> = [];</td></tr>
<tr class="separator:a24f218dcf317c181537192847614ed53"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a8811f45553bf58b7a57bc15203f500"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5a8811f45553bf58b7a57bc15203f500">caferror.rmlog</a> = 0;</td></tr>
<tr class="separator:a5a8811f45553bf58b7a57bc15203f500"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a70ca6a2fc086dda87f5d1398822192c3"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a70ca6a2fc086dda87f5d1398822192c3">caferror.FilterFlag</a> = 0;</td></tr>
<tr class="separator:a70ca6a2fc086dda87f5d1398822192c3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae453d67e8bcdc0f33bb19c3d0437f46c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ae453d67e8bcdc0f33bb19c3d0437f46c">caferror.inFile</a> = open(inFilename, "r");</td></tr>
<tr class="separator:ae453d67e8bcdc0f33bb19c3d0437f46c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8a5d5acbbfc35fa4f032e9275a824365"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a8a5d5acbbfc35fa4f032e9275a824365">caferror.inLines</a> = inFile.readlines();</td></tr>
<tr class="separator:a8a5d5acbbfc35fa4f032e9275a824365"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3006a1dda89738e67c32ad72b2f1a073"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a3006a1dda89738e67c32ad72b2f1a073">caferror.CafePath</a> = inLines[x].replace("\n","");</td></tr>
<tr class="separator:a3006a1dda89738e67c32ad72b2f1a073"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8467c97a1a48f313f0841ba3f7f3f423"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a8467c97a1a48f313f0841ba3f7f3f423">caferror.FamFile</a> = inLines[x][(inLines[x].index("-i") + 3):];</td></tr>
<tr class="separator:a8467c97a1a48f313f0841ba3f7f3f423"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1152ce5f1bf7e2b465fa0f22edec3991"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a1152ce5f1bf7e2b465fa0f22edec3991">caferror.Tree</a> = inLines[x].replace('\n', '');</td></tr>
<tr class="separator:a1152ce5f1bf7e2b465fa0f22edec3991"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a928e8fc1e300249ff34c61e316234a6a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a928e8fc1e300249ff34c61e316234a6a">caferror.LamStruct</a> = inLines[x].replace('\n', '');</td></tr>
<tr class="separator:a928e8fc1e300249ff34c61e316234a6a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a139f3c745da6222303ede423588379e7"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a139f3c745da6222303ede423588379e7">caferror.t_struct</a> = LamStruct[LamStruct.index("-t"):];</td></tr>
<tr class="separator:a139f3c745da6222303ede423588379e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a978fc27af5dd023a1d5e9f24ec10eb1b"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a978fc27af5dd023a1d5e9f24ec10eb1b">caferror.treestring</a> = <a class="el" href="tree_8h.html#a9cc86f30992d5873169ac7a2be85e1bf">Tree</a>[Tree.index("("):];</td></tr>
<tr class="separator:a978fc27af5dd023a1d5e9f24ec10eb1b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ababb58cc826bdd81e0254afd077e3dfa"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ababb58cc826bdd81e0254afd077e3dfa">caferror.errSpec</a> = treestring.replace("(","").replace(")","").replace(";","").split(",");</td></tr>
<tr class="separator:ababb58cc826bdd81e0254afd077e3dfa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a23d177bb8a27417f77820799bf25675f"><td class="memItemLeft" align="right" valign="top">dictionary </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a23d177bb8a27417f77820799bf25675f">caferror.mainSpecDict</a> = {};</td></tr>
<tr class="separator:a23d177bb8a27417f77820799bf25675f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad501d603f96fca7b23322c5513d9dc2c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ad501d603f96fca7b23322c5513d9dc2c">caferror.prevList</a> = os.listdir(os.getcwd());</td></tr>
<tr class="memdesc:ad501d603f96fca7b23322c5513d9dc2c"><td class="mdescLeft"> </td><td class="mdescRight">This block creates a new default directory for each run of <a class="el" href="caferror_8py.html">caferror.py</a>. <a href="namespacecaferror.html#ad501d603f96fca7b23322c5513d9dc2c">More...</a><br /></td></tr>
<tr class="separator:ad501d603f96fca7b23322c5513d9dc2c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4354662ead2da4357f29493abf3791b0"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a4354662ead2da4357f29493abf3791b0">caferror.isDirMade</a> = 0;</td></tr>
<tr class="separator:a4354662ead2da4357f29493abf3791b0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abfc6e00664acd02cfe4b980e4a5ce762"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#abfc6e00664acd02cfe4b980e4a5ce762">caferror.x</a> = 1</td></tr>
<tr class="separator:abfc6e00664acd02cfe4b980e4a5ce762"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4227a5d61649b28c24a74d8e2ba2ddc9"><td class="memItemLeft" align="right" valign="top">string </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a4227a5d61649b28c24a74d8e2ba2ddc9">caferror.dirName</a> = "caferror_" + str(x);</td></tr>
<tr class="separator:a4227a5d61649b28c24a74d8e2ba2ddc9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acfc8e606261fa153c0dd090e9bc9204d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#acfc8e606261fa153c0dd090e9bc9204d">caferror.clogfile</a> = open(caferrorLog, "w");</td></tr>
<tr class="separator:acfc8e606261fa153c0dd090e9bc9204d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a74f06f6610ba99dfea20c2106c42e517"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a74f06f6610ba99dfea20c2106c42e517">caferror.outFile</a> = open(outFilename, "w");</td></tr>
<tr class="separator:a74f06f6610ba99dfea20c2106c42e517"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc0bf06605822e778b3e5e902c3d33e7"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#abc0bf06605822e778b3e5e902c3d33e7">caferror.pad</a> = 35</td></tr>
<tr class="memdesc:abc0bf06605822e778b3e5e902c3d33e7"><td class="mdescLeft"> </td><td class="mdescRight">Begin input info block! <a href="namespacecaferror.html#abc0bf06605822e778b3e5e902c3d33e7">More...</a><br /></td></tr>
<tr class="separator:abc0bf06605822e778b3e5e902c3d33e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af2058dd58ff665fa5f829fb4f5f2b926"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#af2058dd58ff665fa5f829fb4f5f2b926">caferror.numruns</a> = 1;</td></tr>
<tr class="memdesc:af2058dd58ff665fa5f829fb4f5f2b926"><td class="mdescLeft"> </td><td class="mdescRight">End input info block! <a href="namespacecaferror.html#af2058dd58ff665fa5f829fb4f5f2b926">More...</a><br /></td></tr>
<tr class="separator:af2058dd58ff665fa5f829fb4f5f2b926"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a685f381439774f5adba75fa6513b938d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a685f381439774f5adba75fa6513b938d">caferror.lastScore</a> = currentScore;</td></tr>
<tr class="separator:a685f381439774f5adba75fa6513b938d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1fc1e20224b50878f8f01fe7b21e5378"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a1fc1e20224b50878f8f01fe7b21e5378">caferror.lastLam</a></td></tr>
<tr class="separator:a1fc1e20224b50878f8f01fe7b21e5378"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a025ef669e886928b194e5f966f97bba1"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a025ef669e886928b194e5f966f97bba1">caferror.preScore</a> = lastScore;</td></tr>
<tr class="separator:a025ef669e886928b194e5f966f97bba1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a607ba80d54f43317955e34719fe093eb"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a607ba80d54f43317955e34719fe093eb">caferror.preLam</a> = lastLam;</td></tr>
<tr class="separator:a607ba80d54f43317955e34719fe093eb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1a75ed6c7fe7607dff05f377c1fe3a63"><td class="memItemLeft" align="right" valign="top">list </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a1a75ed6c7fe7607dff05f377c1fe3a63">caferror.errList</a> = [];</td></tr>
<tr class="memdesc:a1a75ed6c7fe7607dff05f377c1fe3a63"><td class="mdescLeft"> </td><td class="mdescRight">Global error estimation begins here for -c 0 (default) <a href="namespacecaferror.html#a1a75ed6c7fe7607dff05f377c1fe3a63">More...</a><br /></td></tr>
<tr class="separator:a1a75ed6c7fe7607dff05f377c1fe3a63"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6694201d2bf2191092bae2299fc1ff4c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a6694201d2bf2191092bae2299fc1ff4c">caferror.errMin</a> = initError;</td></tr>
<tr class="separator:a6694201d2bf2191092bae2299fc1ff4c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a886c94486c4f4467056f0fd5ba1d7076"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a886c94486c4f4467056f0fd5ba1d7076">caferror.minScore</a> = lastScore;</td></tr>
<tr class="memdesc:a886c94486c4f4467056f0fd5ba1d7076"><td class="mdescLeft"> </td><td class="mdescRight">Global error estimation begins here for -c 1. <a href="namespacecaferror.html#a886c94486c4f4467056f0fd5ba1d7076">More...</a><br /></td></tr>
<tr class="separator:a886c94486c4f4467056f0fd5ba1d7076"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a58db6718d9ae4486f98b7f325cbccc76"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a58db6718d9ae4486f98b7f325cbccc76">caferror.lastError</a> = initError;</td></tr>
<tr class="separator:a58db6718d9ae4486f98b7f325cbccc76"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5305656aba16c126ce91f772b5300834"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5305656aba16c126ce91f772b5300834">caferror.nextError</a> = 0.0;</td></tr>
<tr class="memdesc:a5305656aba16c126ce91f772b5300834"><td class="mdescLeft"> </td><td class="mdescRight">The main logic statements of the code are below. <a href="namespacecaferror.html#a5305656aba16c126ce91f772b5300834">More...</a><br /></td></tr>
<tr class="separator:a5305656aba16c126ce91f772b5300834"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab35b342dc8b730495ccc8c9bae73d06b"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ab35b342dc8b730495ccc8c9bae73d06b">caferror.posLimit</a> = 1.0;</td></tr>
<tr class="separator:ab35b342dc8b730495ccc8c9bae73d06b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2bd5e95d0f6b09fa8bb6b2dda914077d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a2bd5e95d0f6b09fa8bb6b2dda914077d">caferror.posLimScore</a> = lastScore;</td></tr>
<tr class="separator:a2bd5e95d0f6b09fa8bb6b2dda914077d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5df227a5a78cfd289e6b6968d04cb362"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5df227a5a78cfd289e6b6968d04cb362">caferror.negLimit</a> = 0.0;</td></tr>
<tr class="separator:a5df227a5a78cfd289e6b6968d04cb362"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaaf196e7832d45b77f1763c41580b7b6"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aaaf196e7832d45b77f1763c41580b7b6">caferror.negLimScore</a> = 0.0;</td></tr>
<tr class="separator:aaaf196e7832d45b77f1763c41580b7b6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1c9e7a7aeb73b580a24e471204c8547d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a1c9e7a7aeb73b580a24e471204c8547d">caferror.currentError</a> = initError / 2;</td></tr>
<tr class="memdesc:a1c9e7a7aeb73b580a24e471204c8547d"><td class="mdescLeft"> </td><td class="mdescRight">if Mode == 1 or Mode == 3: overallMinScore = currentScore; Toggle this line to either keep the background constant (commented) or update it each time a species is minimized. <a href="namespacecaferror.html#a1c9e7a7aeb73b580a24e471204c8547d">More...</a><br /></td></tr>
<tr class="separator:a1c9e7a7aeb73b580a24e471204c8547d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a06a3181614adf3ff3d646cf245f22f65"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a06a3181614adf3ff3d646cf245f22f65">caferror.tally</a> = 0;</td></tr>
<tr class="separator:a06a3181614adf3ff3d646cf245f22f65"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a32631d33dbd3e6d1e0c8a24f443a1f17"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a32631d33dbd3e6d1e0c8a24f443a1f17">caferror.keepGoing</a> = 1;</td></tr>
<tr class="memdesc:a32631d33dbd3e6d1e0c8a24f443a1f17"><td class="mdescLeft"> </td><td class="mdescRight">These are the termination scenarios. <a href="namespacecaferror.html#a32631d33dbd3e6d1e0c8a24f443a1f17">More...</a><br /></td></tr>
<tr class="separator:a32631d33dbd3e6d1e0c8a24f443a1f17"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac8629f1b2cfeedc9ab6234b67cbb52be"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ac8629f1b2cfeedc9ab6234b67cbb52be">caferror.currentScore</a></td></tr>
<tr class="separator:ac8629f1b2cfeedc9ab6234b67cbb52be"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5e4b4fd0fddb4905695ce4a5ae722839"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a5e4b4fd0fddb4905695ce4a5ae722839">caferror.currentLam</a></td></tr>
<tr class="separator:a5e4b4fd0fddb4905695ce4a5ae722839"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a06372f18e5a14dec9dc166d40bebf82d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a06372f18e5a14dec9dc166d40bebf82d">caferror.megLimScore</a> = lastScore;</td></tr>
<tr class="separator:a06372f18e5a14dec9dc166d40bebf82d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad72186ea549cf6e51d32bd05ff1d0e5f"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ad72186ea549cf6e51d32bd05ff1d0e5f">caferror.minLam</a> = currentLam;</td></tr>
<tr class="separator:ad72186ea549cf6e51d32bd05ff1d0e5f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad9fe6b0b08a06a30363a4c2854ebf7d9"><td class="memItemLeft" align="right" valign="top">dictionary </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ad9fe6b0b08a06a30363a4c2854ebf7d9">caferror.finalSpecDict</a> = {};</td></tr>
<tr class="memdesc:ad9fe6b0b08a06a30363a4c2854ebf7d9"><td class="mdescLeft"> </td><td class="mdescRight">Individual species error estimation begins here if -s 1. <a href="namespacecaferror.html#ad9fe6b0b08a06a30363a4c2854ebf7d9">More...</a><br /></td></tr>
<tr class="separator:ad9fe6b0b08a06a30363a4c2854ebf7d9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a58f51f2f651018ada0aef5aed619b549"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a58f51f2f651018ada0aef5aed619b549">caferror.overallMinScore</a> = minScore;</td></tr>
<tr class="separator:a58f51f2f651018ada0aef5aed619b549"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9d3aa7a4f0b961597b4880c6d8776802"><td class="memItemLeft" align="right" valign="top">list </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a9d3aa7a4f0b961597b4880c6d8776802">caferror.moreErrSpec</a> = [];</td></tr>
<tr class="separator:a9d3aa7a4f0b961597b4880c6d8776802"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7e9fd5f5b26b0de9ae70e2bf7c3bd3c6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a7e9fd5f5b26b0de9ae70e2bf7c3bd3c6">caferror.specMinScore</a> = minScore;</td></tr>
<tr class="separator:a7e9fd5f5b26b0de9ae70e2bf7c3bd3c6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab0bad6bdc5521350d7cb8848a381e54d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ab0bad6bdc5521350d7cb8848a381e54d">caferror.oldspecMin</a> = minScore;</td></tr>
<tr class="separator:ab0bad6bdc5521350d7cb8848a381e54d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9107e53c0148bfc44e1e120871efa597"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a9107e53c0148bfc44e1e120871efa597">caferror.zcheck</a> = 0;</td></tr>
<tr class="separator:a9107e53c0148bfc44e1e120871efa597"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afe4fb521d1289e6eda5d73e8135eab74"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#afe4fb521d1289e6eda5d73e8135eab74">caferror.minimized</a> = 0;</td></tr>
<tr class="separator:afe4fb521d1289e6eda5d73e8135eab74"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa4be1b7c01638c72113aa69b017e3217"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aa4be1b7c01638c72113aa69b017e3217">caferror.specMinErr</a> = errMin;</td></tr>
<tr class="memdesc:aa4be1b7c01638c72113aa69b017e3217"><td class="mdescLeft"> </td><td class="mdescRight"><h1>if Mode == 1 or Mode == 3:</h1>
<a href="namespacecaferror.html#aa4be1b7c01638c72113aa69b017e3217">More...</a><br /></td></tr>
<tr class="separator:aa4be1b7c01638c72113aa69b017e3217"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeba854b8443a04f53e5790ac8e7fd377"><td class="memItemLeft" align="right" valign="top">string </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aeba854b8443a04f53e5790ac8e7fd377">caferror.check</a> = "higher than";</td></tr>
<tr class="separator:aeba854b8443a04f53e5790ac8e7fd377"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af71a942bc1806a362edbf0253f052381"><td class="memItemLeft" align="right" valign="top">string </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#af71a942bc1806a362edbf0253f052381">caferror.check2</a> = "will not be further minimized.";</td></tr>
<tr class="separator:af71a942bc1806a362edbf0253f052381"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6cb06ef6ddbadab897f04fa89294c057"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a6cb06ef6ddbadab897f04fa89294c057">caferror.numrnuns</a> = cafeRun(FamFile, <a class="el" href="tree_8h.html#a9cc86f30992d5873169ac7a2be85e1bf">Tree</a>, LamStruct, CafePath, tmpDir, caferrorLog, finalSpecDict, spec_to_min, rmlog, FilterFlag, numruns, vOpt);</td></tr>
<tr class="memdesc:a6cb06ef6ddbadab897f04fa89294c057"><td class="mdescLeft"> </td><td class="mdescRight">The final CAFE run which generates a report with the minimized error. <a href="namespacecaferror.html#a6cb06ef6ddbadab897f04fa89294c057">More...</a><br /></td></tr>
<tr class="separator:a6cb06ef6ddbadab897f04fa89294c057"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae1d596be75879e1b52efa8142c98a319"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ae1d596be75879e1b52efa8142c98a319">caferror.finalScore</a></td></tr>
<tr class="separator:ae1d596be75879e1b52efa8142c98a319"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3f4b3d15819a1a8bb3d36e0bef7ccf52"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a3f4b3d15819a1a8bb3d36e0bef7ccf52">caferror.finalLam</a></td></tr>
<tr class="separator:a3f4b3d15819a1a8bb3d36e0bef7ccf52"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aceba7a9e5ec4d4a1f25cb2e4552403d9"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#aceba7a9e5ec4d4a1f25cb2e4552403d9">caferror.endsec</a> = time.time();</td></tr>
<tr class="memdesc:aceba7a9e5ec4d4a1f25cb2e4552403d9"><td class="mdescLeft"> </td><td class="mdescRight">Main output block. <a href="namespacecaferror.html#aceba7a9e5ec4d4a1f25cb2e4552403d9">More...</a><br /></td></tr>
<tr class="separator:aceba7a9e5ec4d4a1f25cb2e4552403d9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8a7e87906db814b7da7c31d46c46ef20"><td class="memItemLeft" align="right" valign="top">tuple </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#a8a7e87906db814b7da7c31d46c46ef20">caferror.runtime</a> = (float(endsec) - float(startsec)) / float(60.0);</td></tr>
<tr class="separator:a8a7e87906db814b7da7c31d46c46ef20"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac41d9b114a793d385683c0e4d502941c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacecaferror.html#ac41d9b114a793d385683c0e4d502941c">caferror.end</a> = datetime.datetime.now().strftime("%m.%d.%Y | %I:%M:%S");</td></tr>
<tr class="separator:ac41d9b114a793d385683c0e4d502941c"><td class="memSeparator" colspan="2"> </td></tr>
</table>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.12
</small></address>
</body>
</html>