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duplicated_report.html
7847 lines (7838 loc) · 476 KB
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duplicated_report.html
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<HTML>
<HEAD>
<TITLE> CloneDigger Report </TITLE>
<script type="text/javascript">
function unhide(divID) {
var item = document.getElementById(divID);
if (item) {
item.className=(item.className=='hidden')?'unhidden':'hidden';
}
}
</script>
<style type="text/css">
.hidden { display: none; }
.unhidden { display: block; }
.preformatted {
border: 1px dashed #3c78b5;
font-size: 11px;
font-family: Courier;
margin: 10px;
line-height: 13px;
}
.preformattedHeader {
background-color: #f0f0f0;
border-bottom: 1px dashed #3c78b5;
padding: 3px;
text-align: center;
}
.preformattedContent {
background-color: #f0f0f0;
padding: 3px;
}
<!--
<div class="preformatted"><div class="preformattedContent">
<pre>Clone Digger
</pre>
</div></div>
-->
</style>
</HEAD>
<BODY>
<P>Source files: 12</P>
<a href = "javascript:unhide('files');">Click here to show/hide file names</a><div id="files" class="hidden"><P><B>Source files:</B><BR>report/html.py, <BR>report/table.py, <BR>report/reportables.py, <BR>report/results.py, <BR>report/generation.py, <BR>report/__init__.py, <BR>report/formatter.py, <BR>report/latex.py, <BR>report/resultcache.py, <BR>report/plotting.py, <BR>report/figure.py, <BR>report/ppt.py</P></div>
<P>Clones detected: 236</P>
<P>1928 of 5060 lines are duplicates (38.10%) </P>
<P>
<B>Parameters<BR> </B>
clustering_threshold = 10<BR>
distance_threshold = 5<BR>
size_threshold = 5<BR>
hashing_depth = 1<BR>
clusterize_using_hash = False<BR>
clusterize_using_dcup = False<BR>
</P>
<B>Time elapsed</B><BR>Construction of AST : 1.45 seconds<BR>
Building statement hash : 0.01 seconds<BR>
Building patterns : 3.38 seconds<BR>
Marking similar statements : 5.24 seconds<BR>
Finding similar sequences of statements : 0.59 seconds<BR>
Refining candidates : 5.61 seconds<BR>
Total time: 16.28<BR>
Started at: Mon Aug 1 06:56:49 2016<BR>
Finished at: Mon Aug 1 06:57:01 2016
<P><B>Clone # 1</B><BR>Distance between two fragments = 3 <BR>Clone size = 27<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 3337</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 1567</TD></TR><TR>
<TD>
<span style="font-family: monospace;">qtys['settoggles'] += "\\toggle%s{<span style="color:rgb(255,0,0);">LsA</span>nd<span style="color:rgb(255,0,0);">GermsSet</span>}\n" % \<BR>
("true" if <span style="color:rgb(255,0,0);">s</span>e<span style="color:rgb(255,0,0);">lf._Ls</span>A<span style="color:rgb(255,0,0);"></span>nd<span style="color:rgb(255,0,0);">GermInfoSet</span> else "false")<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;">qtys['settoggles'] += "\\toggle%s{<span style="color:rgb(255,0,0);">whackamoleappe</span>nd<span style="color:rgb(255,0,0);">ix</span>}\n" % \<BR>
("true" if <span style="color:rgb(255,0,0);">whackamol</span>e<span style="color:rgb(255,0,0);"></span>A<span style="color:rgb(255,0,0);">ppe</span>nd<span style="color:rgb(255,0,0);">ix</span> else "false")<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">qtys['confidenceLevel'] = "%g" % \<BR>
confidenceLevel if confidenceLevel is not None else "NOT-SET"<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="font-family: monospace;">qtys['confidenceLevel'] = "%g" % \<BR>
confidenceLevel if confidenceLevel is not None else "NOT-SET"<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
qtys['linlg_pcntle'] = self.parameters['linlogPercentile']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
qtys['linlg_pcntle'] = self.parameters['linlogPercentile']</TD>
</TR>
<TR>
<TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
</TR>
<TR>
<TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
</TR>
<TR>
<TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
</TR>
<TR>
<TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
</TR>
<TR>
<TD>
D = (report_base) + ('_files')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
D = (report_base) + ('_files')</TD>
</TR>
<TR>
<TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
</TR>
<TR>
<TD>
printer.log('*** Generating tables ***')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('*** Generating tables ***')</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 2</B><BR>Distance between two fragments = 2 <BR>Clone size = 26<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 2796</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 2394</TD></TR><TR>
<TD>
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):<BR>
fig = self.figures.get(figkey, verbosity=v)<BR>
fig.save_to(_os.path.join(report_dir, D, figFilenm))<BR>
qtys[figkey] = incgr(figFilenm, W, H)<BR>
qtys[('tt_') + (figkey)] = <span style="color: rgb(255, 0, 0);">tooltiptext</span>((".figures['%s']") % (figkey))<BR>
return fig</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
def set_fig_qtys(figkey, figFilenm, v, W=None, H=None):<BR>
fig = self.figures.get(figkey, verbosity=v)<BR>
fig.save_to(_os.path.join(report_dir, D, figFilenm))<BR>
qtys[figkey] = incgr(figFilenm, W, H)<BR>
qtys[('tt_') + (figkey)] = <span style="color: rgb(255, 0, 0);">tooltiptex</span>((".figures['%s']") % (figkey))<BR>
return fig</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;"> if self._LsAndGermInfoSet:<BR>
baseStr_dict = self._getBaseStrDict()<BR>
<BR>
Ls = self.parameters['max length list']<BR>
st = 1 if Ls[0] == 0 else 0 #start index: skip LGST col in box plots<BR>
nPlots = (len(Ls[st:])-1)+1 if pixelPlotAppendix else 1<BR>
<BR>
if self.parameters['objective'] == "chi2":<BR>
plotFnName,plotFnLatex = "Chi2", "$\chi^2$"<BR>
elif self.parameters['objective'] == "logl":<BR>
plotFnName,plotFnLatex = "LogL", "$\\log(\\mathcal{L})$"<BR>
else:<BR>
raise ValueError("Invalid objective value: %s"<span style="color:rgb(255,0,0);"> \</span><BR>
% self.parameters['objective'])<BR>
<BR>
printer.log(" -- %s plots (%d): " % (plotFnName, nPlots), end='')<BR>
with printer.progress_logging(1):<BR>
printer.show_progress(0, 0, prefix='', end='')<BR>
fig = set_fig_qtys("bestEstimateColorBoxPlot",<BR>
"best%sBoxes.p<span style="color:rgb(255,0,0);">ng</span>" % plotFnName, printer - 1)<BR>
maxX = fig.get_extra_info()['nUsedXs']<BR>
maxY = fig.get_extra_info()['nUsedYs']<BR>
<BR>
else:<BR>
for figkey in ["bestEstimateColorBoxPlot"]:<BR>
qtys[figkey] = qtys["tt_"+figkey] = ""<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;"> if self._LsAndGermInfoSet:<BR>
baseStr_dict = self._getBaseStrDict()<BR>
<BR>
Ls = self.parameters['max length list']<BR>
st = 1 if Ls[0] == 0 else 0 #start index: skip LGST col in box plots<BR>
nPlots = (len(Ls[st:])-1)+1 if pixelPlotAppendix else 1<BR>
<BR>
if self.parameters['objective'] == "chi2":<BR>
plotFnName,plotFnLatex = "Chi2", "$\chi^2$"<BR>
elif self.parameters['objective'] == "logl":<BR>
plotFnName,plotFnLatex = "LogL", "$\\log(\\mathcal{L})$"<BR>
else:<BR>
raise ValueError("Invalid objective value: %s"<span style="color:rgb(255,0,0);"></span><BR>
% self.parameters['objective'])<BR>
<BR>
printer.log(" -- %s plots (%d): " % (plotFnName, nPlots), end='')<BR>
with printer.progress_logging(1):<BR>
printer.show_progress(0, 0, prefix='', end='')<BR>
fig = set_fig_qtys("bestEstimateColorBoxPlot",<BR>
"best%sBoxes.p<span style="color:rgb(255,0,0);">df</span>" % plotFnName, printer - 1)<BR>
maxX = fig.get_extra_info()['nUsedXs']<BR>
maxY = fig.get_extra_info()['nUsedYs']<BR>
<BR>
else:<BR>
for figkey in ["bestEstimateColorBoxPlot"]:<BR>
qtys[figkey] = qtys["tt_"+figkey] = ""<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 3</B><BR>Distance between two fragments = 3 <BR>Clone size = 26<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/plotting.py"<BR>The first line is 3092</TD><TD></TD><TD>Source file "report/plotting.py"<BR>The first line is 2911</TD></TR><TR>
<TD>
if fidPairs is None:<BR>
gatestringsToWhack = [((prepStr) + (gatestringToWhack)) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ]<BR>
else:<BR>
gatestringsToWhack = [((prepStrs[i]) + (gatestringToWhack)) + (effectStrs[j]) for i, j in fidPairs ]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if fidPairs is None:<BR>
gatestringsToWhack = [((prepStr) + (gatestringToWhack)) + (effectStr) for prepStr in prepStrs for effectStr in effectStrs ]<BR>
else:<BR>
gatestringsToWhack = [((prepStrs[i]) + (gatestringToWhack)) + (effectStrs[j]) for i, j in fidPairs ]</TD>
</TR>
<TR>
<TD>
whacked_indices = [<span style="color: rgb(255, 0, 0);">allGatestringsUsedInLogLOpt</span>.index(s) for s in gatestringsToWhack ]</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
whacked_indices = [<span style="color: rgb(255, 0, 0);">allGatestringsUsedInChi2Opt</span>.index(s) for s in gatestringsToWhack ]</TD>
</TR>
<TR>
<TD>
<span style="color: rgb(255, 0, 0);">whacked_DlogL</span> = _np.take(<span style="color: rgb(255, 0, 0);">DlogL</span>, whacked_indices, axis=1)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">whacked_Dchi2</span> = _np.take(<span style="color: rgb(255, 0, 0);">Dchi2</span>, whacked_indices, axis=1)</TD>
</TR>
<TR>
<TD>
grad = (-1.0) * (_np.sum(<span style="color: rgb(255, 0, 0);">whacked_DlogL</span>, axis=(0, 1)))</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
grad = (-1.0) * (_np.sum(<span style="color: rgb(255, 0, 0);">whacked_Dchi2</span>, axis=(0, 1)))</TD>
</TR>
<TR>
<TD>
dx = ((whackWith) * (grad)) / (_np.dot(grad, grad))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
dx = ((whackWith) * (grad)) / (_np.dot(grad, grad))</TD>
</TR>
<TR>
<TD>
delta = _np.sum(_np.dot(<span style="color: rgb(255, 0, 0);">DlogL</span>, dx), axis=0)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
delta = _np.sum(_np.dot(<span style="color: rgb(255, 0, 0);">Dchi2</span>, dx), axis=0)</TD>
</TR>
<TR>
<TD>
def mx_fn(gateStr):<BR>
if gateStr is None:<BR>
return (_np.nan) * (_np.zeros((len(effectStrs), len(prepStrs)), 'd'))<BR>
if fidPairs is None:<BR>
return _np.array([[delta[<span style="color: rgb(255, 0, 0);">allGatestringsUsedInLogLOpt</span>.index(((prepStr) + (gateStr)) + (effectStr))] for prepStr in prepStrs ] for effectStr in effectStrs ])<BR>
else:<BR>
ret = (_np.nan) * (_np.ones((len(effectStrs), len(prepStrs)), 'd'))<BR>
for i, j in fidPairs:<BR>
ret[j,i] = delta[<span style="color: rgb(255, 0, 0);">allGatestringsUsedInLogLOpt</span>.index(((prepStrs[i]) + (gateStr)) + (effectStrs[j]))]<BR>
return ret</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
def mx_fn(gateStr):<BR>
if gateStr is None:<BR>
return (_np.nan) * (_np.zeros((len(effectStrs), len(prepStrs)), 'd'))<BR>
if fidPairs is None:<BR>
return _np.array([[delta[<span style="color: rgb(255, 0, 0);">allGatestringsUsedInChi2Opt</span>.index(((prepStr) + (gateStr)) + (effectStr))] for prepStr in prepStrs ] for effectStr in effectStrs ])<BR>
else:<BR>
ret = (_np.nan) * (_np.ones((len(effectStrs), len(prepStrs)), 'd'))<BR>
for i, j in fidPairs:<BR>
ret[j,i] = delta[<span style="color: rgb(255, 0, 0);">allGatestringsUsedInChi2Opt</span>.index(((prepStrs[i]) + (gateStr)) + (effectStrs[j]))]<BR>
return ret</TD>
</TR>
<TR>
<TD>
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
xvals, yvals, subMxs, n_boxes, dof = _computeSubMxs(xvals, yvals, xy_gatestring_dict, mx_fn, sumUp)</TD>
</TR>
<TR>
<TD>
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
max_abs = max([_np.max(_np.abs(subMxs[iy][ix])) for ix in range(len(xvals)) for iy in range(len(yvals)) ])</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">m = -max_abs if m is None else m<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="font-family: monospace;">m = -max_abs if m is None else m<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">M = +max_abs if M is None else M<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="font-family: monospace;">M = +max_abs if M is None else M<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
stdcmap = StdColormapFactory('div', n_boxes=n_boxes, vmin=m, vmax=M, dof=dof, midpoint=0)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
stdcmap = StdColormapFactory('div', n_boxes=n_boxes, vmin=m, vmax=M, dof=dof, midpoint=0)</TD>
</TR>
<TR>
<TD>
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
return generate_boxplot(xvals, yvals, xy_gatestring_dict, subMxs, stdcmap, xlabel, ylabel, scale, prec, title, sumUp, boxLabels, histogram, histBins, save_to, ticSize, invert, prepStrs, effectStrs, '$\\rho_i$', '$E_i$')</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 4</B><BR>Distance between two fragments = 4 <BR>Clone size = 23<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 859</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 831</TD></TR><TR>
<TD>
<span style="color: rgb(255, 0, 0);">expr3</span> = <span style="color: rgb(255, 0, 0);">'whack(.+?)MoleBoxesSummed'</span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="color: rgb(255, 0, 0);">expr2</span> = <span style="color: rgb(255, 0, 0);">'whack(.+?)MoleBoxes'</span></TD>
</TR>
<TR>
<TD>
def fn(key, confidenceLevel, vb):<BR>
noConfidenceLevelDependence(confidenceLevel)<BR>
Ls, germs, gsBest, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()<BR>
highestL = Ls[-1]<BR>
hammerWeight = 10.0<BR>
mpc = getMPC()<BR>
gateLabel = _re.match(<span style="color: rgb(255, 0, 0);">expr3</span>, key).group(1)<BR>
strToWhack = _gs.GateString(((gateLabel)) * (highestL))<BR>
whackAMolePlotFn = getWhackAMolePlotFn()<BR>
return whackAMolePlotFn(strToWhack, self.gatestring_lists['all'], Ls[st:], germs, baseStr_dict, self.dataset, gsBest, strs, '$L$', 'germ', scale=1.0, sumUp=<span style="color: rgb(255, 0, 0);">True</span>, title='', whackWith=hammerWeight, save_to='', minProbClipForWeighting=mpc, ticSize=20, fidPairs=fidPairs)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
def fn(key, confidenceLevel, vb):<BR>
noConfidenceLevelDependence(confidenceLevel)<BR>
Ls, germs, gsBest, fidPairs, _, _, baseStr_dict, strs, st = plot_setup()<BR>
highestL = Ls[-1]<BR>
hammerWeight = 10.0<BR>
mpc = getMPC()<BR>
gateLabel = _re.match(<span style="color: rgb(255, 0, 0);">expr2</span>, key).group(1)<BR>
strToWhack = _gs.GateString(((gateLabel)) * (highestL))<BR>
whackAMolePlotFn = getWhackAMolePlotFn()<BR>
return whackAMolePlotFn(strToWhack, self.gatestring_lists['all'], Ls[st:], germs, baseStr_dict, self.dataset, gsBest, strs, '$L$', 'germ', scale=1.0, sumUp=<span style="color: rgb(255, 0, 0);">False</span>, title='', whackWith=hammerWeight, save_to='', minProbClipForWeighting=mpc, ticSize=20, fidPairs=fidPairs)</TD>
</TR>
<TR>
<TD>
def fn_validate(key):<BR>
if not self._LsAndGermInfoSet:<BR>
return []<BR>
len1GermFirstEls = [g[0] for g in self.gatestring_lists['germs'] if len(g) == 1]<BR>
keys = [(<span style="color: rgb(255, 0, 0);">'whack%sMoleBoxesSummed'</span>) % (gl) for gl in len1GermFirstEls ]<BR>
if key == <span style="color: rgb(255, 0, 0);">expr3</span>:<BR>
return keys<BR>
elif key in keys:<BR>
return [key]<BR>
else:<BR>
return []</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
def fn_validate(key):<BR>
if not self._LsAndGermInfoSet:<BR>
return []<BR>
len1GermFirstEls = [g[0] for g in self.gatestring_lists['germs'] if len(g) == 1]<BR>
keys = [(<span style="color: rgb(255, 0, 0);">'whack%sMoleBoxes'</span>) % (gl) for gl in len1GermFirstEls ]<BR>
if key == <span style="color: rgb(255, 0, 0);">expr2</span>:<BR>
return keys<BR>
elif key in keys:<BR>
return [key]<BR>
else:<BR>
return []</TD>
</TR>
<TR>
<TD>
fns[<span style="color: rgb(255, 0, 0);">expr3</span>] = (fn, fn_validate)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
fns[<span style="color: rgb(255, 0, 0);">expr2</span>] = (fn, fn_validate)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 5</B><BR>Distance between two fragments = 0 <BR>Clone size = 23<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 3276</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 1498</TD></TR><TR>
<TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
</TR>
<TR>
<TD>
default_dir = self.parameters['defaultDirectory']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_dir = self.parameters['defaultDirectory']</TD>
</TR>
<TR>
<TD>
default_base = self.parameters['defaultBasename']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_base = self.parameters['defaultBasename']</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] \<BR>
+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None) \<BR>
else "GSTReport"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] \<BR>
+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None) \<BR>
else "GSTReport"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
</TR>
<TR>
<TD>
if title == 'auto':<BR>
title = ('GST report for %s') % (datasetLabel)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if title == 'auto':<BR>
title = ('GST report for %s') % (datasetLabel)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 6</B><BR>Distance between two fragments = 2 <BR>Clone size = 22<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/latex.py"<BR>The first line is 199</TD><TD></TD><TD>Source file "report/html.py"<BR>The first line is 208</TD></TR><TR>
<TD>
TOL = 1e-09</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
TOL = 1e-09</TD>
</TR>
<TR>
<TD>
def render(x):<BR>
if abs(x) < (5) * ((10) ** (-(precision) + (1))):<BR>
s = ('%.0e') % (x)<BR>
elif abs(x) < 1:<BR>
s = ('%.*f') % ((precision, x))<BR>
elif abs(x) <= (10) ** (precision):<BR>
s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))<BR>
else:<BR>
s = ('%.0e') % (x)<BR>
p = s.split('e')<BR>
if len(p) == 2:<BR>
ex = str(int(p[1]))<BR>
s = (((p[0]) + (<span style="color: rgb(255, 0, 0);">'\\e{'</span>)) + (ex)) + (<span style="color: rgb(255, 0, 0);">'}'</span>)<BR>
if '.' in s:<BR>
while s.endswith('0'):<BR>
s = s[:-1]<BR>
if s.endswith('.'):<BR>
s = s[:-1]<BR>
return s</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
def render(x):<BR>
if abs(x) < (5) * ((10) ** (-(precision) + (1))):<BR>
s = ('%.0e') % (x)<BR>
elif abs(x) < 1:<BR>
s = ('%.*f') % ((precision, x))<BR>
elif abs(x) <= (10) ** (precision):<BR>
s = ('%.*f') % (((precision) - (int(_np.log10(abs(x)))), x))<BR>
else:<BR>
s = ('%.0e') % (x)<BR>
p = s.split('e')<BR>
if len(p) == 2:<BR>
ex = str(int(p[1]))<BR>
s = (((p[0]) + (<span style="color: rgb(255, 0, 0);">'×10<sup>'</span>)) + (ex)) + (<span style="color: rgb(255, 0, 0);">'</sup>'</span>)<BR>
if '.' in s:<BR>
while s.endswith('0'):<BR>
s = s[:-1]<BR>
if s.endswith('.'):<BR>
s = s[:-1]<BR>
return s</TD>
</TR>
<TR>
<TD>
if isinstance(el, basestring):<BR>
return el</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if isinstance(el, basestring):<BR>
return el</TD>
</TR>
<TR>
<TD>
if type(el) in (int, _np.int64):<BR>
return ('%d') % (el)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if type(el) in (int, _np.int64):<BR>
return ('%d') % (el)</TD>
</TR>
<TR>
<TD>
if (el is None) or (_np.isnan(el)):<BR>
return '--'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if (el is None) or (_np.isnan(el)):<BR>
return '--'</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 7</B><BR>Distance between two fragments = 4 <BR>Clone size = 22<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 2037</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 2311</TD></TR><TR>
<TD>
<span style="font-family: monospace;">qtys['gofObjective'] = "$2\\Delta\\log{\\mathcal{L}}$" \<BR>
if <span style="color:rgb(255,0,0);"></span>obj<span style="color:rgb(255,0,0);"></span> == "logl" else "$\\chi^2$"<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;">qtys['gofObjective'] = "$2\\Delta\\log{\\mathcal{L}}$" \<BR>
if <span style="color:rgb(255,0,0);">self.parameters['</span>obj<span style="color:rgb(255,0,0);">ective']</span> == "logl" else "$\\chi^2$"<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
</TR>
<TR>
<TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
</TR>
<TR>
<TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
</TR>
<TR>
<TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
</TR>
<TR>
<TD>
D = (report_base) + ('_files')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
D = (report_base) + ('_files')</TD>
</TR>
<TR>
<TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
</TR>
<TR>
<TD>
printer.log('*** Generating tables ***')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('*** Generating tables ***')</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 8</B><BR>Distance between two fragments = 2 <BR>Clone size = 23<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 3276</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 1974</TD></TR><TR>
<TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
</TR>
<TR>
<TD>
default_dir = self.parameters['defaultDirectory']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_dir = self.parameters['defaultDirectory']</TD>
</TR>
<TR>
<TD>
default_base = self.parameters['defaultBasename']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_base = self.parameters['defaultBasename']</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] <span style="color:rgb(255,0,0);">\<BR>
</span>+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None)<span style="color:rgb(255,0,0);"> \<BR>
</span> else "GST<span style="color:rgb(255,0,0);">Report</span>"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] <span style="color:rgb(255,0,0);"></span>+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None)<span style="color:rgb(255,0,0);"></span> else "GST<span style="color:rgb(255,0,0);">Brief</span>"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
</TR>
<TR>
<TD>
if title == 'auto':<BR>
title = (<span style="color: rgb(255, 0, 0);">'GST report for %s'</span>) % (datasetLabel)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if title == 'auto':<BR>
title = (<span style="color: rgb(255, 0, 0);">'Brief GST report for %s'</span>) % (datasetLabel)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 9</B><BR>Distance between two fragments = 2 <BR>Clone size = 23<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 1498</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 1974</TD></TR><TR>
<TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if tips:<BR>
def tooltiptex(directive):<BR>
return ((('\\pdftooltip{{\\color{blue}\\texttt{%s}}\\quad}') % (directive)) + ('{Access this information in pyGSTi via')) + (('<ResultsObject>%s}') % (directive))<BR>
else:<BR>
def tooltiptex(directive):<BR>
return ''</TD>
</TR>
<TR>
<TD>
default_dir = self.parameters['defaultDirectory']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_dir = self.parameters['defaultDirectory']</TD>
</TR>
<TR>
<TD>
default_base = self.parameters['defaultBasename']</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
default_base = self.parameters['defaultBasename']</TD>
</TR>
<TR>
<TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] <span style="color:rgb(255,0,0);">\<BR>
</span>+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None)<span style="color:rgb(255,0,0);"> \<BR>
</span> else "GST<span style="color:rgb(255,0,0);">Report</span>"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
<span style="font-family: monospace;">if filename != "auto":<BR>
report_dir = _os.path.dirname(filename)<BR>
report_base = _os.path.splitext( _os.path.basename(filename) )[0] <span style="color:rgb(255,0,0);"></span>+ suffix<BR>
else:<BR>
cwd = _os.getcwd()<BR>
report_dir = default_dir if (default_dir is not None) else cwd<BR>
report_base = default_base if (default_base is not None)<span style="color:rgb(255,0,0);"></span> else "GST<span style="color:rgb(255,0,0);">Brief</span>"<BR>
report_base += suffix<span style="color:rgb(255,0,0);"></span></span></TD>
</TR>
<TR>
<TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if datasetLabel == 'auto':<BR>
if default_base is not None:<BR>
datasetLabel = _latex.latex_escaped(default_base)<BR>
else:<BR>
datasetLabel = '$\\mathcal{D}$'</TD>
</TR>
<TR>
<TD>
if title == 'auto':<BR>
title = (<span style="color: rgb(255, 0, 0);">'GST report for %s'</span>) % (datasetLabel)</TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
if title == 'auto':<BR>
title = (<span style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">'Brief GST report for %s'</span></span>) % (datasetLabel)</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 10</B><BR>Distance between two fragments = 1 <BR>Clone size = 20<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 3729</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 2141</TD></TR><TR>
<TD>
if bWasInteractive:<BR>
_matplotlib.pyplot.ion()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if bWasInteractive:<BR>
_matplotlib.pyplot.ion()</TD>
</TR>
<TR>
<TD>
printer.log('*** Merging into template file ***')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('*** Merging into template file ***')</TD>
</TR>
<TR>
<TD>
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
mainTexFilename = _os.path.join(report_dir, (report_base) + ('.tex'))</TD>
</TR>
<TR>
<TD>
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
appendicesTexFilename = _os.path.join(report_dir, (report_base) + ('_appendices.tex'))</TD>
</TR>
<TR>
<TD>
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfFilename = _os.path.join(report_dir, (report_base) + ('.pdf'))</TD>
</TR>
<TR>
<TD>
mainTemplate = <span style="color: rgb(255, 0, 0);">'report_general_main.tex'</span></TD>
<TD style="width: 10px;" BGCOLOR=RED> </TD><TD>
mainTemplate = <span style="color: rgb(255, 0, 0);">'brief_report_main.tex'</span></TD>
</TR>
<TR>
<TD>
self._merge_template(qtys, mainTemplate, mainTexFilename)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
self._merge_template(qtys, mainTemplate, mainTexFilename)</TD>
</TR>
<TR>
<TD>
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('Latex file(s) successfully generated. Attempting to compile with pdflatex...')</TD>
</TR>
<TR>
<TD>
cwd = _os.getcwd()</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
cwd = _os.getcwd()</TD>
</TR>
<TR>
<TD>
if len(report_dir) > 0:<BR>
_os.chdir(report_dir)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if len(report_dir) > 0:<BR>
_os.chdir(report_dir)</TD>
</TR>
<TR>
<TD>
try:<BR>
try:<BR>
self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)<BR>
except _subprocess.CalledProcessError, e:<BR>
printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))<BR>
finally:<BR>
_os.chdir(cwd)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
try:<BR>
try:<BR>
self._compile_latex_report(report_dir, report_base, self.options.latex_call, printer)<BR>
except _subprocess.CalledProcessError, e:<BR>
printer.error((('pdflatex returned code %d ') % (e.returncode)) + (('Check %s.log to see details.') % (report_base)))<BR>
finally:<BR>
_os.chdir(cwd)</TD>
</TR>
<TR>
<TD>
return None</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
return None</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 11</B><BR>Distance between two fragments = 0 <BR>Clone size = 22<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 2040</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 3351</TD></TR><TR>
<TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
</TR>
<TR>
<TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
</TR>
<TR>
<TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
</TR>
<TR>
<TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
</TR>
<TR>
<TD>
D = (report_base) + ('_files')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
D = (report_base) + ('_files')</TD>
</TR>
<TR>
<TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
</TR>
<TR>
<TD>
printer.log('*** Generating tables ***')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('*** Generating tables ***')</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 12</B><BR>Distance between two fragments = 0 <BR>Clone size = 22<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 2040</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 1573</TD></TR><TR>
<TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
</TR>
<TR>
<TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
</TR>
<TR>
<TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
</TR>
<TR>
<TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
qtys['pdfinfo'] = _to_pdfinfo(pdfInfo)</TD>
</TR>
<TR>
<TD>
D = (report_base) + ('_files')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
D = (report_base) + ('_files')</TD>
</TR>
<TR>
<TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if not _os.path.isdir(_os.path.join(report_dir, D)):<BR>
_os.mkdir(_os.path.join(report_dir, D))</TD>
</TR>
<TR>
<TD>
printer.log('*** Generating tables ***')</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
printer.log('*** Generating tables ***')</TD>
</TR>
</TABLE> </P> <HR><BR>
<P><B>Clone # 13</B><BR>Distance between two fragments = 0 <BR>Clone size = 22<TABLE NOWRAP WIDTH=100% BORDER=1><TD>Source file "report/results.py"<BR>The first line is 3351</TD><TD></TD><TD>Source file "report/results.py"<BR>The first line is 2314</TD></TR><TR>
<TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
if confidenceLevel is not None:<BR>
cri = self._get_confidence_region(confidenceLevel)<BR>
qtys['confidenceIntervalScaleFctr'] = ('%.3g') % (cri.intervalScaling)<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = ('%d') % (cri.nNonGaugeParams)<BR>
else:<BR>
cri = None<BR>
qtys['confidenceIntervalScaleFctr'] = 'NOT-SET'<BR>
qtys['confidenceIntervalNumNonGaugeParams'] = 'NOT-SET'</TD>
</TR>
<TR>
<TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
pdfInfo = [('Author', 'pyGSTi'), ('Title', title), ('Keywords', 'GST'), ('pyGSTi Version', _version.__version__), ('opt_long_tables', self.options.long_tables), ('opt_table_class', self.options.table_class), ('opt_template_path', self.options.template_path), ('opt_latex_cmd', self.options.latex_cmd)]</TD>
</TR>
<TR>
<TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
<TD style="width: 10px;" BGCOLOR=AQUA> </TD><TD>
for key in sorted(list(self.parameters.keys())):<BR>
pdfInfo.append((key, self.parameters[key]))</TD>
</TR>
<TR>