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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/microbegps">Debian Med / microbegps</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/2ad535451c262c6835929a5cd5da65e6597992b7">2ad53545</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-06T10:59:31Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More PyQt5 changes
</pre>
</li>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#f24cf5396101d28a103d31c2ef9c1ad7d27b1969">
debian/patches/PyQt5.patch
</a>
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<h4>Changes:</h4>
<li id="f24cf5396101d28a103d31c2ef9c1ad7d27b1969">
<a href="https://salsa.debian.org/med-team/microbegps/commit/2ad535451c262c6835929a5cd5da65e6597992b7#f24cf5396101d28a103d31c2ef9c1ad7d27b1969"><strong>debian/patches/PyQt5.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,47 +37,144 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> def __init__(self,mainWindow):</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> super(Pipeline, self).__init__()</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> self.mainWindow = mainWindow</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="p">@@ -126,13 +126,13 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> sublayout = QtGui.QHBoxLayout()</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -101,13 +101,13 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> self.step_visualize]</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> self.currentPipelineThread = None</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- recipeLbl = QtGui.QLabel('Pipeline')</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- settingsLbl = QtGui.QLabel('Settings')</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ recipeLbl = QtWidgets.QLabel('Pipeline')</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ settingsLbl = QtWidgets.QLabel('Settings')</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.recipeList = QtGui.QListWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.recipeList = QtWidgets.QListWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> itemNames = ['Load Data', 'Raw Filter', 'Calculate Reference Table', 'Quality Filtering', 'Calculate Candidates', 'Visualize Results'] </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> for name in itemNames:</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- item = QtGui.QListWidgetItem(self.redIcon,name)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ item = QtWidgets.QListWidgetItem(self.redIcon,name)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> self.recipeList.addItem(item)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> self.recipeList.setMinimumWidth(230)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -116,119 +116,119 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # create all settings pages</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.settingsBox = QtGui.QStackedWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.settingsBox = QtWidgets.QStackedWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # page 0: load data</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.fileNameEdit = QtGui.QLineEdit()</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- selectButton = QtGui.QPushButton(self.openIcon,'')</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.fileNameEdit = QtWidgets.QLineEdit()</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ selectButton = QtWidgets.QPushButton(self.openIcon,'')</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> selectButton.clicked.connect(self.selectDirectory)</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> selectButton.setToolTip('Open directory containing SAM files')</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sublayout = QtGui.QHBoxLayout()</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sublayout = QtWidgets.QHBoxLayout()</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> sublayout.addWidget(self.fileNameEdit,stretch=4)</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> sublayout.addWidget(selectButton,stretch=1)</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subwidget = QtGui.QWidget()</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subwidget = QtWidgets.QWidget()</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> subwidget.setLayout(sublayout)</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> layout = QtGui.QGridLayout()</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QGridLayout()</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QGridLayout()</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)</span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> layout.addWidget(QtGui.QLabel('Input Directory'),0,0)</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addWidget(QtGui.QLabel('Input Directory'),0,0)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addWidget(QtWidgets.QLabel('Input Directory'),0,0)</span></span>
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50
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> layout.addWidget(subwidget,0,1)</span>
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51
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- loadDataWidget = QtGui.QWidget()</span></span>
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52
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ loadDataWidget = QtWidgets.QWidget()</span></span>
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53
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> loadDataWidget.setLayout(layout)</span>
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54
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> self.settingsBox.addWidget(loadDataWidget)</span>
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55
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> </span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="p">@@ -167,7 +167,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> # page 1: Raw Filter</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.minSupportBox = QtGui.QSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.minSupportBox = QtWidgets.QSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> self.minSupportBox.setRange(1,1000000000)</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> self.minSupportBox.setValue(50)</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> self.minSupportBox.setMinimumWidth(100)</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> self.minSupportBox.valueChanged.connect(lambda: self.modifiedSettings(1))</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.maxMatchesBox = QtGui.QSpinBox()</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.maxMatchesBox = QtWidgets.QSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> self.maxMatchesBox.setRange(2,1000000000)</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> self.maxMatchesBox.setValue(80)</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> self.maxMatchesBox.setMinimumWidth(100)</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> self.maxMatchesBox.valueChanged.connect(lambda: self.modifiedSettings(1))</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.maxMappingError = QtGui.QDoubleSpinBox()</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.maxMappingError = QtWidgets.QDoubleSpinBox()</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> self.maxMappingError.setDecimals(2)</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> self.maxMappingError.setRange(0,1)</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> self.maxMappingError.setValue(1)</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> self.maxMappingError.setSingleStep(0.05)</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> self.maxMappingError.setMinimumWidth(100)</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> self.maxMappingError.valueChanged.connect(lambda: self.modifiedSettings(1))</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.mappingErrorQuantile = QtGui.QDoubleSpinBox()</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.mappingErrorQuantile = QtWidgets.QDoubleSpinBox()</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> self.mappingErrorQuantile.setDecimals(2)</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> self.mappingErrorQuantile.setRange(0,1)</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> self.mappingErrorQuantile.setValue(1)</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> self.mappingErrorQuantile.setSingleStep(0.05)</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> self.mappingErrorQuantile.setMinimumWidth(100)</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> self.mappingErrorQuantile.valueChanged.connect(lambda: self.modifiedSettings(1))</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QFormLayout()</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QFormLayout()</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Minimum Genome Support'),self.minSupportBox)</span></span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)</span></span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)</span></span>
</pre>
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60
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rawFilterWidget = QtGui.QWidget()</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Minimum Genome Support'),self.minSupportBox)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Max. Read Matches'),self.maxMatchesBox)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Max. Read Mapping Error'),self.maxMappingError)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)</span></span>
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61
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rawFilterWidget = QtWidgets.QWidget()</span></span>
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62
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> rawFilterWidget.setLayout(layout)</span>
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63
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> self.settingsBox.addWidget(rawFilterWidget)</span>
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64
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> </span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="p">@@ -191,12 +191,12 @@</span> class Pipeline(QtGui.QWidget):</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> sublayout1 = QtGui.QHBoxLayout()</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> # page 2: Calculate Reference Table</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.useIdMapping = QtGui.QRadioButton('No Mapping')</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.useIdMapping = QtWidgets.QRadioButton('No Mapping')</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> self.useIdMapping.toggled.connect(lambda: self.modifiedSettings(2))</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.useMappingFile = QtGui.QRadioButton('Mapping File')</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.useMappingFile = QtWidgets.QRadioButton('Mapping File')</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> self.useMappingFile.toggled.connect(lambda: self.modifiedSettings(2))</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.mappingFileEdit = QtGui.QLineEdit()</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.useNCBIFiles = QtGui.QRadioButton('NCBI catalog')</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.mappingFileEdit = QtWidgets.QLineEdit()</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.useNCBIFiles = QtWidgets.QRadioButton('NCBI catalog')</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> self.useNCBIFiles.setChecked(True)</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> self.useNCBIFiles.toggled.connect(lambda: self.modifiedSettings(2))</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.NCBICatalogPath = QtGui.QLineEdit('<default>')</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.NCBICatalogPath = QtWidgets.QLineEdit('<default>')</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> self.NCBICatalogPath.setToolTip('Clear this field to use the default catalog.')</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- selectButton1 = QtGui.QPushButton(self.openIcon,'')</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ selectButton1 = QtWidgets.QPushButton(self.openIcon,'')</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> selectButton1.clicked.connect(self.selectMappingFile)</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> selectButton1.setToolTip('Load Mapping File')</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- selectButton2 = QtGui.QPushButton(self.openIcon,'')</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ selectButton2 = QtWidgets.QPushButton(self.openIcon,'')</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> selectButton2.clicked.connect(self.selectNCBICatalog)</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> selectButton2.setToolTip('Load NCBI catalog file')</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sublayout1 = QtGui.QHBoxLayout()</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sublayout1 = QtWidgets.QHBoxLayout()</span></span>
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67
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> sublayout1.addWidget(self.mappingFileEdit,stretch=4)</span>
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68
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="diff"> sublayout1.addWidget(selectButton1,stretch=1)</span>
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69
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subwidget1 = QtGui.QWidget()</span></span>
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70
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subwidget1 = QtWidgets.QWidget()</span></span>
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71
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> subwidget1.setLayout(sublayout1)</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> sublayout2 = QtGui.QHBoxLayout()</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sublayout2 = QtGui.QHBoxLayout()</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sublayout2 = QtWidgets.QHBoxLayout()</span></span>
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73
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="diff"> sublayout2.addWidget(self.NCBICatalogPath,stretch=4)</span>
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74
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="diff"> sublayout2.addWidget(selectButton2,stretch=1)</span>
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75
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subwidget2 = QtGui.QWidget()</span></span>
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76
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subwidget2 = QtWidgets.QWidget()</span></span>
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77
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"> subwidget2.setLayout(sublayout2)</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> layout = QtGui.QGridLayout()</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QGridLayout()</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QGridLayout()</span></span>
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79
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="diff"> layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="p">@@ -205,7 +205,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> layout.addWidget(self.useIdMapping,0,0)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> layout.addWidget(self.useMappingFile,1,0)</span>
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81
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="diff"> layout.addWidget(subwidget1,1,1)</span>
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82
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="diff"> layout.addWidget(self.useNCBIFiles,2,0)</span>
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83
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="diff"> layout.addWidget(subwidget2,2,1)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,51 +183,160 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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86
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff"> referenceTableWidget.setLayout(layout)</span>
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87
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="diff"> self.settingsBox.addWidget(referenceTableWidget)</span>
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88
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="p">@@ -228,7 +228,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> # page 3: Quality Filtering</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.minAbsoluteUnique = QtGui.QSpinBox()</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.minAbsoluteUnique = QtWidgets.QSpinBox()</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> self.minAbsoluteUnique.setRange(0,1000000000)</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> self.minAbsoluteUnique.setValue(20)</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> self.minAbsoluteUnique.setMinimumWidth(100)</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> self.minAbsoluteUnique.valueChanged.connect(lambda: self.modifiedSettings(3))</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.maxHomogeneity = QtGui.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.maxHomogeneity = QtWidgets.QDoubleSpinBox()</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> self.maxHomogeneity.setDecimals(3)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> self.maxHomogeneity.setValue(0.6)</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> self.maxHomogeneity.setRange(0.,1.)</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> self.maxHomogeneity.setSingleStep(0.05)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> self.maxHomogeneity.setMinimumWidth(100)</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> self.maxHomogeneity.valueChanged.connect(lambda: self.modifiedSettings(3))</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.minValidity = QtGui.QDoubleSpinBox()</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QFormLayout()</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.minValidity = QtWidgets.QDoubleSpinBox()</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QFormLayout()</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Max. Homogeneity'),self.maxHomogeneity)</span></span>
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92
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="diff"> </span>
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93
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qualFilterWidget = QtGui.QWidget()</span></span>
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94
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qualFilterWidget = QtWidgets.QWidget()</span></span>
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95
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="diff"> qualFilterWidget.setLayout(layout)</span>
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96
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="diff"> self.settingsBox.addWidget(qualFilterWidget)</span>
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97
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="p">@@ -266,7 +266,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="p">@@ -239,75 +239,75 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> self.minValidity.setSingleStep(0.05)</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> self.minValidity.setMinimumWidth(100)</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> self.minValidity.valueChanged.connect(lambda: self.modifiedSettings(4))</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.coverageSimilarity = QtGui.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.coverageSimilarity = QtWidgets.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> self.coverageSimilarity.setDecimals(2)</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> self.coverageSimilarity.setValue(0.2)</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> self.coverageSimilarity.setMinimum(0)</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> self.coverageSimilarity.setSingleStep(0.05)</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> self.coverageSimilarity.setMinimumWidth(100)</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> self.coverageSimilarity.valueChanged.connect(lambda: self.modifiedSettings(4))</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.sharedFractionUSR = QtGui.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.sharedFractionUSR = QtWidgets.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> self.sharedFractionUSR.setDecimals(2)</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> self.sharedFractionUSR.setValue(0.2) </span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> self.sharedFractionUSR.setRange(0.,1.)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> self.sharedFractionUSR.setSingleStep(0.05)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> self.sharedFractionUSR.setMinimumWidth(100)</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> self.sharedFractionUSR.valueChanged.connect(lambda: self.modifiedSettings(4))</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.sharedFractionAll = QtGui.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.sharedFractionAll = QtWidgets.QDoubleSpinBox()</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> self.sharedFractionAll.setDecimals(2)</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> self.sharedFractionAll.setValue(0.6) </span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> self.sharedFractionAll.setRange(0.,1.)</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> self.sharedFractionAll.setSingleStep(0.05)</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> self.sharedFractionAll.setMinimumWidth(100)</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> self.sharedFractionAll.valueChanged.connect(lambda: self.modifiedSettings(4))</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QFormLayout()</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QFormLayout()</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Min. Genome Validity'),self.minValidity)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)</span></span>
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102
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- extractUSRWidget = QtGui.QWidget()</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Min. Genome Validity'),self.minValidity)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Coverage Similarity'),self.coverageSimilarity)</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Fraction Shared USR'),self.sharedFractionUSR)</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout.addRow(QtWidgets.QLabel('Fraction Shared Reads'),self.sharedFractionAll)</span></span>
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103
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ extractUSRWidget = QtWidgets.QWidget()</span></span>
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104
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="diff"> extractUSRWidget.setLayout(layout)</span>
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105
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="diff"> self.settingsBox.addWidget(extractUSRWidget)</span>
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106
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="p">@@ -274,7 +274,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> layout = QtGui.QVBoxLayout()</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> # page 5: Visualize</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- layout = QtGui.QVBoxLayout()</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.closeOnFinish = QtWidgets.QCheckBox('Close this window after visualizing results')</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ layout = QtWidgets.QVBoxLayout()</span></span>
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110
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="diff"> layout.addWidget(self.closeOnFinish)</span>
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111
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- visualizeWidget = QtGui.QWidget()</span></span>
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112
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ visualizeWidget = QtWidgets.QWidget()</span></span>
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113
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="diff"> visualizeWidget.setLayout(layout)</span>
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114
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="diff"> self.settingsBox.addWidget(visualizeWidget) </span>
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115
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="p">@@ -294,7 +294,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> consoleLayout = QtGui.QVBoxLayout()</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> # Text boxes</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.descriptionText = QtGui.QTextEdit()</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.descriptionText = QtWidgets.QTextEdit()</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> self.descriptionText.setReadOnly(True)</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.consoleText = QtGui.QTextEdit()</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.consoleText = QtWidgets.QTextEdit()</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> self.consoleText.setReadOnly(True)</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> consoleFont = self.consoleText.font()</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> consoleFont.setPointSize(self.font().pointSize()-1)</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> self.consoleText.setFont(consoleFont)</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> # Progress bar</span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.progress = QtGui.QProgressBar()</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.progress = QtWidgets.QProgressBar()</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> </span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- consoleLayout = QtGui.QVBoxLayout()</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ consoleLayout = QtWidgets.QVBoxLayout()</span></span>
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118
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="diff"> consoleLayout.addWidget(self.progress)</span>
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119
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="diff"> consoleLayout.addWidget(self.consoleText)</span>
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120
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- consoleWidget = QtGui.QWidget()</span></span>
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121
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ consoleWidget = QtWidgets.QWidget()</span></span>
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122
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="diff"> consoleWidget.setLayout(consoleLayout)</span>
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123
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> self.runStepBtn = QtGui.QPushButton("Run Step")</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="p">@@ -304,7 +304,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"> buttonLayout = QtGui.QHBoxLayout()</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.runStepBtn = QtGui.QPushButton("Run Step")</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.runStepBtn = QtWidgets.QPushButton("Run Step")</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> self.runStepBtn.clicked.connect(self.runOneStep)</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.runPipelineBtn = QtGui.QPushButton("Run Pipeline")</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.runPipelineBtn = QtWidgets.QPushButton("Run Pipeline")</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> self.runPipelineBtn.clicked.connect(self.runPipeline)</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- buttonLayout = QtGui.QHBoxLayout()</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buttonLayout = QtWidgets.QHBoxLayout()</span></span>
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127
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="diff"> buttonLayout.addWidget(self.runStepBtn)</span>
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128
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="diff"> buttonLayout.addWidget(self.runPipelineBtn)</span>
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129
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- buttonBar = QtGui.QWidget()</span></span>
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130
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ buttonBar = QtWidgets.QWidget()</span></span>
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131
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="diff"> buttonBar.setLayout(buttonLayout)</span>
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132
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"> gridLayout = QtGui.QGridLayout()</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gridLayout = QtGui.QGridLayout()</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gridLayout = QtWidgets.QGridLayout()</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> gridLayout.setColumnStretch(0,2)</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> gridLayout.setColumnStretch(1,2)</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> gridLayout.addWidget(recipeLbl,0,0)</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="p">@@ -805,14 +805,14 @@</span> class Pipeline(QtGui.QWidget):</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> self.stepsDone = min(step-1,self.stepsDone)</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> def selectDirectory(self):</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fname = str(QtGui.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fname = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> if len(fname):</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> self.pr("Input directory for SAM files: "+fname)</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> self.fileNameEdit.setText(fname)</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> self.modifiedSettings(0)</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> def selectMappingFile(self):</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fname = str(QtGui.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fname = str(QtWidgets.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> if len(fname):</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> self.pr("Using ID Mapping File "+fname)</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> self.mappingFileEdit.setText(fname)</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -820,7 +820,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> self.useMappingFile.setChecked(True)</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> </span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> def selectNCBICatalog(self):</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fname = str(QtGui.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fname = str(QtWidgets.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> if len(fname):</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> self.pr("Using NCBI catalog "+fname)</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> self.NCBICatalogPath.setText(fname)</span>
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134
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="diff"><span class="p">@@ -871,7 +871,7 @@</span> class Pipeline(QtGui.QWidget):</span>
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135
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="diff"> self.sharedFractionAll.setValue(settings.get('fraction_shared_all',0.8))</span>
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136
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,22 +346,31 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="diff"> def __init__(self):</span>
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141
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> super(GPSAnalyzer, self).__init__()</span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="diff"> self.initUI()</span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="p">@@ -901,19 +901,19 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"> self.graphicDock = QtGui.QDockWidget('Graphic',self)</span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"> self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -898,22 +898,22 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> self.pipelineGui = Pipeline(self)</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> # Prepare the Docks on the right hand side</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.graphicDock = QtGui.QDockWidget('Graphic',self)</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.graphicDock = QtWidgets.QDockWidget('Graphic',self)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.graphicDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="diff"> self.graphicDock.setMinimumSize(450,300)</span>
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.graphicDock.setTitleBarWidget(QtGui.QWidget())</span></span>
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.graphicDock.setTitleBarWidget(QtWidgets.QWidget())</span></span>
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149
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"> self.toolsDock = QtGui.QDockWidget('Tools',self)</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toolsDock = QtGui.QDockWidget('Tools',self)</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toolsDock = QtWidgets.QDockWidget('Tools',self)</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toolsDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)</span></span>
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="diff"> self.toolsDock.setMinimumHeight(150)</span>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="diff"> self.toolsDock.setMaximumHeight(250)</span>
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154
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toolsDock.setTitleBarWidget(QtGui.QWidget())</span></span>
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155
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toolsDock.setTitleBarWidget(QtWidgets.QWidget())</span></span>
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156
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> self.consoleDock = QtGui.QDockWidget('Console',self)</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.consoleDock = QtGui.QDockWidget('Console',self)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.consoleDock = QtWidgets.QDockWidget('Console',self)</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.consoleDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)</span></span>
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159
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="diff"> self.consoleDock.setMinimumHeight(150)</span>
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160
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="diff"> self.consoleDock.setMaximumHeight(450)</span>
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161
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.consoleDock.setTitleBarWidget(QtGui.QWidget())</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,7 +378,60 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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163
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="diff"> self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.graphicDock)</span>
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165
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="diff"> self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.toolsDock)</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="p">@@ -966,7 +966,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="p">@@ -924,72 +924,72 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> self.figure = plt.figure()</span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> self.canvas = FigureCanvas(self.figure)</span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> </span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.phyloTreeWidget = QtGui.QTreeWidget()</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.phyloTreeWidget = QtWidgets.QTreeWidget()</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> self.phyloTreeWidget.setHeaderHidden(True)</span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> self.phyloTreeWidget.setUniformRowHeights(False)</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> self.phyloTreeWidget.setAutoScrollMargin(50)</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.phyloTreeWidget.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.phyloTreeWidget.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.phyloTreeWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.phyloTreeWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> self.phyloTreeWidget.setMouseTracking(True)</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> self.phyloTreeWidget.itemClicked.connect(self.view_tree_selection)</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> self.phyloTreeWidget.setColumnCount(2)</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> self.phyloTreeWidget.itemCollapsed.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> self.phyloTreeWidget.itemExpanded.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> </span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.graphicsTab = QtGui.QTabWidget()</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.graphicsTab.setTabPosition(QtGui.QTabWidget.South)</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.graphicsTab = QtWidgets.QTabWidget()</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.graphicsTab.setTabPosition(QtWidgets.QTabWidget.South)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> self.graphicsTab.addTab(self.canvas,"Figure")</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> self.graphicsTab.addTab(self.phyloTreeWidget,"Tree")</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> </span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> self.graphicDock.setWidget(self.graphicsTab) </span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> </span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> # Fill the Tools Dock</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.enablePlottingBox = QtGui.QCheckBox('Draw Graphics')</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.enablePlottingBox = QtWidgets.QCheckBox('Draw Graphics')</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> self.enablePlottingBox.setChecked(True)</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.enableTaxonomyTree = QtGui.QCheckBox('Interactive Tree')</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.enableTaxonomyTree = QtWidgets.QCheckBox('Interactive Tree')</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> self.enableTaxonomyTree.setChecked(True)</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> </span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exportFigureQualityLabel = QtGui.QLabel('Image export quality (DPI)')</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.exportFigureQuality = QtGui.QSpinBox()</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exportFigureQualityLabel = QtWidgets.QLabel('Image export quality (DPI)')</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.exportFigureQuality = QtWidgets.QSpinBox()</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> self.exportFigureQuality.setMinimum(10)</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> self.exportFigureQuality.setMaximum(1200)</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> self.exportFigureQuality.setValue(150)</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> self.exportFigureQuality.setSingleStep(10)</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> </span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- showPipelineBtn = QtGui.QPushButton('Show GPS Pipeline')</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ showPipelineBtn = QtWidgets.QPushButton('Show GPS Pipeline')</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> showPipelineBtn.clicked.connect(self.pipelineGui.show)</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> </span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- toolsGrid = QtGui.QGridLayout()</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ toolsGrid = QtWidgets.QGridLayout()</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> toolsGrid.addWidget(self.enablePlottingBox,0,0)</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> toolsGrid.addWidget(self.enableTaxonomyTree,0,1)</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> toolsGrid.addWidget(exportFigureQualityLabel,1,0)</span>
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167
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="diff"> toolsGrid.addWidget(self.exportFigureQuality,1,1)</span>
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168
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="diff"> toolsGrid.addWidget(showPipelineBtn,2,0)</span>
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169
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +439,301 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ toolsWidget = QtWidgets.QWidget()</span></span>
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172
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="diff"> toolsWidget.setLayout(toolsGrid)</span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="diff"> </span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"> self.toolsTab = QtGui.QTabWidget()</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toolsTab = QtGui.QTabWidget()</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toolsTab = QtWidgets.QTabWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> self.toolsTab.currentChanged.connect(self.show_module_help)</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toolsTab.setTabPosition(QtGui.QTabWidget.South)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toolsTab.setTabPosition(QtWidgets.QTabWidget.South)</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> self.toolsTab.addTab(toolsWidget,"Settings")</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> self.toolsDock.setWidget(self.toolsTab)</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> </span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> # Fill the Console Dock</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.helpText = QtGui.QTextEdit()</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.helpText = QtWidgets.QTextEdit()</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> self.helpText.setReadOnly(True)</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.consoleText = QtGui.QTextBrowser()</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.consoleText = QtWidgets.QTextBrowser()</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> self.consoleText.setReadOnly(True)</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> </span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.textTabs = QtGui.QTabWidget()</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.textTabs.setTabPosition(QtGui.QTabWidget.South)</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.textTabs = QtWidgets.QTabWidget()</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.textTabs.setTabPosition(QtWidgets.QTabWidget.South)</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> self.textTabs.addTab(self.helpText,"Help")</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> self.textTabs.addTab(self.consoleText,"Console")</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> self.consoleDock.setWidget(self.textTabs)</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> </span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> # Insert the main Tree Widget</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.treeView = QtGui.QTreeWidget()</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.treeView = QtWidgets.QTreeWidget()</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> self.treeView.setColumnCount(7)</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> self.treeView.setColumnWidth(0,300)</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> self.treeView.setHeaderLabels(['Name','Reads','Unique','Coverage','Validity','Homogeneity','Mapping Error'])</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="p">@@ -998,8 +998,8 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> self.treeView.itemSelectionChanged.connect(self.selection_changed_handler)</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> self.treeView.setUniformRowHeights(False)</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> self.treeView.setAutoScrollMargin(50)</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.treeView.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.treeView.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.treeView.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.treeView.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> self.treeView.setMinimumWidth(400)</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> self.treeView.setMouseTracking(True)</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> self.treeView.header().setClickable(True)</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="p">@@ -1007,43 +1007,43 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> self.setCentralWidget(self.treeView)</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> </span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> # New Analysis action</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_analysis = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_analysis = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> new_analysis.triggered.connect(self.new_analysis)</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> </span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> # Load Data action</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- load_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ load_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> load_data.triggered.connect(self.load_data)</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> </span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> # Save Data action</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- save_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ save_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> save_data.triggered.connect(self.save_data)</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> </span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> # Exit Program action</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exit_program = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exit_program = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> exit_program.triggered.connect(self.close)</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> # Export iTOL tree</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- export_iTOL_tree = QtGui.QAction('Export Tree to iTOL', self)</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ export_iTOL_tree = QtWidgets.QAction('Export Tree to iTOL', self)</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> export_iTOL_tree.setToolTip('Export a set of files that can be loaded with the online tree visualizer iTOL.')</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> export_iTOL_tree.triggered.connect(self.export_iTOL)</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> </span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> # Export current graphic</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- export_graphic = QtGui.QAction('Export Figure', self)</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ export_graphic = QtWidgets.QAction('Export Figure', self)</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> export_graphic.setToolTip('Export the figure currently shown in the graphics panel to file.')</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> export_graphic.triggered.connect(self.export_graphic)</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> </span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> # Show the program information on the console</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- show_program_info = QtGui.QAction('About MicrobeGPS', self)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ show_program_info = QtWidgets.QAction('About MicrobeGPS', self)</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> show_program_info.setToolTip('Show the program information on the console.')</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> show_program_info.triggered.connect(self.show_program_info)</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> # Load online help</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- show_online_help = QtGui.QAction('Online help', self)</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ show_online_help = QtWidgets.QAction('Online help', self)</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> show_online_help.setToolTip('Redirect to the online help of MicrobeGPS.')</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> show_online_help.triggered.connect(self.show_online_help)</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> # Show the license on the console</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- show_license = QtGui.QAction('Show License', self)</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ show_license = QtWidgets.QAction('Show License', self)</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> show_license.setToolTip('Show the licensing information on the console.')</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> show_license.triggered.connect(self.show_license)</span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> </span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="p">@@ -1079,18 +1079,18 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> def closeEvent(self, event):</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> if self.saving:</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"> quit_msg = "Data saving in progress. Are you sure you want to exit the program? Unsaved data will be lost!"</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- reply = QtGui.QMessageBox.question(self, 'Message', </span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if reply == QtGui.QMessageBox.Yes:</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reply = QtWidgets.QMessageBox.question(self, 'Message', </span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if reply == QtWidgets.QMessageBox.Yes:</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> event.accept()</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> self.pipelineGui.close()</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> else:</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> event.ignore() </span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> else:</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> quit_msg = "Are you sure you want to exit the program?"</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- reply = QtGui.QMessageBox.question(self, 'Message', </span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if reply == QtGui.QMessageBox.Yes:</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reply = QtWidgets.QMessageBox.question(self, 'Message', </span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if reply == QtWidgets.QMessageBox.Yes:</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> event.accept()</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> self.pipelineGui.close()</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> else:</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="p">@@ -1129,7 +1129,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> # find member with most unique reads -> use as representative</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> most_unique = max([(m,grp.members[m].unique) for m in grp.members],key=lambda x:x[1])</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> cand_name = most_unique[0]</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gr_item = QtGui.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gr_item = QtWidgets.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> '%i'%grp.reads,'%i'%grp.unique, '%f'%grp.cov, '%f'%grp.max_val,</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> '%f'%grp.cov_homog, '%f'%grp.map_qual],QtCore.Qt.AlignHCenter)</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> gr_item.setIcon(0,candidateIcon)</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="p">@@ -1153,7 +1153,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> for m in sorted_members:</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> mbr = grp.members[m]</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> self.mapq = [min(self.mapq[0],mbr.map_qual),max(self.mapq[1],mbr.map_qual)]</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m_item = QtGui.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m_item = QtWidgets.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> '%i'%mbr.unique, '%f'%mbr.coverage, '%f'%mbr.validity,</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> '%f'%mbr.cov_homog, '%f'%mbr.map_qual])</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> m_item.setIcon(0,sequenceIcon)</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="p">@@ -1168,13 +1168,13 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> for i in range(1,m_item.columnCount()):</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> m_item.setTextColor(i,QtCore.Qt.black)</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> # Sub-Item: all reads</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ar_item = QtGui.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ar_item = QtWidgets.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> ar_item.i_type = "all reads"</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> # Sub-Item: unique reads</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ur_item = QtGui.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ur_item = QtWidgets.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> ur_item.i_type = "unique reads"</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> # Sub-Item: Top Shared Genomes</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rg_item = QtGui.QTreeWidgetItem(m_item,['Related genomes'])</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rg_item = QtWidgets.QTreeWidgetItem(m_item,['Related genomes'])</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> rg_item.i_type = "related"</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> </span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> # Iterate over all items and colorize the fields</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="p">@@ -1182,19 +1182,19 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> for g in range(root.childCount()):</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> group = root.child(g)</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> frac = int(255*(1.-group.unique/float(group.reads)))</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- group.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ group.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> for m in range(group.childCount()):</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> m_item = group.child(m)</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> frac = 255-int(m_item.unique/float(m_item.reads)*255)</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m_item.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m_item.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> frac = int(255*(1-m_item.validity))</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m_item.setBackground(4,QtGui.QBrush(QtGui.QColor(frac,255,frac)))</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m_item.setBackground(4,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> frac = int(128.*(m_item.map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m_item.setBackground(6,QtGui.QBrush(QtGui.QColor(127+frac,255-frac,0)))</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(127+frac,255-frac,0)))</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> </span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> d_max = math.sqrt(math.log(2/0.05))/math.sqrt(2*m_item.reads)</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> if m_item.cov_homog < d_max:</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m_item.setBackground(5,QtGui.QBrush(QtGui.QColor(0,0,255)))</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m_item.setBackground(5,QtWidgets.QBrush(QtWidgets.QColor(0,0,255)))</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> m_item.setTextColor(5,QtCore.Qt.white)</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> </span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> # Build the taxonomy tree for all observed genomes</span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="p">@@ -1216,7 +1216,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> continue</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> if not tid in self.taxid_to_item:</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> # add item to tree if not already found</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.taxid_to_item[tid] = QtGui.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.taxid_to_item[tid] = QtWidgets.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> par = self.taxid_to_item[tid]</span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="p">@@ -1235,10 +1235,10 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> for rd in reads:</span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"> map_qual = reads[rd]</span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> num_matches = len(self.reads[rd].matches)</span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rd_item = QtGui.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> rd_item.i_type = "read"</span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> if item.i_type == "unique reads":</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> ref_name = str(item.parent().text(0))</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> self.pr("Collecting all unique reads for "+ref_name,False)</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="p">@@ -1250,10 +1250,10 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"> reads[rd] = trg.reads[rd][2]</span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> for rd in reads:</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> map_qual = reads[rd]</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rd_item = QtGui.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> rd_item.i_type = "unique read"</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> if item.i_type == "read":</span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> rd_name = str(item.text(0))</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> self.pr("Collecting all matches of read "+rd_name,False)</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="p">@@ -1263,10 +1263,10 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> if rd_name in trg.reads:</span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> map_qual = trg.reads[rd_name][2]</span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> break</span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mt_item = QtGui.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mt_item = QtWidgets.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> mt_item.i_type = "match"</span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))</span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mt_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mt_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"> if item.i_type == "match":</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> match_name = str(item.text(0))</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> group_id = self.ref2group[match_name]</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="p">@@ -1292,10 +1292,10 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> # Sort by size, descending</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> sorted_names = sorted([(d,related[d]) for d in related],key=lambda x:-x[1])</span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> for name,shared in sorted_names:</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mt_item = QtGui.QTreeWidgetItem(item,[name,'%i'%shared])</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mt_item = QtWidgets.QTreeWidgetItem(item,[name,'%i'%shared])</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> mt_item.i_type = "match"</span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> frac = int(255*(1-shared/float(self.references[ref_name].reads)))</span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mt_item.setBackground(1,QtGui.QBrush(QtGui.QColor(255,frac,frac)))</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mt_item.setBackground(1,QtWidgets.QBrush(QtWidgets.QColor(255,frac,frac)))</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> </span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> def tree_item_clicked_handler(self,item,column):</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="p">@@ -1492,7 +1492,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> # now color the tree</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> for taxid,item in self.taxid_to_item.items():</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> if not taxid == 1:</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- item.setBackground(0,QtGui.QBrush(QtGui.QColor(255,255,255)))</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ item.setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(255,255,255)))</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> item.setText(1,'')</span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> if 1 in reads:</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> total_reads = float(len(reads[1]))</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="p">@@ -1501,7 +1501,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> N_reads = len(reads.get(taxid,set()))</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> frac =100+ int((1.-N_reads/total_reads)*155)</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> if taxid in self.taxid_to_item:</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.taxid_to_item[taxid].setBackground(0,QtGui.QBrush(QtGui.QColor(frac,frac,255)))</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.taxid_to_item[taxid].setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(frac,frac,255)))</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"> self.phyloTreeWidget.expandItem(self.taxid_to_item[taxid])</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> self.taxid_to_item[taxid].setText(1,'%i'%N_reads)</span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> self.phyloTreeWidget.resizeColumnToContents(0)</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="p">@@ -1613,7 +1613,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> self.pipelineGui.show()</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> </span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> def save_data(self):</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fname = str(QtGui.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fname = str(QtWidgets.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> if len(fname):</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> if not fname.endswith('.gpsa'):</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> if not '.' in fname:</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="p">@@ -1641,7 +1641,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> </span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> </span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> def load_data(self):</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dialog = QtGui.QFileDialog(self,'Load Data')</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dialog = QtWidgets.QFileDialog(self,'Load Data')</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> fname = str(dialog.getOpenFileName(caption='Load Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> if len(fname):</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> self.pr("Loading data from file "+fname)</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="p">@@ -1676,7 +1676,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"> """ Export the whole tree to files that can be loaded with iTOL.</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> http://itol.embl.de/upload.cgi"""</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> try:</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outdir = str(QtGui.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outdir = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"> taxonomy.candidates_to_LCA_tree(self.sgroups,self.taxonomy_nodes,self.taxonomy_names,outdir)</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> except Exception as e:</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> self.pr('Error while saving iTOL files: '+e.message)</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="p">@@ -1686,7 +1686,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> def export_graphic(self):</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> """ export the current content of the figure to file. Use the DPI </span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> quality specified in exportFigureQuality """</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dialog = QtGui.QFileDialog(self,'Save Graphic as ...')</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dialog = QtWidgets.QFileDialog(self,'Save Graphic as ...')</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> fname = str(dialog.getSaveFileName(caption='Save Graphic as ...',filter="Raster Images (*.png *.tiff *.jpg);;Vector Images (*.pdf *.eps)",parent=self))</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> if len(fname) > 0:</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> self.figure.savefig(fname,dpi=self.exportFigureQuality.value())</span>
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175
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="diff"><span class="p">@@ -1734,7 +1734,7 @@</span> the LICENSE file shipped with this softw</span>
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176
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="diff"> self.treeView.scrollToItem(sel)</span>
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177
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,6 +751,29 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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189
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="diff"> import matplotlib.pyplot as plt</span>
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190
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="diff"> </span>
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191
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="diff"> class GPSModule:</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="p">@@ -23,18 +23,18 @@</span> class GPSModule:</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"> self.selectedTaxa = []</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> self.selectedParent = ''</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> </span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.initialAnalysisLabel = QtGui.QLabel('Initial setup')</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.initialAnalysisLabel = QtWidgets.QLabel('Initial setup')</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"> self.initialAnalysis = QtGui.QPushButton('Scan GPS results')</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"> self.initialAnalysis.setToolTip('Run the initial analysis required for the following steps. This may take some time depending on the amount of data.')</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> self.initialAnalysis.clicked.connect(self.initial_analysis)</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> </span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.taxRankBoxLabel = QtGui.QLabel('Select a Taxonomic rank')</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.taxRankBoxLabel = QtWidgets.QLabel('Select a Taxonomic rank')</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> self.taxRankBox = QtGui.QComboBox()</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> self.taxRankBox.currentIndexChanged.connect(self.select_tax_rank)</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.taxGroupBoxLabel = QtGui.QLabel('Select group')</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.taxGroupBoxLabel = QtWidgets.QLabel('Select group')</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"> self.taxGroupBox = QtGui.QComboBox()</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"> self.taxGroupBox.currentIndexChanged.connect(self.select_taxon)</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.taxSelectedText = QtGui.QLabel('Found 0 [Not found]')</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.taxSelectedText = QtWidgets.QLabel('Found 0 [Not found]')</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> self.getFromTree = QtGui.QPushButton('Get from tree')</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> self.getFromTree.setToolTip('Use the currently selected taxon from the tree.')</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> self.getFromTree.clicked.connect(self.select_taxon_from_tree)</span>
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192
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="diff"><span class="p">@@ -56,7 +56,7 @@</span> class GPSModule:</span>
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193
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="diff"> tabGrid.addWidget(self.getFromTree, 3,1)</span>
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194
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="diff"> tabGrid.addWidget(self.taxSelectedText,4,0)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -206,6 +791,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="diff"> from os import linesep</span>
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207
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="diff"> from microbegps import taxonomy</span>
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208
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="diff"> </span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> class GPSModule:</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"> self.exportSupporting.setToolTip('Also export the supporting genomes of each candidate.')</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"> self.exportSupporting.setChecked(False)</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> </span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- columnsLabel = QtGui.QLabel('Columns:')</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ columnsLabel = QtWidgets.QLabel('Columns:')</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"> </span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"> self.numReads = QtGui.QCheckBox('Number of Reads')</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"> self.numReads.setToolTip('The total number of reads mapped to the candidate/genome.')</span>
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209
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span> class GPSModule:</span>
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="diff"> tabGrid.addWidget(self.genomeValidity,4,1)</span>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="diff"> tabGrid.addWidget(self.homogeneity,5,0)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,6 +818,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="diff"> class GPSModule:</span>
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="diff"> """ This GPS Module implements a search tab, that allows the user to</span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="p">@@ -15,7 +15,7 @@</span> class GPSModule:</span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> self.searchText.returnPressed.connect(self.find_reference)</span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> self.searchBtn = QtGui.QPushButton('Find Reference')</span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"> self.searchBtn.clicked.connect(self.find_reference)</span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.searchRes = QtGui.QListWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.searchRes = QtWidgets.QListWidget()</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"> self.searchRes.setMinimumHeight(150)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"> self.searchRes.itemClicked.connect(self.view_search_result)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
227
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<td class="diff-line-num new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span> class GPSModule:</span>
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<td class="diff-line-num old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
228
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<td class="diff-line-num new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="diff"> searchGrid.addWidget(self.searchBtn, 0,1)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
229
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<td class="diff-line-num new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
832
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC832" class="line" lang="diff"> searchGrid.addWidget(self.searchRes, 1,0,1,2)</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,6 +836,18 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200</td>
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<td class="diff-line-num old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
233
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<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="diff"> searchWidget.setLayout(searchGrid)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
234
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<td class="diff-line-num new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
235
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<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
838
</td>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="diff"> GPS.toolsTab.addTab(searchWidget,"Search")</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="p">@@ -38,9 +38,9 @@</span> class GPSModule:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> self.searchRes.clear()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> if len(search_results) > 0:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> for ref in sorted(search_results):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.searchRes.addItem(QtGui.QListWidgetItem(ref))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.searchRes.addItem(QtWidgets.QListWidgetItem(ref))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.searchRes.addItem(QtGui.QListWidgetItem('No matching references found.'))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.searchRes.addItem(QtWidgets.QListWidgetItem('No matching references found.'))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> def view_search_result(self, item):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> # View the item selected in the search results in the main window</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
236
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<td class="diff-line-num new_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="diff"><span class="p">@@ -54,4 +54,4 @@</span> class GPSModule:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
237
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<td class="diff-line-num new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="diff"> self.GPS.treeView.setCurrentItem(sel)</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
238
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<td class="diff-line-num new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
853
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC853" class="line" lang="diff"> self.GPS.treeView.expand(self.GPS.treeView.currentIndex())</span>
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