Update Generalized D class

Author: travisbenedict

gui_layout.py

@@ -2,8 +2,7 @@
 
 # Form implementation generated from reading ui file 'gui_layout.ui'
 #
-# Created: Sun Feb 11 21:44:47 2018
-#      by: PyQt4 UI code generator 4.10
+# Created by: PyQt4 UI code generator 4.11.4
 #
 # WARNING! All changes made in this file will be lost!
 

main.py

@@ -250,6 +250,8 @@ def __init__(self, parent=None):
         self.lAlignmentDirBtn.clicked.connect(lambda: self.openDirectory(self.lAlignmentDirEntry))
         self.lSpeciesTreeBtn.clicked.connect(lambda: self.getFileName(self.lSpeciesTreeEntry))
         self.lStatisticFileBtn.clicked.connect(lambda: self.getFileName(self.lStatisticFileEntry))
+        self.calcGenD.plot = False
+        self.calcGenD.meta = ""
 
         # when an alignment is selected update the combo boxes
         self.connect(self.lAlignmentEntry, QtCore.SIGNAL('FILE_SELECTED'), lambda: self.updateTaxonComboBoxes(self.lStatisticSourceComboBoxes, self.lAlignmentEntry))

module/gui_layout.py

@@ -541,7 +541,7 @@ def setupUi(self, PhylogeneticVisualization):
         self.verticalLayout_21.addWidget(self.widget)
         self.raxmlToolBox.addItem(self.raxmlOptionsPage, _fromUtf8(""))
         self.graphOptionsPage = QtGui.QWidget()
-        self.graphOptionsPage.setGeometry(QtCore.QRect(0, 0, 949, 659))
+        self.graphOptionsPage.setGeometry(QtCore.QRect(0, 0, 949, 542))
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
@@ -1696,12 +1696,16 @@ def setupUi(self, PhylogeneticVisualization):
         self.lineEdit.setObjectName(_fromUtf8("lineEdit"))
         self.horizontalLayout_73.addWidget(self.lineEdit)
         self.verticalLayout_29.addLayout(self.horizontalLayout_73)
-        self.horizontalLayout_62 = QtGui.QHBoxLayout()
-        self.horizontalLayout_62.setObjectName(_fromUtf8("horizontalLayout_62"))
+        self.horizontalLayout_74 = QtGui.QHBoxLayout()
+        self.horizontalLayout_74.setContentsMargins(-1, -1, -1, 0)
+        self.horizontalLayout_74.setObjectName(_fromUtf8("horizontalLayout_74"))
+        self.checkBox = QtGui.QCheckBox(self.groupBox_3)
+        self.checkBox.setObjectName(_fromUtf8("checkBox"))
+        self.horizontalLayout_74.addWidget(self.checkBox)
         self.generatePlotCB = QtGui.QCheckBox(self.groupBox_3)
         self.generatePlotCB.setObjectName(_fromUtf8("generatePlotCB"))
-        self.horizontalLayout_62.addWidget(self.generatePlotCB)
-        self.verticalLayout_29.addLayout(self.horizontalLayout_62)
+        self.horizontalLayout_74.addWidget(self.generatePlotCB)
+        self.verticalLayout_29.addLayout(self.horizontalLayout_74)
         self.horizontalLayout_66.addLayout(self.verticalLayout_29)
         self.verticalLayout_22.addLayout(self.horizontalLayout_66)
         self.lStatisticWrapperVL.addWidget(self.groupBox_3)
@@ -1827,7 +1831,7 @@ def setupUi(self, PhylogeneticVisualization):
         self.scrollArea.setWidgetResizable(True)
         self.scrollArea.setObjectName(_fromUtf8("scrollArea"))
         self.verboseOutputScrollable = QtGui.QWidget()
-        self.verboseOutputScrollable.setGeometry(QtCore.QRect(0, 0, 98, 48))
+        self.verboseOutputScrollable.setGeometry(QtCore.QRect(0, 0, 57, 48))
         self.verboseOutputScrollable.setObjectName(_fromUtf8("verboseOutputScrollable"))
         self.verticalLayout_28 = QtGui.QVBoxLayout(self.verboseOutputScrollable)
         self.verticalLayout_28.setObjectName(_fromUtf8("verticalLayout_28"))
@@ -2059,6 +2063,7 @@ def retranslateUi(self, PhylogeneticVisualization):
         self.label_43.setText(_translate("PhylogeneticVisualization", "Alpha:", None))
         self.lAlphaEntry.setText(_translate("PhylogeneticVisualization", "0.01", None))
         self.label_50.setText(_translate("PhylogeneticVisualization", "Outgroup:", None))
+        self.checkBox.setText(_translate("PhylogeneticVisualization", "Use Inverse", None))
         self.generatePlotCB.setText(_translate("PhylogeneticVisualization", "Generate Plot", None))
         self.lImageLabel.setText(_translate("PhylogeneticVisualization", "input species tree for visualization", None))
         self.label_39.setText(_translate("PhylogeneticVisualization", "Reticulations", None))

module/gui_layout.ui

@@ -1313,7 +1313,7 @@
                <x>0</x>
                <y>0</y>
                <width>949</width>
-               <height>659</height>
+               <height>542</height>
               </rect>
              </property>
              <property name="sizePolicy">
@@ -3896,7 +3896,17 @@ Run RAxML -&gt; Advanced</string>
                       </layout>
                      </item>
                      <item>
-                      <layout class="QHBoxLayout" name="horizontalLayout_62">
+                      <layout class="QHBoxLayout" name="horizontalLayout_74">
+                       <property name="bottomMargin">
+                        <number>0</number>
+                       </property>
+                       <item>
+                        <widget class="QCheckBox" name="checkBox">
+                         <property name="text">
+                          <string>Use Inverse</string>
+                         </property>
+                        </widget>
+                       </item>
                        <item>
                         <widget class="QCheckBox" name="generatePlotCB">
                          <property name="text">
@@ -4179,7 +4189,7 @@ Run RAxML -&gt; Advanced</string>
                       <rect>
                        <x>0</x>
                        <y>0</y>
-                       <width>98</width>
+                       <width>57</width>
                        <height>48</height>
                       </rect>
                      </property>
@@ -4329,4 +4339,4 @@ Run RAxML -&gt; Advanced</string>
  </widget>
  <resources/>
  <connections/>
-</ui>
+</ui>