<commit_before><?xml version="1.0" encoding="UTF-8"?>

<?import javafx.scene.Cursor?>
<?import javafx.scene.canvas.Canvas?>
<?import javafx.scene.control.Button?>
<?import javafx.scene.control.CheckBox?>
<?import javafx.scene.control.Label?>
<?import javafx.scene.control.Menu?>
<?import javafx.scene.control.MenuBar?>
<?import javafx.scene.control.MenuItem?>
<?import javafx.scene.control.ProgressBar?>
<?import javafx.scene.control.ScrollBar?>
<?import javafx.scene.control.SplitPane?>
<?import javafx.scene.control.TextArea?>
<?import javafx.scene.control.TextField?>
<?import javafx.scene.layout.AnchorPane?>
<?import javafx.scene.layout.BorderPane?>
<?import javafx.scene.text.Font?>

<AnchorPane maxHeight="1080.0" maxWidth="1920.0" prefHeight="768.0" prefWidth="1366.0" xmlns="http://javafx.com/javafx/8.0.111" xmlns:fx="http://javafx.com/fxml/1" fx:controller="gui.MenuController">
   <children>
      <BorderPane maxHeight="1080.0" maxWidth="1920.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
         <bottom>
          <AnchorPane maxHeight="-Infinity" minHeight="-Infinity" minWidth="-Infinity" style="-fx-background-color: white;" BorderPane.alignment="CENTER">
               <children>
              <AnchorPane minHeight="0.0" minWidth="0.0" prefHeight="180.0" prefWidth="150.0" style="-fx-background-color: white;">
                     <children>
                        <Label layoutX="14.0" layoutY="14.0" text="Nodes:" />
                        <Label layoutX="14.0" layoutY="43.0" text="Edges:" />
                        <Label fx:id="numNodesLabel" layoutX="63.0" layoutY="14.0" text="0" />
                        <Label fx:id="numEdgesLabel" layoutX="63.0" layoutY="43.0" text="0" />
                     </children>
                  </AnchorPane>
                  <SplitPane dividerPositions="0.5" layoutX="150.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="150.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
                     <items>
                        <TextArea fx:id="sequenceInfo" editable="false" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" prefHeight="162.0" style="-fx-background-color: transparent; -fx-background-insets: 0px;" text="Node info &lt;click&gt;" wrapText="true" />
                        <TextArea fx:id="sequenceInfoAlt" editable="false" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" prefHeight="162.0" style="-fx-background-color: transparent; fx-background-insets: 0px;" text="Node info &lt;ctrl click&gt;" wrapText="true" />
                     </items>
                  </SplitPane>
                  <ProgressBar fx:id="progressBar" prefHeight="40.0" prefWidth="1366.0" progress="0.0" visible="false" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" />
               </children>
            </AnchorPane>
         </bottom>
         <top>
            <MenuBar prefHeight="32.0" BorderPane.alignment="CENTER">
              <menus>
                <Menu mnemonicParsing="false" text="File">
                  <items>
                    <MenuItem mnemonicParsing="false" onAction="#openGfaFileClicked" text="Open gfa file" />
                      <MenuItem fx:id="gffItem" disable="true" mnemonicParsing="false" onAction="#openGffFileClicked" text="Open gff file" />
                      <Menu mnemonicParsing="false" text="Recent">
                          <items>
                              <MenuItem fx:id="file1" mnemonicParsing="false" onAction="#file1Press" text="&lt;No recent file&gt;" />
                              <MenuItem fx:id="file2" mnemonicParsing="false" onAction="#file2Press" text="&lt;No recent file&gt;" />
                              <MenuItem fx:id="file3" mnemonicParsing="false" onAction="#file3Press" text="&lt;No recent file&gt;" />
                          </items>
                      </Menu>
                  </items>
                </Menu>
                <Menu mnemonicParsing="false" text="Help">
                  <items>
                    <MenuItem mnemonicParsing="false" text="About" />
                  </items>
                </Menu>
                  <Menu mnemonicParsing="false" text="Bookmarks">
                    <items>
                        <Menu mnemonicParsing="false" text="Open bookmarks">
                          <items>
                            <MenuItem fx:id="bookmark1" mnemonicParsing="false" onAction="#pressNewBookmark1" text="-" />
                              <MenuItem fx:id="bookmark2" mnemonicParsing="false" onAction="#pressNewBookmark2" text="-" />
                              <MenuItem fx:id="bookmark3" mnemonicParsing="false" onAction="#pressNewBookmark3" text="-" />
                          </items>
                        </Menu>
                        <MenuItem fx:id="saveBookmark" mnemonicParsing="false" onAction="#newSaveBookmarkPress" text="Add bookmark" />
                        <MenuItem mnemonicParsing="false" onAction="#manageBookmarks" text="Manage bookmarks" />
                    </items>
                  </Menu>
                  <Menu mnemonicParsing="false" text="Genomes">
                    <items>
                        <Menu mnemonicParsing="false" text="Open genomes">
                          <items>
                            <MenuItem fx:id="genome1" mnemonicParsing="false" onAction="#genome1Click" text="-" />
                              <MenuItem fx:id="genome2" mnemonicParsing="false" onAction="#genome2Click" text="-" />
                              <MenuItem fx:id="genome3" mnemonicParsing="false" onAction="#genome3Click" text="-" />
                          </items>
                        </Menu>
                    </items>
                  </Menu>
              </menus>
            </MenuBar>
         </top>
         <left>
          <AnchorPane maxWidth="150.0" minHeight="-Infinity" minWidth="-Infinity" prefWidth="150.0" BorderPane.alignment="CENTER">
               <children>
                  <TextField fx:id="nodeTextField" alignment="CENTER" disable="true" layoutX="10.0" layoutY="30.0" prefHeight="29.0" prefWidth="97.0" promptText="Centre node">
                     <font>
                        <Font size="12.0" />
                     </font></TextField>
                  <Button fx:id="goToNodeBut" disable="true" layoutX="10.0" layoutY="72.0" mnemonicParsing="false" onAction="#traverseGraphClicked" text="Go to this node">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <TextField fx:id="radiusTextField" alignment="CENTER" disable="true" layoutX="10.0" layoutY="111.0" prefHeight="29.0" prefWidth="97.0" promptText="Radius">
                     <font>
                        <Font size="12.0" />
                     </font></TextField>
                  <Button fx:id="chooseGenome" disable="true" layoutX="10.0" layoutY="171.0" mnemonicParsing="false" onAction="#chooseGenomePress" prefHeight="25.0" prefWidth="120.0" text="Specific Genome">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <Button fx:id="annoBut" disable="true" layoutX="12.0" layoutY="208.0" mnemonicParsing="false" onAction="#chooseAnnoClicked" prefHeight="25.0" prefWidth="120.0" text="Choose Annotation">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <CheckBox fx:id="rainbowBut" disable="true" layoutX="10.0" layoutY="255.0" mnemonicParsing="false" onAction="#rainbowButtonClicked" selected="true" text="Rainbow view">
                     <font>
                        <Font size="12.0" />
                     </font>
                  </CheckBox>
                  <CheckBox fx:id="collapseSNPButton" disable="true" layoutX="10.0" layoutY="285.0" mnemonicParsing="false" onAction="#collapseSNPClicked" selected="true" text="Collapse SNPs">
                     <font>
                        <Font size="12.0" />
                     </font>
                  </CheckBox>
               </children>
            </AnchorPane>
         </left>
         <center>
          <AnchorPane fx:id="canvasPanel" focusTraversable="true" minHeight="0.0" minWidth="0.0" prefHeight="520.0" prefWidth="1200.0" style="-fx-background-color: WHITE;" BorderPane.alignment="CENTER">
               <children>
                  <Canvas fx:id="canvas" onMouseClicked="#clickMouse" onScroll="#scrollZoom" />
                  <Button fx:id="zoomInBut" disable="true" mnemonicParsing="false" onAction="#zoomInClicked" prefHeight="32.0" prefWidth="32.0" text="+" AnchorPane.rightAnchor="40.0" AnchorPane.topAnchor="20.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <Button fx:id="zoomOutBut" disable="true" mnemonicParsing="false" onAction="#zoomOutClicked" prefHeight="32.0" prefWidth="32.0" text="-" AnchorPane.rightAnchor="40.0" AnchorPane.topAnchor="60.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <Button fx:id="rightPannButton" disable="true" mnemonicParsing="false" prefHeight="80.0" prefWidth="200.0" text="Right" AnchorPane.bottomAnchor="30.0" AnchorPane.rightAnchor="40.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <Button fx:id="leftPannButton" disable="true" mnemonicParsing="false" prefHeight="80.0" prefWidth="200.0" text="Left" AnchorPane.bottomAnchor="30.0" AnchorPane.leftAnchor="20.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <ScrollBar fx:id="scrollBar" layoutX="1184.0" layoutY="125.0" max="10.0" orientation="VERTICAL" visibleAmount="10.0" AnchorPane.bottomAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0" />
               </children>
            </AnchorPane>
         </center>
      </BorderPane>
   </children>
</AnchorPane><commit_msg>Give the GUI a better look<commit_after><?xml version="1.0" encoding="UTF-8"?>

<?import javafx.scene.Cursor?>
<?import javafx.scene.canvas.Canvas?>
<?import javafx.scene.control.Button?>
<?import javafx.scene.control.CheckBox?>
<?import javafx.scene.control.Label?>
<?import javafx.scene.control.Menu?>
<?import javafx.scene.control.MenuBar?>
<?import javafx.scene.control.MenuItem?>
<?import javafx.scene.control.ProgressBar?>
<?import javafx.scene.control.ScrollBar?>
<?import javafx.scene.control.Separator?>
<?import javafx.scene.control.SplitPane?>
<?import javafx.scene.control.TextArea?>
<?import javafx.scene.control.TextField?>
<?import javafx.scene.layout.AnchorPane?>
<?import javafx.scene.layout.BorderPane?>
<?import javafx.scene.text.Font?>

<AnchorPane maxHeight="1080.0" maxWidth="1920.0" prefHeight="768.0" prefWidth="1366.0" xmlns="http://javafx.com/javafx/8.0.111" xmlns:fx="http://javafx.com/fxml/1" fx:controller="gui.MenuController">
   <children>
      <BorderPane maxHeight="1080.0" maxWidth="1920.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
         <bottom>
          <AnchorPane maxHeight="-Infinity" minHeight="-Infinity" minWidth="-Infinity" BorderPane.alignment="CENTER">
               <children>
              <AnchorPane minHeight="0.0" minWidth="0.0" prefHeight="180.0" prefWidth="150.0" style="-fx-border-color: grey;">
                     <children>
                        <Label layoutX="14.0" layoutY="14.0" text="Nodes:" />
                        <Label layoutX="14.0" layoutY="43.0" text="Edges:" />
                        <Label fx:id="numNodesLabel" layoutX="63.0" layoutY="14.0" text="0" />
                        <Label fx:id="numEdgesLabel" layoutX="63.0" layoutY="43.0" text="0" />
                     </children>
                  </AnchorPane>
                  <SplitPane dividerPositions="0.5" layoutX="150.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="150.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
                     <items>
                        <TextArea fx:id="sequenceInfo" editable="false" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" prefHeight="162.0" style="-fx-background-color: transparent; -fx-background-insets: 0px;" text="Node info &lt;click&gt;" wrapText="true" />
                        <TextArea fx:id="sequenceInfoAlt" editable="false" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" prefHeight="162.0" style="-fx-background-color: transparent; fx-background-insets: 0px;" text="Node info &lt;ctrl click&gt;" wrapText="true" />
                     </items>
                  </SplitPane>
                  <ProgressBar fx:id="progressBar" prefHeight="40.0" prefWidth="1366.0" progress="0.0" visible="false" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" />
               </children>
            </AnchorPane>
         </bottom>
         <top>
            <MenuBar prefHeight="32.0" BorderPane.alignment="CENTER">
              <menus>
                <Menu mnemonicParsing="false" text="File">
                  <items>
                    <MenuItem mnemonicParsing="false" onAction="#openGfaFileClicked" text="Open gfa file" />
                      <MenuItem fx:id="gffItem" disable="true" mnemonicParsing="false" onAction="#openGffFileClicked" text="Open gff file" />
                      <Menu mnemonicParsing="false" text="Recent">
                          <items>
                              <MenuItem fx:id="file1" mnemonicParsing="false" onAction="#file1Press" text="&lt;No recent file&gt;" />
                              <MenuItem fx:id="file2" mnemonicParsing="false" onAction="#file2Press" text="&lt;No recent file&gt;" />
                              <MenuItem fx:id="file3" mnemonicParsing="false" onAction="#file3Press" text="&lt;No recent file&gt;" />
                          </items>
                      </Menu>
                  </items>
                </Menu>
                <Menu mnemonicParsing="false" text="Help">
                  <items>
                    <MenuItem mnemonicParsing="false" text="About" />
                  </items>
                </Menu>
                  <Menu mnemonicParsing="false" text="Bookmarks">
                    <items>
                        <Menu mnemonicParsing="false" text="Open bookmarks">
                          <items>
                            <MenuItem fx:id="bookmark1" mnemonicParsing="false" onAction="#pressNewBookmark1" text="-" />
                              <MenuItem fx:id="bookmark2" mnemonicParsing="false" onAction="#pressNewBookmark2" text="-" />
                              <MenuItem fx:id="bookmark3" mnemonicParsing="false" onAction="#pressNewBookmark3" text="-" />
                          </items>
                        </Menu>
                        <MenuItem fx:id="saveBookmark" mnemonicParsing="false" onAction="#newSaveBookmarkPress" text="Add bookmark" />
                        <MenuItem mnemonicParsing="false" onAction="#manageBookmarks" text="Manage bookmarks" />
                    </items>
                  </Menu>
                  <Menu mnemonicParsing="false" text="Genomes">
                    <items>
                        <Menu mnemonicParsing="false" text="Open genomes">
                          <items>
                            <MenuItem fx:id="genome1" mnemonicParsing="false" onAction="#genome1Click" text="-" />
                              <MenuItem fx:id="genome2" mnemonicParsing="false" onAction="#genome2Click" text="-" />
                              <MenuItem fx:id="genome3" mnemonicParsing="false" onAction="#genome3Click" text="-" />
                          </items>
                        </Menu>
                    </items>
                  </Menu>
              </menus>
            </MenuBar>
         </top>
         <left>
          <AnchorPane maxWidth="150.0" minHeight="-Infinity" minWidth="-Infinity" prefWidth="150.0" style="-fx-border-color: GREY;" BorderPane.alignment="CENTER">
               <children>
                  <TextField fx:id="nodeTextField" alignment="CENTER" disable="true" layoutX="27.0" layoutY="64.0" prefHeight="29.0" prefWidth="97.0" promptText="Centre node">
                     <font>
                        <Font size="12.0" />
                     </font></TextField>
                  <Button fx:id="goToNodeBut" disable="true" layoutX="26.0" layoutY="28.0" mnemonicParsing="false" onAction="#traverseGraphClicked" text="Go to this node">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <TextField fx:id="radiusTextField" alignment="CENTER" disable="true" layoutX="27.0" layoutY="101.0" prefHeight="29.0" prefWidth="97.0" promptText="Radius">
                     <font>
                        <Font size="12.0" />
                     </font></TextField>
                  <Button fx:id="chooseGenome" disable="true" layoutX="15.0" layoutY="171.0" mnemonicParsing="false" onAction="#chooseGenomePress" prefHeight="25.0" prefWidth="120.0" text="Specific Genome">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <Button fx:id="annoBut" disable="true" layoutX="17.0" layoutY="208.0" mnemonicParsing="false" onAction="#chooseAnnoClicked" prefHeight="25.0" prefWidth="120.0" text="Choose Annotation">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="12.0" />
                     </font>
                  </Button>
                  <CheckBox fx:id="rainbowBut" disable="true" layoutX="29.0" layoutY="278.0" mnemonicParsing="false" onAction="#rainbowButtonClicked" selected="true" text="Rainbow view">
                     <font>
                        <Font size="12.0" />
                     </font>
                  </CheckBox>
                  <CheckBox fx:id="collapseSNPButton" disable="true" layoutX="29.0" layoutY="308.0" mnemonicParsing="false" onAction="#collapseSNPClicked" selected="true" text="Collapse SNPs">
                     <font>
                        <Font size="12.0" />
                     </font>
                  </CheckBox>
                  <Separator layoutX="-23.0" layoutY="148.0" prefWidth="200.0" AnchorPane.leftAnchor="10.0" AnchorPane.rightAnchor="10.0" />
                  <Separator layoutX="9.0" layoutY="257.0" prefWidth="200.0" AnchorPane.leftAnchor="10.0" AnchorPane.rightAnchor="10.0" />
               </children>
            </AnchorPane>
         </left>
         <center>
          <AnchorPane fx:id="canvasPanel" focusTraversable="true" minHeight="0.0" minWidth="0.0" prefHeight="520.0" prefWidth="1200.0" style="-fx-background-color: WHITE;" BorderPane.alignment="CENTER">
               <children>
                  <Canvas fx:id="canvas" onMouseClicked="#clickMouse" onScroll="#scrollZoom" />
                  <Button fx:id="zoomInBut" disable="true" layoutX="1080.0" layoutY="451.0" mnemonicParsing="false" onAction="#zoomInClicked" prefHeight="32.0" prefWidth="32.0" text="+" AnchorPane.bottomAnchor="70.0" AnchorPane.rightAnchor="100.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <Button fx:id="zoomOutBut" disable="true" layoutX="1080.0" layoutY="495.0" mnemonicParsing="false" onAction="#zoomOutClicked" prefHeight="32.0" prefWidth="32.0" text="-" AnchorPane.bottomAnchor="30.0" AnchorPane.rightAnchor="100.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                  </Button>
                  <Button fx:id="rightPannButton" disable="true" mnemonicParsing="false" prefHeight="30.0" prefWidth="50.0" text="→" AnchorPane.bottomAnchor="30.0" AnchorPane.rightAnchor="40.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="14.0" />
                     </font>
                  </Button>
                  <Button fx:id="leftPannButton" disable="true" layoutX="1014.0" layoutY="496.0" mnemonicParsing="false" prefHeight="30.0" prefWidth="50.0" text="←" AnchorPane.bottomAnchor="30.0" AnchorPane.rightAnchor="142.0">
                     <cursor>
                        <Cursor fx:constant="OPEN_HAND" />
                     </cursor>
                     <font>
                        <Font size="14.0" />
                     </font>
                  </Button>
                  <ScrollBar fx:id="scrollBar" layoutX="1184.0" layoutY="125.0" max="10.0" orientation="VERTICAL" visibleAmount="10.0" AnchorPane.bottomAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0" />
               </children>
            </AnchorPane>
         </center>
      </BorderPane>
   </children>
</AnchorPane>
{'fraction_non_alphanumeric': 0.14793881487462432, 'fraction_numerical': 0.04005741712645225, 'mean_word_length': 1.894572838223838, 'pattern_counts': {'":': 0, '<': 352, '<?xml version=': 2, '>': 352, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6625891', 'n_tokens_mistral': 6958, 'n_tokens_neox': 6324, 'n_words': 1008}