working on generating documentation

src/main/java/splitstree6/io/nexus/GenomesNexusInput.java

@@ -47,9 +47,9 @@ public class GenomesNexusInput extends NexusIOBase implements INexusInput<Genome
 					[FILES={YES|NO}]
 				;]
 				MATRIX
-				  [label] [accession] length {sequence | [#parts] length {sequence|{file:.. offset}} .. length {sequence|{file offset}}},
-				  ...
-				  [label] [accession] length {sequence | [#parts] length {sequence|{file:.. offset}} .. length {sequence|{file offset}}}
+				 	[label] [accession] length {sequence | [#parts] length {sequence|{file:.. offset}} .. length {sequence|{file offset}}},
+				 	...
+				 	[label] [accession] length {sequence | [#parts] length {sequence|{file:.. offset}} .. length {sequence|{file offset}}}
 				;]
 			END;
 			""";

src/main/java/splitstree6/io/nexus/TaxaNexusInput.java

@@ -49,9 +49,9 @@ public class TaxaNexusInput extends NexusIOBase {
 
 	public static final String DESCRIPTION = """
 			This block maintains the list of all taxa in the analysis.
-			There is a fixed number (nTax) of taxa and each has an id 1..nTax and label associated with it.
+			There is a fixed number (nTax) of taxa and each has an id 1..nTax and an unique label.
 			Optionally, an info string can be provided for each taxon.
-			Optionally, a display label can be provided for each taxon. This many include certain HTML tags
+			Also, a display label may be provided for each taxon. This can include certain HTML tags
 			that are used to render the label.
 			""";
 

src/main/java/splitstree6/io/nexus/TraitsNexusInput.java

@@ -54,6 +54,11 @@ public class TraitsNexusInput extends NexusIOBase implements INexusInput<TraitsB
 			END;
 			""";
 
+	public static final String DESCRIPTION = """
+			This block contains traits associated with the input taxa. Each trait has a label,
+			optional latitude and longitude, and a value, which can either be a number or a string.
+			""";
+
 	public String getSyntax() {
 		return SYNTAX;
 	}
@@ -101,13 +106,13 @@ public List<String> parse(NexusStreamParser np, TaxaBlock taxaBlock, TraitsBlock
 				throw new IOExceptionWithLineNumber("Format 'no labels' invalid because no taxLabels given in TAXA block", np.lineno());
 
 			final var separator = np.findIgnoreCase(formatTokens, "separator=", StringUtils.toString(TraitsNexusFormat.Separator.values(), " "), "");
-			if (separator.length() > 0) {
+			if (!separator.isEmpty()) {
 				format.setOptionSeparator(separator);
 			}
 
 			format.setOptionMissingCharacter(Character.toLowerCase(np.findIgnoreCase(formatTokens, "missing=", null, '?')));
 
-			if (formatTokens.size() != 0)
+			if (!formatTokens.isEmpty())
 				throw new IOExceptionWithLineNumber("Unexpected in FORMAT: '" + StringUtils.toString(formatTokens, " ") + "'", np.lineno());
 		}
 

src/main/java/splitstree6/io/readers/ImportManager.java

@@ -23,6 +23,7 @@
 import jloda.util.Basic;
 import splitstree6.data.SplitsBlock;
 import splitstree6.data.TreesBlock;
+import splitstree6.io.readers.characters.StockholmReader;
 import splitstree6.io.utils.DataReaderBase;
 import splitstree6.io.utils.IDataReaderNoAutoDetect;
 import splitstree6.workflow.DataBlock;
@@ -45,7 +46,7 @@ public synchronized static ImportManager getInstance() {
 	private ImportManager() {
 		readers.add(new splitstree6.io.readers.characters.FastAReader());
 		readers.add(new splitstree6.io.readers.characters.MSFReader());
-		readers.add(new splitstree6.io.readers.characters.StockholmImporter());
+		readers.add(new StockholmReader());
 		readers.add(new splitstree6.io.readers.characters.NexusReader());
 		readers.add(new splitstree6.io.readers.characters.PhylipReader());
 		readers.add(new splitstree6.io.readers.distances.NexusReader());

src/main/java/splitstree6/io/readers/characters/StockholmImporter.java → src/main/java/splitstree6/io/readers/characters/StockholmReader.java

@@ -1,5 +1,5 @@
 /*
- * StockholmImporter.java Copyright (C) 2024 Daniel H. Huson
+ * StockholmReader.java Copyright (C) 2024 Daniel H. Huson
  *
  * (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -32,9 +32,9 @@
 
 import static splitstree6.io.readers.characters.FastAReader.checkIfCharactersValid;
 
-public class StockholmImporter extends CharactersReader {
+public class StockholmReader extends CharactersReader {
 
-	public StockholmImporter() {
+	public StockholmReader() {
 		setFileExtensions("stk", "sto", "stockholm");
 	}
 

src/main/java/splitstree6/main/SplitsTree6.java

@@ -81,7 +81,6 @@ public static void main(String[] args) {
 		SplashScreen.setVersionString(ProgramProperties.getProgramVersion());
 		SplashScreen.setImageResourceName("SplitsTree6-splash.png");
 
-
 		try {
 			parseArguments(args);
 		} catch (Throwable th) {

src/main/java/splitstree6/window/MainWindow.java

@@ -35,6 +35,7 @@
 import jloda.fx.selection.SetSelectionModel;
 import jloda.fx.util.MemoryUsage;
 import jloda.fx.util.ProgramProperties;
+import jloda.fx.util.RunAfterAWhile;
 import jloda.fx.util.StatementFilter;
 import jloda.fx.window.IMainWindow;
 import jloda.fx.window.MainWindowManager;
@@ -53,6 +54,7 @@
 import splitstree6.view.alignment.AlignmentView;
 import splitstree6.workflow.Workflow;
 import splitstree6.workflowtree.WorkflowTreeView;
+import splitstree6.xtra.latex.MenusToLaTeX;
 
 import java.io.IOException;
 import java.util.Objects;
@@ -143,6 +145,11 @@ public MainWindow() {
 		name.set("Untitled");
 
 		presenter = new MainWindowPresenter(this);
+
+		if (true) {
+			var obj = new Object();
+			RunAfterAWhile.applyInFXThread(obj, () -> System.out.println(MenusToLaTeX.apply(controller.getMenuBar())));
+		}
 	}
 
 	@Override

src/main/java/splitstree6/window/MainWindowController.java

@@ -161,9 +161,6 @@ public class MainWindowController {
 	@FXML
 	private MenuItem gotoLineMenuItem;
 
-	@FXML
-	private MenuItem preferencesMenuItem;
-
 	@FXML
 	private MenuItem selectAllMenuItem;
 
@@ -752,10 +749,6 @@ public MenuItem getGotoLineMenuItem() {
 		return gotoLineMenuItem;
 	}
 
-	public MenuItem getPreferencesMenuItem() {
-		return preferencesMenuItem;
-	}
-
 	public MenuItem getSelectAllMenuItem() {
 		return selectAllMenuItem;
 	}

src/main/java/splitstree6/window/MainWindowPresenter.java

@@ -495,8 +495,6 @@ private void setupCommonMenuItems(MainWindow mainWindow, MainWindowController co
 
 		// controller.getGotoLineMenuItem().setOnAction(null);
 
-		controller.getPreferencesMenuItem().setOnAction(null);
-
 		controller.getSelectAllMenuItem().setOnAction(e -> mainWindow.getTaxonSelectionModel().selectAll(mainWindow.getWorkflow().getWorkingTaxaBlock().getTaxa()));
 		controller.getSelectAllMenuItem().disableProperty().bind(mainWindow.emptyProperty());
 

src/main/java/splitstree6/xtra/latex/AlgorithmsToLaTeX.java

@@ -29,34 +29,15 @@
 import java.util.HashMap;
 import java.util.List;
 
+import static splitstree6.xtra.latex.IOToLaTeX.FOOTER;
+import static splitstree6.xtra.latex.IOToLaTeX.HEADER;
+
 /**
  * outputs a LaTeX document containing a description of all algorithms
  * Daniel Huson, 3.2024
  */
 public class AlgorithmsToLaTeX {
 	public static void main(String[] args) {
-		var header = """
-				\\documentclass{article}
-				\\usepackage{graphicx}
-				\\usepackage{hyperref}
-				\\usepackage{fullpage}
-				\\usepackage{parskip}\s
-				     
-				\\title{SplitsTree Community Edition - Algorithms}
-				\\author{Daniel H. Huson and Dave Bryant}
-				\\date{March 2024}
-				    
-				\\begin{document}
-				    
-				\\maketitle
-								
-				\\section{Algorithms}
-								
-				""";
-
-		var footer = """
-				\\end{document}
-				""";
 		var ordering = List.of("Characters Block", "Distances Block", "Splits Block", "Trees Block", "Network Block", "View Block", "Report Block");
 
 		var fromLineMap = new HashMap<String, List<String>>();
@@ -107,7 +88,7 @@ public static void main(String[] args) {
 			}
 		}
 
-		System.out.println(header);
+		System.out.println(HEADER);
 
 		if (true) {
 			System.out.println("\\section{List of algorithms sorted by input}\n\n");
@@ -132,7 +113,7 @@ public static void main(String[] args) {
 				}
 			}
 		}
-		System.out.println(footer);
+		System.out.println(FOOTER);
 
 	}
 }

src/main/java/splitstree6/xtra/latex/BlocksToLaTeX.java

@@ -0,0 +1,54 @@
+/*
+ *  BlocksToLaTeX.java Copyright (C) 2024 Daniel H. Huson
+ *
+ *  (Some files contain contributions from other authors, who are then mentioned separately.)
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package splitstree6.xtra.latex;
+
+import splitstree6.io.nexus.*;
+
+import static splitstree6.xtra.latex.IOToLaTeX.FOOTER;
+import static splitstree6.xtra.latex.IOToLaTeX.HEADER;
+
+public class BlocksToLaTeX {
+	public static void main(String[] args) {
+
+		System.out.println(HEADER +
+						   "\\section{Main data blocks and their `Nexus format' syntax}\n\n" +
+						   output("Taxa block", TaxaNexusInput.DESCRIPTION, TaxaNexusInput.SYNTAX) +
+						   output("Traits block", TraitsNexusInput.DESCRIPTION, TraitsNexusInput.SYNTAX) +
+						   output("Characters block", CharactersNexusInput.DESCRIPTION, CharactersNexusInput.SYNTAX) +
+						   output("Distances block", DistancesNexusInput.DESCRIPTION, DistancesNexusInput.SYNTAX) +
+						   output("Trees block", TreesNexusInput.DESCRIPTION, TreesNexusInput.SYNTAX) +
+						   output("Splits block", SplitsNexusInput.DESCRIPTION, SplitsNexusInput.SYNTAX) +
+						   output("Network block", NetworkNexusInput.DESCRIPTION, NetworkNexusInput.SYNTAX) +
+						   output("View block", ViewNexusInput.DESCRIPTION, ViewNexusInput.SYNTAX) +
+						   output("Algorithms block", AlgorithmNexusInput.DESCRIPTION, AlgorithmNexusInput.SYNTAX) +
+						   output("Report block", ReportNexusInput.DESCRIPTION, ReportNexusInput.SYNTAX) +
+						   output("Sets block", SetsNexusInput.DESCRIPTION, SetsNexusInput.SYNTAX) +
+						   output("SplitsTree6 block", SplitsTree6NexusInput.DESCRIPTION, SplitsTree6NexusInput.SYNTAX) +
+						   output("Genomes block", GenomesNexusInput.DESCRIPTION, GenomesNexusInput.SYNTAX) +
+						   FOOTER);
+	}
+
+	public static String output(String name, String description, String syntax) {
+		return "\\subsection{%s}\n%n%s%n".formatted(name, description.replaceAll("\t", "    ")) +
+			   "{\\footnotesize\\begin{verbatim}\n" +
+			   syntax.replaceAll("\t", "  ") +
+			   "\\end{verbatim}}\n\n";
+	}
+}

src/main/java/splitstree6/xtra/latex/IOToLaTeX.java

@@ -1,5 +1,5 @@
 /*
- *  NexusToLaTeX.java Copyright (C) 2024 Daniel H. Huson
+ *  BlocksToLaTeX.java Copyright (C) 2024 Daniel H. Huson
  *
  *  (Some files contain contributions from other authors, who are then mentioned separately.)
  *
@@ -29,29 +29,21 @@
 import java.lang.reflect.InvocationTargetException;
 
 public class IOToLaTeX {
-	public static void main(String[] args) throws InvocationTargetException, NoSuchMethodException, InstantiationException, IllegalAccessException {
-		var header = """
+	public static final String HEADER = """
 				\\documentclass{article}
 				\\usepackage{graphicx}
 				\\usepackage{hyperref}
 				\\usepackage{fullpage}
 				\\usepackage{parskip}\s
 				     
-				\\title{SplitsTree Community Edition - Importers}
-				\\author{Daniel H. Huson and Dave Bryant}
-				\\date{March 2024}
-				    
 				\\begin{document}
-				    
-				\\maketitle
-								
+			    								
 				""";
 
-		var footer = """
-				\\end{document}
-				""";
+	public static final String FOOTER = "\n\\end{document}\n";
 
-		System.out.println(header);
+	public static void main(String[] args) throws InvocationTargetException, NoSuchMethodException, InstantiationException, IllegalAccessException {
+		System.out.println(HEADER);
 
 		System.out.println("\\section{Supported import formats}\n");
 
@@ -72,7 +64,7 @@ public static void main(String[] args) throws InvocationTargetException, NoSuchM
 						   outputExporters(NetworkBlock.class) +
 						   outputExporters(GenomesBlock.class));
 
-		System.out.println(footer);
+		System.out.println(FOOTER);
 	}
 
 	public static String outputImporters(Class<? extends DataBlock> clazz) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
@@ -96,7 +88,7 @@ public static String outputExporters(Class<? extends DataBlock> clazz) throws No
 		var exportManager = ExportManager.getInstance();
 		var formats = exportManager.getExporters(clazz).stream().map(ReaderWriterBase::getName).filter(n -> !n.equals("PlainText")).toList();
 
-		buf.append("Can import %s data in the following formats: %s.%n%n"
+		buf.append("Can export %s data in the following formats: %s.%n%n"
 				.formatted(blockName, StringUtils.toString(formats, ", ")));
 		return buf.toString();
 	}

src/main/java/splitstree6/xtra/latex/MenusToLaTeX.java

@@ -0,0 +1,62 @@
+/*
+ *  MenusToLaTeX.java Copyright (C) 2024 Daniel H. Huson
+ *
+ *  (Some files contain contributions from other authors, who are then mentioned separately.)
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package splitstree6.xtra.latex;
+
+import javafx.scene.control.Menu;
+import javafx.scene.control.MenuBar;
+import javafx.scene.control.SeparatorMenuItem;
+
+/**
+ * write out all items in the menu bar in LaTeX
+ */
+public class MenusToLaTeX {
+	public static String apply(MenuBar menuBar) {
+		var buf = new StringBuilder("\\section{The main menu bar}\n\n");
+		for (var menu : menuBar.getMenus()) {
+			buf.append(applyRec(menu, 0));
+		}
+		return buf.toString();
+	}
+
+	public static String applyRec(Menu menu, int level) {
+		var buf = new StringBuilder();
+		if (level == 0) {
+			buf.append("\\subsection{The %s menu}%n%n%n".formatted(menu.getText()));
+			buf.append("This menu has the following items:\n\n");
+		} else {
+			buf.append("This %s-menu has the following items:\n\n".formatted("sub".repeat(level)));
+		}
+		buf.append("\\begin{itemize}\n");
+		for (var item : menu.getItems()) {
+			if (!(item instanceof SeparatorMenuItem)) {
+				if (item instanceof Menu subMenu) {
+					applyRec(subMenu, level + 1);
+				} else {
+					var text = item.getText();
+					if (item.getUserData() != null)
+						text += " - " + item.getUserData().toString();
+					buf.append("\\item %s%n".formatted(text));
+				}
+			}
+		}
+		buf.append("\\end{itemize}\n\n");
+		return buf.toString();
+	}
+}