more work on automatic generation of documentation

Author: dhuson

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

@@ -74,6 +74,7 @@ public static void main(String[] args) {
 
 				var options = OptionIO.optionsUsage(algorithm);
 				if (!options.isBlank()) {
+					buf.append("The algorithm has the following options:\n");
 					buf.append("\n{\\footnotesize\\obeylines\n");
 					for (var line : StringUtils.toList(options)) {
 						var pos = line.indexOf("-");

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

@@ -0,0 +1,56 @@
+/*
+ *  AlgorithmsToLaTeX.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.algorithms.AlgorithmList;
+import splitstree6.workflow.DataTaxaFilter;
+import splitstree6.workflow.interfaces.DoNotLoadThisAlgorithm;
+
+import java.util.TreeSet;
+
+/**
+ * outputs a LaTeX document containing a description of all algorithms
+ * Daniel Huson, 3.2024
+ */
+public class ExtractReferences {
+	public static void main(String[] args) {
+		var set = new TreeSet<String>();
+
+		for (var algorithm : AlgorithmList.list()) {
+			if (!(algorithm instanceof DataTaxaFilter || algorithm instanceof DoNotLoadThisAlgorithm)) {
+
+
+				var citations = algorithm.getCitation();
+				if (citations != null && !citations.isBlank()) {
+					var pos = citations.indexOf(";");
+					if (pos > 0)
+						citations = citations.substring(pos + 1);
+					set.add(citations);
+				}
+			}
+		}
+
+		for (var line : set) {
+			System.out.println("\n- " + line);
+		}
+
+
+	}
+}