Examples with Program com.github.lindenb.jvarkit.util.jcommander.Program used on opensource projects

Example 1 with Program

use of com.github.lindenb.jvarkit.util.jcommander.Program in project jvarkit by lindenb.

the class JvarkitCentral method start.

@Override
public void start(Stage primaryStage) throws Exception {
    primaryStage.setTitle("Jvarkit-Central");
    StackPane root = new StackPane();
    root.setPadding(new Insets(2));
    final TableView<Class<?>> tableView = new TableView<>();
    final TableColumn<Class<?>, String> nameCol = new TableColumn<>("Name");
    nameCol.setCellValueFactory(CB -> {
        final String value;
        Class<?> clazz = CB.getValue();
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null) {
            value = null;
        } else {
            value = program.name();
        }
        return new SimpleStringProperty(value);
    });
    final TableColumn<Class<?>, String> descCol = new TableColumn<>("Description");
    descCol.setCellValueFactory(CB -> {
        final String value;
        Class<?> clazz = CB.getValue();
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null) {
            value = null;
        } else {
            value = program.description();
        }
        return new SimpleStringProperty(value);
    });
    tableView.getColumns().addAll(nameCol, descCol);
    final BorderPane borderPane1 = new BorderPane(tableView);
    borderPane1.setPadding(new Insets(10));
    final Button but = new Button("New Instance...");
    but.setOnAction(AE -> {
        final Class<?> clazz = tableView.getSelectionModel().getSelectedItem();
        if (clazz == null)
            return;
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null)
            return;
        createNewInstanceOf(clazz);
    });
    FlowPane bottom = new FlowPane(but);
    borderPane1.setBottom(bottom);
    tableView.getItems().addAll(String.class, Integer.class, VCFFilterJS.class, BioAlcidae.class);
    root.getChildren().add(borderPane1);
    // root.getChildren().add(btn);
    primaryStage.setScene(new Scene(root, 300, 250));
    primaryStage.show();
}

Example 2 with Program

use of com.github.lindenb.jvarkit.util.jcommander.Program in project jvarkit by lindenb.

the class JVarkitAnnotationProcessor method process.

@Override
public boolean process(final Set<? extends TypeElement> annotations, final RoundEnvironment roundEnv) {
    final String mainClass = System.getProperty("jvarkit.main.class");
    final String thisDir = System.getProperty("jvarkit.this.dir");
    roundEnv.getElementsAnnotatedWith(IncludeSourceInJar.class).stream().filter(E -> E.getKind() == ElementKind.CLASS).filter(E -> E.getAnnotation(IncludeSourceInJar.class) != null).forEach(E -> {
        if (thisDir == null || thisDir.isEmpty())
            return;
        copySource(E);
    });
    /* find if roundEnv contains main class annotated with 'Program' annotation
		 * if true: generate a file that will tell Make to compile the markdown
		 * documentation
		 */
    roundEnv.getElementsAnnotatedWith(Program.class).stream().filter(E -> E.getKind() == ElementKind.CLASS).filter(E -> {
        final Program prog = E.getAnnotation(Program.class);
        return prog != null && prog.generate_doc();
    }).forEach(E -> {
        copySource(E);
        final String className = E.toString();
        if (mainClass == null)
            return;
        if (!mainClass.equals(className))
            return;
        final Program prog = E.getAnnotation(Program.class);
        if (prog == null || !prog.generate_doc())
            return;
        try {
            final Filer filer = super.processingEnv.getFiler();
            FileObject fo = filer.createResource(StandardLocation.CLASS_OUTPUT, "", "markdown.flag");
            fo.openWriter().append(String.valueOf(mainClass)).close();
        } catch (final Exception err) {
            LOG.warn(err);
        }
        if (thisDir != null) {
            final File index_html = new File(thisDir, "docs/index.html");
            if (index_html.exists()) {
                try {
                    final Document dom = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(index_html);
                    Element tr = dom.createElement("tr");
                    tr.setAttribute("id", prog.name());
                    // name
                    Element td = dom.createElement("th");
                    tr.appendChild(td);
                    Element a = dom.createElement("a");
                    a.setAttribute("href", E.getSimpleName() + ".html");
                    a.setAttribute("title", E.getSimpleName().toString());
                    td.appendChild(a);
                    a.appendChild(dom.createTextNode(prog.name()));
                    // desc
                    td = dom.createElement("td");
                    tr.appendChild(td);
                    td.appendChild(dom.createTextNode(prog.description()));
                    // keywords
                    td = dom.createElement("td");
                    tr.appendChild(td);
                    td.appendChild(dom.createTextNode(Arrays.asList(prog.keywords()).stream().collect(Collectors.joining(" "))));
                    // terms
                    td = dom.createElement("td");
                    tr.appendChild(td);
                    td.appendChild(dom.createTextNode(Arrays.asList(prog.terms()).stream().map(T -> "[" + T.getAccession() + "]" + T.getLabel()).collect(Collectors.joining(" "))));
                    // misc
                    td = dom.createElement("td");
                    tr.appendChild(td);
                    final DocumentFragment misc = dom.createDocumentFragment();
                    if (prog.deprecatedMsg() != null && !prog.deprecatedMsg().isEmpty()) {
                        Element span = dom.createElement("span");
                        span.setAttribute("style", "color:orange;");
                        span.setAttribute("title", "deprecated");
                        span.appendChild(dom.createTextNode(prog.deprecatedMsg()));
                        misc.appendChild(span);
                        misc.appendChild(dom.createTextNode(". "));
                    }
                    td.appendChild(misc);
                    final XPath xpath = XPathFactory.newInstance().newXPath();
                    final NodeList nodeList = (NodeList) xpath.evaluate("//table[1]/tbody/tr[@id='" + prog.name() + "']", dom, XPathConstants.NODESET);
                    for (int i = 0; i < nodeList.getLength(); ++i) {
                        Node oldTr = nodeList.item(i);
                        if (tr != null) {
                            oldTr.getParentNode().replaceChild(tr, oldTr);
                            tr = null;
                        } else {
                            oldTr.getParentNode().removeChild(oldTr);
                        }
                    }
                    if (tr != null) {
                        Node tbody = (Node) xpath.evaluate("//table[1]/tbody", dom, XPathConstants.NODE);
                        if (tbody != null) {
                            tbody.appendChild(tr);
                            tbody.appendChild(dom.createTextNode("\n"));
                            tr = null;
                        }
                    }
                    if (tr != null) {
                        LOG.warn("Cannot insert new doc in " + index_html);
                    } else {
                        final Transformer transformer = TransformerFactory.newInstance().newTransformer();
                        transformer.setOutputProperty(OutputKeys.INDENT, "no");
                        transformer.setOutputProperty(OutputKeys.METHOD, "xml");
                        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
                        transformer.transform(new DOMSource(dom), new StreamResult(index_html));
                    }
                } catch (final Exception err) {
                    LOG.warn(err);
                }
            } else {
                LOG.warn("Cannot get " + index_html);
            }
        }
    });
    return true;
}