Examples with BookmarksUtil org.cytoscape.property.bookmark.BookmarksUtil used on opensource projects

Example 1 with BookmarksUtil

use of org.cytoscape.property.bookmark.BookmarksUtil in project cytoscape-impl by cytoscape.

the class OntologyPanelBuilder method setAnnotationComboBox.

@SuppressWarnings("unchecked")
protected void setAnnotationComboBox() throws JAXBException, IOException {
    final CyProperty<Bookmarks> bookmarksProp = serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=bookmarks)");
    final BookmarksUtil bkUtil = serviceRegistrar.getService(BookmarksUtil.class);
    final Bookmarks bookmarks = bookmarksProp.getProperties();
    final List<DataSource> annotations = bkUtil.getDataSourceList("annotation", bookmarks.getCategory());
    String key = null;
    panel.annotationComboBox.addItem(DEF_ANNOTATION_ITEM);
    for (DataSource source : annotations) {
        key = source.getName();
        panel.annotationComboBox.addItem(key);
        annotationUrlMap.put(key, source.getHref());
        annotationFormatMap.put(key, source.getFormat());
        final Map<String, String> attrMap = new HashMap<String, String>();
        for (Attribute attr : source.getAttribute()) attrMap.put(attr.getName(), attr.getContent());
        annotationAttributesMap.put(key, attrMap);
    }
    panel.annotationComboBox.setToolTipText(getAnnotationTooltip());
}

Example 2 with BookmarksUtil

use of org.cytoscape.property.bookmark.BookmarksUtil in project cytoscape-impl by cytoscape.

the class OntologyPanelBuilder method setOntologyComboBox.

@SuppressWarnings("unchecked")
protected void setOntologyComboBox() {
    final CyProperty<Bookmarks> bookmarksProp = serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=bookmarks)");
    final BookmarksUtil bkUtil = serviceRegistrar.getService(BookmarksUtil.class);
    final Bookmarks bookmarks = bookmarksProp.getProperties();
    final List<DataSource> annotations = bkUtil.getDataSourceList("ontology", bookmarks.getCategory());
    String key = null;
    for (DataSource source : annotations) {
        key = source.getName();
        panel.ontologyComboBox.addItem(key);
        ontologyUrlMap.put(key, source.getHref());
        ontologyDescriptionMap.put(key, bkUtil.getAttribute(source, "description"));
        ontologyTypeMap.put(key, bkUtil.getAttribute(source, "ontologyType"));
    }
    panel.ontologyComboBox.setToolTipText(getOntologyTooltip());
}

Example 3 with BookmarksUtil

use of org.cytoscape.property.bookmark.BookmarksUtil in project cytoscape-impl by cytoscape.

the class BookmarkDataSourceBuilder method buildDataSource.

private void buildDataSource() {
    final BookmarksUtil bookmarksUtil = serviceRegistrar.getService(BookmarksUtil.class);
    final Bookmarks bookMarks = (Bookmarks) serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=bookmarks)").getProperties();
    final List<Category> categoryList = bookMarks.getCategory();
    for (final Category category : categoryList) {
        final DataCategory dataType = CONVERSION_MAP.get(category.getName());
        if (dataType == null)
            continue;
        final List<DataSource> theDataSourceList = bookmarksUtil.getDataSourceList(category.getName(), categoryList);
        if (theDataSourceList != null) {
            for (final DataSource ds : theDataSourceList) {
                final String location = ds.getHref();
                final String name = ds.getName();
                final String description = "From Bookmarks";
                final String provider = "Example";
                URL url = null;
                try {
                    url = new URL(location);
                } catch (MalformedURLException e) {
                    logger.warn("Bookmark file coniatin invalid URL: " + location);
                    continue;
                }
                final org.cytoscape.io.datasource.DataSource dataSource = new DefaultDataSource(name, provider, description, dataType, url);
                datasourceSet.add(dataSource);
            }
        }
    }
}