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

Example 1 with Bookmarks

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

the class Cy2SessionReaderImpl method extractBookmarks.

private void extractBookmarks(InputStream is, String entryName) throws Exception {
    CyPropertyReader reader = propertyReaderMgr.getReader(is, entryName);
    reader.run(taskMonitor);
    final Bookmarks bookmarks = (Bookmarks) reader.getProperty();
    final CyProperty<Bookmarks> cyProps = new SimpleCyProperty<Bookmarks>("bookmarks", bookmarks, Bookmarks.class, CyProperty.SavePolicy.SESSION_FILE);
    properties.add(cyProps);
}

Example 2 with Bookmarks

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

the class Cy3SessionReaderImpl method extractProperties.

private void extractProperties(InputStream is, String entryName) throws Exception {
    CyPropertyReader reader = propertyReaderMgr.getReader(is, entryName);
    if (reader == null)
        return;
    reader.run(taskMonitor);
    CyProperty<?> cyProps = null;
    Object obj = reader.getProperty();
    if (obj instanceof Properties) {
        Properties props = (Properties) obj;
        Matcher matcher = PROPERTIES_PATTERN.matcher(entryName);
        if (matcher.matches()) {
            String propsName = matcher.group(2);
            if (propsName != null) {
                cyProps = new SimpleCyProperty<>(propsName, props, Properties.class, CyProperty.SavePolicy.SESSION_FILE);
            }
        }
    } else if (obj instanceof Bookmarks) {
        cyProps = new SimpleCyProperty<>("bookmarks", (Bookmarks) obj, Bookmarks.class, CyProperty.SavePolicy.SESSION_FILE);
    } else {
        // TODO: get name and create the CyProperty for unknown types
        logger.error("Cannot extract CyProperty name from: " + entryName);
    }
    if (cyProps != null)
        properties.add(cyProps);
}

Example 3 with Bookmarks

use of org.cytoscape.property.bookmark.Bookmarks 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 4 with Bookmarks

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

the class BookmarksCyProperty method setup.

@Before
public void setup() {
    Properties coreP = new Properties();
    coreP.setProperty("cyPropertyName", "cytoscape3.props");
    Properties p = new Properties();
    p.setProperty("cyPropertyName", "bookmarks");
    CyProperty<Properties> cyProp = new BasicCyProperty(new Properties(), CyProperty.SavePolicy.CONFIG_DIR);
    registerMockService(CyProperty.class, cyProp, coreP);
    BookmarksCyProperty cyBookProp = new BookmarksCyProperty(new Bookmarks(), CyProperty.SavePolicy.CONFIG_DIR);
    registerMockService(CyProperty.class, cyBookProp, p);
    registerMockService(BookmarksUtil.class);
    registerMockService(FileUtil.class);
}

Example 5 with Bookmarks

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

the class BookmarksUtilImpl method saveBookmark.

public void saveBookmark(Bookmarks pBookmarks, String pCategoryName, DataSource pDataSource, String pProvider) {
    if (pBookmarks == null) {
        pBookmarks = new Bookmarks();
    }
    List<Category> theCategoryList = pBookmarks.getCategory();
    // if the category does not exist, create it
    if (theCategoryList.size() == 0) {
        Category theCategory = new Category();
        theCategory.setName(pCategoryName);
        theCategoryList.add(theCategory);
    }
    Category theCategory = getCategory(pCategoryName, theCategoryList);
    if (theCategory == null) {
        Category newCategory = new Category();
        newCategory.setName(pCategoryName);
        theCategoryList.add(newCategory);
        theCategory = newCategory;
    }
    List<Object> theObjList = theCategory.getCategoryOrDataSource();
    if (!theObjList.contains(pDataSource))
        theObjList.add(pDataSource);
    org.cytoscape.io.datasource.DataSource data = convertToDataSource(pBookmarks, pCategoryName, pDataSource, pProvider);
    if (data != null && !dataSourceMap.containsKey(pDataSource)) {
        register.registerService(data, org.cytoscape.io.datasource.DataSource.class, new Properties());
        dataSourceMap.put(pDataSource, data);
    }
}