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Example 6 with Bookmarks

use of org.cytoscape.property.bookmark.Bookmarks 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());
}
Also used : Bookmarks(org.cytoscape.property.bookmark.Bookmarks) BookmarksUtil(org.cytoscape.property.bookmark.BookmarksUtil) DataSource(org.cytoscape.property.bookmark.DataSource)

Example 7 with Bookmarks

use of org.cytoscape.property.bookmark.Bookmarks 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);
            }
        }
    }
}
Also used : Bookmarks(org.cytoscape.property.bookmark.Bookmarks) DataCategory(org.cytoscape.io.DataCategory) MalformedURLException(java.net.MalformedURLException) DataCategory(org.cytoscape.io.DataCategory) Category(org.cytoscape.property.bookmark.Category) BookmarksUtil(org.cytoscape.property.bookmark.BookmarksUtil) DefaultDataSource(org.cytoscape.io.datasource.DefaultDataSource) URL(java.net.URL) DataSource(org.cytoscape.property.bookmark.DataSource) DefaultDataSource(org.cytoscape.io.datasource.DefaultDataSource)

Aggregations

Bookmarks (org.cytoscape.property.bookmark.Bookmarks)7 Properties (java.util.Properties)3 BookmarksUtil (org.cytoscape.property.bookmark.BookmarksUtil)3 DataSource (org.cytoscape.property.bookmark.DataSource)3 DataCategory (org.cytoscape.io.DataCategory)2 CyPropertyReader (org.cytoscape.io.read.CyPropertyReader)2 SimpleCyProperty (org.cytoscape.property.SimpleCyProperty)2 Category (org.cytoscape.property.bookmark.Category)2 MalformedURLException (java.net.MalformedURLException)1 URL (java.net.URL)1 HashMap (java.util.HashMap)1 Matcher (java.util.regex.Matcher)1 DefaultDataSource (org.cytoscape.io.datasource.DefaultDataSource)1 BasicCyProperty (org.cytoscape.property.BasicCyProperty)1 Attribute (org.cytoscape.property.bookmark.Attribute)1 Before (org.junit.Before)1