Examples of org.broad.igv.ui.action.SearchCommand.runSearch()

org.broad.igv.ui.action.SearchCommand.runSearch()

Given a string, search for the appropriate data to show the user. Different syntaxes are accepted.

In general, whitespace delimited tokens are treated separately and each are shown. There is 1 exception to this. A locus of form chr1 1 10000 will be treated the same as chr1:1-10000. Only one entry of this form can be entered, chr1 1 10000 chr2:1-1000 will not be recognized. @param searchString Feature name (EGFR), chromosome (chr1), or locus string (chr1:1-100 or chr1:6)Partial matches to a feature name (EG) will return multiple results, and ask the user which they want. @return resultList describing the results of the search. Will never be null, field type will equal ResultType.ERROR if something went wrong.

        //Need to call this to attach listener
        MongoFeatureSource.loadFeatureTrack(MongoCollabPluginTest.getTestLocator(), new ArrayList<Track>());


        String searchStr = testFeat.getName();
        SearchCommand cmd = new SearchCommand(null, searchStr, false);
        List<SearchCommand.SearchResult> list = cmd.runSearch(searchStr);


        assertEquals(1, list.size());
        SearchCommand.SearchResult result = list.get(0);


        assertEquals(SearchCommand.ResultType.FEATURE, result.getType());

     * @param flankingRegion
     * @return The found locus, null if not found
     */
    public static Locus getLocus(String searchString, int flankingRegion) {
        SearchCommand cmd = new SearchCommand(getDefaultFrame(), searchString);
        List<SearchCommand.SearchResult> results = cmd.runSearch(searchString);
        Locus locus = null;
        for (SearchCommand.SearchResult result : results) {
            if (result.getType() != SearchCommand.ResultType.ERROR) {
                int delta = 0;

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.