Examples of org.broad.igv.ui.action.SearchCommand

org.broad.igv.ui.action.SearchCommand
A class for performing search actions. The class takes a view context and search string as parameters. The search string can be either (a) a feature (e.g. gene), or (b) a locus string in the UCSC form, e.g. chr1:100,000-200,000
Note: Currently the only recognized features are genes
Custom searchers can be registered, see {@link #registerNamedFeatureSearcher(org.broad.igv.dev.api.NamedFeatureSearcher)} @author jrobinso


        //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());

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     * @param searchString
     * @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;

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            log.debug("Enter search by locus: " + searchText);
        }


        if ((searchText != null) && (searchText.length() > 0)) {
            searchTextField.setText(searchText);
            (new SearchCommand(getDefaultReferenceFrame(), searchText)).execute();
            //This is not necessary, since we receive a ViewChange.Result later
            //chromosomeComboBox.setSelectedItem(getDefaultReferenceFrame().getChrName());
        }


        if (log.isDebugEnabled()) {

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                IGV.getInstance().setGeneList(GeneListManager.getInstance().getGeneList(listName), false);
            } else {
                if (FrameManager.isGeneListMode()) {
                    IGV.getInstance().setGeneList(null, false);
                }
                (new SearchCommand(FrameManager.getDefaultFrame(), locus, false)).execute();
                //Zoom should be implicit in the locus
                //FrameManager.getDefaultFrame().setZoom(entry.getZoom());
            }


        }

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