/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package org.broad.igv.feature.tribble.reader;

import org.broad.igv.util.FileUtils;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.AbstractFeatureReader;

import java.io.IOException;
import java.net.URL;

public class IGVComponentMethods extends AbstractFeatureReader.ComponentMethods {

    public boolean isTabix(String resourcePath, String tabxIndex) throws IOException {
        ResourceLocator locator = new ResourceLocator(resourcePath);
        if (tabxIndex == null) {
            if (HttpUtils.isRemoteURL(locator.getPath())) {
                final URL url = new URL(locator.getPath());
                String path = url.getPath();
                String indexPath = path + ".tbi";   // Strip off parameters
                tabxIndex = locator.getPath().replace(path, indexPath);
            } else {
                tabxIndex = locator.getPath() + ".tbi";
            }
        }
        boolean isTabix =  (locator.getPath().endsWith(".gz") || locator.getPath().endsWith(".bgz")) && FileUtils.resourceExists(tabxIndex);
        if(isTabix) {
            locator.setIndexPath(tabxIndex);
        }
        return isTabix;
    }

}