/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.track;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* Used to wrap multiple files as a single logical unit for tracks that break data by chromosome.
*/
public class MultiFileWrapper {
String name;
Map<String, ResourceLocator> locators;
public MultiFileWrapper(String name, Map<String, ResourceLocator> locators) {
this.name = name;
this.locators = locators;
}
public String getName() {
return name;
}
public Map<String, ResourceLocator> getLocators() {
return locators;
}
public static MultiFileWrapper parse(ResourceLocator rl) {
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(rl);
String name = reader.readLine();
String serverURL = reader.readLine();
Map<String, ResourceLocator> locators = new LinkedHashMap();
String nextLine = null;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
String chr = tokens[0];
String file = tokens[1];
ResourceLocator loc = new ResourceLocator(file);
locators.put(chr, loc);
}
return new MultiFileWrapper(name, locators);
}
catch (IOException e) {
e.printStackTrace();
return null;
}
finally {
if (reader != null) {
reader.close();
}
}
}
}