/*
* 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.util;
//~--- non-JDK imports --------------------------------------------------------
import biz.source_code.base64Coder.Base64Coder;
import org.apache.log4j.Logger;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.zip.CRC32;
/**
*
*/
public class Utilities {
private static Logger log = Logger.getLogger(Utilities.class);
public static String base64Encode(String str) {
return Base64Coder.encodeString(str);
}
public static String base64Decode(String str) {
return Base64Coder.decodeString(str);
}
/**
* Changes a files extension.
*/
final public static File changeFileExtension(File file, String extension) {
if ((file == null) || (extension == null) || extension.trim().equals("")) {
return null;
}
String path = file.getAbsolutePath();
String newPath = "";
String filename = file.getName().trim();
if ((filename != null) && !filename.equals("")) {
int periodIndex = path.lastIndexOf(".");
newPath = path.substring(0, periodIndex);
newPath += extension;
}
return new File(newPath);
}
/**
* Reads an xml from an input stream and creates DOM document.
*
* @param inStream
* @return
* @throws ParserConfigurationException
* @throws IOException
* @throws SAXException
*/
public static Document createDOMDocumentFromXmlStream(InputStream inStream)
throws ParserConfigurationException, IOException, SAXException {
DocumentBuilder documentBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document xmlDocument = documentBuilder.parse(inStream);
return xmlDocument;
}
public static Map<String, String> getAttributes(Node node) {
HashMap<String, String> attributes = new HashMap();
NamedNodeMap tNodeMap = node.getAttributes();
if(tNodeMap != null){
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node nd = tNodeMap.item(i);
String value = nd.getNodeValue();
if (value != null && value.length() > 0) {
attributes.put(nd.getNodeName(), value);
}
}
}
return attributes;
}
public static String getString(Document document) {
StreamResult streamResult;
try {
TransformerFactory factory = TransformerFactory.newInstance();
Transformer transformer = factory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
streamResult = new StreamResult(new StringWriter());
DOMSource source = new DOMSource(document);
transformer.transform(source, streamResult);
} catch (TransformerException e) {
return null;
}
return streamResult.getWriter().toString();
}
/**
* Get the node value of the attribute {@code key} from
* the set {@code attr}. If that attribute is not present, null is returned
*
* @param attr
* @param key
* @return
*/
public static String getNullSafe(NamedNodeMap attr, String key) {
Node node = attr.getNamedItem(key);
return node != null ? node.getNodeValue() : null;
}
static public Comparator getNumericStringComparator() {
Comparator comparator = new Comparator<String>() {
public int compare(String s1, String s2) {
StringTokenizer st1 = new StringTokenizer(s1, " ");
StringTokenizer st2 = new StringTokenizer(s2, " ");
while (st1.hasMoreTokens() && st2.hasMoreTokens()) {
String t1 = st1.nextToken();
String t2 = st2.nextToken();
int c;
try {
Integer i1 = new Integer(t1);
Integer i2 = new Integer(t2);
c = i1.compareTo(i2);
} catch (NumberFormatException e) {
c = t1.compareTo(t2);
}
if (c != 0) {
return c;
}
}
return 0;
}
};
return comparator;
}
/**
* @param buffer
* @return
* @throws java.io.IOException
*/
static private long getCrc(byte[] buffer) throws IOException {
CRC32 crc = new CRC32();
crc.reset();
crc.update(buffer, 0, buffer.length);
return crc.getValue();
}
/**
* Parses the file name from a URL.
*
* @param url
* @return
*/
static public String getFileNameFromURL(String url) {
int lastIndexOfSlash = url.lastIndexOf("/");
String fileName = null;
if (lastIndexOfSlash > -1) {
fileName = url.substring(lastIndexOfSlash+1, url.length());
} else {
fileName = url;
}
return fileName;
}
public static boolean objectEqual(Object str1, Object str2) {
if(str1 == null) {
return str2 == null;
}
else if(str2 == null) {
return str1 == null;
}
else {
return str1.equals(str2);
}
}
}