/*
* 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;
import org.apache.log4j.Logger;
import org.broad.igv.renderer.SequenceRenderer;
import java.io.IOException;
import java.text.DecimalFormat;
import java.util.*;
import java.util.List;
import java.util.regex.Pattern;
/**
* User: jrobinso
* Date: Feb 3, 2010
*/
public class Globals {
private static Logger log = Logger.getLogger(Globals.class);
public static final int DESIGN_DPI = 96;
public static final DecimalFormat DECIMAL_FORMAT = new DecimalFormat();
final static public String HISTORY_DELIMITER = ";";
public static final String DEFAULT_GENOME = "hg19";
// External resoure URLs
public static final String DEFAULT_GENOME_URL = "http://igv.broadinstitute.org/genomes/genomes.txt";
public static final String DEFAULT_DATA_URL = "https://data.broadinstitute.org/igvdata/$$_dataServerRegistry.txt";
public static final String CHR_ALL = "All";
public static final String TRACK_NAME_ATTRIBUTE = "NAME";
public static final String TRACK_DATA_FILE_ATTRIBUTE = "DATA FILE";
public static final String TRACK_DATA_TYPE_ATTRIBUTE = "DATA TYPE";
private static boolean headless = false;
private static boolean suppressMessages = false;
private static boolean batch = false;
private static boolean testing = false;
public static int CONNECT_TIMEOUT = 20000; // 20 seconds
public static int READ_TIMEOUT = 1000 * 3 * 60; // 3 minutes
/**
* Field description
*/
final public static String SESSION_FILE_EXTENSION = ".xml";
/**
* GENOME ARCHIVE CONSTANTS
*/
final public static String GENOME_FILE_EXTENSION = ".genome";
final public static String ZIP_EXTENSION = ".zip";
final public static String GZIP_FILE_EXTENSION = ".gz";
final public static String GENOME_ARCHIVE_PROPERTY_FILE_NAME = "property.txt";
final public static String GENOME_ARCHIVE_ID_KEY = "id";
final public static String GENOME_ARCHIVE_NAME_KEY = "name";
final public static String GENOME_ARCHIVE_VERSION_KEY = "version";
final public static String GENOME_ORDERED_KEY = "ordered";
final public static String GENOME_GENETRACK_NAME = "geneTrackName";
final public static String GENOME_URL_KEY = "url";
final public static String GENOME_ARCHIVE_CYTOBAND_FILE_KEY = "cytobandFile";
final public static String GENOME_ARCHIVE_GENE_FILE_KEY = "geneFile";
final public static String GENOME_ARCHIVE_SEQUENCE_FILE_LOCATION_KEY = "sequenceLocation";
/**
* Whether the sequenceLocation has been modified from the version of the .genome
* file on the server
*/
public static final String GENOME_ARCHIVE_CUSTOM_SEQUENCE_LOCATION_KEY = "customSequenceLocation";
public static final String GENOME_CHR_ALIAS_FILE_KEY = "chrAliasFile";
// Default user folder
final static public Pattern commaPattern = Pattern.compile(",");
final static public Pattern tabPattern = Pattern.compile("\t");
final static public Pattern colonPattern = Pattern.compile(":");
final static public Pattern dashPattern = Pattern.compile("-");
final static public Pattern equalPattern = Pattern.compile("=");
final static public Pattern semicolonPattern = Pattern.compile(";");
final static public Pattern singleTabMultiSpacePattern = Pattern.compile("\t|( +)");
final static public Pattern forwardSlashPattern = Pattern.compile("/");
final static public Pattern whitespacePattern = Pattern.compile("\\s+");
public static List emptyList = new ArrayList();
public static String VERSION;
public static String BUILD;
public static String TIMESTAMP;
public static double log2 = Math.log(2);
final public static boolean IS_WINDOWS =
System.getProperty("os.name").toLowerCase().startsWith("windows");
final public static boolean IS_MAC =
System.getProperty("os.name").toLowerCase().startsWith("mac");
final public static boolean IS_LINUX =
System.getProperty("os.name").toLowerCase().startsWith("linux");
final public static boolean IS_JWS =
System.getProperty("webstart.version", null) != null || System.getProperty("javawebstart.version", null) != null;
public static final String JAVA_VERSION_STRING = "java.version";
//Location of bedtools executable
//Note: It is recommended you use an absolute path here.
//System paths can be finnicky and vary depending on how IGV is launched
//However, the path environment variable will be checked if the executable
//is named rather than the full path given
public static String BEDtoolsPath = "/usr/local/bin/bedtools"; //"bedtools"
public static boolean toolsMenuEnabled = false;
public static boolean development = false;
public static String versionURL = "https://data.broadinstitute.org/igv/projects/current/version.txt";
public static String downloadURL = "http://www.broadinstitute.org/igv/download";
static {
Properties properties = new Properties();
try {
properties.load(Globals.class.getResourceAsStream("/resources/about.properties"));
} catch (IOException e) {
log.error("*** Error retrieving version and build information! ***", e);
}
VERSION = properties.getProperty("version", "???");
BUILD = properties.getProperty("build", "???");
TIMESTAMP = properties.getProperty("timestamp", "???");
BEDtoolsPath = System.getProperty("BEDtoolsPath", BEDtoolsPath);
//Runtime property overrides compile-time property, if both exist.
//If neither exist we default to false
final String developmentProperty = System.getProperty("development", properties.getProperty("development", "false"));
development = Boolean.parseBoolean(developmentProperty);
if(development){
log.warn("Development mode is enabled");
}
}
public static void setHeadless(boolean bool) {
headless = bool;
}
public static boolean isHeadless() {
return headless;
}
public static void setTesting(boolean testing) {
Globals.testing = testing;
}
public static boolean isTesting() {
return testing;
}
public static void setSuppressMessages(boolean bool) {
suppressMessages = bool;
}
public static boolean isSuppressMessages() {
return suppressMessages;
}
public static String applicationString() {
return "IGV Version " + VERSION + " " + TIMESTAMP;
}
public static String versionString() {
return "<html>Version " + VERSION + " " + TIMESTAMP;
}
public static boolean isDevelopment() {
return development;
}
public static boolean isBatch() {
return batch;
}
public static void setBatch(boolean batch) {
Globals.batch = batch;
}
/**
* Checks whether the current JVM is the minimum specified version
* or higher. Only compares up to as many characters as
* in {@code minVersion}
*
* @param minVersion
* @return
*/
public static boolean checkJavaVersion(String minVersion) {
String curVersion = System.getProperty(JAVA_VERSION_STRING);
if (curVersion.length() >= minVersion.length()) {
curVersion = curVersion.substring(0, minVersion.length());
}
return curVersion.compareTo(minVersion) >= 0;
}
/**
* Return the URL to fetch the current IGV version (note: not Java version)
* @return
*/
public static String getVersionURL() {
return versionURL;
}
}