/*
* 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;
import htsjdk.samtools.util.ftp.FTPClient;
import htsjdk.samtools.util.ftp.FTPReply;
import org.broad.igv.util.ftp.FTPUtils;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.renderer.*;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.track.WindowFunction;
import org.broad.igv.ui.color.ColorUtilities;
import org.broad.igv.ui.util.MessageUtils;
import htsjdk.tribble.readers.AsciiLineReader;
import java.awt.*;
import java.io.*;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
/**
* @author jrobinso
*/
public class ParsingUtils {
private static Logger log = Logger.getLogger(ParsingUtils.class);
public static final Pattern TAB_PATTERN = Pattern.compile("\t");
public static final Pattern COMMA_PATTERN = Pattern.compile(",");
public static final Pattern SEMI_COLON_PATTERN = Pattern.compile(";");
public static final Pattern EQ_PATTERN = Pattern.compile("=");
public static final Pattern PERIOD_PATTERN = Pattern.compile("\\.");
public static final Pattern WHITESPACE_PATTERN = Pattern.compile("\\s+");
/**
* Open a BufferedReader on the path, which might be a local file or URL, and might be gzipped or not.
*
* @param pathOrUrl
* @return
* @throws IOException
*/
public static BufferedReader openBufferedReader(String pathOrUrl) throws IOException {
BufferedReader reader = new BufferedReader(new InputStreamReader(openInputStream(pathOrUrl)));
return reader;
}
public static BufferedReader openBufferedReader(ResourceLocator locator) throws IOException {
InputStream stream = openInputStreamGZ(locator);
return new BufferedReader(new InputStreamReader(stream));
}
public static AsciiLineReader openAsciiReader(ResourceLocator locator) throws IOException {
InputStream stream = openInputStreamGZ(locator);
return new AsciiLineReader(stream);
}
public static InputStream openInputStream(String path) throws IOException {
return openInputStreamGZ(new ResourceLocator(path));
}
/**
* Open an InputStream on the resource. Wrap it in a GZIPInputStream if necessary.
*
* @param locator
* @return
* @throws IOException
*/
public static InputStream openInputStreamGZ(ResourceLocator locator) throws IOException {
InputStream inputStream = null;
if (HttpUtils.isRemoteURL(locator.getPath())) {
URL url = new URL(locator.getPath());
inputStream = HttpUtils.getInstance().openConnectionStream(url);
} else {
String path = locator.getPath();
if (path.startsWith("file://")) {
path = path.substring(7);
}
File file = new File(path);
inputStream = new FileInputStream(file);
}
if (locator.getPath().endsWith("gz")) {
return new GZIPInputStream(inputStream);
} else {
return inputStream;
}
}
/**
* Parse the string and return the result as an integer. This method supports scientific notation for integers,
* which Integer.parseInt() does not.
*
* @param string
* @return
*/
public static int parseInt(String string) {
return (int) Double.parseDouble(string);
}
/**
* Load a text file of format
* {@code key}={@code value}
* <p/>
* Lines beginning with a "#" are skipped
* <p/>
* The {@code value} field must not contain any "=", no allowance is made for quoting or escaping
* or anything like that.
*
* @param inputStream
* @return
*/
public static Map<String, String> loadMap(InputStream inputStream) {
BufferedReader reader = null;
Map<String, String> map = new HashMap<String, String>();
try {
reader = new BufferedReader(new InputStreamReader(inputStream));
String nextLine = null;
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("#")) continue;
String[] tokens = nextLine.split("=");
if (tokens.length == 2) {
map.put(tokens[0], tokens[1]);
} else {
throw new IllegalArgumentException("Incorrect number of tokens at line: " + nextLine);
}
}
} catch (IOException e) {
throw new RuntimeException(e);
} finally {
try {
if (reader != null) {
reader.close();
}
} catch (IOException ex) {
log.error(ex.getMessage(), ex);
}
}
return map;
}
private static final String codeFilePath = "resources/iupac_regex_table.txt";
public static Map<String, String> loadIUPACMap() {
return loadMap(ParsingUtils.class.getResourceAsStream(codeFilePath));
}
private static final DateFormat ftpDateFormat = new SimpleDateFormat("yyyyMMddHHmmss");
/**
* Returns the number of milliseconds since January 1, 1970, 00:00:00 GMT
* since the specified resource was modified, or 0 if not known/error
*
* @param path
* @return
*/
public static long getLastModified(String path) {
if (HttpUtils.isRemoteURL(path)) {
String resp = null;
try {
URL url = new URL(path);
if (path.startsWith("ftp:")) {
String host = url.getHost();
FTPClient ftp = FTPUtils.connect(host, url.getUserInfo(), new UserPasswordInputImpl());
ftp.pasv();
FTPReply reply = ftp.executeCommand("MDTM " + url.getPath());
resp = reply.getReplyString();
return ftpDateFormat.parse(resp).getTime();
} else {
return HttpUtils.getInstance().getLastModified(url);
}
} catch (MalformedURLException e) {
log.error("Malformed url " + path, e);
} catch (IOException e) {
log.error("Error getting modified date for " + path, e);
} catch (ParseException e) {
log.error("Error parsing Last-Modified " + resp, e);
} catch (NumberFormatException e) {
log.error("Error parsing Last-Modified " + resp, e);
}
return 0;
} else {
File f = new File(path);
return f.exists() ? f.lastModified() : 0;
}
}
public static long getContentLength(String path) {
try {
long contentLength = -1;
if (path.startsWith("http:") || path.startsWith("https:")) {
URL url = new URL(path);
contentLength = HttpUtils.getInstance().getContentLength(url);
} else if (path.startsWith("ftp:")) {
// Use JDK url
URL url = new URL(path);
URLConnection connection = url.openConnection();
connection.setConnectTimeout(Globals.CONNECT_TIMEOUT);
//For reasons beyond my ken, on Java 7 getContentLength
//returns -1 without attempting a connection
//contentLength = connection.getContentLength();
contentLength = connection.getInputStream().available();
} else {
contentLength = (new File(path)).length();
}
return contentLength;
} catch (IOException e) {
log.error("Error getting content length for: " + path, e);
return -1;
}
}
public static int estimateLineCount(String path) {
AsciiLineReader reader = null;
try {
final int defaultLength = 100000;
long fileLength = getContentLength(path);
if (fileLength <= 0) {
return defaultLength;
}
reader = openAsciiReader(new ResourceLocator(path));
String nextLine;
int lines = 0;
// Skip the first 10 lines (headers, etc)
int nSkip = 10;
while (nSkip-- > 0 && reader.readLine() != null) {
}
long startPos = reader.getPosition();
while ((nextLine = reader.readLine()) != null & lines < 100) {
lines++;
}
if (lines == 0) {
return defaultLength;
}
double bytesPerLine = (double) ((reader.getPosition() - startPos) / lines);
int nLines = (int) (fileLength / bytesPerLine);
return nLines;
} catch (Exception e) {
log.error("Error estimating line count", e);
return 1000;
} finally {
try {
reader.close();
} catch (Exception e) {
// Ignore errors closing reader
}
}
}
/**
* Method description
*
* @param file
* @return
*/
public static List<String> loadRegions(File file) {
try {
FileInputStream fileInput = new FileInputStream(file);
BufferedReader reader = new BufferedReader(new InputStreamReader(fileInput));
String nextLine;
List<String> features = new ArrayList<String>();
while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
try {
if (nextLine.startsWith("chr")) {
String[] tokens = nextLine.split("\t");
String region = tokens[0] + ":" + tokens[1] + "-" + tokens[2];
features.add(region);
}
} catch (NumberFormatException e) {
log.error("Error parsing numer in line: " + nextLine);
}
}
reader.close();
return features;
} catch (IOException e) {
e.printStackTrace();
return null;
}
}
/**
* graphType bar|points # default is bar
* yLineMark real-value # default is 0.0
* yLineOnOff on|off # default is off
* windowingFunction maximum|mean|minimum # default is maximum
* smoothingWindow off|[2-16] # default is off
*
* @param nextLine
* @param trackProperties
* @throws NumberFormatException
*/
public static boolean parseTrackLine(String nextLine, TrackProperties trackProperties)
throws NumberFormatException {
boolean foundProperties = false;
try {
trackProperties.setTrackLine(nextLine);
// track type=wiggle_0 name="CSF +" description="CSF +" visibility=full autoScale=off viewLimits=-50:50
List<String> tokens = StringUtils.breakQuotedString(nextLine, ' ');
for (String pair : tokens) {
List<String> kv = StringUtils.breakQuotedString(pair, '=');
if (kv.size() == 2) {
foundProperties = true;
String key = kv.get(0).toLowerCase().trim();
String value = kv.get(1).replaceAll("\"", "");
if (key.equals("coords")) {
if (value.equals("0")) {
trackProperties.setBaseCoord(TrackProperties.BaseCoord.ZERO);
} else if (value.equals("1")) {
trackProperties.setBaseCoord(TrackProperties.BaseCoord.ONE);
}
}
if (key.equals("name")) {
trackProperties.setName(value);
//dhmay adding name check for TopHat junctions files. graphType is also checked.
if (value.equals("junctions")) {
trackProperties.setRendererClass(SpliceJunctionRenderer.class);
trackProperties.setHeight(60);
}
} else if (key.equals("description")) {
trackProperties.setDescription(value);
} else {
final String valueLowerCase = value.toLowerCase();
if (key.equals("itemrgb")) {
trackProperties.setItemRGB(valueLowerCase.equals("on") || value.equals("1"));
} else if (key.equals("usescore")) {
trackProperties.setUseScore(value.equals("1"));
} else if (key.equals("color")) {
Color color = ColorUtilities.stringToColor(value);
trackProperties.setColor(color);
} else if (key.equals("altcolor")) {
Color color = ColorUtilities.stringToColor(value);
trackProperties.setAltColor(color);
} else if (key.equals("midcolor")) {
Color color = ColorUtilities.stringToColor(value);
trackProperties.setMidColor(color);
} else if (key.equals("autoscale")) {
boolean autoscale = value.equals("on");
trackProperties.setAutoScale(autoscale);
} else if (key.equals("maxheightpixels")) {
try {
// There should be 3 values per UCSC spec, max:default:min. In the past we have accepted
// 2 values, def:min, so keep this for backwards compatibility. IGV currently doesn't
// have a "max height" UPDATE -- apparently 1 value is also allowed!
String[] maxDefMin = value.split(":");
if (maxDefMin.length >= 2) {
int defIDX = (maxDefMin.length == 2 ? 0 : 1);
trackProperties.setHeight(Integer.parseInt(maxDefMin[defIDX].trim()));
trackProperties.setMinHeight(Integer.parseInt(maxDefMin[defIDX + 1].trim()));
} else {
// Single value
trackProperties.setHeight(Integer.parseInt(value));
}
} catch (NumberFormatException e) {
log.error("height must be an integer: " + value);
}
} else if ("height".equals(key)) {
try {
trackProperties.setHeight(Integer.parseInt(value));
} catch (NumberFormatException e) {
log.error("height must be an integer: " + value);
}
} else if (key.equals("url")) {
trackProperties.setUrl(value);
} else if (key.equals("graphtype")) {
if (value.equals("bar")) {
trackProperties.setRendererClass(BarChartRenderer.class);
} else if (value.equals("points")) {
trackProperties.setRendererClass(PointsRenderer.class);
trackProperties.setWindowingFunction(WindowFunction.none);
} else if (value.equals("line")) {
trackProperties.setRendererClass(LineplotRenderer.class);
} else if (value.equals("heatmap")) {
trackProperties.setRendererClass(HeatmapRenderer.class);
} else if (value.equals("junctions")) {
//dhmay adding check for graphType=junctions. name is also checked
trackProperties.setRendererClass(SpliceJunctionRenderer.class);
} else if (value.equals("genotype")) {
trackProperties.setRendererClass(GenotypeRenderer.class);
} else if ("arc".equals(value)) {
trackProperties.setRendererClass(ArcRenderer.class);
}
} else if (key.toLowerCase().equals("viewlimits")) {
String[] limits = value.split(":");
if (limits.length == 2) {
try {
float min = Float.parseFloat(limits[0].trim());
float max = Float.parseFloat(limits[1].trim());
trackProperties.setMinValue(min);
trackProperties.setMaxValue(max);
} catch (NumberFormatException e) {
log.error("viewLimits values must be numeric: " + value);
}
}
} else if (key.equals("midrange")) {
String[] limits = value.split(":");
if (limits.length == 2) {
try {
float from = Float.parseFloat(limits[0].trim());
float to = Float.parseFloat(limits[1].trim());
trackProperties.setNeutralFromValue(from);
trackProperties.setNeutralToValue(to);
} catch (NumberFormatException e) {
log.error("midrange values must be numeric: " + value);
}
}
} else if (key.equals("ylinemark")) {
try {
float yLine = Float.parseFloat(value);
trackProperties.setyLine(yLine);
} catch (NumberFormatException e) {
log.error("Number format exception in track line (ylinemark): " + nextLine);
}
} else if (key.equals("ylineonoff")) {
trackProperties.setDrawYLine(value.equals("on"));
} else if (key.equals("windowingfunction")) {
WindowFunction wf = WindowFunction.getWindowFunction(value);
trackProperties.setWindowingFunction(wf);
} else if (key.equals("maxfeaturewindow") || key.equals("featurevisibilitywindow") ||
key.equals("visibilitywindow")) {
try {
int windowSize = Integer.parseInt(value);
trackProperties.setFeatureVisibilityWindow(windowSize);
} catch (NumberFormatException e) {
log.error(key + " must be numeric: " + nextLine);
}
} else if (key.equals("scaletype")) {
if (value.equals("log")) {
trackProperties.setLogScale(true);
}
} else if (key.equals("gfftags")) {
// Any value other than 0 or off => on
boolean gffTags = !(value.equals("0") || (valueLowerCase.equals("off")));
trackProperties.setGffTags(gffTags);
} else if (key.equals("sortable")) {
// Any value other than 0 or off => on
boolean sortable = (value.equals("1") || (valueLowerCase.equals("true")));
trackProperties.setSortable(sortable);
} else if (key.equals("alternateexoncolor")) {
trackProperties.setAlternateExonColor(valueLowerCase.equals("on") || value.equals("1"));
} else if (key.equals("visibility")) {
if (valueLowerCase.equals("1") || valueLowerCase.equals("dense") || valueLowerCase.equals("collapsed")) {
trackProperties.setDisplayMode(Track.DisplayMode.COLLAPSED);
} else if (valueLowerCase.equals("2") || valueLowerCase.equals("3") || valueLowerCase.equals("pack") || valueLowerCase.equals("expanded")) {
trackProperties.setDisplayMode(Track.DisplayMode.EXPANDED);
} else if (valueLowerCase.equals("4") || valueLowerCase.equals("squish") || valueLowerCase.equals("squished")) {
trackProperties.setDisplayMode(Track.DisplayMode.SQUISHED);
}
} else if (key.equals("genome") || key.equals("db")) {
trackProperties.setGenome(value);
} else if (key.equals("bigdataurl") || key.equals("dataurl")) {
trackProperties.setDataURL(value);
} else if (key.equals("indexurl")) {
trackProperties.setIndexURL(value);
} else if (key.equals("coverageurl")) {
trackProperties.setCoverageURL(value);
} else if (key.equals("meta")) {
trackProperties.setMetaData(value);
}
}
}
}
} catch (Exception exception) {
MessageUtils.showMessage("Error parsing track line: " + nextLine + " (" + exception.getMessage() + ")");
}
return foundProperties;
}
public static boolean pathExists(String covPath) {
if (covPath == null) return false;
try {
return (new File(covPath)).exists() ||
(HttpUtils.isRemoteURL(covPath) && HttpUtils.getInstance().resourceAvailable(new URL(covPath)));
} catch (MalformedURLException e) {
log.error(e.getMessage(), e);
return false;
}
}
/**
* Return the "IGV extension" (basically the extension after stripping trailing qualifiers) for the input path.
* his is the string IGV uses to identify the format and data type of the file.
*
* @param path
* @return
*/
public static String getIGVExtension(String path) {
// String off gzip first
if (path.endsWith(".gz")) path = path.substring(0, path.length() - 3);
// Now common qualifiers
if (path.endsWith(".txt") || path.endsWith(".xls")) path = path.substring(0, path.length() - 4);
int idx = path.lastIndexOf('.');
return idx < 0 ? path : path.substring(idx + 1, path.length());
}
}