@Test
public void testParseTrackLine() {
String trackLine = "track type=bigWig name=\"Track 196\" visibility=2 " +
"description=\" CD34 - H3K27me3 - hg19 - 18.7 M/20.9 M - 61P7DAAXX.6\" " +
"maxHeightPixels=70 viewLimits=0:18 windowingFunction=mean autoScale=off " +
"bigDataUrl=http://www.broadinstitute.org/epigenomics/dataportal/track_00196.portal.bw " +
"color=255,0,0";
TrackProperties props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
assertEquals("Track 196", props.getName());
assertEquals(Track.DisplayMode.EXPANDED, props.getDisplayMode());
assertEquals(" CD34 - H3K27me3 - hg19 - 18.7 M/20.9 M - 61P7DAAXX.6", props.getDescription());
assertEquals(70, props.getHeight());
assertEquals(0, props.getMinValue(), 1.0e-9);
assertEquals(18, props.getMaxValue(), 1.0e-9);
assertEquals(WindowFunction.mean, props.getWindowingFunction());
assertEquals(false, props.isAutoScale());
assertEquals(new Color(255, 0, 0), props.getColor());
assertEquals("http://www.broadinstitute.org/epigenomics/dataportal/track_00196.portal.bw", props.getDataURL());
}
/**
* Load all features in this file.
*
* @param reader
* @param maxLines
* @return
*/
public List<org.broad.tribble.Feature> loadFeatures(BufferedReader reader, int maxLines) {
List<org.broad.tribble.Feature> features = new ArrayList<org.broad.tribble.Feature>();
String nextLine = null;
int nLines = 0;
try {
while ((nextLine = reader.readLine()) != null) {
nextLine = nextLine.trim();
if (nextLine.length() == 0) continue;
nLines++;
if ((maxLines > 0) && (nLines > maxLines)) {
break;
}
try {
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#type")) {
String[] tokens = Globals.equalPattern.split(nextLine);
if (tokens.length > 1) {
try {
// TODO: type is not currently used, is there any reason to keep this?
TrackType type = TrackType.valueOf(tokens[1]);
} catch (Exception e) {
log.error("Error converting track type: " + tokens[1]);
}
}
} else if (nextLine.startsWith("#track")) {
TrackProperties tp = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, tp);
setTrackProperties(tp);
if (tp.isGffTags()) {
gffTags = true;
}
} else if (nextLine.startsWith("#coords")) {
try {
String[] tokens = Globals.equalPattern.split(nextLine);
startBase = Integer.parseInt(tokens[1]);
} catch (Exception e) {
log.error("Error parsing coords line: " + nextLine, e);
}
} else if (nextLine.startsWith("#gffTags")) {
gffTags = true;
}
} else {
Feature feature = parseLine(nextLine);
if (feature != null) {
features.add(feature);
}
}
} catch (NumberFormatException e) {
// Expected condition -- for example comments. don't log as it slows down
// the parsing and is not useful information.
}
}
} catch (java.io.EOFException e) {
// This exception is due to a known bug with java zip library. Not
// in general a real error, and nothing we can do about it in any
// event.
return features;
} catch (Exception e) {
if (nextLine != null && nLines != 0) {
throw new ParserException(e.getMessage(), e, nLines, nextLine);
} else {
throw new RuntimeException(e);
}
}
// TODO -- why is this test here? This will break igvtools processing of expression files
// if (IGV.hasInstance() || Globals.isTesting()) {
FeatureDB.addFeatures(features);
// }
return features;
}