/**
* Note: This is an exact copy of the method in ExpressionFileParser. Refactor to merge these two
* parsers, or share a common base class.
*
* @param comment
* @param dataset
*/
private void parseDirective(String comment, IGVDataset dataset) {
String tmp = comment.substring(1, comment.length());
if (tmp.startsWith("track")) {
ParsingUtils.parseTrackLine(tmp, dataset.getTrackProperties());
} else if (tmp.startsWith("columns")) {
parseColumnLine(tmp);
} else {
String[] tokens = tmp.split("=");
if (tokens.length != 2) {
return;
}
String key = tokens[0].trim().toLowerCase();
if (key.equals("name")) {
dataset.setName(tokens[1].trim());
} else if (key.equals("type")) {
try {
dataset.setTrackType(TrackType.valueOf(tokens[1].trim().toUpperCase()));
} catch (Exception exception) {
// Ignore
}
} else if (key.equals("coords")) {
startBase = Integer.parseInt(tokens[1].trim());
}
}
}
private void updateWholeGenome(
String currentChromosome,
IGVDataset dataset,
String[] headings,
IGVDatasetParser.WholeGenomeData wgData) {
if (!genome.getHomeChromosome().equals(Globals.CHR_ALL)) {
return;
}
// Update whole genome data
int[] locations = wgData.locations.toArray();
if (locations.length > 0) {
Map<String, float[]> tmp = new HashMap(wgData.data.size());
for (String s : wgData.headings) {
tmp.put(s, wgData.data.get(s).toArray());
}
GenomeSummaryData genomeSummary = dataset.getGenomeSummary();
if (genomeSummary == null) {
genomeSummary = new GenomeSummaryData(genome, headings);
dataset.setGenomeSummary(genomeSummary);
}
genomeSummary.addData(currentChromosome, locations, tmp);
}
}
private void loadIGVFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
String dsName = locator.getTrackName();
IGVDataset ds = new IGVDataset(locator, genome);
ds.setName(dsName);
TrackProperties trackProperties = ds.getTrackProperties();
String path = locator.getPath();
TrackType type = ds.getType();
for (String trackName : ds.getTrackNames()) {
DatasetDataSource dataSource = new DatasetDataSource(trackName, ds, genome);
String trackId = path + "_" + trackName;
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
// track.setRendererClass(HeatmapRenderer.class);
track.setTrackType(ds.getType());
track.setProperties(trackProperties);
if (type == TrackType.ALLELE_FREQUENCY) {
track.setRendererClass(PointsRenderer.class);
track.setHeight(40);
}
newTracks.add(track);
}
}
/**
* Scan the datafile for chromosome breaks.
*
* @param dataset
* @return
*/
public List<ChromosomeSummary> scan(IGVDataset dataset) {
int estLineCount = ParsingUtils.estimateLineCount(dataResourceLocator.getPath());
Map<String, Integer> longestFeatureMap = new HashMap();
float dataMin = 0;
float dataMax = 0;
InputStream is = null;
AsciiLineReader reader = null;
String nextLine = null;
ChromosomeSummary chrSummary = null;
List<ChromosomeSummary> chrSummaries = new ArrayList();
String[] headings = null;
WholeGenomeData wgData = null;
int nRows = 0;
int headerRows = 0;
int count = 0;
boolean logNormalized;
try {
int skipColumns = hasCalls ? 2 : 1;
// BufferedReader reader = ParsingUtils.openBufferedReader(dataResourceLocator);
is = ParsingUtils.openInputStreamGZ(dataResourceLocator);
reader = new AsciiLineReader(is);
// Infer datatype from extension. This can be overriden in the
// comment section
if (isCopyNumberFileExt(dataResourceLocator.getPath())) {
dataset.setTrackType(TrackType.COPY_NUMBER);
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
} else if (isLOHFileExt(dataResourceLocator.getPath())) {
dataset.setTrackType(TrackType.LOH);
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
} else {
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
}
// Parse comments and directives, if any
nextLine = reader.readLine();
while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
headerRows++;
if (nextLine.length() > 0) {
parseDirective(nextLine, dataset);
}
nextLine = reader.readLine();
}
if (chrColumn < 0) {
setColumnDefaults();
}
// Parse column headings
String[] data = nextLine.trim().split("\t");
// Set last data column
if (lastDataColumn < 0) {
lastDataColumn = data.length - 1;
}
headings = getHeadings(data, skipColumns);
dataset.setDataHeadings(headings);
// Infer if the data is logNormalized by looking for negative data values.
// Assume it is not until proven otherwise
logNormalized = false;
wgData = new WholeGenomeData(headings);
int chrRowCount = 0;
// Update
int updateCount = 5000;
long lastPosition = 0;
while ((nextLine = reader.readLine()) != null) {
if (igv != null && ++count % updateCount == 0) {
igv.setStatusBarMessage("Loaded: " + count + " / " + estLineCount + " (est)");
}
// Distance since last sample
String[] tokens = Globals.tabPattern.split(nextLine, -1);
int nTokens = tokens.length;
if (nTokens > 0) {
String thisChr = genome.getChromosomeAlias(tokens[chrColumn]);
if (chrSummary == null || !thisChr.equals(chrSummary.getName())) {
// Update whole genome and previous chromosome summary, unless this is
// the first chromosome
if (chrSummary != null) {
updateWholeGenome(chrSummary.getName(), dataset, headings, wgData);
chrSummary.setNDataPoints(nRows);
}
// Shart the next chromosome
chrSummary = new ChromosomeSummary(thisChr, lastPosition);
chrSummaries.add(chrSummary);
nRows = 0;
wgData = new WholeGenomeData(headings);
chrRowCount = 0;
}
lastPosition = reader.getPosition();
int location = -1;
try {
location = ParsingUtils.parseInt(tokens[startColumn]) - startBase;
} catch (NumberFormatException numberFormatException) {
log.error("Column " + tokens[startColumn] + " is not a number");
throw new ParserException(
"Column "
+ (startColumn + 1)
+ " must contain an integer value."
+ " Found: "
+ tokens[startColumn],
count + headerRows,
nextLine);
}
int length = 1;
if (hasEndLocations) {
try {
length = ParsingUtils.parseInt(tokens[endColumn].trim()) - location + 1;
} catch (NumberFormatException numberFormatException) {
log.error("Column " + tokens[endColumn] + " is not a number");
throw new ParserException(
"Column "
+ (endColumn + 1)
+ " must contain an integer value."
+ " Found: "
+ tokens[endColumn],
count + headerRows,
nextLine);
}
}
updateLongestFeature(longestFeatureMap, thisChr, length);
if (wgData.locations.size() > 0
&& wgData.locations.get(wgData.locations.size() - 1) > location) {
throw new ParserException(
"File is not sorted, .igv and .cn files must be sorted by start position."
+ " Use igvtools (File > Run igvtools..) to sort the file.",
count + headerRows);
}
wgData.locations.add(location);
for (int idx = 0; idx < headings.length; idx++) {
int i = firstDataColumn + idx * skipColumns;
float copyNo = i < tokens.length ? readFloat(tokens[i]) : Float.NaN;
if (!Float.isNaN(copyNo)) {
dataMin = Math.min(dataMin, copyNo);
dataMax = Math.max(dataMax, copyNo);
}
if (copyNo < 0) {
logNormalized = true;
}
String heading = headings[idx];
wgData.data.get(heading).add(copyNo);
}
nRows++;
}
chrRowCount++;
}
dataset.setLongestFeatureMap(longestFeatureMap);
} catch (ParserException pe) {
throw pe;
} catch (FileNotFoundException e) {
// DialogUtils.showError("SNP file not found: " + dataSource.getCopyNoFile());
log.error("File not found: " + dataResourceLocator);
throw new RuntimeException(e);
} catch (Exception e) {
log.error("Exception when loading: " + dataResourceLocator.getPath(), e);
if (nextLine != null && (count + headerRows != 0)) {
throw new ParserException(e.getMessage(), e, count + headerRows, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (is != null) {
try {
is.close();
} catch (IOException e) {
log.error("Error closing IGVDataset stream", e);
}
}
}
// Update last chromosome
if (chrSummary != null) {
updateWholeGenome(chrSummary.getName(), dataset, headings, wgData);
chrSummary.setNDataPoints(nRows);
}
dataset.setLogNormalized(logNormalized);
dataset.setDataMin(dataMin);
dataset.setDataMax(dataMax);
return chrSummaries;
}
