private boolean forceNotTribble(String typeString) {
List<String> nonTribble = Arrays.asList("fpkm_tracking", "exp_diff", "_exp.diff");
for (String s : nonTribble) {
if (typeString.endsWith(s)) {
return true;
}
}
return false;
}
/** User: jrobinso Date: Feb 14, 2010 */
public class TrackLoader {
private static Logger log = Logger.getLogger(TrackLoader.class);
private static Collection<? extends Class> NOLogExceptions =
Arrays.asList(TribbleIndexNotFoundException.class);
/**
* Switches on various attributes of locator (mainly locator path extension and whether the
* locator is indexed) to call the appropriate loading method.
*
* @param locator
* @param genome
* @return
*/
public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadException {
final String path = locator.getPath().trim();
log.info("Loading resource, path " + path);
try {
String typeString = locator.getTypeString();
if (typeString.endsWith(".tbi")) {
MessageUtils.showMessage(
"<html><b>Error:</b>File type '.tbi' is not recognized. If this is a 'tabix' index <br>"
+ " load the associated gzipped file, which should have an extension of '.gz'");
}
// This list will hold all new tracks created for this locator
List<Track> newTracks = new ArrayList<Track>();
String dbUrl = locator.getDBUrl();
LoadHandler handler = getTrackLoaderHandler(typeString);
if (dbUrl != null) {
this.loadFromDatabase(locator, newTracks, genome);
} else if (typeString.endsWith(".dbxml")) {
loadFromDBProfile(locator, newTracks);
} else if (typeString.endsWith(".gmt")) {
loadGMT(locator);
} else if (typeString.equals("das")) {
loadDASResource(locator, newTracks);
} else if (typeString.endsWith(".vcf.list")) {
loadVCFListFile(locator, newTracks, genome);
} else if (typeString.endsWith(".trio")) {
loadTrioData(locator);
} else if (typeString.endsWith("varlist")) {
VariantListManager.loadVariants(locator);
} else if (typeString.endsWith("samplepathmap")) {
VariantListManager.loadSamplePathMap(locator);
} else if (typeString.endsWith(".rnai.gct")) {
loadRnaiGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gct")
|| typeString.endsWith("res")
|| typeString.endsWith("tab")) {
loadGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gbk") || typeString.endsWith(".gb")) {
loadGbkFile(locator, newTracks, genome);
} else if (typeString.endsWith(".cn")
|| typeString.endsWith(".xcn")
|| typeString.endsWith(".snp")
|| typeString.endsWith(".igv")
|| typeString.endsWith(".loh")) {
loadIGVFile(locator, newTracks, genome);
} else if (typeString.endsWith(".cbs")
|| typeString.endsWith(".seg")
|| typeString.endsWith("glad")
|| typeString.endsWith("birdseye_canary_calls")
|| typeString.endsWith(".seg.zip")) {
loadSegFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gistic")) {
loadGisticFile(locator, newTracks);
} else if (typeString.endsWith(".gs")) {
loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.GENE_SCORE, genome);
} else if (typeString.endsWith(".riger")) {
loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.POOLED, genome);
} else if (typeString.endsWith(".hp")) {
loadRNAiHPScoreFile(locator);
} else if (typeString.contains(".tabblastn") || typeString.endsWith(".orthologs")) {
loadSyntentyMapping(locator, newTracks);
} else if (typeString.endsWith(".sam")
|| typeString.endsWith(".bam")
|| typeString.endsWith(".cram")
|| typeString.endsWith(".sam.list")
|| typeString.endsWith(".bam.list")
|| typeString.endsWith(".aligned")
|| typeString.endsWith(".sai")
|| typeString.endsWith(".bai")
|| typeString.equals("alist")
|| typeString.equals(Ga4ghAPIHelper.RESOURCE_TYPE)) {
loadAlignmentsTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".wig")
|| typeString.endsWith(".bedgraph")
|| typeString.endsWith(".bdg")
|| typeString.endsWith("cpg.txt")
|| typeString.endsWith(".expr")) {
loadWigFile(locator, newTracks, genome);
} else if (typeString.endsWith("fpkm_tracking")
|| typeString.endsWith("gene_exp.diff")
|| typeString.endsWith("cds_exp.diff")) {
loadCufflinksFile(locator, newTracks, genome);
} else if (typeString.contains(".dranger")) {
loadDRangerFile(locator, newTracks, genome);
} else if (typeString.endsWith(".ewig.tdf") || (typeString.endsWith(".ewig.ibf"))) {
loadEwigIBFFile(locator, newTracks, genome);
} else if (typeString.endsWith(".bw")
|| typeString.endsWith(".bb")
|| typeString.endsWith(".bigwig")
|| typeString.endsWith(".bigbed")) {
loadBWFile(locator, newTracks, genome);
} else if (typeString.endsWith(".ibf") || typeString.endsWith(".tdf")) {
loadTDFFile(locator, newTracks, genome);
} else if (typeString.endsWith(".counts")) {
loadGobyCountsArchive(locator, newTracks, genome);
} else if (WiggleParser.isWiggle(locator)) {
loadWigFile(locator, newTracks, genome);
} else if (typeString.endsWith(".maf")) {
loadMultipleAlignmentTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".maf.dict")) {
loadMultipleAlignmentTrack(locator, newTracks, genome);
} else if (typeString.contains(".peak.bin")) {
loadPeakTrack(locator, newTracks, genome);
} else if (typeString.endsWith("mage-tab")
|| ExpressionFileParser.parsableMAGE_TAB(locator)) {
locator.setDescription("MAGE_TAB");
loadGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".bp")) {
loadBasePairFile(locator, newTracks, genome);
} else if (GWASParser.isGWASFile(typeString)) {
loadGWASFile(locator, newTracks, genome);
} else if (GobyAlignmentQueryReader.supportsFileType(path)) {
loadAlignmentsTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".list")) {
// This should be deprecated
loadListFile(locator, newTracks, genome);
} else if (typeString.endsWith(".smap")) {
loadSMAPFile(locator, newTracks, genome);
} else if (CodecFactory.hasCodec(locator, genome) && !forceNotTribble(typeString)) {
loadTribbleFile(locator, newTracks, genome);
} else if (handler != null) {
// Custom loader specified
log.info(String.format("Loading %s with %s", path, handler));
handler.load(path, newTracks);
} else if (AttributeManager.isSampleInfoFile(locator)) {
// This might be a sample information file.
AttributeManager.getInstance().loadSampleInfo(locator);
} else {
MessageUtils.showMessage("<html>Unknown file type: " + path + "<br>Check file extension");
}
// Track line
TrackProperties tp = null;
String trackLine = locator.getTrackLine();
if (trackLine != null) {
tp = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, tp);
}
for (Track track : newTracks) {
if (locator.getFeatureInfoURL() != null) {
track.setUrl(locator.getFeatureInfoURL());
}
if (tp != null) {
track.setProperties(tp);
}
if (locator.getColor() != null) {
track.setColor(locator.getColor());
}
if (locator.getSampleId() != null) {
track.setSampleId(locator.getSampleId());
}
}
return newTracks;
} catch (Exception e) {
if (!NOLogExceptions.contains(e.getClass())) {
log.error(e.getMessage(), e);
}
throw new DataLoadException(e.getMessage());
}
}
private void loadSMAPFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
List<Feature> features = SMAPParser.parseFeatures(locator, genome);
FeatureCollectionSource src = new FeatureCollectionSource(features, genome);
FeatureTrack track = new FeatureTrack(locator, locator.getName(), src);
track.setRendererClass(SMAPRenderer.class);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
newTracks.add(track);
}
private boolean forceNotTribble(String typeString) {
List<String> nonTribble = Arrays.asList("fpkm_tracking", "exp_diff", "_exp.diff");
for (String s : nonTribble) {
if (typeString.endsWith(s)) {
return true;
}
}
return false;
}
private void loadGMT(ResourceLocator locator) throws IOException {
List<GeneList> lists = GeneListManager.getInstance().loadGMTFile(locator.getPath());
if (lists.size() == 1) {
GeneList gl = lists.get(0);
IGV.getInstance().setGeneList(gl, true);
} else {
MessageUtils.showMessage("Loaded " + lists.size() + " gene lists.");
}
}
private void loadVCF(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(locator, genome);
VCFHeader header = (VCFHeader) src.getHeader();
// Test if the input VCF file contains methylation rate data:
// This is determined by testing for the presence of two sample format fields: MR and GB, used
// in the
// rendering of methylation rate.
// MR is the methylation rate on a scale of 0 to 100% and GB is the number of bases that pass
// filter for the position. GB is needed to avoid displaying positions for which limited
// coverage
// prevents reliable estimation of methylation rate.
boolean enableMethylationRateSupport =
(header.getFormatHeaderLine("MR") != null && header.getFormatHeaderLine("GB") != null);
List<String> allSamples = new ArrayList(header.getGenotypeSamples());
VariantTrack t = new VariantTrack(locator, src, allSamples, enableMethylationRateSupport);
// VCF tracks handle their own margin
t.setMargin(0);
newTracks.add(t);
}
private void loadVCFListFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
TribbleListFeatureSource src = new TribbleListFeatureSource(locator.getPath(), genome);
VCFHeader header = (VCFHeader) src.getHeader();
// Test if the input VCF file contains methylation rate data:
// This is determined by testing for the presence of two sample format fields: MR and GB, used
// in the
// rendering of methylation rate.
// MR is the methylation rate on a scale of 0 to 100% and GB is the number of bases that pass
// filter for the position. GB is needed to avoid displaying positions for which limited
// coverage
// prevents reliable estimation of methylation rate.
boolean enableMethylationRateSupport =
(header.getFormatHeaderLine("MR") != null && header.getFormatHeaderLine("GB") != null);
List<String> allSamples = new ArrayList(header.getGenotypeSamples());
VariantTrack t = new VariantTrack(locator, src, allSamples, enableMethylationRateSupport);
// VCF tracks handle their own margin
t.setMargin(0);
newTracks.add(t);
}
private void loadSyntentyMapping(ResourceLocator locator, List<Track> newTracks) {
List<BlastMapping> mappings = (new BlastParser()).parse(locator.getPath());
List<htsjdk.tribble.Feature> features = new ArrayList<htsjdk.tribble.Feature>(mappings.size());
features.addAll(mappings);
Genome genome = GenomeManager.getInstance().getCurrentGenome();
FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
track.setName(locator.getTrackName());
// track.setRendererClass(AlignmentBlockRenderer.class);
newTracks.add(track);
}
private void loadDRangerFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
DRangerParser parser = new DRangerParser();
newTracks.addAll(parser.loadTracks(locator, genome));
}
/**
* Load the input file as a feature, mutation, or maf (multiple alignment) file.
*
* @param locator
* @param newTracks
*/
private void loadTribbleFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
String typeString = locator.getTypeString();
// Mutation (mut, maf, vcf) files are handled special. Check here, rather than depend on order
// in giant case statement.
if (MutationTrackLoader.isMutationAnnotationFile(locator)) {
loadMutFile(locator, newTracks, genome); // Must be tried before generic "loadIndexed" below
} else if (VariantTrack.isVCF(typeString)) {
loadVCF(locator, newTracks, genome);
} else {
TribbleFeatureSource tribbleFeatureSource =
TribbleFeatureSource.getFeatureSource(locator, genome);
FeatureSource src =
GFFFeatureSource.isGFF(locator.getPath())
? new GFFFeatureSource(tribbleFeatureSource)
: tribbleFeatureSource;
// Create feature source and track
FeatureTrack t = new FeatureTrack(locator, src);
t.setName(locator.getTrackName());
// t.setRendererClass(BasicTribbleRenderer.class);
// Set track properties from header
Object header = tribbleFeatureSource.getHeader();
if (header != null && header instanceof FeatureFileHeader) {
FeatureFileHeader ffh = (FeatureFileHeader) header;
if (ffh.getTrackType() != null) {
t.setTrackType(ffh.getTrackType());
}
if (ffh.getTrackProperties() != null) {
t.setProperties(ffh.getTrackProperties());
}
if (ffh.getTrackType() == TrackType.REPMASK) {
t.setHeight(15);
}
}
if (locator.getPath().contains(".narrowPeak")
|| locator.getPath().contains(".broadPeak")
|| locator.getPath().contains(".gappedPeak")) {
t.setUseScore(true);
}
newTracks.add(t);
}
}
/**
* Load GWAS PLINK result file
*
* @param locator
* @param newTracks
* @throws IOException
*/
private void loadGWASFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
GWASParser gwasParser = new GWASParser(locator, genome);
GWASData gwasData = gwasParser.parse();
GWASTrack gwasTrack =
new GWASTrack(locator, locator.getPath(), locator.getFileName(), gwasData, gwasParser);
newTracks.add(gwasTrack);
}
private void loadRnaiGctFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
RNAIGCTDatasetParser parser = new RNAIGCTDatasetParser(locator, genome);
Collection<RNAIDataSource> dataSources = parser.parse();
if (dataSources != null) {
String path = locator.getPath();
for (RNAIDataSource ds : dataSources) {
String trackId = path + "_" + ds.getName();
DataSourceTrack track = new DataSourceTrack(locator, trackId, ds.getName(), ds);
// Set attributes.
track.setAttributeValue("SCREEN", ds.getScreen());
track.setHeight(80);
newTracks.add(track);
}
}
}
private void loadGctFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
ExpressionFileParser parser = null;
ExpressionDataset ds = null;
parser = new ExpressionFileParser(locator, null, genome);
ds = parser.createDataset();
if (ds.isEmpty()) {
String message =
"The probes in the file <br> "
+ locator.getPath()
+ "<br>"
+ "could not be mapped to genomic positions. This can be corrected by specify a probe mapping<br>"
+ "file from the Preferences window (Probes tab), or by specifing the genomic positions in the<br>"
+ "expression data file. Please see the user guide for more details.";
MessageUtils.showMessage(message);
} else {
ds.setName(locator.getTrackName());
ds.setNormalized(true);
ds.setLogValues(true);
/*
* File outputFile = new File(IGV.DEFAULT_USER_DIRECTORY, file.getName() + ".h5");
* OverlappingProcessor proc = new OverlappingProcessor(ds);
* proc.setZoomMax(0);
* proc.process(outputFile.getAbsolutePath());
* loadH5File(outputFile, messages, attributeList, group);
*/
// Counter for generating ID
TrackProperties trackProperties = ds.getTrackProperties();
String path = locator.getPath();
for (String trackName : ds.getTrackNames()) {
DatasetDataSource dataSource = new DatasetDataSource(trackName, ds, genome);
String trackId = path + "_" + trackName;
Track track = new DataSourceTrack(locator, trackId, trackName, dataSource);
track.setRendererClass(HeatmapRenderer.class);
track.setProperties(trackProperties);
newTracks.add(track);
}
}
}
/**
* Load features from a genbank (.gbk)file. This method ignores the fasta section. To define a
* genome from a genbank file use GenomeManager.
*
* @param newTracks
* @param genome
* @throws IOException
*/
private void loadGbkFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
GenbankParser genbankParser = new GenbankParser(locator.getPath());
genbankParser.readFeatures(false);
FeatureCollectionSource src = new FeatureCollectionSource(genbankParser.getFeatures(), genome);
FeatureTrack track = new FeatureTrack(locator, src);
newTracks.add(track);
}
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);
}
}
private void loadCufflinksFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
final String path = locator.getPath();
final String s = path.toLowerCase();
List<DataTrack> cuffTracks = new ArrayList<DataTrack>();
if (s.endsWith("fpkm_tracking")) {
FPKMTrackingCodec codec = new FPKMTrackingCodec(path);
List<FPKMValue> values = CufflinksParser.parse(codec, path);
for (int sampleIndex = 0; sampleIndex < codec.getNumSamples(); sampleIndex++) {
CufflinksDataSource ds = new CufflinksDataSource(sampleIndex, values, genome);
String supId = String.format("q%02d", sampleIndex);
DataTrack track =
new DataSourceTrack(
locator, locator.getPath() + " " + supId, locator.getTrackName() + " " + supId, ds);
cuffTracks.add(track);
}
} else if (s.endsWith("gene_exp.diff") || s.endsWith("cds_exp.diff")) {
AsciiFeatureCodec<ExpDiffValue> codec = new ExpDiffCodec(path);
List<ExpDiffValue> values = CufflinksParser.parse(codec, path);
CufflinksDataSource ds = new CufflinksDataSource(values, genome);
DataTrack track = new DataSourceTrack(locator, locator.getPath(), locator.getTrackName(), ds);
cuffTracks.add(track);
} else {
throw new RuntimeException("Unsupported file type: " + path);
}
for (DataTrack track : cuffTracks) {
track.setTrackType(TrackType.FPKM);
CufflinksTrack.setCufflinksScale(track);
newTracks.add(track);
}
}
private static boolean checkSize(ResourceLocator locator) {
if (!PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_SIZE_WARNING)) {
return true;
}
final String path = locator.getPath();
long size = FileUtils.getLength(path);
int maxSize = 50000000; // 50 mb
if (path.endsWith(".gz") || path.endsWith(".bgz")) {
maxSize /= 4;
}
if (size > maxSize) {
String message =
"The file "
+ path
+ " is large ("
+ (size / 1000000)
+ " mb). It is recommended "
+ "that large files be converted to the binary <i>.tdf</i> format using the IGVTools "
+ "<b>tile</b> command. Loading unconverted ascii fies of this size can lead to poor "
+ "performance or unresponsiveness (freezing). "
+ "<br><br>IGVTools can be launched from the <b>Tools</b> menu or separately as a "
+ "command line program. See the user guide for more details.<br><br>Click <b>Continue</b> "
+ "to continue loading, or <b>Cancel</b> to skip this file.";
return ConfirmDialog.optionallyShowConfirmDialog(
message, PreferenceManager.SHOW_SIZE_WARNING, true);
}
return true;
}
private void loadDOTFile(ResourceLocator locator, List<Track> newTracks) {
// GraphTrack gt = new GraphTrack(locator);
// gt.setHeight(80);
// newTracks.add(gt);
}
private void loadWigFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
WiggleDataset ds = (new WiggleParser(locator, genome)).parse();
TrackProperties props = ds.getTrackProperties();
// In case of conflict between the resource locator display name and the track properties name,
// use the resource locator
String name = props == null ? null : props.getName();
String label = locator.getName();
if (name == null) {
name = locator.getFileName();
} else if (label != null) {
props.setName(label); // erase name rom track properties
}
String path = locator.getPath();
boolean multiTrack = ds.getTrackNames().length > 1;
for (String heading : ds.getTrackNames()) {
String trackId = multiTrack ? path + "_" + heading : path;
String trackName = multiTrack ? heading : name;
DatasetDataSource dataSource = new DatasetDataSource(trackId, ds, genome);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
String displayName = (label == null || multiTrack) ? heading : label;
track.setName(displayName);
track.setProperties(props);
track.setTrackType(ds.getType());
if (ds.getType() == TrackType.EXPR) {
track.setWindowFunction(WindowFunction.none);
}
newTracks.add(track);
}
}
public void loadTDFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
log.debug("Loading TDF file " + locator.getPath());
TDFReader reader = TDFReader.getReader(locator);
TrackType type = reader.getTrackType();
TrackProperties props = null;
String trackLine = reader.getTrackLine();
if (trackLine != null && trackLine.length() > 0) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
}
// In case of conflict between the resource locator display name and the track properties name,
// use the resource locator
String name = locator.getName();
if (name != null && props != null) {
props.setName(name);
}
if (name == null) {
name = props == null ? locator.getTrackName() : props.getName();
}
int trackNumber = 0;
String path = locator.getPath();
boolean multiTrack = reader.getTrackNames().length > 1;
for (String heading : reader.getTrackNames()) {
String trackId = multiTrack ? path + "_" + heading : path;
String trackName = multiTrack ? heading : name;
final DataSource dataSource =
locator.getPath().endsWith(".counts")
? new GobyCountArchiveDataSource(locator)
: new TDFDataSource(reader, trackNumber, heading, genome);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
String displayName = (name == null || multiTrack) ? heading : name;
track.setName(displayName);
track.setTrackType(type);
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
trackNumber++;
}
}
public void loadBWFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
String trackName = locator.getTrackName();
String trackId = locator.getPath();
String path = locator.getPath();
BBFileReader reader = new BBFileReader(path);
BigWigDataSource bigwigSource = new BigWigDataSource(reader, genome);
if (reader.isBigWigFile()) {
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, bigwigSource);
newTracks.add(track);
} else if (reader.isBigBedFile()) {
if (locator.getPath().contains("RRBS_cpgMethylation")
|| locator.getPath().contains("BiSeq_cpgMethylation")
|| (reader.getAutoSql() != null
&& reader.getAutoSql().startsWith("table BisulfiteSeq"))) {
loadMethylTrack(locator, reader, newTracks, genome);
} else {
FeatureTrack track = new FeatureTrack(locator, trackId, trackName, bigwigSource);
newTracks.add(track);
}
} else {
throw new RuntimeException("Unknown BIGWIG type: " + locator.getPath());
}
}
private void loadMethylTrack(
ResourceLocator locator, BBFileReader reader, List<Track> newTracks, Genome genome)
throws IOException {
MethylTrack track = new MethylTrack(locator, reader, genome);
newTracks.add(track);
}
private void loadGobyCountsArchive(
ResourceLocator locator, List<Track> newTracks, Genome genome) {
if (log.isDebugEnabled()) {
log.debug("Loading Goby counts archive: " + locator.toString());
}
String trackId = locator.getSampleId() + " coverage";
String trackName = locator.getFileName();
final DataSource dataSource = new GobyCountArchiveDataSource(locator);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
newTracks.add(track);
}
private void loadEwigIBFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
TDFReader reader = TDFReader.getReader(locator.getPath());
TrackProperties props = null;
String trackLine = reader.getTrackLine();
if (trackLine != null && trackLine.length() > 0) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
}
EWigTrack track = new EWigTrack(locator, genome);
if (props != null) {
track.setProperties(props);
}
track.setName(locator.getTrackName());
newTracks.add(track);
}
private void loadListFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
try {
FeatureSource source = new FeatureDirSource(locator, genome);
FeatureTrack track = new FeatureTrack(locator, source);
track.setName(locator.getTrackName());
track.setVisibilityWindow(0);
newTracks.add(track);
} catch (IOException ex) {
throw new RuntimeException(ex);
}
}
private void loadGisticFile(ResourceLocator locator, List<Track> newTracks) {
GisticTrack track = GisticFileParser.loadData(locator);
track.setName(locator.getTrackName());
newTracks.add(track);
}
/**
* Load a rnai gene score file and create a datasource and track.
*
* <p>
*
* @param locator
* @param newTracks
*/
private void loadRNAiGeneScoreFile(
ResourceLocator locator,
List<Track> newTracks,
RNAIGeneScoreParser.Type type,
Genome genome) {
RNAIGeneScoreParser parser = new RNAIGeneScoreParser(locator.getPath(), type, genome);
Collection<RNAIDataSource> dataSources = parser.parse();
String path = locator.getPath();
for (RNAIDataSource ds : dataSources) {
String name = ds.getName();
String trackId = path + "_" + name;
DataSourceTrack track = new DataSourceTrack(locator, trackId, name, ds);
// Set attributes. This "hack" is neccessary to register these attributes with the
// attribute manager to get displayed.
track.setAttributeValue("SCREEN", ds.getScreen());
if ((ds.getCondition() != null) && (ds.getCondition().length() > 0)) {
track.setAttributeValue("CONDITION", ds.getCondition());
}
track.setHeight(80);
// track.setDataRange(new DataRange(-3, 0, 3));
newTracks.add(track);
}
}
/**
* Load a RNAi haripin score file. The results of this action are hairpin scores added to the
* RNAIDataManager. Currently no tracks are created for hairpin scores, although this could
* change.
*
* @param locator
*/
private void loadRNAiHPScoreFile(ResourceLocator locator) {
(new RNAIHairpinParser(locator.getPath())).parse();
}
private void loadMultipleAlignmentTrack(
ResourceLocator locator, List<Track> newTracks, Genome genome) throws IOException {
MultipleAlignmentTrack t = new MultipleAlignmentTrack(locator, genome);
t.setName("Multiple Alignments");
newTracks.add(t);
}
private void loadPeakTrack(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
PeakTrack t = new PeakTrack(locator, genome);
newTracks.add(t);
}
private void loadAlignmentsTrack(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
try {
String dsName = locator.getTrackName();
// If the user tried to load the index, look for the file (this is a common mistake)
if (locator.getTypeString().endsWith(".sai") || locator.getTypeString().endsWith(".bai")) {
MessageUtils.showMessage(
"<html><b>ERROR:</b> Loading SAM/BAM index files are not supported: "
+ locator.getPath()
+ "<br>Load the SAM or BAM file directly. ");
return;
}
AlignmentDataManager dataManager = new AlignmentDataManager(locator, genome);
// Check that alignments we loaded actually match some data. Many BAM files will contain some
// sequences
// not represented in the genome, buf if there are no matches warn the user.
List<String> seqNames = dataManager.getSequenceNames();
if (seqNames != null && seqNames.size() > 0) {
if (!checkSequenceNames(locator.getPath(), genome, seqNames)) {
return;
}
}
if (locator.getTypeString().endsWith("bam") || locator.getTypeString().endsWith("cram")) {
if (!dataManager.hasIndex()) {
MessageUtils.showMessage(
"<html>Could not load index file for: "
+ locator.getPath()
+ "<br> An index file is required for SAM & BAM files.");
return;
}
}
AlignmentTrack alignmentTrack =
new AlignmentTrack(locator, dataManager, genome); // parser.loadTrack(locator, dsName);
alignmentTrack.setName(dsName);
alignmentTrack.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_ALIGNMENT_TRACK));
// Create coverage track
CoverageTrack covTrack =
new CoverageTrack(locator, dsName + " Coverage", alignmentTrack, genome);
covTrack.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_COV_TRACK));
newTracks.add(covTrack);
covTrack.setDataManager(dataManager);
dataManager.setCoverageTrack(covTrack);
alignmentTrack.setCoverageTrack(covTrack);
// Search for precalculated coverage data
// Skip for GA4GH & SU2C resources
if (!(Ga4ghAPIHelper.RESOURCE_TYPE.equals(locator.getType())
|| locator.getPath().contains("dataformat=.bam")
|| OAuthUtils.isGoogleCloud(locator.getPath()))) {
String covPath = locator.getCoverage();
if (covPath == null) {
boolean bypassFileAutoDiscovery =
PreferenceManager.getInstance()
.getAsBoolean(PreferenceManager.BYPASS_FILE_AUTO_DISCOVERY);
String path = locator.getPath();
if (!bypassFileAutoDiscovery && !path.contains("/query.cgi?")) {
covPath = path + ".tdf";
}
}
if (covPath != null) {
if (FileUtils.resourceExists(covPath)) {
log.debug("Loading TDF for coverage: " + covPath);
try {
TDFReader reader = TDFReader.getReader(covPath);
TDFDataSource ds = new TDFDataSource(reader, 0, dsName + " coverage", genome);
covTrack.setDataSource(ds);
} catch (Exception e) {
log.error("Error loading coverage TDF file", e);
}
}
}
}
boolean showSpliceJunctionTrack =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_JUNCTION_TRACK);
SpliceJunctionTrack spliceJunctionTrack =
new SpliceJunctionTrack(
locator,
dsName + " Junctions",
dataManager,
alignmentTrack,
SpliceJunctionTrack.StrandOption.BOTH);
spliceJunctionTrack.setHeight(60);
spliceJunctionTrack.setVisible(showSpliceJunctionTrack);
newTracks.add(spliceJunctionTrack);
alignmentTrack.setSpliceJunctionTrack(spliceJunctionTrack);
newTracks.add(alignmentTrack);
log.debug("Alignment track loaded");
} catch (IndexNotFoundException e) {
MessageUtils.showMessage(
"<html>Could not find the index file for <br><br> "
+ e.getSamFile()
+ "<br><br>Note: The index file can be created using igvtools and must be in the same directory as the .sam file.");
}
}
/**
* Compare the sequence names against sequence (chromosome) names in the genome. If no matches
* warn the user.
*
* @param filename
* @param genome
* @param seqNames
* @return true if there is at least one sequence match, false otherwise
*/
private boolean checkSequenceNames(String filename, Genome genome, List<String> seqNames) {
boolean atLeastOneMatch = false;
for (String seqName : seqNames) {
if (genome.getChromosome(seqName) != null) {
atLeastOneMatch = true;
break;
}
}
if (!atLeastOneMatch) {
StringBuffer message = new StringBuffer();
message.append(
"<html>File: "
+ filename
+ "<br>does not contain any sequence names which match the current genome.");
message.append("<br><br>File: ");
int n = 0;
for (String sn : seqNames) {
message.append(sn + ", ");
n++;
if (n > 3) {
message.append(" ...");
break;
}
}
message.append("<br>Genome: ");
n = 0;
for (String cn : genome.getAllChromosomeNames()) {
message.append(cn + ", ");
n++;
if (n > 3) {
message.append(" ...");
break;
}
}
MessageUtils.showMessage(message.toString());
}
return atLeastOneMatch;
}
/**
* Load a mutation file (".mut" or ".maf").
*
* @param locator
* @param newTracks
*/
private void loadMutFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
MutationTrackLoader loader = new MutationTrackLoader();
List<FeatureTrack> mutationTracks = loader.loadMutationTracks(locator, genome);
for (FeatureTrack track : mutationTracks) {
track.setTrackType(TrackType.MUTATION);
track.setRendererClass(MutationRenderer.class);
newTracks.add(track);
}
}
private void loadFromDBProfile(ResourceLocator profileLocator, List<Track> newTracks)
throws IOException {
DBProfile dbProfile = DBProfile.parseProfile(profileLocator.getPath());
for (DBProfile.DBTable table : dbProfile.getTableList()) {
SQLCodecSource source = SQLCodecSource.getFromTable(table);
if (source != null) {
CachingFeatureSource cachingReader = new CachingFeatureSource(source);
FeatureTrack track = new FeatureTrack(profileLocator, cachingReader);
track.setName(source.getTableName());
newTracks.add(track);
} else if (table.getFormat().equals("seg")) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
SegmentedAsciiDataSet ds =
(new SegmentedReader(table.getDbLocator(), genome)).loadFromDB(table);
loadSegTrack(table.getDbLocator(), newTracks, genome, ds);
} else if (table.getFormat().equals("sample.info")) {
// TODO sampleIdColumnLabel was previously hardcoded as "SAMPLE_ID_ARRAY"
// TODO Basically I'm shoehorning this information into a field usually used for something
// else. Only slightly better
String sampleIdColumnLabel = table.getBinColName();
if (sampleIdColumnLabel == null) {
throw new IllegalArgumentException(
"Profile must have binColName specifying the sample id column label");
}
(new SampleInfoSQLReader(table, sampleIdColumnLabel)).load();
}
}
}
/**
* @param locator
* @param newTracks
* @param genome
* @deprecated See loadFromDBProfile, which loads from an xml file specifying table
* characteristics
*/
@Deprecated
private void loadFromDatabase(ResourceLocator locator, List<Track> newTracks, Genome genome) {
// For backwards/forwards compatibility
// We used to put path in the serverURL field
ResourceLocator dbLocator = new ResourceLocator(locator.getDBUrl());
if (".seg".equals(locator.getTypeString())) {
// TODO Don't hardcode table name, this might note even be right for our target case
SegmentedAsciiDataSet ds = (new SegmentedSQLReader(dbLocator, "CNV", genome)).load();
loadSegTrack(locator, newTracks, genome, ds);
} else {
(new SampleInfoSQLReader(dbLocator, "SAMPLE_INFO", "SAMPLE_ID_ARRAY")).load();
}
}
private void loadSegFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
// TODO - -handle remote resource
SegmentedDataSet ds;
String path = locator.getPath().toLowerCase();
if (path.endsWith("seg.zip")) {
ds = new SegmentedBinaryDataSet(locator);
} else {
SegmentFileParser parser = new SegmentFileParser(locator);
ds = parser.loadSegments(locator, genome);
}
loadSegTrack(locator, newTracks, genome, ds);
}
/**
* Add the provided SegmentedDataSet to the list of tracks, set other relevant properties
*
* @param locator
* @param newTracks
* @param genome
* @param ds
*/
private void loadSegTrack(
ResourceLocator locator, List<Track> newTracks, Genome genome, SegmentedDataSet ds) {
String path = locator.getPath();
TrackProperties props = null;
if (ds instanceof SegmentedAsciiDataSet) {
props = ((SegmentedAsciiDataSet) ds).getTrackProperties();
}
// The "freq" track. TODO - make this optional
if ((ds.getType() == TrackType.COPY_NUMBER || ds.getType() == TrackType.CNV)
&& ds.getSampleNames().size() > 1) {
FreqData fd = new FreqData(ds, genome);
String freqTrackId = path;
String freqTrackName = "CNV Summary";
CNFreqTrack freqTrack = new CNFreqTrack(locator, freqTrackId, freqTrackName, fd);
newTracks.add(freqTrack);
}
for (String trackName : ds.getSampleNames()) {
String trackId = path + "_" + trackName;
SegmentedDataSource dataSource = new SegmentedDataSource(trackName, ds);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
track.setRendererClass(HeatmapRenderer.class);
track.setTrackType(ds.getType());
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
}
}
private void loadDASResource(ResourceLocator locator, List<Track> currentTracks)
throws DataLoadException {
// TODO Connect and get all the attributes of the DAS server, and run the appropriate load
// statements
// TODO Currently we are only going to be doing features
// TODO -- move the source creation to a factory
DASFeatureSource featureSource = null;
try {
featureSource = new DASFeatureSource(locator);
} catch (MalformedURLException e) {
log.error("Malformed URL", e);
throw new DataLoadException("Error: Malformed URL ");
}
FeatureTrack track = new FeatureTrack(locator, featureSource);
// Try to create a sensible name from the path
String name = locator.getName();
if (name == null || name.length() == 0) {
if (locator.getPath().contains("genome.ucsc.edu")) {
name = featureSource.getType();
} else {
name = featureSource.getPath().replace("/das/", "").replace("/features", "");
}
}
track.setName(name);
// A hack until we can notate this some other way
if (locator.getPath().contains("cosmic")) {
track.setRendererClass(CosmicFeatureRenderer.class);
track.setMinimumHeight(2);
track.setHeight(20);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
} else {
track.setRendererClass(IGVFeatureRenderer.class);
track.setMinimumHeight(35);
track.setHeight(45);
}
currentTracks.add(track);
}
private void loadTrioData(ResourceLocator locator) throws IOException {
PedigreeUtils.parseTrioFile(locator.getPath());
}
private void loadBasePairFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
BasePairFileParser parser = new BasePairFileParser();
newTracks.add(parser.loadTrack(locator, genome)); // should create one track from the given file
}
public static boolean isIndexed(ResourceLocator locator, Genome genome) {
// Checking for the index is expensive over HTTP. First see if this is an indexable format by
// fetching the codec
String fullPath = locator.getPath();
String pathNoQuery = locator.getURLPath();
if (!CodecFactory.hasCodec(locator, genome)) {
return false;
}
String indexExtension = pathNoQuery.endsWith("gz") ? ".tbi" : ".idx";
String indexPath = fullPath + indexExtension;
if (HttpUtils.isRemoteURL(fullPath)) {
// Handle query string, if it exists
String[] toks = fullPath.split("\\?", 2);
if (toks.length == 2) {
indexPath = String.format("%s%s?%s", toks[0], indexExtension, toks[1]);
}
}
return FileUtils.resourceExists(indexPath);
}
public static TrackProperties getTrackProperties(Object header) {
try {
FeatureFileHeader ffHeader = (FeatureFileHeader) header;
if (ffHeader != null) {
return ffHeader.getTrackProperties();
} else {
return null;
}
} catch (ClassCastException e) {
return null;
}
}
private static Map<String, LoadHandler> handlers = new HashMap<String, LoadHandler>();
/**
* Register a custom handler for the given extension. Note that this does NOT override built-in
* IGV behavior
*
* @param extension
* @param loader
* @api
*/
public static void registerHandler(String extension, LoadHandler loader) {
handlers.put(extension, loader);
}
/**
* Get the registered {@link org.broad.igv.dev.api.LoadHandler} for this path/typeString, or null
* if one not found
*
* @param typeString
* @return
* @api
*/
private LoadHandler getTrackLoaderHandler(String typeString) {
String lower = typeString.toLowerCase();
for (Map.Entry<String, LoadHandler> entry : handlers.entrySet()) {
if (lower.endsWith(entry.getKey().toLowerCase())) {
return entry.getValue();
}
}
return null;
}
}