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 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 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.");
}
}