public static List<FeatureTrack> loadTracks(
Iterable<Feature> features,
ResourceLocator locator,
Genome genome,
TrackProperties trackProperties) {
FeatureCollectionSource source = new FeatureCollectionSource(features, genome);
// Load into FeatureDB for searching
if (IGV.hasInstance() || Globals.isTesting()) {
Set<String> chrs = source.getChrs();
for (String chr : chrs) {
List<Feature> feats = source.getFeatures(chr);
for (Feature f : feats) {
if (f instanceof NamedFeature) {
FeatureDB.addFeature((NamedFeature) f);
}
}
}
}
FeatureTrack track = new FeatureTrack(locator, source);
track.setName(locator.getTrackName());
track.setRendererClass(IGVFeatureRenderer.class);
track.setHeight(45);
if (trackProperties != null) {
track.setProperties(trackProperties);
}
List<FeatureTrack> tracks = new ArrayList();
tracks.add(track);
return tracks;
}
public static String getGSUser() throws IOException {
if (gsUser == null && !Globals.isTesting()) {
BufferedReader br = null;
try {
File tokenFile = getUsernameFile();
if (tokenFile.exists()) {
br = new BufferedReader(new FileReader(tokenFile));
gsUser = br.readLine().trim();
}
} finally {
try {
if (br != null) br.close();
} catch (Exception e) {
}
}
}
return gsUser;
}
public static void setGSUser(String newUser) {
if (gsUser == null || !gsUser.equals(newUser)) {
gsUser = newUser;
if (Globals.isTesting()) {
return;
}
File gsDir = getTokenSaveDir();
if (!gsDir.isDirectory()) {
log.error(
"Could not store token for SSO. File "
+ gsDir.getAbsolutePath()
+ "exists and is not a directory.");
return; // someone made a file with this name...
}
File userFile = getUsernameFile();
if (userFile.exists()) userFile.delete();
writeToFile(gsUser, userFile);
}
}
public static String getGSToken() {
if (gsToken == null && !Globals.isTesting()) {
File file = GSUtils.getTokenFile();
if (file.exists()) {
BufferedReader br = null;
try {
br = new BufferedReader(new FileReader(file));
gsToken = br.readLine();
} catch (IOException e) {
log.error("Error reading GS cookie", e);
} finally {
if (br != null)
try {
br.close();
} catch (IOException e) {
// Ignore
}
}
}
}
return gsToken;
}
public static void setGSToken(String newToken) {
if (gsToken == null || !gsToken.equals(newToken)) {
gsToken = newToken;
if (Globals.isTesting()) {
return;
}
BufferedWriter bw = null;
File gsDir = getTokenSaveDir();
if (!gsDir.isDirectory()) {
log.error(
"Could not store token for SSO. File "
+ gsDir.getAbsolutePath()
+ "exists and is not a directory.");
return; // someone made a file with this name...
}
File tokenFile = getTokenFile();
if (tokenFile.exists()) tokenFile.delete();
writeToFile(gsToken, tokenFile);
}
}