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;
}
/**
* Main method. Used to run igvtools from the command line
*
* @param argv
* @throws IOException
* @throws PreprocessingException
*/
public static void main(String[] argv) {
try {
initLogger();
Globals.setHeadless(true);
(new IgvTools()).run(argv);
System.out.println("Done");
System.exit(0);
} catch (Exception e) {
e.printStackTrace();
System.exit(-1);
}
}
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);
}
}
/**
* Load a gui with the specified genome file. No genome is loaded if null
*
* @param genomeFile
* @return
* @throws IOException
*/
protected static IGV startGUI(String genomeFile) throws IOException {
Globals.setHeadless(false);
IGV igv;
// If IGV is already open, we get the instance.
if (IGV.hasInstance()) {
igv = IGV.getInstance();
IGV.getMainFrame().setVisible(true);
System.out.println("Using old IGV");
} else {
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
Main.open(frame);
System.out.println("Started new IGV");
igv = IGV.getInstance();
assertTrue(IGV.getInstance().waitForNotify(1000));
}
if (genomeFile != null) {
igv.loadGenome(genomeFile, null);
genome = igv.getGenomeManager().getCurrentGenome();
}
return igv;
}
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);
}
}
private static ConnectionWrapper connect(String url) {
try {
return new ConnectionWrapper(DriverManager.getConnection(url, username, password));
} catch (SQLException e) {
int errorCode = e.getErrorCode();
if (errorCode == 1044 || errorCode == 1045) {
String host = PreferenceManager.getInstance().get(PreferenceManager.DB_HOST);
Frame parent = Globals.isHeadless() ? null : IGV.getMainFrame();
LoginDialog dlg = new LoginDialog(parent, false, host, false);
dlg.setVisible(true);
if (dlg.isCanceled()) {
throw new RuntimeException("Must login to access" + host);
}
username = dlg.getUsername();
password = new String(dlg.getPassword());
return connect(url);
} else {
MessageUtils.showMessage("<html>Error connecting to database: <br>" + e.getMessage());
return null;
}
}
}
/**
* Generate the "tools" menu. This is imperative, it is written to field {@code toolsMenu}. Reason
* being, when we add (TODO remove) a new tool, we need to refresh just this menu
*/
void refreshToolsMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>(10);
// batch script
MenuAction menuAction = new RunScriptMenuAction("Run Batch Script...", KeyEvent.VK_X, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// igvtools
// menuItems.add(new JSeparator());
menuAction =
new SortTracksMenuAction("Run igvtools...", KeyEvent.VK_T, igv) {
@Override
public void actionPerformed(ActionEvent e) {
IgvToolsGui.launch(false, igv.getGenomeManager().getGenomeId());
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
List<JComponent> otherToolMenus = igv.getOtherToolMenus();
if (otherToolMenus.size() > 0) {
for (JComponent entry : otherToolMenus) {
menuItems.add(entry);
}
}
// menuItems.add(new JSeparator());
// -------------------------------------//
// "Add tool" option, for loading cli_plugin from someplace else
JMenuItem addTool = new JMenuItem("Add Tool...");
addTool.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File pluginFi = FileDialogUtils.chooseFile("Select cli_plugin .xml spec");
if (pluginFi == null) return;
try {
PluginSpecReader.addCustomPlugin(pluginFi.getAbsolutePath());
refreshToolsMenu();
} catch (IOException e1) {
MessageUtils.showErrorMessage("Error loading custom cli_plugin", e1);
}
}
});
// menuItems.add(addTool);
// menuItems.add(new JSeparator());
// -------------------------------------//
for (final PluginSpecReader pluginSpecReader : PluginSpecReader.getPlugins()) {
for (final PluginSpecReader.Tool tool : pluginSpecReader.getTools()) {
final String toolName = tool.name;
boolean toolVisible = tool.visible;
JMenuItem toolMenu;
if (toolVisible) {
final String toolPath = pluginSpecReader.getToolPath(tool);
final String tool_url = tool.toolUrl;
boolean isValid = PluginSpecReader.isToolPathValid(toolPath);
ActionListener invalidActionListener =
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String msg = String.format("%s executable not found at %s", toolName, toolPath);
if (tool_url != null) {
msg += "<br/>See " + tool_url + " to install";
}
MessageUtils.showMessage(msg);
}
};
toolMenu = new JMenu(toolName);
// Kind of overlaps with the side-pull menu, doesn't look great
// toolMenu.setToolTipText(tool.getAttribute("description"));
for (final PluginSpecReader.Command command : tool.commandList) {
final String cmdName = command.name;
JMenuItem cmdItem = new JMenuItem(cmdName);
toolMenu.add(cmdItem);
if (isValid || toolPath == null) {
cmdItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
RunPlugin runPlugin = null;
try {
runPlugin =
new RunPlugin(IGV.getMainFrame(), pluginSpecReader, tool, command);
} catch (IllegalStateException e1) {
MessageUtils.showErrorMessage(e1.getMessage(), e1);
return;
}
runPlugin.setVisible(true);
}
});
cmdItem.setEnabled(true);
} else {
cmdItem.setEnabled(false);
}
}
// Hack so we can have a tool which is just general command line stuff
// Don't let the user change the path in that case
if (tool.defaultPath != null) {
JMenuItem setPathItem = new JMenuItem(String.format("Set path to %s...", toolName));
setPathItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
(new SetPluginPathDialog(IGV.getMainFrame(), pluginSpecReader, tool))
.setVisible(true);
refreshToolsMenu();
}
});
toolMenu.add(setPathItem);
}
menuItems.add(toolMenu);
}
}
}
// -------------------------------------//
// -----------SQL DB Tools--------------//
boolean showDBEditor = Globals.isDevelopment();
if (showDBEditor) {
JMenu sqlDBProfileEditor = new JMenu("SQL DB Profile Editor");
JMenuItem createNewProfile = new JMenuItem("Create New Profile");
createNewProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file =
FileDialogUtils.chooseFile(
"Save DB Profile", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE);
if (file != null) {
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
JMenuItem editExistingProfile = new JMenuItem("Edit Existing Profile");
editExistingProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file = FileDialogUtils.chooseFile("Select .dbxml database profile");
if (file != null) {
if (!file.exists()) {}
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
sqlDBProfileEditor.add(createNewProfile);
sqlDBProfileEditor.add(editExistingProfile);
menuItems.add(sqlDBProfileEditor);
}
// -------------------------------------//
// DataTrack Math------------------------//
if (Globals.isDevelopment()) {
JMenuItem combineDataItem = new JMenuItem("Combine Data Tracks");
combineDataItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
CombinedDataSourceDialog dialog = new CombinedDataSourceDialog(IGV.getMainFrame());
dialog.setVisible(true);
}
});
menuItems.add(combineDataItem);
}
// -------------------------------------//
MenuAction toolsMenuAction = new MenuAction("Tools", null);
if (toolsMenu == null) {
toolsMenu = MenuAndToolbarUtils.createMenu(menuItems, toolsMenuAction);
toolsMenu.setName("Tools");
} else {
toolsMenu.removeAll();
for (JComponent item : menuItems) {
toolsMenu.add(item);
}
}
}
private void processResources(Session session, Element element, HashMap additionalInformation) {
dataFiles = new ArrayList();
missingDataFiles = new ArrayList();
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
if (missingDataFiles.size() > 0) {
StringBuffer message = new StringBuffer();
message.append("<html>The following data file(s) could not be located.<ul>");
for (ResourceLocator file : missingDataFiles) {
if (file.isLocal()) {
message.append("<li>");
message.append(file.getPath());
message.append("</li>");
} else {
message.append("<li>Server: ");
message.append(file.getServerURL());
message.append(" Path: ");
message.append(file.getPath());
message.append("</li>");
}
}
message.append("</ul>");
message.append("Common reasons for this include: ");
message.append("<ul><li>The session or data files have been moved.</li> ");
message.append(
"<li>The data files are located on a drive that is not currently accessible.</li></ul>");
message.append("</html>");
MessageUtils.showMessage(message.toString());
}
if (dataFiles.size() > 0) {
final List<String> errors = new ArrayList<String>();
// Load files concurrently -- TODO, put a limit on # of threads?
List<Thread> threads = new ArrayList(dataFiles.size());
long t0 = System.currentTimeMillis();
int i = 0;
List<Runnable> synchronousLoads = new ArrayList<Runnable>();
for (final ResourceLocator locator : dataFiles) {
final String suppliedPath = locator.getPath();
final String relPath = fullToRelPathMap.get(suppliedPath);
Runnable runnable =
new Runnable() {
public void run() {
List<Track> tracks = null;
try {
tracks = igv.load(locator);
for (Track track : tracks) {
if (track == null) {
log.info("Null track for resource " + locator.getPath());
continue;
}
String id = track.getId();
if (id == null) {
log.info("Null track id for resource " + locator.getPath());
continue;
}
if (relPath != null) {
id = id.replace(suppliedPath, relPath);
}
List<Track> trackList = trackDictionary.get(id);
if (trackList == null) {
trackList = new ArrayList();
trackDictionary.put(id, trackList);
}
trackList.add(track);
}
} catch (Exception e) {
log.error("Error loading resource " + locator.getPath(), e);
String ms =
"<b>" + locator.getPath() + "</b><br>&nbs;p " + e.toString() + "<br>";
errors.add(ms);
}
}
};
boolean isAlignment =
locator.getPath().endsWith(".bam")
|| locator.getPath().endsWith(".entries")
|| locator.getPath().endsWith(".sam");
// Run synchronously if in batch mode or if there are no "track" elments, or if this is an
// alignment file
if (isAlignment || Globals.isBatch() || !hasTrackElments) {
synchronousLoads.add(runnable);
} else {
Thread t = new Thread(runnable);
threads.add(t);
t.start();
}
i++;
}
// Wait for all threads to complete
for (Thread t : threads) {
try {
t.join();
} catch (InterruptedException ignore) {
}
}
// Now load data that must be loaded synchronously
for (Runnable runnable : synchronousLoads) {
runnable.run();
}
long dt = System.currentTimeMillis() - t0;
log.debug("Total load time = " + dt);
if (errors.size() > 0) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Errors were encountered loading the session:<br>");
for (String msg : errors) {
buf.append(msg);
}
MessageUtils.showMessage(buf.toString());
}
}
dataFiles = null;
}
public static String getVersionString() {
return Globals.applicationString();
}
public static void main(String[] argv)
throws IOException, CmdLineParser.UnknownOptionException,
CmdLineParser.IllegalOptionValueException {
if (argv.length < 4) {
System.out.println("Usage: hictools pre <options> <inputFile> <outputFile> <genomeID>");
System.out.println(" <options>: -d only calculate intra chromosome (diagonal) [false]");
System.out.println(
" : -o calculate densities (observed/expected), write to file [false]");
System.out.println(" : -t <int> only write cells with count above threshold t [0]");
System.out.println(
" : -c <chromosome ID> only calculate map on specific chromosome");
System.exit(0);
}
Globals.setHeadless(true);
CommandLineParser parser = new CommandLineParser();
parser.parse(argv);
String[] args = parser.getRemainingArgs();
if (args[0].equals("sort")) {
AlignmentsSorter.sort(args[1], args[2], null);
} else if (args[0].equals("pairsToBin")) {
String ifile = args[1];
String ofile = args[2];
String genomeId = args[3];
List<Chromosome> chromosomes = loadChromosomes(genomeId);
AsciiToBinConverter.convert(ifile, ofile, chromosomes);
} else if (args[0].equals("binToPairs")) {
String ifile = args[1];
String ofile = args[2];
AsciiToBinConverter.convertBack(ifile, ofile);
} else if (args[0].equals("printmatrix")) {
if (args.length < 5) {
System.err.println(
"Usage: hictools printmatrix <observed/oe/pearson> hicFile chr1 chr2 binsize");
System.exit(-1);
}
String type = args[1];
String file = args[2];
String chr1 = args[3];
String chr2 = args[4];
String binSizeSt = args[5];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
dumpMatrix(file, chr1, chr2, binSize, type);
} else if (args[0].equals("eigenvector")) {
if (args.length < 4) {
System.err.println("Usage: hictools eigenvector hicFile chr binsize");
}
String file = args[1];
String chr = args[2];
String binSizeSt = args[3];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
calculateEigenvector(file, chr, binSize);
} else if (args[0].equals("pre")) {
String genomeId = "";
try {
genomeId = args[3];
} catch (ArrayIndexOutOfBoundsException e) {
System.err.println("No genome ID given");
System.exit(0);
}
List<Chromosome> chromosomes = loadChromosomes(genomeId);
long genomeLength = 0;
for (Chromosome c : chromosomes) {
if (c != null) genomeLength += c.getSize();
}
chromosomes.set(0, new Chromosome(0, "All", (int) (genomeLength / 1000)));
String[] tokens = args[1].split(",");
List<String> files = new ArrayList<String>(tokens.length);
for (String f : tokens) {
files.add(f);
}
Preprocessor preprocessor = new Preprocessor(new File(args[2]), chromosomes);
preprocessor.setIncludedChromosomes(parser.getChromosomeOption());
preprocessor.setCountThreshold(parser.getCountThresholdOption());
preprocessor.setNumberOfThreads(parser.getThreadedOption());
preprocessor.setDiagonalsOnly(parser.getDiagonalsOption());
preprocessor.setLoadDensities(parser.getDensitiesOption());
preprocessor.preprocess(files);
}
}