/**
* This function is used to re-run the analyser, and re-create the rows corresponding the its
* results.
*/
private void refreshReviewTable() {
reviewPanel.removeAll();
rows.clear();
GridBagLayout gbl = new GridBagLayout();
reviewPanel.setLayout(gbl);
GridBagConstraints gbc = new GridBagConstraints();
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.gridy = 0;
try {
Map<String, Long> sums =
analyser.processLogFile(config.getLogFilename(), fromDate.getDate(), toDate.getDate());
for (Entry<String, Long> entry : sums.entrySet()) {
String project = entry.getKey();
double hours = 1.0 * entry.getValue() / (1000 * 3600);
addRow(gbl, gbc, project, hours);
}
for (String project : main.getProjectsTree().getTopLevelProjects())
if (!rows.containsKey(project)) addRow(gbl, gbc, project, 0);
gbc.insets = new Insets(10, 0, 0, 0);
addLeftLabel(gbl, gbc, "TOTAL");
gbc.gridx = 1;
gbc.weightx = 1;
totalLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 3));
gbl.setConstraints(totalLabel, gbc);
reviewPanel.add(totalLabel);
gbc.weightx = 0;
addRightLabel(gbl, gbc);
} catch (IOException e) {
e.printStackTrace();
}
recomputeTotal();
pack();
}
void lookUpTaxonID(String taxonID) {
URI url;
try {
// We should look up the miITIS_TSN status, but since we don't
// have any options there ...
url =
new URI(
"http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="
+ taxonID);
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
try {
Desktop desktop = Desktop.getDesktop();
desktop.browse(url);
} catch (IOException e) {
MessageBox.messageBox(
mainFrame,
"Could not open URL '" + url + "'",
"The following error occurred while looking up URL '" + url + "': " + e.getMessage(),
MessageBox.ERROR);
}
}
void searchName(String nameToMatch) {
URI url;
try {
// We should look up the miITIS_TSN status, but since we don't
// have any options there ...
url = new URI("http", "www.google.com", "/search", "q=" + nameToMatch);
// I think the URI handles the URL encoding?
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
try {
Desktop desktop = Desktop.getDesktop();
desktop.browse(url);
} catch (IOException e) {
MessageBox.messageBox(
mainFrame,
"Could not open URL '" + url + "'",
"The following error occurred while looking up URL '" + url + "': " + e.getMessage(),
MessageBox.ERROR);
}
}
public final boolean replace(int num, String replacement) {
buf.buffer.replace(buf.cursor - num, buf.cursor, replacement);
try {
moveCursor(-num);
drawBuffer(Math.max(0, num - replacement.length()));
moveCursor(replacement.length());
} catch (IOException e) {
e.printStackTrace();
return false;
}
return true;
}
public static void showDesktop() { // Windows only
try {
if (SystemUtils.isWinPlatform())
RUNTIME.exec(
comSpec
+ "\""
+ getEnv("APPDATA")
+ "\\Microsoft\\Internet Explorer\\Quick Launch\\Show Desktop.scf\"");
} catch (IOException e) {
e.printStackTrace();
}
}
public File getCurrentFile(boolean shouldSave) {
if (shouldSave && _editingFile == null && isDirty()) {
try {
saveAsFile(Settings.isMac());
} catch (IOException e) {
Debug.error(
me + "getCurrentFile: Problem while trying to save %s\n%s",
_editingFile.getAbsolutePath(),
e.getMessage());
}
}
return _editingFile;
}
/** Execute the system command 'cmd' and fill an ArrayList with the results. */
public static ArrayList<String> executeSystemCommand(String cmd) {
if (debug) System.out.println("cmd: " + cmd);
ArrayList<String> list = new ArrayList<>();
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec(/*comSpec +*/ cmd).getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
if (debug) System.out.println(line);
list.add(line);
}
} catch (IOException e) {
e.printStackTrace();
}
return list;
}
public File copyFileToBundle(String filename) {
File f = new File(filename);
String bundlePath = getSrcBundle();
if (f.exists()) {
try {
File newFile = FileManager.smartCopy(filename, bundlePath);
return newFile;
} catch (IOException e) {
Debug.error(
me + "copyFileToBundle: Problem while trying to save %s\n%s", filename, e.getMessage());
return f;
}
}
return null;
}
public static String ping(String address) {
String reply = "Request timed out";
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec("ping " + address).getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
if (line.trim().startsWith("Reply ")) {
reply = line;
break;
}
}
} catch (IOException e) {
e.printStackTrace();
}
return reply;
}
/**
* Handle the -biojava option
*
* <p>Command line syntax: art -biojava org.biojava.bio.seq.io.EmblLikeFormat foo.embl
*
* <p>BioJava formats: EmblLikeFormat, FastaFormat, GAMEFormat, GenbankFormat, PhredFormat
*/
private void handleBioJava(final String[] args) {
if (args.length == 3) {
final String class_name = args[1];
final String location = args[2];
final Document location_document = DocumentFactory.makeDocument(location);
try {
final Object biojava_object = Class.forName(class_name).newInstance();
final EntryInformation entry_information = Options.getArtemisEntryInformation();
final uk.ac.sanger.artemis.io.BioJavaEntry emblEntry;
if (biojava_object instanceof SequenceFormat) {
final SequenceFormat sequence_format = (SequenceFormat) biojava_object;
emblEntry =
new uk.ac.sanger.artemis.io.BioJavaEntry(
entry_information, location_document, sequence_format);
final Entry new_entry = new Entry(emblEntry);
final EntryEdit new_entry_edit = makeEntryEdit(new_entry);
new_entry_edit.setVisible(true);
} else new MessageDialog(this, "not a SequenceFormat: " + class_name);
} catch (IllegalAccessException e) {
new MessageDialog(this, "cannot create class: " + class_name + " - IllegalAccessException");
} catch (ClassNotFoundException e) {
new MessageDialog(this, "cannot find class: " + class_name);
} catch (ClassCastException e) {
new MessageDialog(this, class_name + " is not a sub-class of " + "SequenceFormat");
} catch (IOException e) {
new MessageDialog(this, "I/O error while reading from " + location + ": " + e.getMessage());
} catch (NoSequenceException e) {
new MessageDialog(this, location + " contained no sequence");
} catch (InstantiationException e) {
new MessageDialog(this, "cannot instantiate " + class_name);
} catch (OutOfRangeException e) {
new MessageDialog(
this,
"read failed: one of the features in "
+ location
+ " has an out of range location: "
+ e.getMessage());
}
} else new MessageDialog(this, "the -biojava option needs two arguments");
}
public static Properties getEnvironmentVariables() {
synchronized (cygstartPath) {
if (envVars != null) return envVars;
envVars = new Properties();
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec(comSpec + "env").getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
// if (debug) System.out.println("getEnvironmentVariables(): line=" + line);
int idx = line.indexOf('=');
if (idx > 0) envVars.put(line.substring(0, idx), line.substring(idx + 1));
}
} catch (IOException e) {
e.printStackTrace();
}
return envVars;
}
}
private void jMenuItemLoadProjectActionPerformed(
java.awt.event.ActionEvent evt) // GEN-FIRST:event_jMenuItemLoadProjectActionPerformed
{ // GEN-HEADEREND:event_jMenuItemLoadProjectActionPerformed
JFileChooser jfc = new JFileChooser();
if (lastPath != null) {
jfc.setCurrentDirectory(lastPath);
}
int fileDialogReturnVal = jfc.showOpenDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File inputFile = jfc.getSelectedFile();
FileInputStream fis = new FileInputStream(inputFile);
ObjectInputStream ois = new ObjectInputStream(fis);
this.theProject = (Project) ois.readObject();
this.currentResults = (LSAResults) ois.readObject();
lastPath = new File(jfc.getSelectedFile().getPath());
} catch (IOException e) {
if (this.theProject == null) {
log.log(Log.ERROR, "Failed to load project");
}
if (this.currentResults == null) {
log.log(Log.WARNING, "Failed to load results");
}
log.log(Log.WARNING, e.getMessage());
} catch (ClassNotFoundException e) {
log.log(Log.ERROR, "Class not found error, version mismatch");
}
}
if (this.theProject != null) {
jMenuItemViewDocuments.setEnabled(true);
jMenuItemSaveProject.setEnabled(true);
this.setTitle(theProject.getProjectName());
log.log(Log.INFO, "Project Loaded");
}
if (this.currentResults != null) {
log.log(Log.INFO, "Results loaded");
}
} // GEN-LAST:event_jMenuItemLoadProjectActionPerformed
private void jMenuItemSaveLSAResultsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_jMenuItemSaveLSAResultsActionPerformed
if (this.currentResults != null) {
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showSaveDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File outputFile = jfc.getSelectedFile();
FileOutputStream fos = new FileOutputStream(outputFile);
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(this.currentResults);
} catch (IOException e) {
System.out.println("IOexception");
System.out.println(e.getMessage());
}
}
}
} // GEN-LAST:event_jMenuItemSaveLSAResultsActionPerformed
private void jMenuItemLoadLSAResultsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_jMenuItemLoadLSAResultsActionPerformed
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showOpenDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File inputFile = jfc.getSelectedFile();
FileInputStream fis = new FileInputStream(inputFile);
ObjectInputStream ois = new ObjectInputStream(fis);
this.currentResults = (LSAResults) ois.readObject();
} catch (IOException e) {
log.log(Log.ERROR, "Failed to load LSA results\n" + e.getMessage());
} catch (ClassNotFoundException e) {
log.log(Log.ERROR, "Class not found : Error loading LSA results due to version mismatch");
}
System.out.println(currentResults == null);
}
} // GEN-LAST:event_jMenuItemLoadLSAResultsActionPerformed
private void jMenuItemSaveProjectActionPerformed(
java.awt.event.ActionEvent evt) // GEN-FIRST:event_jMenuItemSaveProjectActionPerformed
{ // GEN-HEADEREND:event_jMenuItemSaveProjectActionPerformed
if (this.theProject != null) {
JFileChooser jfc = new JFileChooser();
int fileDialogReturnVal = jfc.showSaveDialog(this);
if (fileDialogReturnVal == JFileChooser.APPROVE_OPTION) {
try {
File outputFile = jfc.getSelectedFile();
FileOutputStream fos = new FileOutputStream(outputFile);
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(this.theProject);
if (this.currentResults != null) {
oos.writeObject(this.currentResults);
}
} catch (IOException e) {
log.log(Log.ERROR, "Failed to save file\n" + e.getMessage());
}
}
}
} // GEN-LAST:event_jMenuItemSaveProjectActionPerformed
/**
* Try to determine whether this application is running under Windows or some other platform by
* examining the "os.name" property.
*/
static {
String os = System.getProperty("os.name");
// String version = System.getProperty("os.version"); // for Win7, reports "6.0" on JDK7, should
// be "6.1"; for Win8, reports "6.2" as of JDK7u17
if (SystemUtils.startsWithIgnoreCase(os, "windows 7"))
isWin7 = true; // reports "Windows Vista" on JDK7
else if (SystemUtils.startsWithIgnoreCase(os, "windows 8"))
isWin7 = true; // reports "Windows 8" as of JDK7u17
else if (SystemUtils.startsWithIgnoreCase(os, "windows vista")) isVista = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows xp")) isWinXP = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows 2000")) isWin2k = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows nt")) isWinNT = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows"))
isWin9X = true; // win95 or win98 (what about WinME?)
else if (SystemUtils.startsWithIgnoreCase(os, "mac")) isMac = true;
else if (SystemUtils.startsWithIgnoreCase(os, "so")) isSolaris = true; // sunos or solaris
else if (os.equalsIgnoreCase("linux")) isLinux = true;
else isUnix = true; // assume UNIX, e.g. AIX, HP-UX, IRIX
String osarch = System.getProperty("os.arch");
String arch = (osarch != null && osarch.contains("64")) ? "_x64" /* eg. 'amd64' */ : "_x32";
String syslib = SYSLIB + arch;
try { // loading a native lib in a static initializer ensures that it is available before any
// method in this class is called:
System.loadLibrary(syslib);
System.out.println(
"Done loading '" + System.mapLibraryName(syslib) + "', PID=" + getProcessID());
} catch (Error e) {
System.err.println(
"Native library '"
+ System.mapLibraryName(syslib)
+ "' not found in 'java.library.path': "
+ System.getProperty("java.library.path"));
throw e; // re-throw
}
if (isWinPlatform()) {
System.setProperty(
"line.separator", "\n"); // so we won't have to mess with DOS line endings ever again
comSpec =
getEnv(
"comSpec"); // use native method here since getEnvironmentVariable() needs to know
// comSpec
comSpec = (comSpec != null) ? comSpec + " /c " : "";
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(
RUNTIME.exec(comSpec + "ver").getInputStream()))) { // fix for Win7,8
for (String line = null; (line = br.readLine()) != null; ) {
if (isVista && (line.contains("6.1" /*Win7*/) || line.contains("6.2" /*Win8*/))) {
isVista = false;
isWin7 = true;
}
}
} catch (IOException e) {
e.printStackTrace();
}
String cygdir = getEnv("cygdir"); // this is set during CygWin install to "?:/cygwin/bin"
isCygWin = (cygdir != null && !cygdir.equals("%cygdir%"));
cygstartPath = cygdir + "/cygstart.exe"; // path to CygWin's cygutils' "cygstart" binary
if (getDebug() && Desktop.isDesktopSupported()) {
Desktop desktop = Desktop.getDesktop();
for (Desktop.Action action : Desktop.Action.values())
System.out.println(
"Desktop action " + action + " supported? " + desktop.isSupported(action));
}
}
}