/**
* Returns date in the format: neededDatePattern, in case if year or month isn't entered, current
* year/month is put.
*
* @return correct date.
*/
private Date getCorrectedDate(String enteredDate) {
Queue<String> dateParts = new ArrayDeque<>(3);
StringBuilder number = new StringBuilder();
for (char symbol : enteredDate.toCharArray()) {
if (Character.isDigit(symbol)) {
number.append(symbol);
} else if (number.length() > 0) {
dateParts.add(number.toString());
number = new StringBuilder();
}
}
if (number.length() > 0) {
dateParts.add(number.toString());
}
Calendar currentDate = Calendar.getInstance();
switch (dateParts.size()) {
case 1:
dateParts.add(Integer.toString(currentDate.get(Calendar.MONTH) + 1));
case 2:
dateParts.add(Integer.toString(currentDate.get(Calendar.YEAR)));
}
try {
return new SimpleDateFormat("dd.MM.yyyy")
.parse(dateParts.remove() + '.' + dateParts.remove() + '.' + dateParts.remove());
} catch (ParseException e) {
throw new RuntimeException(e); // todo change exception
}
}
public void insertString(FilterBypass fb, int offset, String string, AttributeSet attr)
throws BadLocationException {
StringBuilder builder = new StringBuilder(string);
for (int i = builder.length() - 1; i >= 0; i--) {
int cp = builder.codePointAt(i);
if (!Character.isDigit(cp) && cp != '-') {
builder.deleteCharAt(i);
if (Character.isSupplementaryCodePoint(cp)) {
i--;
builder.deleteCharAt(i);
}
}
}
super.insertString(fb, offset, builder.toString(), attr);
}
@Override
public void insertString(final int offs, final String str, final AttributeSet a)
throws BadLocationException {
// NavigatorLogger.printMessage("Offset:"+offs+" STr:"+str+"L:"+getLength()+"attr:"+a);
if ((getLength() + str.length()) <= maxLength) {
final char[] source = str.toCharArray();
final char[] result = new char[source.length];
int j = 0;
for (int i = 0; i < result.length; i++) {
if (Character.isDigit(source[i])) {
result[j++] = source[i];
} else {
toolkit.beep();
if (log.isDebugEnabled()) {
log.debug("insertString: " + source[i]); // NOI18N
}
}
}
super.insertString(offs, new String(result, 0, j), a);
checked = false;
} else {
toolkit.beep();
}
if ((getLength()) == maxLength) { // getLength() ist schon aktualisiert
if (bringFocus2Next == true) {
checked = true;
nextField.requestFocus();
}
// NavigatorLogger.printMessage("Sprung");
// NavigatorLogger.printMessage(nextField);
}
}
public static boolean isNumeric(String str) {
for (int i = str.length(); --i >= 0; ) {
if (!Character.isDigit(str.charAt(i))) {
return false;
}
}
return true;
}
private String readInt(JTextComponent textComponent) throws IncorrectInputException {
String text = textComponent.getText();
if (Character.isDigit(text.charAt(0))) {
return text;
} else {
throw new IncorrectInputException("wrong input");
}
}
@Override
protected void processKeyEvent(KeyEvent e) {
if (e.getID() == KeyEvent.KEY_TYPED) {
if (!Character.isDigit(e.getKeyChar()) && !(!positiveOnly && e.getKeyChar() == '-')) {
e.consume();
}
}
super.processKeyEvent(e);
}
public void processKeyEvent(KeyEvent evt) {
evt = KeyEventWorkaround.processKeyEvent(evt);
if (evt == null) return;
switch (evt.getID()) {
case KeyEvent.KEY_TYPED:
char ch = evt.getKeyChar();
if (!nonDigit && Character.isDigit(ch)) {
super.processKeyEvent(evt);
repeat = true;
repeatCount = Integer.parseInt(action.getText());
} else {
nonDigit = true;
if (repeat) {
passToView(evt);
} else super.processKeyEvent(evt);
}
break;
case KeyEvent.KEY_PRESSED:
int keyCode = evt.getKeyCode();
if (evt.isActionKey()
|| evt.isControlDown()
|| evt.isAltDown()
|| evt.isMetaDown()
|| keyCode == KeyEvent.VK_BACK_SPACE
|| keyCode == KeyEvent.VK_DELETE
|| keyCode == KeyEvent.VK_ENTER
|| keyCode == KeyEvent.VK_TAB
|| keyCode == KeyEvent.VK_ESCAPE) {
nonDigit = true;
if (repeat) {
passToView(evt);
break;
} else if (keyCode == KeyEvent.VK_TAB) {
complete(true);
evt.consume();
} else if (keyCode == KeyEvent.VK_ESCAPE) {
evt.consume();
if (popup != null) {
popup.dispose();
popup = null;
action.requestFocus();
} else {
if (temp) view.removeToolBar(ActionBar.this);
view.getEditPane().focusOnTextArea();
}
break;
} else if ((keyCode == KeyEvent.VK_UP || keyCode == KeyEvent.VK_DOWN)
&& popup != null) {
popup.list.processKeyEvent(evt);
break;
}
}
super.processKeyEvent(evt);
break;
}
}
/**
* Checks if a string contains anything but spaces - needed for text field validation
*
* @param inputSting
* @return
* @param inputString
*/
private static boolean containsText(final String inputString) {
boolean stringContainsText = false;
if (!inputString.equals("")) {
for (int i = 0; i < inputString.length(); i++) {
char chr = inputString.charAt(i);
if (Character.isDigit(chr) || Character.isLetter(chr)) stringContainsText = true;
}
}
return stringContainsText;
}
// The insert string method
public void insertString(int offs, String src, AttributeSet a) throws BadLocationException {
char[] source = src.toCharArray();
char[] result = new char[source.length];
int j = 0;
for (int i = 0; i < result.length; i++) {
if (Character.isDigit(source[i])) result[j++] = source[i];
}
super.insertString(offs, new String(result, 0, j), a);
}
// helper function to check if String is either a number or a string (first and last name)
public static boolean isValidInput(String x) {
boolean hasNumber = false;
for (int i = 0; i < x.trim().length(); i++) {
if (Character.isDigit(x.trim().charAt(i))) {
hasNumber = true;
break;
}
}
// if it has a number, check that it is all numbers
if (hasNumber) {
for (int i = 0; i < x.trim().length(); i++) {
if (!Character.isDigit(x.trim().charAt(i)) && !(x.trim().charAt(i) == '-')) {
return false;
}
}
return isValidNumber(x);
}
// else check that there are 2 inputs for first and last name;
else return (x.split("\\s+")).length >= 2; // delimiting using any kind of white space
}
/** Handle remove. */
public void remove(int offs, int length) throws BadLocationException {
int sourceLength = getLength();
// Allow user to restore uninitialized state again by removing all
if (offs == 0 && sourceLength == length) {
super.remove(0, sourceLength);
return;
}
// Do custom remove
String sourceText = getText(0, sourceLength);
StringBuffer strBuffer = new StringBuffer(sourceText.substring(0, offs));
int counter;
for (counter = offs; counter < offs + length; counter++) {
// Only remove digits and intDelims
char currChar = sourceText.charAt(counter);
if (Character.isDigit(currChar) || currChar == intDelim) {
continue;
}
strBuffer.append(currChar);
}
// Append last part of sourceText
if (counter < sourceLength) {
strBuffer.append(sourceText.substring(counter));
}
// Set text in field
super.remove(0, sourceLength);
insertString(0, strBuffer.toString(), (AttributeSet) getDefaultRootElement());
// Set caret pos
int newDiff = sourceLength - getLength() - 1;
if (newDiff < 0) {
newDiff = 0;
}
if (offs - newDiff < 0) {
newDiff = 0;
}
textField.setCaretPosition(offs - newDiff);
}
public void insertString(int offs, String str, AttributeSet a) throws BadLocationException {
char[] source = str.toCharArray();
char[] result = new char[source.length];
int j = 0;
for (int i = 0; i < result.length; i++) {
if (Character.isDigit(source[i])) result[j++] = source[i];
else {
toolkit.beep();
// System.err.println("insertString: " + source[i]);
}
}
super.insertString(offs, new String(result, 0, j), a);
}
public void insertString(int offs, String str, AttributeSet a) throws BadLocationException {
final boolean rgb = isRGBMode();
char[] source = str.toCharArray();
if (mySrc != null) {
final int selected = mySrc.getSelectionEnd() - mySrc.getSelectionStart();
int newLen = mySrc.getText().length() - selected + str.length();
if (newLen > (myHex ? 6 : 3)) {
Toolkit.getDefaultToolkit().beep();
return;
}
}
char[] result = new char[source.length];
int j = 0;
for (int i = 0; i < result.length; i++) {
if (myHex
? "0123456789abcdefABCDEF".indexOf(source[i]) >= 0
: Character.isDigit(source[i])) {
result[j++] = source[i];
} else {
Toolkit.getDefaultToolkit().beep();
}
}
final String toInsert = StringUtil.toUpperCase(new String(result, 0, j));
final String res = new StringBuilder(mySrc.getText()).insert(offs, toInsert).toString();
try {
if (!myHex) {
final int num = Integer.parseInt(res);
if (rgb) {
if (num > 255) {
Toolkit.getDefaultToolkit().beep();
return;
}
} else {
if ((mySrc == myRed && num > 359)
|| ((mySrc == myGreen || mySrc == myBlue) && num > 100)) {
Toolkit.getDefaultToolkit().beep();
return;
}
}
}
} catch (NumberFormatException ignore) {
}
super.insertString(offs, toInsert, a);
}
public void actionPerformed(ActionEvent arg0) {
//
String s = arg0.getActionCommand();
if (faxNumButton.isSelected()) {
if (Character.isDigit(s.charAt(0))) faxNumberWork(s);
if (s.equals("-")) faxNumberWork(s);
} else {
if (!(check_control_key(s))) {
BroadcastDBWork(s);
}
}
if (s.equals("Send")) {
SendWork(s);
} else if (s.equals("Clear")) {
ClearWork(s);
} else if (s.equals("Cancel")) {
CancelWork(s);
}
}
@Override
public void replace(
DocumentFilter.FilterBypass fp, int offset, int length, String string, AttributeSet aset)
throws BadLocationException {
Document doc = fp.getDocument();
String oldText = doc.getText(0, doc.getLength());
StringBuilder sb = new StringBuilder(oldText);
sb.replace(offset, offset + length, oldText);
int len = string.length();
boolean isValidInteger = true;
for (int i = 0; i < len; i++) {
if (!Character.isDigit(string.charAt(i))) {
isValidInteger = false;
break;
}
}
if (isValidInteger && verifyText(sb.toString())) {
super.replace(fp, offset, length, string, aset);
} else Toolkit.getDefaultToolkit().beep();
}
/** Remove delimiters */
public String getRealString(String oldString) {
char addChar;
String newString = "";
realDelimFound = false;
int length = oldString.length();
for (int i = 0; i < length; i++) {
addChar = oldString.charAt(i);
if (Character.isDigit(addChar)) {
newString += addChar;
} else if (addChar == realDelim) {
if (realDelimFound == true) {
break;
}
realDelimFound = true;
newString += ".";
}
}
return newString;
}
public static double getOSVersion() {
if (osVersion == null) {
try {
String ver = System.getProperties().getProperty("os.version");
String version = "";
boolean firstPoint = true;
for (int i = 0; i < ver.length(); i++) {
if (ver.charAt(i) == '.') {
if (firstPoint) {
version += ver.charAt(i);
}
firstPoint = false;
} else if (Character.isDigit(ver.charAt(i))) {
version += ver.charAt(i);
}
}
osVersion = new Double(version);
} catch (Exception ex) {
osVersion = new Double(1.0);
}
}
return osVersion.doubleValue();
}
private DarkBotMCSpambot(
DarkBot darkBot,
String server,
String username,
String password,
String sessionId,
String loginProxy,
String proxy,
String owner) {
synchronized (bots) {
bots.add(this);
// slotsTaken.incrementAndGet();
synchronized (slotsTaken) {
slotsTaken.notifyAll();
}
}
MinecraftBotData.Builder builder = MinecraftBotData.builder();
// botData.nickname = "";
// for(int i = 0; i < 10; i++)
// botData.nickname += alphas[random.nextInt(alphas.length)];
if (proxy != null && !proxy.isEmpty()) {
int port = 80;
ProxyType type = ProxyType.SOCKS;
if (proxy.contains(":")) {
String[] parts = proxy.split(":");
proxy = parts[0];
port = Integer.parseInt(parts[1]);
if (parts.length > 2) type = ProxyType.values()[Integer.parseInt(parts[2]) - 1];
}
builder.withSocksProxy(new ProxyData(proxy, port, type));
this.proxy = new Proxy(Proxy.Type.SOCKS, new InetSocketAddress(proxy, port));
}
if (loginProxy != null && !loginProxy.isEmpty()) {
int port = 80;
if (loginProxy.contains(":")) {
String[] parts = loginProxy.split(":");
loginProxy = parts[0];
port = Integer.parseInt(parts[1]);
}
builder.withHttpProxy(new ProxyData(loginProxy, port, ProxyType.HTTP));
this.loginProxy = new Proxy(Proxy.Type.HTTP, new InetSocketAddress(loginProxy, port));
}
builder.withUsername(username);
if (sessionId != null) builder.withSessionId(sessionId);
else builder.withPassword(password);
if (server != null && !server.isEmpty()) {
int port = 25565;
if (server.contains(":")) {
String[] parts = server.split(":");
server = parts[0];
port = Integer.parseInt(parts[1]);
}
builder.withServer(server).withPort(port);
} else throw new IllegalArgumentException("Unknown server!");
this.owner = owner;
MinecraftBotData botData = builder.build();
System.setProperty("socksProxyHost", "");
System.setProperty("socksProxyPort", "");
System.out.println("[" + username + "] Connecting...");
bot = new MinecraftBot(darkBot, botData);
bot.setMovementDisabled(true);
connectionHandler = bot.getConnectionHandler();
Session session = bot.getSession();
// System.gc();
System.out.println("[" + username + "] Done! (" + amountJoined.incrementAndGet() + ")");
bot.getEventManager().registerListener(this);
bot.getGameHandler().registerListener(this);
long lastShoutTime = System.currentTimeMillis();
while (bot.isConnected()) {
if (die) {
connectionHandler.sendPacket(new Packet255KickDisconnect("Goodbye"));
return;
}
try {
Thread.sleep(3000 + random.nextInt(1000));
} catch (InterruptedException exception) {
exception.printStackTrace();
}
if (!bot.hasSpawned()) continue;
connectionHandler.sendPacket(new Packet0KeepAlive(random.nextInt()));
if (spamMessage == null || !canSpam) continue;
String message = spamMessage;
if (message.contains("%skill")) message = message.replace("%skill", skills[nextSkill++]);
if (nextSkill >= skills.length) nextSkill = 0;
if (message.contains("%bot")) {
synchronized (bots) {
message =
message.replace(
"%bot",
bots.get(nextBot > bots.size() ? (nextBot = 0) * 0 : nextBot++)
.bot
.getSession()
.getUsername());
}
}
if (message.contains("%spamlist"))
message = message.replace("%spamlist", spamList[nextSpamList++]);
if (nextSpamList >= spamList.length) nextSpamList = 0;
if (message.contains("%rnd")) {
int length = 1;
int index = message.indexOf("%rnd") + "%rnd".length();
int lastIndex;
for (lastIndex = index; lastIndex < message.length(); lastIndex++)
if (Character.isDigit(message.charAt(lastIndex))) lastIndex++;
else break;
if (lastIndex > message.length()) lastIndex--;
try {
System.out.println(index + "," + lastIndex + "," + message.length());
length = Integer.parseInt(message.substring(index, lastIndex));
} catch (Exception exception) {
}
String randomChars = "";
for (int i = 0; i < length; i++) randomChars += alphas[random.nextInt(alphas.length)];
message = message.replace("%rnd", randomChars);
}
if (message.contains("%msg"))
message = "/msg " + msgChars[nextMsgChar++] + " " + message.replace("%msg", "");
if (message.contains("%ernd")) {
message = message.replace("%ernd", "");
int extraMessageLength = 15 + random.nextInt(6);
message = message.substring(0, Math.min(100 - extraMessageLength, message.length())) + " [";
extraMessageLength -= 3;
for (int i = 0; i < extraMessageLength; i++)
message += alphas[random.nextInt(alphas.length)];
message += "]";
} else message = message.substring(0, Math.min(100, message.length()));
connectionHandler.sendPacket(new Packet3Chat(message));
}
synchronized (bots) {
bots.remove(this);
}
amountJoined.decrementAndGet();
slotsTaken.decrementAndGet();
synchronized (slotsTaken) {
slotsTaken.notifyAll();
}
}
@NotNull
private Pattern getPattern(String pattern) {
if (!Comparing.strEqual(pattern, myPattern)) {
myCompiledPattern = null;
myPattern = pattern;
}
if (myCompiledPattern == null) {
boolean allowToLower = true;
final int eol = pattern.indexOf('\n');
if (eol != -1) {
pattern = pattern.substring(0, eol);
}
if (pattern.length() >= 80) {
pattern = pattern.substring(0, 80);
}
final @NonNls StringBuffer buffer = new StringBuffer();
if (containsOnlyUppercaseLetters(pattern)) {
allowToLower = false;
}
if (allowToLower) {
buffer.append(".*");
}
boolean firstIdentifierLetter = true;
for (int i = 0; i < pattern.length(); i++) {
final char c = pattern.charAt(i);
if (Character.isLetterOrDigit(c)) {
// This logic allows to use uppercase letters only to catch the name like PDM for
// PsiDocumentManager
if (Character.isUpperCase(c) || Character.isDigit(c)) {
if (!firstIdentifierLetter) {
buffer.append("[^A-Z]*");
}
buffer.append("[");
buffer.append(c);
if (allowToLower || i == 0) {
buffer.append('|');
buffer.append(Character.toLowerCase(c));
}
buffer.append("]");
} else if (Character.isLowerCase(c)) {
buffer.append('[');
buffer.append(c);
buffer.append('|');
buffer.append(Character.toUpperCase(c));
buffer.append(']');
} else {
buffer.append(c);
}
firstIdentifierLetter = false;
} else if (c == '*') {
buffer.append(".*");
firstIdentifierLetter = true;
} else if (c == '.') {
buffer.append("\\.");
firstIdentifierLetter = true;
} else if (c == ' ') {
buffer.append("[^A-Z]*\\ ");
firstIdentifierLetter = true;
} else {
firstIdentifierLetter = true;
// for standard RegExp engine
// buffer.append("\\u");
// buffer.append(Integer.toHexString(c + 0x20000).substring(1));
// for OROMATCHER RegExp engine
buffer.append("\\x");
buffer.append(Integer.toHexString(c + 0x20000).substring(3));
}
}
buffer.append(".*");
try {
myCompiledPattern = new Perl5Compiler().compile(buffer.toString());
} catch (MalformedPatternException e) {
// do nothing
}
}
return myCompiledPattern;
}
private int findItOffset(
@NotNull Editor editor, int startOffset, int count, int dir, boolean noSmartCase) {
boolean wrap = Options.getInstance().isSet("wrapscan");
TextRange range = findIt(editor, startOffset, count, dir, noSmartCase, wrap, true, true);
if (range == null) {
return -1;
}
// highlightMatch(editor, range.getStartOffset(), range.getEndOffset());
ParsePosition pp = new ParsePosition(0);
int res = range.getStartOffset();
if (lastOffset == null) {
return -1;
}
if (lastOffset.length() == 0) {
return range.getStartOffset();
} else if (Character.isDigit(lastOffset.charAt(0))
|| lastOffset.charAt(0) == '+'
|| lastOffset.charAt(0) == '-') {
int lineOffset = 0;
if (lastOffset.equals("+")) {
lineOffset = 1;
} else if (lastOffset.equals("-")) {
lineOffset = -1;
} else {
if (lastOffset.charAt(0) == '+') {
lastOffset = lastOffset.substring(1);
}
NumberFormat nf = NumberFormat.getIntegerInstance();
pp = new ParsePosition(0);
Number num = nf.parse(lastOffset, pp);
if (num != null) {
lineOffset = num.intValue();
}
}
int line = editor.offsetToLogicalPosition(range.getStartOffset()).line;
int newLine = EditorHelper.normalizeLine(editor, line + lineOffset);
res = VimPlugin.getMotion().moveCaretToLineStart(editor, newLine);
} else if ("ebs".indexOf(lastOffset.charAt(0)) != -1) {
int charOffset = 0;
if (lastOffset.length() >= 2) {
if ("+-".indexOf(lastOffset.charAt(1)) != -1) {
charOffset = 1;
}
NumberFormat nf = NumberFormat.getIntegerInstance();
pp = new ParsePosition(lastOffset.charAt(1) == '+' ? 2 : 1);
Number num = nf.parse(lastOffset, pp);
if (num != null) {
charOffset = num.intValue();
}
}
int base = range.getStartOffset();
if (lastOffset.charAt(0) == 'e') {
base = range.getEndOffset() - 1;
}
res = Math.max(0, Math.min(base + charOffset, EditorHelper.getFileSize(editor) - 1));
}
int ppos = pp.getIndex();
if (ppos < lastOffset.length() - 1 && lastOffset.charAt(ppos) == ';') {
int flags;
if (lastOffset.charAt(ppos + 1) == '/') {
flags = Command.FLAG_SEARCH_FWD;
} else if (lastOffset.charAt(ppos + 1) == '?') {
flags = Command.FLAG_SEARCH_REV;
} else {
return res;
}
if (lastOffset.length() - ppos > 2) {
ppos++;
}
res = search(editor, lastOffset.substring(ppos + 1), res, 1, flags);
return res;
} else {
return res;
}
}
/*
* Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
*/
private static void doTests(neuronEditorFrame nef, String fileName) {
System.out.println(
"Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
+ fileName);
File tempDir = new File("temp");
if (!tempDir.exists()) tempDir.mkdir();
neuronEditorPanel nep = nef.getNeuronEditorPanel();
String rootFileName = fileName;
if (rootFileName.toLowerCase().endsWith(".swc")) {
rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
}
if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
rootFileName =
rootFileName.substring(
rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
}
// NEURON save...
String neuronFileName = rootFileName + ".hoc";
File neuronFile = new File(tempDir, neuronFileName);
File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");
nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());
StringBuilder sbNeuTest = new StringBuilder();
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
sbNeuTest.append("forall morph()\n");
System.out.println("--------------------------------------------------------------");
nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());
System.out.println(
"Saved NEURON representation of the file to: "
+ neuronFile.getAbsolutePath()
+ ": "
+ neuronFile.exists());
System.out.println("--------------------------------------------------------------");
// GENESIS save...
String genesisFileName = rootFileName + ".p";
File genesisFile = new File(tempDir, genesisFileName);
File genesisTestFile = new File(tempDir, rootFileName + "_test.g");
nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());
StringBuilder sbGenTest = new StringBuilder();
sbGenTest.append("include compartments \n");
sbGenTest.append("create neutral /library\n");
sbGenTest.append("disable /library\n");
sbGenTest.append("ce /library\n");
sbGenTest.append("make_cylind_compartment\n");
sbGenTest.append("make_cylind_symcompartment\n");
sbGenTest.append("make_sphere_compartment\n");
sbGenTest.append("ce /\n");
sbGenTest.append(
"echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");
sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
sbGenTest.append(
"create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
sbGenTest.append(
"setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
sbGenTest.append(
"create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
sbGenTest.append("xcolorscale hot\n");
sbGenTest.append("xshow /form\n\n");
sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");
nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());
System.out.println(
"Saved GENESIS representation of the file to: "
+ genesisFile.getAbsolutePath()
+ ": "
+ genesisFile.exists());
System.out.println("--------------------------------------------------------------");
// NeuroML save...
String nml1FileName = rootFileName + ".xml";
File nml1File = new File(tempDir, nml1FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
String nml2FileName = rootFileName + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(tempDir, nml2FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}
@Override
public boolean isValidInputCharacter(final char c, final int offs) {
return Character.isDigit(c) && offs < DBSchema.getFieldLength(DBSchema.OWNER_INDEX);
}