public static boolean processNoContigAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return false;
boolean changed = false;
MesquiteFile file = data.getProject().getHomeFile();
int count = 0;
int originalChars = editedData.getNumChars();
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (ChromaseqUtil.reprocessContig(editedData, it)) {
AceDirectoryProcessor aceDirProcessor = new AceDirectoryProcessor();
aceDirProcessor.reprocessAceFileDirectory(file, ownerModule, editedData, it);
count++;
}
if (count > 0) {
editedData.getTaxa().notifyListeners(ownerModule, new Notification(ownerModule.PARTS_ADDED));
MesquiteMessage.discreetNotifyUser(
"Some of the contigs have been reprocessed; this will be lost permanently unless you resave the file.");
changed = true;
}
if (originalChars < editedData.getNumChars())
editedData.notifyListeners(ownerModule, new Notification(ownerModule.PARTS_ADDED));
else if (originalChars > editedData.getNumChars())
editedData.notifyListeners(ownerModule, new Notification(ownerModule.PARTS_DELETED));
ChromaseqUtil.removeAssociatedObjects(editedData, ChromaseqUtil.reprocessContigRef);
return changed;
}
/*.................................................................................................................*/
boolean checkUsernamePassword(boolean tellUserAboutCipres) {
if (StringUtil.blank(username) || StringUtil.blank(password)) {
MesquiteBoolean answer = new MesquiteBoolean(false);
MesquiteString usernameString = new MesquiteString();
if (username != null) usernameString.setValue(username);
MesquiteString passwordString = new MesquiteString();
if (password != null) passwordString.setValue(password);
String help =
"You will need an account on the CIPRes REST system to use this service. To register, go to https://www.phylo.org/restusers/register.action";
new UserNamePasswordDialog(
ownerModule.containerOfModule(),
"Sign in to CIPRes",
help,
"",
"Username",
"Password",
answer,
usernameString,
passwordString);
if (answer.getValue()) {
username = usernameString.getValue();
password = passwordString.getValue();
}
ownerModule.storePreferences();
}
boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
if (!success && tellUserAboutCipres) {
MesquiteMessage.discreetNotifyUser(
"Use of the CIPRes service requires an account with CIPRes's REST service. Go to https://www.phylo.org/restusers/register.action to register for an account");
}
return success;
}
public void readTabbedTranslationFile(String translationList) {
Parser parser = new Parser();
parser.setString(translationList);
Parser subParser = new Parser();
String line = parser.getRawNextDarkLine();
numCodes = 0;
while (!StringUtil.blank(line)) {
numCodes++;
line = parser.getRawNextDarkLine();
}
if (numCodes == 0) {
MesquiteMessage.discreetNotifyUser("File is empty.");
return;
}
initializeArrays(numCodes);
int count = -1;
parser.setPosition(0);
subParser.setPunctuationString("\t");
line = parser.getRawNextDarkLine();
String token = "";
while (!StringUtil.blank(line)) {
count++;
subParser.setString(line);
token = subParser.getFirstToken();
if (StringUtil.notEmpty(token)) {
originalSampleCodes[count] = token;
token = subParser.getNextToken();
if (StringUtil.notEmpty(token)) {
translatedSampleCodes[count] = token;
}
}
line = parser.getRawNextDarkLine();
}
}