public static boolean checkNoContigAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return false;
int count = 0;
boolean resave = false;
boolean warn = false;
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (AceFile.hasAceFilePath(editedData, it)) {
if (!AceFile.hasAceFile(ownerModule, editedData, it)) {}
AceFile ace = AceFile.getAceFile(ownerModule, editedData, it);
if (ace != null) {
if (ace.getNumContigs() <= 0 || ace.getContig(0).getNumBases() == 0) {
if (!warn
&& !AlertDialog.query(
ownerModule.containerOfModule(),
"Reprocess and save file?",
"Some of the contigs need to be reprocessed, which will"
+ " alter the modified .ace files produced by Phrap and Chromaseq. To be compatible with these altered .ace files, the Mesquite file "
+ "would then need to be re-saved. If instead you choose not to reprocess contigs, they will not be fully editable in Chromaseq.",
"Reprocess and Save",
"Do not reprocess",
-1)) {
return false;
} else resave = true;
warn = true;
ChromaseqUtil.setReprocessContig(editedData, it);
}
}
count++;
}
return resave;
}
/*.................................................................................................................*/
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;
}
/*..........................................MContinuousStates................*/
public int userQueryItem(String message, MesquiteModule module) {
int numItems = getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(getItemName(i))) items[i] = "(unnamed)";
else items[i] = getItemName(i);
}
return ListDialog.queryList(
module.containerOfModule(), "Select item", message, MesquiteString.helpString, items, 0);
}