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;
}
/*.................................................................................................................*/
public static boolean hasDisconnectedAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return true;
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (AceFile.hasAceFilePath(editedData, it)
&& !AceFile.hasAceFile(ownerModule, editedData, it)) {
// boolean db = AceFile.hasAceFile(ownerModule, editedData,it);
return true;
}
return false;
}