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;
}
/*.................................................................................................................*/
public void fillNameTranslation(DNAData editedData, int it, int numReads) {
Associable as = editedData.getTaxaInfo(false);
if (as == null) return;
String[] fileNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.origReadFileNamesRef, it);
String[] primerNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.primerForEachReadNamesRef, it);
String[] sampleCodes =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.sampleCodeNamesRef, it);
for (int i = 0; i < numReads; i++) {
if (fileNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"fileNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < fileNames.length) {
fileNameTranslation[0][i] = fileNames[i * 2];
fileNameTranslation[1][i] = fileNames[i * 2 + 1];
} else
MesquiteMessage.warnProgrammer(
"fileNames.length too small in AceDirectoryProcess.fileNameTranslation: fileNames.length = "
+ fileNames.length
+ ", numReads: "
+ numReads);
if (primerNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"primerNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < primerNames.length) fileNameTranslation[2][i] = primerNames[i * 2 + 1];
else
MesquiteMessage.warnProgrammer(
"primerNames.length too small in AceDirectoryProcess.fileNameTranslation: primerNames.length = "
+ primerNames.length
+ ", numReads: "
+ numReads);
if (sampleCodes == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"sampleCodes NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 3 + 2 < sampleCodes.length) {
fileNameTranslation[3][i] = sampleCodes[i * 3 + 1];
fileNameTranslation[4][i] = sampleCodes[i * 3 + 2];
} else
MesquiteMessage.warnProgrammer(
"sampleCodes.length too small in AceDirectoryProcess.fileNameTranslation: sampleCodes.length = "
+ sampleCodes.length
+ ", numReads: "
+ numReads);
}
}