/*.................................................................................................................*/
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);
}
}
