/*.................................................................................................................*/
public void processAceFileWithoutContig(
DNAData data,
String processedAceFilePath,
AceFile ace,
String geneName,
MesquiteString fullName,
int it,
MesquiteString voucherCode) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
DNAData originalData = ChromaseqUtil.getOriginalData(data);
Taxa taxa = data.getTaxa();
ace.processFailedContig(polyThreshold);
ace.setNameTranslation(fileNameTranslation);
ace.renameContigs(fullName.toString(), addFragName, geneName);
ace.setLowQualityToLowerCase(qualThresholdForLowerCase);
ace.writeToPropertiesFile(contigPropertiesFileBuffer, fullName.toString());
if (truncateMixedEnds) {
ace.trimMixedEnds(mixedEndThreshold, mixedEndWindow, qualThresholdForTrim, addPhrapFailures);
}
MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
ace.importSequence(
taxa,
editedData,
it,
originalData,
ChromaseqUtil.getQualityData(data),
ChromaseqUtil.getRegistryData(data),
singleTaxaBlock,
processPolymorphisms,
maxChar,
"",
true,
voucherCode);
}
/*.................................................................................................................*/
public void processAceFileWithContig(
CharacterData data,
MesquiteModule ownerModule,
String processedAceFilePath,
String fragmentDirPath,
AceFile ace,
SequenceUploader uploader,
String geneName,
MesquiteString fullName,
String baseName,
MesquiteString voucherCode,
int it) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
DNAData originalData = ChromaseqUtil.getOriginalData(data);
Taxa taxa = data.getTaxa();
ace.setNameTranslation(fileNameTranslation);
ownerModule.log(ace.contigListForLog() + StringUtil.lineEnding());
if (processPolymorphisms) ace.processPolys(); // creates an additional CO that has polys in it
if (renameContigsInAceFiles) ace.renameContigs(fullName.toString(), addFragName, geneName);
ace.setLowQualityToLowerCase(qualThresholdForLowerCase);
ace.writeToPropertiesFile(contigPropertiesFileBuffer, fullName.toString());
if (truncateMixedEnds)
ace.trimMixedEnds(mixedEndThreshold, mixedEndWindow, qualThresholdForTrim, addPhrapFailures);
/* if (uploadResultsToDatabase && StringUtil.notEmpty(databaseURL)) {
uploader.uploadAceFileToServer(MesquiteXMLToLUtilities.getTOLPageDatabaseURL(databaseURL), ace, processPolymorphisms, qualThresholdForTrim);
}
*/
System.out.println("\n\nfasta file name: " + baseName + " ace file: " + ace);
MesquiteFile.putFileContents(
fragmentDirPath
+ MesquiteFile.fileSeparator
+ ChromaseqUtil.processedFastaFolder
+ MesquiteFile.fileSeparator
+ baseName
+ ".fas",
ace.toFASTAString(processPolymorphisms, qualThresholdForTrim),
true);
MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
ace.importSequence(
taxa,
editedData,
it,
originalData,
ChromaseqUtil.getQualityData(data),
ChromaseqUtil.getRegistryData(data),
singleTaxaBlock,
processPolymorphisms,
maxChar,
" contig ",
false,
voucherCode);
}