/*.................................................................................................................*/
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);
}
/*.................................................................................................................*/
String getComDelim() {
if (externalProcRunner.isWindows()) return ";" + StringUtil.lineEnding();
else return ";" + StringUtil.lineEnding();
}
/*.................................................................................................................*/
void formCommandFile(String dataFileName, int firstOutgroup) {
if (parallel) {
commands = "";
}
commands += getTNTCommand("mxram " + mxram);
commands += getTNTCommand("report+0/1/0");
commands += getTNTCommand("log " + logFileName);
commands += getTNTCommand("p " + dataFileName);
commands += getTNTCommand("vversion");
if (MesquiteInteger.isCombinable(firstOutgroup) && firstOutgroup >= 0)
commands += getTNTCommand("outgroup " + firstOutgroup);
if (bootstrapOrJackknife()) {
if (parallel) {
commands += indentTNTCommand("ptnt begin parallelRun " + numSlaves + "/ram x 2 = ");
}
if (StringUtil.notEmpty(bootSearchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(bootSearchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else
commands += StringUtil.lineEnding() + bootstrapSearchArguments + StringUtil.lineEnding();
String saveTreesString = "";
if (resamplingAllConsensusTrees) saveTreesString = " savetrees ";
String bootSearchString = " [xmult; bb]";
bootSearchString = "";
if (parallel) {
int numRepsPerSlave = bootstrapreps / numSlaves;
if (numRepsPerSlave * numSlaves < bootstrapreps) numRepsPerSlave++;
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
commands += getTNTCommand("return");
commands += getTNTCommand("ptnt wait parallelRun");
commands += getTNTCommand("ptnt get parallelRun");
} else {
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("macro=");
commands += getTNTCommand("ttags =");
}
commands += getTNTCommand("tsave *" + treeFileName);
if (bootstrapAllowed) {
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
}
if (!resamplingAllConsensusTrees) commands += getTNTCommand("save *");
else commands += getTNTCommand("save");
commands += getTNTCommand("tsave/");
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("ttags -/");
commands += getTNTCommand("macro-");
}
}
// commands += getTNTCommand("proc/") ;
commands += getTNTCommand("log/");
// if (!parallel)
commands += getTNTCommand("quit");
} else {
// commands += getTNTCommand("tsave !5 " + treeFileName) ; // if showing intermediate trees
commands += getTNTCommand("tsave *" + treeFileName);
if (StringUtil.notEmpty(searchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(searchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else commands += searchArguments;
commands += otherOptions;
if (harvestOnlyStrictConsensus) commands += getTNTCommand("nelsen *");
commands += getTNTCommand("save");
commands += getTNTCommand("log/");
commands += getTNTCommand("tsave/");
commands += getTNTCommand("quit");
}
}