/*.................................................................................................................*/
public void modifyTree(Tree tree, MesquiteTree modified, RandomBetween rng) {
if (tree == null || modified == null) return;
if (tree.getTaxa().anySelected()) { // error fixed in 1. 12
int[] terminals = tree.getTerminalTaxa(tree.getRoot());
if (terminals == null) return;
int numTerminals = 0;
for (int i = 0; i < terminals.length; i++)
if (tree.getTaxa().getSelected(terminals[i])) numTerminals++;
if (numTerminals > numExcluded) {
int[] selTerminals = new int[numTerminals];
int icount = 0;
for (int i = 0; i < terminals.length; i++)
if (tree.getTaxa().getSelected(terminals[i])) {
selTerminals[icount] = terminals[i];
icount++;
}
terminals = selTerminals;
for (int it = 0; it < numExcluded; it++) {
int taxon = -1;
int count = 0;
int ntries = 100000;
while (terminals[taxon = rng.randomIntBetween(0, numTerminals - 1)] < 0
&& count < ntries) {
count++;
}
if (count >= ntries)
discreetAlert(
"ERROR: Rarefy tree failed to find taxon to delete in " + ntries + " tries.");
else {
int nT = modified.nodeOfTaxonNumber(terminals[taxon]);
modified.deleteClade(nT, false);
terminals[taxon] = -1;
}
}
} else
MesquiteMessage.warnUser(
"Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
} else {
int numTerminals = tree.numberOfTerminalsInClade(tree.getRoot());
if (numTerminals > numExcluded) {
for (int it = 0; it < numExcluded; it++) {
int taxon = rng.randomIntBetween(0, numTerminals - it - 1);
int nT = modified.getTerminalNode(modified.getRoot(), taxon);
modified.deleteClade(nT, false);
}
} else
MesquiteMessage.warnUser(
"Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
}
}
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;
}
/** monitors the run. */
public boolean monitorAndCleanUpShell() {
lastModified = null;
boolean stillGoing = true;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
if (!StringUtil.blank(
runningFilePath)) // is file at runningFilePath; watch for its disappearance
while (MesquiteFile.fileExists(runningFilePath) && stillGoing) {
processOutputFiles();
try {
Thread.sleep(sleepTime);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer(
"InterruptedException in shell script executed by " + name);
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(proc);
}
if (outputFileProcessor != null)
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
return true;
}
/*.................................................................................................................*/
boolean checkUsernamePassword(boolean tellUserAboutCipres) {
if (StringUtil.blank(username) || StringUtil.blank(password)) {
MesquiteBoolean answer = new MesquiteBoolean(false);
MesquiteString usernameString = new MesquiteString();
if (username != null) usernameString.setValue(username);
MesquiteString passwordString = new MesquiteString();
if (password != null) passwordString.setValue(password);
String help =
"You will need an account on the CIPRes REST system to use this service. To register, go to https://www.phylo.org/restusers/register.action";
new UserNamePasswordDialog(
ownerModule.containerOfModule(),
"Sign in to CIPRes",
help,
"",
"Username",
"Password",
answer,
usernameString,
passwordString);
if (answer.getValue()) {
username = usernameString.getValue();
password = passwordString.getValue();
}
ownerModule.storePreferences();
}
boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
if (!success && tellUserAboutCipres) {
MesquiteMessage.discreetNotifyUser(
"Use of the CIPRes service requires an account with CIPRes's REST service. Go to https://www.phylo.org/restusers/register.action to register for an account");
}
return success;
}
public boolean clipBoardHasString() {
Clipboard clip = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable t = clip.getContents(this);
try {
String s = (String) t.getTransferData(DataFlavor.stringFlavor);
if (s != null) {
return true;
}
} catch (Exception e) {
MesquiteMessage.printStackTrace(e);
}
return false;
}
/*.................................................................................................................*/
public boolean monitorAndCleanUpShell(String jobURL) {
boolean stillGoing = true;
if (!checkUsernamePassword(true)) {
return false;
}
lastModified = null;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
String status = "";
while (!jobCompleted(jobURL) && stillGoing) {
if (StringUtil.blank(status))
ownerModule.logln(
"CIPRes Job Status: " + getJobStatus(jobURL) + " (" + StringUtil.getDateTime() + ")");
// if (jobSubmitted(jobURL))
// processOutputFiles();
try {
Thread.sleep(minPollIntervalSeconds * 1000);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(null);
String newStatus = getJobStatus(jobURL);
if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
ownerModule.logln(
"CIPRes Job Status: " + newStatus + " (" + StringUtil.getDateTime() + ")");
status = newStatus;
} else ownerModule.log(".");
if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
processOutputFiles(jobURL);
}
}
ownerModule.logln("CIPRes job completed.");
if (outputFileProcessor != null) {
if (rootDir != null) {
ownerModule.logln("About to download results from CIPRes.");
if (downloadResults(jobURL, rootDir, false))
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
else return false;
}
}
return true;
}
/*.................................................................................................................*/
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);
}
}
public void readTabbedTranslationFile(String translationList) {
Parser parser = new Parser();
parser.setString(translationList);
Parser subParser = new Parser();
String line = parser.getRawNextDarkLine();
numCodes = 0;
while (!StringUtil.blank(line)) {
numCodes++;
line = parser.getRawNextDarkLine();
}
if (numCodes == 0) {
MesquiteMessage.discreetNotifyUser("File is empty.");
return;
}
initializeArrays(numCodes);
int count = -1;
parser.setPosition(0);
subParser.setPunctuationString("\t");
line = parser.getRawNextDarkLine();
String token = "";
while (!StringUtil.blank(line)) {
count++;
subParser.setString(line);
token = subParser.getFirstToken();
if (StringUtil.notEmpty(token)) {
originalSampleCodes[count] = token;
token = subParser.getNextToken();
if (StringUtil.notEmpty(token)) {
translatedSampleCodes[count] = token;
}
}
line = parser.getRawNextDarkLine();
}
}
/**
* executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then
* Mesquite will create a file there that will serve as a flag to Mesquite that the script is
* running.
*/
public boolean executeInShell() {
proc = null;
try {
ShellScriptUtil.setScriptFileToBeExecutable(scriptPath);
if (!StringUtil.blank(runningFilePath)) {
if (StringUtil.blank(runningFileMessage))
MesquiteFile.putFileContents(runningFilePath, "Script running...", true);
else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true);
if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath))
MesquiteFile.appendFileContents(
scriptPath,
StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath),
true); // append remove command to guarantee that the runningFile is deleted
// +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand()
}
proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal);
} catch (IOException e) {
MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name);
return false;
}
return true;
}