/*.................................................................................................................*/
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;
}
/**
* A request for the MesquiteModule to perform a command. It is passed two strings, the name of
* the command and the arguments. This should be overridden by any module that wants to respond to
* a command.
*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
MesquiteInteger io = new MesquiteInteger(0);
int column = MesquiteInteger.fromString(arguments, io);
int row = MesquiteInteger.fromString(arguments, io);
if (MesquiteInteger.isCombinable(row)) {
if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
else setColor(row, (int) currentColor);
}
} else if (checker.compare(
this.getClass(),
"Sets the color to be used to paint cells",
"[name of color]",
commandName,
"setColor")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
removeColor.setValue(false);
currentColor = bc;
savedColor = bc;
colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
}
} else if (checker.compare(
this.getClass(),
"Sets the color of selected taxa",
"[name of color]",
commandName,
"setColorSelected")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
}
} else if (checker.compare(
this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
removeAllColor(true);
} else if (checker.compare(
this.getClass(),
"Sets the paint brush so that it removes colors from any cells touched",
null,
commandName,
"removeColor")) {
if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
else removeColor.toggleValue(parser.getFirstToken(arguments));
if (removeColor.getValue()) {
colorString = "Remove color";
currentColor = MesquiteLong.unassigned;
} else {
colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
currentColor = savedColor;
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public Snapshot getSnapshot(MesquiteFile file) {
Snapshot temp = new Snapshot();
temp.addLine(
"setColor "
+ ColorDistribution.getStandardColorName(
ColorDistribution.getStandardColor((int) currentColor)));
temp.addLine("removeColor " + removeColor.toOffOnString());
return temp;
}
/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String content) {
if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content);
if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content);
if ("convertGapsToMissing".equalsIgnoreCase(tag))
convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content);
if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag))
resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content);
if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag))
harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content);
if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content);
if ("searchArguments".equalsIgnoreCase(tag))
searchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("bootstrapSearchArguments".equalsIgnoreCase(tag))
bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("otherOptions".equalsIgnoreCase(tag))
otherOptions = StringUtil.cleanXMLEscapeCharacters(content);
// parallel, etc.
preferencesSet = true;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets whether or not to count stops in regions with ambiguous nucleotides that imply a stop OR an amino acid",
"[on; off]",
commandName,
"toggleCountEvenIfOthers")) {
countEvenIfOthers.toggleValue(parser.getFirstToken(arguments));
parametersChanged();
} else if (checker.compare(
this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
return matrixSourceTask;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
logln("Preparing to receive TNT trees.");
boolean success = false;
taxa = treeList.getTaxa();
// TODO finalScore.setValue(finalValue);
suppressProjectPanelReset();
CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
CommandRecord scr = new CommandRecord(true);
MesquiteThread.setCurrentCommandRecord(scr);
// define file paths and set tree files as needed.
setFileNames();
String[] outputFilePaths = externalProcRunner.getOutputFilePaths();
String treeFilePath = outputFilePaths[OUT_TREEFILE];
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
runFilesAvailable();
// read in the tree files
success = false;
Tree t = null;
MesquiteBoolean readSuccess = new MesquiteBoolean(false);
// TreeVector tv = new TreeVector(taxa);
if (bootstrapOrJackknife()) {
if (resamplingAllConsensusTrees)
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Rep",
0,
readSuccess,
false,
false,
null,
namer); // set first tree number as 0 as will remove the first one later.
else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Majority Rule Tree",
1,
readSuccess,
false,
false,
freqRef,
namer);
} else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNTTree",
1,
readSuccess,
false,
harvestOnlyStrictConsensus,
null,
namer);
success = t != null;
if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
t = t.cloneTree();
treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
}
MesquiteThread.setCurrentCommandRecord(oldCR);
success = readSuccess.getValue();
if (!success) {
logln("Execution of TNT unsuccessful [2]");
if (!beanWritten) postBean("unsuccessful [2]", false);
beanWritten = true;
} else {
if (!beanWritten) postBean("successful", false);
beanWritten = true;
}
desuppressProjectPanelReset();
if (data != null) data.decrementEditInhibition();
// manager.deleteElement(tv); // get rid of temporary tree block
externalProcRunner.finalCleanup();
if (success) return t;
return null;
}
/*.................................................................................................................*/
public Snapshot getSnapshot(MesquiteFile file) {
Snapshot temp = new Snapshot();
temp.addLine("getMatrixSource", matrixSourceTask);
temp.addLine("toggleCountEvenIfOthers " + countEvenIfOthers.toOffOnString());
return temp;
}