/**
* 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 String jobStatusFromResponse(Document cipresResponseDoc) {
String status = "Status not available";
Element element = cipresResponseDoc.getRootElement().element("terminalStage");
if (element != null) {
status = element.getText();
if ("true".equalsIgnoreCase(status)) return JOBCOMPLETED;
}
element = cipresResponseDoc.getRootElement().element("messages");
if (element == null) return status;
List entries = element.elements("message");
String reportedJobID = "";
for (Iterator iter = entries.iterator(); iter.hasNext(); ) {
Element nextEntry = (Element) iter.next();
if (nextEntry != null) status = nextEntry.elementText("stage");
}
element = cipresResponseDoc.getRootElement().element("minPollIntervalSeconds");
if (element != null) {
minPollIntervalSeconds = MesquiteInteger.fromString(element.getText());
if (!MesquiteInteger.isCombinable(minPollIntervalSeconds) || minPollIntervalSeconds <= 0)
minPollIntervalSeconds = defaultMinPollIntervalSeconds;
}
if (JOBCOMPLETED.equalsIgnoreCase(status)) return JOBCOMPLETED;
return status;
}
/*.................................................................................................................*/
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 the number of randomly chosen taxa to exclude",
"[number]",
commandName,
"setNumberExcluded")) {
int s = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (!MesquiteInteger.isCombinable(s)) {
s =
MesquiteInteger.queryInteger(
containerOfModule(),
"Number of taxa to exclude",
"Enter the number of randomly chosen taxa to exclude",
numExcluded);
}
if (MesquiteInteger.isCombinable(s)) {
numExcluded = s;
parametersChanged();
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
Tree trt = treeDisplay.getTree();
MesquiteTree t = null;
if (trt instanceof MesquiteTree) t = (MesquiteTree) trt;
if (checker.compare(
this.getClass(),
"Adjust tool has touched branch",
"[branch number][x coordinate touched][y coordinate touched][modifiers]",
commandName,
"touchedPositionAdjust")) {
if (t == null) return null;
MesquiteInteger io = new MesquiteInteger(0);
int node = MesquiteInteger.fromString(arguments, io);
int x = MesquiteInteger.fromString(arguments, io);
int y = MesquiteInteger.fromString(arguments, io);
String mod = ParseUtil.getRemaining(arguments, io);
Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
originalX = newOnLine.x;
originalY = newOnLine.y;
// lastX= newOnLine.x;
// lastY = newOnLine.y;
Graphics g = null;
if (GraphicsUtil.useXORMode(null, false)) {
g = treeDisplay.getGraphics();
g.setXORMode(Color.white);
g.setColor(Color.red);
}
// double bX = treeDisplay.getTreeDrawing().lineBaseX[node];
// double bY = treeDisplay.getTreeDrawing().lineBaseY[node];
// Math.sqrt((originalY-bY)*(originalY-bY) + (originalX-bX)*(originalX-bX));
lastBL = tree.getBranchLength(node);
double shortestAbove = MesquiteDouble.unassigned;
for (int daughter = t.firstDaughterOfNode(node);
t.nodeExists(daughter);
daughter = t.nextSisterOfNode(daughter))
shortestAbove = MesquiteDouble.minimum(shortestAbove, tree.getBranchLength(daughter));
if (shortestAbove == MesquiteDouble.unassigned) upperLimit = MesquiteDouble.infinite;
else if (MesquiteDouble.isCombinable(lastBL)) upperLimit = shortestAbove + lastBL;
else upperLimit = shortestAbove + 1.0;
int ibX = treeDisplay.getTreeDrawing().lineBaseX[node];
int ibY = treeDisplay.getTreeDrawing().lineBaseY[node];
lastX = treeDisplay.getTreeDrawing().lineTipX[node];
lastY = treeDisplay.getTreeDrawing().lineTipY[node];
if (GraphicsUtil.useXORMode(null, false)) {
drawThickLine(g, ibX, ibY, lastX, lastY);
for (int daughter = t.firstDaughterOfNode(node);
t.nodeExists(daughter);
daughter = t.nextSisterOfNode(daughter))
drawThickLine(
g,
treeDisplay.getTreeDrawing().lineTipX[daughter],
treeDisplay.getTreeDrawing().lineTipY[daughter],
lastX,
lastY);
g.fillOval(
lastX - ovalRadius,
lastY - ovalRadius,
ovalRadius + ovalRadius,
ovalRadius + ovalRadius);
try {
g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY);
} catch (InternalError e) { // workaround for bug on windows java 1.7.
} catch (Throwable e) {
}
lineOn = true;
g.dispose();
}
} else if (checker.compare(
this.getClass(),
"Adjust tool has been dropped",
"[branch number][x coordinate dropped][y coordinate dropped]",
commandName,
"droppedPositionAdjust")) {
if (t == null) return null;
if (editorOn) return null;
MesquiteInteger io = new MesquiteInteger(0);
int node = MesquiteInteger.fromString(arguments, io);
int x = MesquiteInteger.fromString(arguments, io);
int y = MesquiteInteger.fromString(arguments, io);
if (lineOn) {
Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
double bX = treeDisplay.getTreeDrawing().lineBaseX[node];
double bY = treeDisplay.getTreeDrawing().lineBaseY[node];
double tX = treeDisplay.getTreeDrawing().lineTipX[node];
double tY = treeDisplay.getTreeDrawing().lineTipY[node];
double lengthLine =
Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX));
double bL;
if (lengthLine != 0) {
double extension =
Math.sqrt(
(newOnLine.y - bY) * (newOnLine.y - bY)
+ (newOnLine.x - bX) * (newOnLine.x - bX))
/ lengthLine;
if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension;
else bL = t.getBranchLength(node) * extension;
} else bL = 1;
if (bL > upperLimit) bL = upperLimit;
else if (bL < lowerLimit) bL = lowerLimit;
double oldBL = t.getBranchLength(node);
if (!MesquiteDouble.isCombinable(oldBL)) oldBL = 1.0;
t.setBranchLength(node, bL, false);
double difference = oldBL - t.getBranchLength(node);
for (int daughter = t.firstDaughterOfNode(node);
t.nodeExists(daughter);
daughter = t.nextSisterOfNode(daughter))
if (MesquiteDouble.isCombinable(t.getBranchLength(daughter)))
t.setBranchLength(daughter, t.getBranchLength(daughter) + difference, false);
t.notifyListeners(this, new Notification(MesquiteListener.BRANCHLENGTHS_CHANGED));
Graphics g = treeDisplay.getGraphics();
g.setPaintMode();
g.dispose();
treeDisplay.pleaseUpdate(true);
lineOn = false;
}
} else if (checker.compare(
this.getClass(),
"Adjust tool is being dragged",
"[branch number][x coordinate][y coordinate]",
commandName,
"draggedPositionAdjust")) {
if (t == null) return null;
if (editorOn) return null;
MesquiteInteger io = new MesquiteInteger(0);
int node = MesquiteInteger.fromString(arguments, io);
int x = MesquiteInteger.fromString(arguments, io);
int y = MesquiteInteger.fromString(arguments, io);
if (lineOn) {
Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
// WARNING": This shouldn't result in length increase if simple click and release with no
// drag; must subtract original X, Y
Graphics g = null;
if (GraphicsUtil.useXORMode(null, false)) {
g = treeDisplay.getGraphics();
g.setXORMode(Color.white);
g.setColor(Color.red);
}
// g.fillOval(lastX-ovalRadius, lastY-ovalRadius, ovalRadius + ovalRadius, ovalRadius +
// ovalRadius);
// g.fillOval(newOnLine.x-ovalRadius, newOnLine.y -ovalRadius, ovalRadius + ovalRadius,
// ovalRadius + ovalRadius);
// g.drawLine(originalX, originalY, lastX, lastY);
// g.drawLine(originalX, originalY, newOnLine.x, newOnLine.y);
// if decreasing, & unassigned involved: push unassigned down and assign values to
// unassigned above; if increasing, push unassigne up
int ibX = treeDisplay.getTreeDrawing().lineBaseX[node];
int ibY = treeDisplay.getTreeDrawing().lineBaseY[node];
int itX = treeDisplay.getTreeDrawing().lineTipX[node];
int itY = treeDisplay.getTreeDrawing().lineTipY[node];
double bX = ibX;
double bY = ibY;
double tX = itX;
double tY = itY;
double lengthLine =
Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX));
if (lengthLine != 0) {
if (GraphicsUtil.useXORMode(null, false)) {
if (MesquiteTrunk.isMacOSX()
&& MesquiteTrunk.getJavaVersionAsDouble() >= 1.5
&& MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug
g.fillRect(lastX, lastY - 20, 100, 20);
g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY);
if (MesquiteTrunk.isMacOSX()
&& MesquiteTrunk.getJavaVersionAsDouble() >= 1.5
&& MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug
g.fillRect(lastX, lastY - 20, 100, 20);
}
double extension =
Math.sqrt(
(newOnLine.y - bY) * (newOnLine.y - bY)
+ (newOnLine.x - bX) * (newOnLine.x - bX))
/ lengthLine;
double bL;
if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension;
else bL = t.getBranchLength(node) * extension;
if (bL > upperLimit) {
bL = upperLimit;
if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node))
extension = upperLimit;
else extension = upperLimit / t.getBranchLength(node);
} else if (bL < lowerLimit) {
bL = lowerLimit;
if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node))
extension = lowerLimit;
else extension = lowerLimit / t.getBranchLength(node);
}
lastBL = bL;
if (GraphicsUtil.useXORMode(null, false)) {
drawThickLine(g, ibX, ibY, lastX, lastY);
for (int daughter = t.firstDaughterOfNode(node);
t.nodeExists(daughter);
daughter = t.nextSisterOfNode(daughter))
drawThickLine(
g,
treeDisplay.getTreeDrawing().lineTipX[daughter],
treeDisplay.getTreeDrawing().lineTipY[daughter],
lastX,
lastY);
g.fillOval(
lastX - ovalRadius,
lastY - ovalRadius,
ovalRadius + ovalRadius,
ovalRadius + ovalRadius);
}
int newX = ibX + (int) (extension * (tX - bX));
int newY = ibY + (int) (extension * (tY - bY));
if (GraphicsUtil.useXORMode(null, false)) {
g.drawString(MesquiteDouble.toString(bL), newX + 10, newY);
drawThickLine(g, ibX, ibY, newX, newY);
for (int daughter = t.firstDaughterOfNode(node);
t.nodeExists(daughter);
daughter = t.nextSisterOfNode(daughter))
drawThickLine(
g,
treeDisplay.getTreeDrawing().lineTipX[daughter],
treeDisplay.getTreeDrawing().lineTipY[daughter],
newX,
newY);
g.fillOval(
newX - ovalRadius,
newY - ovalRadius,
ovalRadius + ovalRadius,
ovalRadius + ovalRadius);
}
lastX = newX;
lastY = newY;
}
// lastX= newOnLine.x;
// lastY = newOnLine.y;
}
}
return null;
}
/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String content) {
if ("availMemory".equalsIgnoreCase(tag)) availMemory = MesquiteInteger.fromString(content);
super.processSingleXMLPreference(tag, content);
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
return matrixSourceTask;
} else if (checker.compare(
this.getClass(), "Copies the data for selected taxon", null, commandName, "copyData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it)) {
StringBuffer sb = new StringBuffer();
data.copyDataFromRowIntoBuffer(it, sb);
if (StringUtil.notEmpty(sb.toString())) {
localCopyDataClipboard = sb.toString();
localCopyData = data;
localCopyDataTaxon = data.getTaxa().getTaxonName(it);
} else {
localCopyDataClipboard = null;
localCopyData = null;
localCopyDataTaxon = null;
}
}
return null;
} else if (checker.compare(
this.getClass(), "Pastes the data for selected taxon", null, commandName, "pasteData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it) && StringUtil.notEmpty(localCopyDataClipboard)) {
data.pasteDataFromStringIntoTaxon(it, localCopyDataClipboard);
}
return null;
} else if (checker.compare(
this.getClass(),
"Pastes the data for selected taxon",
null,
commandName,
"deleteDataTouched")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
Debugg.println("prepare to delete row: " + it);
if (MesquiteInteger.isCombinable(it)) {
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for taxon "
+ data.getTaxa().getTaxonName(it)
+ " in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) {
zapData(data, it);
}
}
return null;
} else if (checker.compare(
this.getClass(), "Deletes the data for selected taxa", null, commandName, "deleteData")) {
if (observedStates == null) return null;
captureCharacterDataFromObservedStates();
if (data == null) return null;
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for these taxa in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) zapData(data);
return null;
} else if (checker.compare(
this.getClass(),
"deleteds () and anything between",
null,
commandName,
"deletePrepended")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("(") >= 0) {
int start = note.indexOf("(");
int end = note.indexOf(")");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(end + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(this.getClass(), "deletes *", null, commandName, "deleteStar")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("*") >= 0) {
int start = note.indexOf("*");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(start + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the sequence length (including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependLength")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + sequenceLength(it) + ")";
else note = "(" + sequenceLength(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the number of non-missing sites (not including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependNumSites")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + numSites(it) + ")";
else note = "(" + numSites(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Deletes the notes for the selected taxa",
null,
commandName,
"deleteAnnotation")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
setNote(it, null);
}
}
outputInvalid();
parametersChanged();
return null;
} else return super.doCommand(commandName, arguments, checker);
}
public void runFilesAvailable(int fileNum) {
String[] logFileNames = getLogFileNames();
if ((progIndicator != null && progIndicator.isAborted()) || logFileNames == null) return;
String[] outputFilePaths = new String[logFileNames.length];
outputFilePaths[fileNum] = externalProcRunner.getOutputFilePath(logFileNames[fileNum]);
String filePath = outputFilePaths[fileNum];
if (fileNum == 0
&& outputFilePaths.length > 0
&& !StringUtil.blank(outputFilePaths[0])
&& !bootstrapOrJackknife()) { // tree file
if (ownerModule instanceof NewTreeProcessor) {
String treeFilePath = filePath;
if (taxa != null) {
TaxaSelectionSet outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, outgroupSet);
} else ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, null);
}
} else if (fileNum == 1
&& outputFilePaths.length > 1
&& !StringUtil.blank(outputFilePaths[1])
&& !bootstrapOrJackknife()) { // log file
if (MesquiteFile.fileExists(filePath)) {
String s = MesquiteFile.getFileLastContents(filePath);
if (!StringUtil.blank(s))
if (progIndicator != null) {
parser.setString(s);
String rep = parser.getFirstToken(); // generation number
logln("");
if (MesquiteInteger.isNumber(rep)) {
int numReps = MesquiteInteger.fromString(rep) + 1;
progIndicator.setText(
"Replicate: " + numReps); // + ", ln L = " + parser.getNextToken());
if (bootstrapOrJackknife()) {
logln("Replicate " + numReps + " of " + bootstrapreps);
}
logln("Replicate " + numReps + " of " + totalNumHits);
progIndicator.spin();
double timePerRep = 0;
if (MesquiteInteger.isCombinable(numReps) && numReps > 0) {
timePerRep = timer.timeSinceVeryStartInSeconds() / numReps; // this is time per rep
}
int timeLeft = 0;
if (bootstrapOrJackknife()) {
timeLeft = (int) ((bootstrapreps - numReps) * timePerRep);
} else {
String token = parser.getNextToken(); // algorithm
token = parser.getNextToken(); // Tree
token = parser.getNextToken(); // Score
String best = parser.getNextToken(); // Best
logln(" Score " + token + "; best found so far " + best);
timeLeft = (int) ((totalNumHits - numReps) * timePerRep);
}
logln(
" Running time so far "
+ StringUtil.secondsToHHMMSS((int) timer.timeSinceVeryStartInSeconds())
+ ", approximate time remaining "
+ StringUtil.secondsToHHMMSS(timeLeft));
}
}
count++;
} else if (MesquiteTrunk.debugMode) logln("*** File does not exist (" + filePath + ") ***");
}
}
/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String flavor, String content) {
if ("userName".equalsIgnoreCase(tag)) username = StringUtil.cleanXMLEscapeCharacters(content);
else if ("jobNumber".equalsIgnoreCase(tag)) jobNumber = MesquiteInteger.fromString(content);
}