/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the number of trees included in each tree block",
"[number of trees]",
commandName,
"setNumberTrees")) {
MesquiteInteger pos = new MesquiteInteger(0);
int newNum = MesquiteInteger.fromFirstToken(arguments, pos);
if (!MesquiteInteger.isCombinable(newNum))
newNum =
MesquiteInteger.queryInteger(
containerOfModule(),
"Set Number of Trees",
"Number of Trees:",
numTrees,
0,
MesquiteInteger.infinite);
if (newNum > 0 && newNum != numTrees) {
numTrees = newNum;
parametersChanged();
}
} else if (checker.compare(
this.getClass(),
"Returns the module supplying trees",
"[name of module]",
commandName,
"getTreeFiller")) {
return fillerTask;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/**
* 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 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 Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the number of trees included in each tree block",
"[number of trees]",
commandName,
"setNumberTrees")) {
MesquiteInteger pos = new MesquiteInteger(0);
int newNum = MesquiteInteger.fromFirstToken(arguments, pos);
if (!MesquiteInteger.isCombinable(newNum))
newNum =
MesquiteInteger.queryInteger(
containerOfModule(),
"Set Number of Trees",
"Number of Trees:",
numTrees,
0,
MesquiteInteger.infinite);
if (newNum > 0 && newNum != numTrees) {
numTrees = newNum;
parametersChanged();
}
} else if (checker.compare(
this.getClass(),
"Sets the module supplying trees",
"[name of module]",
commandName,
"setTreeFiller")) {
TreeBlockFiller temp =
(TreeBlockFiller)
replaceEmployee(
TreeBlockFiller.class, arguments, "Source of trees for tree blocks", fillerTask);
if (temp != null) {
fillerTask = temp;
initialize(preferredTaxa);
parametersChanged(); // ?
}
return temp;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the running file path",
"[file path]",
commandName,
"setRunningFilePath")) {
runningFilePath = parser.getFirstToken(arguments);
} else if (checker.compare(
this.getClass(),
"Sets the output file paths",
"[file paths]",
commandName,
"setOutputFilePaths")) {
int num = parser.getNumberOfTokens(arguments);
outputFilePaths = new String[num];
if (num > 0) outputFilePaths[0] = parser.getFirstToken();
for (int i = 1; i < num; i++) outputFilePaths[i] = parser.getNextToken();
}
return null;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets module supplying characters",
"[name of module]",
commandName,
"setCharacterSource")) {
CharacterObedSource newCharacterSourceTask;
if (hiringCondition != null)
newCharacterSourceTask =
(CharacterObedSource)
replaceCompatibleEmployee(
CharacterObedSource.class,
arguments,
characterSourceTask,
hiringCondition); // , "Source of characters"
else
newCharacterSourceTask =
(CharacterObedSource)
replaceEmployee(
CharacterObedSource.class,
arguments,
"Source of characters",
characterSourceTask);
if (newCharacterSourceTask != null) {
characterSourceTask = newCharacterSourceTask;
characterSourceTask.setHiringCommand(cstC);
charSourceName.setValue(characterSourceTask.getName());
resetContainingMenuBar();
parametersChanged();
return characterSourceTask;
} else {
discreetAlert(
"Unable to activate character source \""
+ arguments
+ "\" for use by "
+ employer.getName());
}
} else if (characterSourceTask != null) { // todo: temporary, for snapshot conversions
return characterSourceTask.doCommand(commandName, arguments, checker);
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Hires the ExternalProcessRunner",
"[name of module]",
commandName,
"setExternalProcessRunner")) {
ExternalProcessRunner temp =
(ExternalProcessRunner)
replaceEmployee(
ExternalProcessRunner.class,
arguments,
"External Process Runner",
externalProcRunner);
if (temp != null) {
externalProcRunner = temp;
parametersChanged();
}
externalProcRunner.setProcessRequester(this);
return externalProcRunner;
} else return super.doCommand(commandName, arguments, checker);
}
/*.................................................................................................................*/
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;
}