/*.................................................................................................................*/
public String getStringForTree(int ic) {
if (treesBlock == null) return "";
Tree tree = treesBlock.getTree(ic);
if (tree == null) return "";
if (tree.hasPolytomies(tree.getRoot())) return "Yes";
else return "No";
}
/*..........................................ContinuousHistory................*/
private void fillDistribution(Tree tree, int node, ContinuousAdjustable dist) {
if (tree.nodeIsTerminal(node)) {
int t = tree.taxonNumberOfNode(node);
for (int i = 0; i < getNumItems(); i++) dist.setState(t, i, getState(node, i));
} else
for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d))
fillDistribution(tree, d, dist);
}
/*..........................................ContinuousHistory................*/
public void calcMinMaxStates(Tree tree, int node) {
for (int i = 0; i < getNumItems(); i++) {
double s = getState(node, i);
maxState = MesquiteDouble.maximum(maxState, s);
minState = MesquiteDouble.minimum(minState, s);
}
for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d))
calcMinMaxStates(tree, d);
}
/**
* Returns a new object indicating the states at the tips (used whether or not History is
* reconstruction)
*/
public CharacterDistribution getStatesAtTips(Tree tree) {
if (observedStates != null) return (CharacterDistribution) observedStates.getAdjustableClone();
else {
ContinuousAdjustable d =
new ContinuousAdjustable(tree.getTaxa(), tree.getTaxa().getNumTaxa());
d.setItemsAs(this);
fillDistribution(tree, tree.getRoot(), d);
return d;
}
}
/**
* This readjust procedure can be called to readjust the size of storage of states of a character
* for nodes.
*/
public CharacterHistory adjustSize(Tree tree) {
if (tree.getNumNodeSpaces() == this.getNumNodes()) return this;
else {
ContinuousHistory soc =
new ContinuousHistory(
tree.getTaxa(), tree.getNumNodeSpaces(), (ContinuousData) getParentData());
soc.setItemsAs(this);
soc.setParentData(getParentData());
soc.setParentCharacter(getParentCharacter());
((CharacterStates) soc).setExplanation(getExplanation());
return soc;
}
}
/*.................................................................................................................*/
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 void calculateNumber(
Tree tree1, Tree tree2, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
if (tree1 == null) return;
if (tree2 == null) return;
int numTaxa = tree1.getTaxa().getNumTaxa();
double[][] patristic1 = null;
patristic1 =
p1.calculatePatristic(
tree1,
numTaxa,
patristic1); // for this tree calculate patristic distances (number of nodes separating
// terminals; no branch lengths)
double[][] patristic2 = null;
patristic2 =
p2.calculatePatristic(
tree2,
numTaxa,
patristic2); // for this tree calculate patristic distances (number of nodes separating
// terminals; no branch lengths)
double correl = offDiagonalPMCorrelationFILTERED(patristic1, patristic2);
if (isDistance && (MesquiteDouble.isCombinable(correl)))
correl = -correl + 1.0; // shifting 1 to -1 to be 0 to 2 to act as distance
result.setValue(correl);
if (resultString != null) {
if (isDistance)
resultString.setValue(
"Patristic correlation (converted to distance): " + result.toString());
else resultString.setValue("Patristic correlation: " + result.toString());
}
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
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;
}
/** gets the current matrix. */
public CharacterDistribution getCurrentCharacter(Tree tree) {
if (tree == null) return null;
else return getCurrentCharacter(tree.getTaxa());
}
/* -- the following are a preliminary attempt to allow matrix sources to know exactly what tree the
matrix will be used with. These can be overridden by modules to do simulations on the trees, or to see if there
is a simulated matrix attached to the tree, or what ---*/
public void initialize(Tree tree) {
if (tree == null) return;
else initialize(tree.getTaxa());
}
/*.................................................................................................................*/
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;
}