/**
* Places into Color array the colors at the node, and returns the number of colors. Uses passed
* stateColors as color key. If null is passed, uses color system of parent data (using maxState
* of this StsOfCharcter) or, if there is not parent data object, the default colors.
*/
public int getColorsAtNode(
int node, ColorDistribution colors, MesquiteColorTable stateColors, boolean showWeights) {
int numBinBoundaries = 10;
double[] binBoundaries = stateColors.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
for (int i = 0; i < 10; i++) colors.initialize();
if (getNumItems() == 1) {
double s = firstItem.getValue(node);
colors.setWeight(0, 1.0);
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, ColorDistribution.unassigned);
else {
int place =
getPlace(s, stateColors); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(0, stateColors.getColor(numBinBoundaries, place));
}
} else {
for (int i = 0; i < getNumItems(); i++) {
double s = getState(node, i);
colors.setWeight(i, 1.0 / getNumItems());
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, ColorDistribution.unassigned);
else {
int place =
getPlace(
s, stateColors); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(i, stateColors.getColor(numBinBoundaries, place));
}
}
}
return getNumItems();
}
/*..........................................ContinuousHistory................*/
public int getLegendStates(
Color[] cs, String[] stateNames, Point[] tableMappings, MesquiteColorTable stateColors) {
int colorCount = 0;
int numBinBoundaries = 10;
double[] binBoundaries = stateColors.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
for (int e = 0; e <= numBinBoundaries; e++) {
if (binBoundaries == null) {
double rangeUnit = (maxState - minState) * 1.0 / numBinBoundaries;
cs[colorCount] = stateColors.getColor(numBinBoundaries, e);
if (tableMappings != null) tableMappings[colorCount] = new Point(numBinBoundaries, e);
stateNames[colorCount++] =
MesquiteDouble.toString(minState + rangeUnit * e)
+ " to "
+ MesquiteDouble.toString(minState + rangeUnit * (e + 1));
} else {
double localMin, localMax;
int localE;
int localNumBoundaries;
// here look for closest defined bin boundaries
localMin = minState;
localMax = MesquiteDouble.unassigned;
int localMinK = -1;
int localMaxK = numBinBoundaries;
for (int k = 0; k < numBinBoundaries; k++) {
if (MesquiteDouble.isCombinable(binBoundaries[k])) {
if (k < e) {
localMin = binBoundaries[k];
localMinK = k;
} else if (!MesquiteDouble.isCombinable(localMax)) {
localMax = binBoundaries[k];
localMaxK = k;
}
}
}
if (!MesquiteDouble.isCombinable(localMax)) localMax = maxState;
if (localMax < localMin) localMax = localMin;
localE = e - localMinK - 1;
localNumBoundaries = localMaxK - localMinK;
double rangeUnit = (localMax - localMin) * 1.0;
if (localNumBoundaries != 0) rangeUnit = rangeUnit / localNumBoundaries;
cs[colorCount] = stateColors.getColor(numBinBoundaries, e);
if (tableMappings != null) tableMappings[colorCount] = new Point(numBinBoundaries, e);
stateNames[colorCount++] =
MesquiteDouble.toString(localMin + rangeUnit * localE)
+ " to "
+ MesquiteDouble.toString(localMin + rangeUnit * (localE + 1));
}
}
return colorCount;
}
/*..........................................MContinuousStates................*/
public boolean allCombinable(int item) {
for (int ic = 0; ic < getNumChars(); ic++)
for (int it = 0; it < getNumNodes(); it++) {
if (!MesquiteDouble.isCombinable(getState(ic, it, item))) return false;
}
return true;
}
double sumSqFILTERED(double[][] m, double mean) {
double sumSq = 0;
for (int i = 0; i < m.length; i++)
for (int j = 0; j < i; j++) {
double d = m[i][j];
if (d >= -0.0000000001 && MesquiteDouble.isCombinable(d)) sumSq += (d - mean) * (d - mean);
}
return sumSq;
}
/**
* places into the already instantiated ColorDistribution the colors corresponding to the
* CharacterState, and returns the number of colors. Uses default colors. Mode is
* MesquiteColorTable.GRAYSCALE, COLORS, COLORS_NO_BW, or DEFAULT (default depends on subclass)
*/
public int getColorsOfState(
CharacterState state, ColorDistribution colors, MesquiteColorTable colorTable) {
if (colors == null || state == null || !(state instanceof ContinuousState)) return 0;
int numBinBoundaries = 10;
double[] binBoundaries = colorTable.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
colors.initialize();
ContinuousState cState = (ContinuousState) state;
if (cState.getNumItems() == 1) {
double s = cState.getValue(0);
colors.setWeight(0, 1.0);
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, Color.white);
else {
int place =
getPlace(s, colorTable); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(
0,
colorTable.getColor(
numBinBoundaries, place)); // bug fixed in 1. 12 that had been introduced in 1. 10
// colors.setColor(0, colorTable.getColor(s, minState, maxState)); 1.10 to 1.11
}
} else {
for (int i = 0; i < cState.getNumItems(); i++) {
double s = cState.getValue(i);
colors.setWeight(i, 1.0 / cState.getNumItems());
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, Color.white);
else {
int place =
getPlace(
s, colorTable); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(
i,
colorTable.getColor(
numBinBoundaries, place)); // bug fixed in 1. 12 that had been introduced in 1. 10
// colors.setColor(i, colorTable.getColor(s, minState, maxState)); 1.10 to 1.11
}
}
}
return cState.getNumItems();
}
/*.......................................... ContinuousHistory ..................................................*/
public int getPlace(double d, MesquiteColorTable colorTable) {
int numBinBoundaries = 10;
double[] binBoundaries = colorTable.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
else return (int) (((d - minState) / (maxState - minState)) * numBinBoundaries);
for (int e = 0; e <= numBinBoundaries; e++) {
double localMin, localMax;
int localE;
int localNumBoundaries;
// here look for closest defined bin boundaries
localMin = minState;
localMax = MesquiteDouble.unassigned;
int localMinK = -1;
int localMaxK = numBinBoundaries;
for (int k = 0; k < numBinBoundaries; k++) {
if (MesquiteDouble.isCombinable(binBoundaries[k])) {
if (k < e) {
localMin = binBoundaries[k];
localMinK = k;
} else if (!MesquiteDouble.isCombinable(localMax)) {
localMax = binBoundaries[k];
localMaxK = k;
}
}
}
if (!MesquiteDouble.isCombinable(localMax)) localMax = maxState;
if (localMax < localMin) localMax = localMin;
localE = e - localMinK - 1;
localNumBoundaries = localMaxK - localMinK;
double rangeUnit = (localMax - localMin) * 1.0;
if (localNumBoundaries != 0) rangeUnit = rangeUnit / localNumBoundaries;
if (d <= localMin + rangeUnit * (localE + 1)) // d > localMin + rangeUnit*localE &&
return e;
}
return numBinBoundaries;
}
/*.......................................... ContinuousHistory ..................................................*/
public double getBinBoundary(int i, MesquiteColorTable colorTable) { // the boundary after bin i
int numBinBoundaries = 10;
double[] binBoundaries = colorTable.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
else return minState + (i + 1) * (maxState - minState) / numBinBoundaries;
double localMin, localMax;
int localE;
localMin = minState;
localMax = MesquiteDouble.unassigned;
int localNumBoundaries;
int localMinK = -1;
int localMaxK = numBinBoundaries;
for (int k = 0;
k < numBinBoundaries;
k++) { // what are the defined boundaries on either side of i?
if (MesquiteDouble.isCombinable(binBoundaries[k])) {
if (k < i) {
localMin = binBoundaries[k];
localMinK = k;
} else if (!MesquiteDouble.isCombinable(localMax)) {
localMax = binBoundaries[k];
localMaxK = k;
}
}
}
if (!MesquiteDouble.isCombinable(localMax)) localMax = maxState;
if (localMax < localMin) localMax = localMin;
localE = i - localMinK - 1;
localNumBoundaries = localMaxK - localMinK;
double rangeUnit = (localMax - localMin) * 1.0;
if (localNumBoundaries > 0) rangeUnit = rangeUnit / localNumBoundaries;
return localMin + rangeUnit * (localE + 1);
}
double meanFILTERED(double[][] m) {
double sum = 0;
int n = 0;
for (int i = 0; i < m.length; i++)
for (int j = 0; j < i; j++) {
double d = m[i][j];
if (d >= -0.0000000001 && MesquiteDouble.isCombinable(d)) {
sum += d;
n++;
}
}
if (n == 0) return MesquiteDouble.unassigned;
return sum / n;
}
// by filtered means -ve and uncombinable numbers excluded
double offDiagonalPMCorrelationFILTERED(double[][] m1, double[][] m2) {
if (m1 == null || m2 == null) return MesquiteDouble.unassigned;
double mean1 = meanFILTERED(m1);
double mean2 = meanFILTERED(m2);
if (!MesquiteDouble.isCombinable(mean1) || !MesquiteDouble.isCombinable(mean2))
return MesquiteDouble.unassigned;
double sumSq1 = sumSqFILTERED(m1, mean1);
double sumSq2 = sumSqFILTERED(m2, mean2);
double sumProd = 0;
for (int i = 0; i < m1.length; i++)
for (int j = 0; j < i; j++) {
double d1 = m1[i][j];
double d2 = m2[i][j];
if (d1 >= -0.0000000001
&& MesquiteDouble.isCombinable(d1)
&& d2 >= -0.0000000001
&& MesquiteDouble.isCombinable(d2)) sumProd += (d1 - mean1) * (d2 - mean2);
}
if (sumSq1 == 0 || sumSq2 == 0) return MesquiteDouble.unassigned;
return sumProd / Math.sqrt(sumSq1 * sumSq2);
}
void reinterpret(MesquiteTree tree, int node) {
if (tree.nodeIsInternal(node)) {
if (tree.nodeHasLabel(node)) {
String label = tree.getNodeLabel(node);
if (isNumber) {
double d = MesquiteDouble.fromString(label);
if (MesquiteDouble.isCombinable(d))
tree.setAssociatedDouble(nameRef, node, d, appliesToBranch);
} else {
tree.setAssociatedObject(nameRef, node, label, appliesToBranch);
}
if (deleteAfter) tree.setNodeLabel(null, node);
}
for (int daughter = tree.firstDaughterOfNode(node);
tree.nodeExists(daughter);
daughter = tree.nextSisterOfNode(daughter)) {
reinterpret(tree, daughter);
}
}
}
/*.................................................................................................................*/
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;
}
/*.......................................... ..................................................*/
public boolean legalValue(int ic, double states) {
return !MesquiteDouble.isCombinable(states)
|| ((ic == LATITUDE && states >= -90.0 && states <= 90.0)
|| (ic == LONGITUDE && states >= -180.0 && states <= 180.0));
}