// 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);
}
/*.................................................................................................................*/
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;
}