public MatrixZoomData getControlZd() {
Matrix matrix = getControlMatrix();
if (matrix == null || currentZoom == null) {
return null;
} else {
return matrix.getZoomData(currentZoom);
}
}
public MatrixZoomData getZd() throws UninitializedObjectException {
Matrix matrix = getMatrix();
if (matrix == null) {
throw new UninitializedObjectException("Uninitialized matrix");
} else if (currentZoom == null) {
throw new UninitializedObjectException("Uninitialized zoom");
} else {
return matrix.getZoomData(currentZoom);
}
}
public void applyMatricesToVertices(MDL mdlr) {
int sz = numVerteces();
for (int i = 0; i < sz; i++) {
GeosetVertex gv = vertex.get(i);
gv.clearBoneAttachments();
Matrix mx = getMatrix(gv.getVertexGroup());
mx.updateIds(mdlr);
int szmx = mx.size();
for (int m = 0; m < szmx; m++) {
gv.addBoneAttachment((Bone) mdlr.getIdObject(mx.getBoneId(m)));
}
}
}
public void applyVerticesToMatrices(MDL mdlr) {
matrix.clear();
for (int i = 0; i < vertex.size(); i++) {
Matrix newTemp = new Matrix(vertex.get(i).bones);
boolean newMatrix = true;
for (int m = 0; m < matrix.size() && newMatrix; m++) {
if (newTemp.equals(matrix.get(m))) {
newTemp = matrix.get(m);
newMatrix = false;
}
}
if (newMatrix) {
matrix.add(newTemp);
newTemp.updateIds(mdlr);
}
vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
vertex.get(i).setMatrix(newTemp);
}
}
private void unsafeSave1DTrackToWigFile(
Chromosome chromosomeForPosition, PrintWriter printWriter, int binStartPosition)
throws IOException {
int resolution = getZoom().getBinSize();
for (Chromosome chromosome : chromosomes) {
if (chromosome.getName().equals(Globals.CHR_ALL)) continue;
Matrix matrix = null;
if (displayOption == MatrixType.OBSERVED) {
matrix = dataset.getMatrix(chromosomeForPosition, chromosome);
} else if (displayOption == MatrixType.CONTROL) {
matrix = controlDataset.getMatrix(chromosomeForPosition, chromosome);
}
if (matrix == null) continue;
MatrixZoomData zd = matrix.getZoomData(currentZoom);
printWriter.println(
"fixedStep chrom=chr"
+ chromosome.getName().replace("chr", "")
+ " start=1 step="
+ resolution
+ " span="
+ resolution);
int[] regionIndices;
if (chromosomeForPosition.getIndex() < chromosome.getIndex()) {
regionIndices = new int[] {binStartPosition, binStartPosition, 0, chromosome.getLength()};
} else {
regionIndices = new int[] {0, chromosome.getLength(), binStartPosition, binStartPosition};
}
zd.dump1DTrackFromCrossHairAsWig(
printWriter,
chromosomeForPosition,
binStartPosition,
chromosomeForPosition.getIndex() == chromosome.getIndex(),
regionIndices,
normalizationType,
displayOption,
getExpectedValues());
}
}
public static void main(String[] args) throws Exception {
fw = new FileWriter("/Users/Main/Desktop/test.csv", false); // ※１
pw = new PrintWriter(new BufferedWriter(fw));
for (range = 1; range < 1000000; range *= 2) {
for (int j = 0; j < 3; j++) {
for (int i = 0; i < 1; i++) {
Vector X = Vector.generate(n, range);
Matrix A = Matrix.generate(n, n, range);
Vector B = A.multi(X);
pw.print(range);
pw.print(",");
pw.print(n);
System.out.println(n);
analysisGaussianEliminationWithPivot(A, B, X);
System.out.println();
}
}
}
pw.close();
}
public void updateToObjects(MDL mdlr) {
// upload the temporary UVLayer and Matrix objects into the vertices themselves
int sz = numVerteces();
for (Matrix m : matrix) {
m.updateBones(mdlr);
}
for (int i = 0; i < sz; i++) {
GeosetVertex gv = vertex.get(i);
gv.clearTVerts();
int szuv = uvlayers.size();
for (int l = 0; l < szuv; l++) {
try {
gv.addTVertex(uvlayers.get(l).getTVertex(i));
} catch (Exception e) {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(),
"Error: Length of TVertices and Vertices chunk differ (Or some other unknown error has occurred)!");
}
}
Matrix mx = getMatrix(gv.getVertexGroup());
int szmx = mx.size();
gv.clearBoneAttachments();
for (int m = 0; m < szmx; m++) {
gv.addBoneAttachment((Bone) mdlr.getIdObject(mx.getBoneId(m)));
}
gv.setNormal(normals.get(i));
for (Triangle t : triangle) {
if (t.containsRef(gv)) {
gv.triangles.add(t);
}
}
gv.geoset = this;
// gv.addBoneAttachment(null);//Why was this here?
}
try {
material = mdlr.getMaterial(materialID);
} catch (ArrayIndexOutOfBoundsException e) {
JOptionPane.showMessageDialog(null, "Error: Material index out of bounds for geoset!");
}
parentModel = mdlr;
}
/**
* Compute the bounding screen extent of a rotated rectangle.
*
* @param rect Rectangle to rotate.
* @param x X coordinate of the rotation point.
* @param y Y coordinate of the rotation point.
* @param rotation Rotation angle.
* @return The smallest rectangle that completely contains {@code rect} when rotated by the
* specified angle.
*/
protected Rectangle computeRotatedScreenExtent(Rectangle rect, int x, int y, Angle rotation) {
Rectangle r = new Rectangle(rect);
// Translate the rectangle to the rotation point.
r.translate(-x, -y);
// Compute corner points
Vec4[] corners = {
new Vec4(r.getMaxX(), r.getMaxY()),
new Vec4(r.getMaxX(), r.getMinY()),
new Vec4(r.getMinX(), r.getMaxY()),
new Vec4(r.getMinX(), r.getMinY())
};
// Rotate the rectangle
Matrix rotationMatrix = Matrix.fromRotationZ(rotation);
for (int i = 0; i < corners.length; i++) {
corners[i] = corners[i].transformBy3(rotationMatrix);
}
// Find the bounding rectangle of rotated points.
int minX = Integer.MAX_VALUE;
int minY = Integer.MAX_VALUE;
int maxX = -Integer.MAX_VALUE;
int maxY = -Integer.MAX_VALUE;
for (Vec4 v : corners) {
if (v.x > maxX) maxX = (int) v.x;
if (v.x < minX) minX = (int) v.x;
if (v.y > maxY) maxY = (int) v.y;
if (v.y < minY) minY = (int) v.y;
}
// Set bounds and translate the rectangle back to where it started.
r.setBounds(minX, minY, maxX - minX, maxY - minY);
r.translate(x, y);
return r;
}
public static void analysisGaussianEliminationWithPivot(Matrix A, Vector B, Vector X) {
System.out.println("GaussianElimination");
pw.print(",");
pw.print("GaussianElimination");
analysis(
X,
() -> {
try {
return Algorithm.gaussianEliminationWithPivot(A.toDoubleArray(), B.toDoubleArray());
} catch (Exception e) {
e.printStackTrace();
pw.print(",");
pw.print("-");
pw.print(",");
pw.print("-");
pw.println();
return new double[0];
}
});
}
public void doSavePrep(MDL mdlr) {
purifyFaces();
// Normals cleared here, in case that becomes a problem later.
normals.clear();
// UV Layers cleared here
uvlayers.clear();
int bigNum = 0;
int littleNum = -1;
for (int i = 0; i < vertex.size(); i++) {
int temp = vertex.get(i).tverts.size();
if (temp > bigNum) {
bigNum = temp;
}
if (littleNum == -1 || temp < littleNum) {
littleNum = temp;
}
}
if (littleNum != bigNum) {
JOptionPane.showMessageDialog(
null,
"Error: Attempting to save a Geoset with Verteces that have differing numbers of TVertices! Empty TVertices will be autogenerated.");
}
for (int i = 0; i < bigNum; i++) {
uvlayers.add(new UVLayer());
}
for (int i = 0; i < vertex.size(); i++) {
normals.add(vertex.get(i).getNormal());
for (int uv = 0; uv < bigNum; uv++) {
TVertex temp = vertex.get(i).getTVertex(uv);
if (temp != null) {
uvlayers.get(uv).addTVertex(temp);
} else {
uvlayers.get(uv).addTVertex(new TVertex(0, 0));
}
}
}
// Clearing matrix list
matrix.clear();
for (int i = 0; i < vertex.size(); i++) {
Matrix newTemp = new Matrix(vertex.get(i).bones);
boolean newMatrix = true;
for (int m = 0; m < matrix.size() && newMatrix; m++) {
if (newTemp.equals(matrix.get(m))) {
newTemp = matrix.get(m);
newMatrix = false;
}
}
if (newMatrix) {
matrix.add(newTemp);
newTemp.updateIds(mdlr);
}
vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
vertex.get(i).setMatrix(newTemp);
}
for (int i = 0; i < triangle.size(); i++) {
triangle.get(i).updateVertexIds(this);
}
int boneRefCount = 0;
for (int i = 0; i < matrix.size(); i++) {
boneRefCount += matrix.get(i).bones.size();
}
for (int i = 0; i < matrix.size(); i++) {
matrix.get(i).updateIds(mdlr);
}
}
public void printTo(PrintWriter writer, MDL mdlr, boolean trianglesTogether) {
purifyFaces();
writer.println("Geoset {");
writer.println("\tVertices " + vertex.size() + " {");
String tabs = "\t\t";
// Normals cleared here, in case that becomes a problem later.
normals.clear();
// UV Layers cleared here
uvlayers.clear();
int bigNum = 0;
int littleNum = -1;
for (int i = 0; i < vertex.size(); i++) {
int temp = vertex.get(i).tverts.size();
if (temp > bigNum) {
bigNum = temp;
}
if (littleNum == -1 || temp < littleNum) {
littleNum = temp;
}
}
if (littleNum != bigNum) {
JOptionPane.showMessageDialog(
null,
"Error: Attempting to save a Geoset with Verteces that have differing numbers of TVertices! Empty TVertices will be autogenerated.");
}
for (int i = 0; i < bigNum; i++) {
uvlayers.add(new UVLayer());
}
for (int i = 0; i < vertex.size(); i++) {
writer.println(tabs + vertex.get(i).toString() + ",");
normals.add(vertex.get(i).getNormal());
for (int uv = 0; uv < bigNum; uv++) {
try {
TVertex temp = vertex.get(i).getTVertex(uv);
if (temp != null) {
uvlayers.get(uv).addTVertex(temp);
} else {
uvlayers.get(uv).addTVertex(new TVertex(0, 0));
}
} catch (IndexOutOfBoundsException e) {
uvlayers.get(uv).addTVertex(new TVertex(0, 0));
}
}
}
writer.println("\t}");
writer.println("\tNormals " + normals.size() + " {");
for (int i = 0; i < normals.size(); i++) {
writer.println(tabs + normals.get(i).toString() + ",");
}
writer.println("\t}");
for (int i = 0; i < uvlayers.size(); i++) {
uvlayers.get(i).printTo(writer, 1, true);
}
// Clearing matrix list
matrix.clear();
writer.println("\tVertexGroup {");
for (int i = 0; i < vertex.size(); i++) {
Matrix newTemp = new Matrix(vertex.get(i).bones);
boolean newMatrix = true;
for (int m = 0; m < matrix.size() && newMatrix; m++) {
if (newTemp.equals(matrix.get(m))) {
newTemp = matrix.get(m);
newMatrix = false;
}
}
if (newMatrix) {
matrix.add(newTemp);
newTemp.updateIds(mdlr);
}
vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
vertex.get(i).setMatrix(newTemp);
writer.println(tabs + vertex.get(i).VertexGroup + ",");
}
writer.println("\t}");
if (trianglesTogether) {
writer.println("\tFaces 1 " + (triangle.size() * 3) + " {");
writer.println("\t\tTriangles {");
String triangleOut = "\t\t\t{ ";
for (int i = 0; i < triangle.size(); i++) {
triangle.get(i).updateVertexIds(this);
if (i != triangle.size() - 1) {
triangleOut = triangleOut + triangle.get(i).toString() + ", ";
} else {
triangleOut = triangleOut + triangle.get(i).toString() + " ";
}
}
writer.println(triangleOut + "},");
writer.println("\t\t}");
} else {
writer.println("\tFaces " + triangle.size() + " " + (triangle.size() * 3) + " {");
writer.println("\t\tTriangles {");
String triangleOut = "\t\t\t{ ";
for (int i = 0; i < triangle.size(); i++) {
triangle.get(i).updateVertexIds(this);
writer.println(triangleOut + triangle.get(i).toString() + " },");
}
writer.println("\t\t}");
}
writer.println("\t}");
int boneRefCount = 0;
for (int i = 0; i < matrix.size(); i++) {
boneRefCount += matrix.get(i).bones.size();
}
writer.println("\tGroups " + matrix.size() + " " + boneRefCount + " {");
for (int i = 0; i < matrix.size(); i++) {
matrix.get(i).updateIds(mdlr);
matrix.get(i).printTo(writer, 2); // 2 is the tab height
}
writer.println("\t}");
if (extents != null) extents.printTo(writer, 1);
for (int i = 0; i < anims.size(); i++) {
anims.get(i).printTo(writer, 1);
}
writer.println("\tMaterialID " + materialID + ",");
writer.println("\tSelectionGroup " + selectionGroup + ",");
for (int i = 0; i < flags.size(); i++) {
writer.println("\t" + flags.get(i) + ",");
}
writer.println("}");
}
public static Geoset read(BufferedReader mdl) {
String line = MDLReader.nextLine(mdl);
System.out.println("geo begins with " + line);
if (line.contains("Geoset")) {
line = MDLReader.nextLine(mdl);
Geoset geo = new Geoset();
if (!line.contains("Vertices")) {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(), "Error: Vertices not found at beginning of Geoset!");
}
while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
geo.addVertex(GeosetVertex.parseText(line));
}
line = MDLReader.nextLine(mdl);
if (line.contains("Normals")) {
// If we have normals:
while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
geo.addNormal(Normal.parseText(line));
}
}
while (((line = MDLReader.nextLine(mdl)).contains("TVertices"))) {
geo.addUVLayer(UVLayer.read(mdl));
}
if (!line.contains("VertexGroup")) {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(), "Error: VertexGroups missing or invalid!");
}
int i = 0;
while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
geo.getVertex(i).setVertexGroup(MDLReader.readInt(line));
i++;
}
line = MDLReader.nextLine(mdl);
if (!line.contains("Faces")) {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(), "Error: Faces missing or invalid!");
}
line = MDLReader.nextLine(mdl);
if (!line.contains("Triangles")) {
System.out.println(line);
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(), "Error: Triangles missing or invalid!");
}
geo.setTriangles(Triangle.read(mdl, geo));
line = MDLReader.nextLine(mdl); // Throw away the \t} closer for faces
line = MDLReader.nextLine(mdl);
if (!line.contains("Groups")) {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(), "Error: Groups (Matrices) missing or invalid!");
}
while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
geo.addMatrix(Matrix.parseText(line));
}
MDLReader.mark(mdl);
line = MDLReader.nextLine(mdl);
while (!line.contains("}") || line.contains("},")) {
if (line.contains("Extent") || line.contains("BoundsRadius")) {
System.out.println("Parsing geoset extLog:" + line);
MDLReader.reset(mdl);
geo.setExtLog(ExtLog.read(mdl));
System.out.println("Completed geoset extLog.");
} else if (line.contains("Anim")) {
MDLReader.reset(mdl);
geo.add(Animation.read(mdl));
MDLReader.mark(mdl);
} else if (line.contains("MaterialID")) {
geo.materialID = MDLReader.readInt(line);
MDLReader.mark(mdl);
} else if (line.contains("SelectionGroup")) {
geo.selectionGroup = MDLReader.readInt(line);
MDLReader.mark(mdl);
} else {
geo.addFlag(MDLReader.readFlag(line));
System.out.println("Reading to geoFlag: " + line);
MDLReader.mark(mdl);
}
line = MDLReader.nextLine(mdl);
}
// JOptionPane.showMessageDialog(MDLReader.getDefaultContainer(),"Geoset reading
// completed!");
System.out.println("Geoset reading completed!");
return geo;
} else {
JOptionPane.showMessageDialog(
MDLReader.getDefaultContainer(),
"Unable to parse Geoset: Missing or unrecognized open statement '" + line + "'.");
}
return null;
}
private static void addSprites(Compositor sh) throws IOException, QTException {
File matchFile =
QTFactory.findAbsolutePath("images/Ship01.pct"); // this file must exist in the directory!!!
ImageDataSequence isp = ImageUtil.createSequence(matchFile);
ImageDataSequence seq = ImageUtil.makeTransparent(isp, QDColor.blue);
// Build Sprites
Matrix matrix1 = new Matrix();
matrix1.setTx(20);
matrix1.setTy(20);
matrix1.setSx(0.8F);
matrix1.setSy(0.8F);
TwoDSprite s1 = new TwoDSprite(seq, 4, matrix1, true, 1);
sh.addMember(s1);
Matrix matrix2 = new Matrix();
matrix2.setTx(4);
matrix2.setTy(4);
TwoDSprite s2 = new TwoDSprite(seq, 1, matrix2, true, 10);
sh.addMember(s2);
// This needs to be a 32bit QDGraphics so the blend mode will
// be applied correctly to this sprite
File shipFile = QTFactory.findAbsolutePath("images/Ship10.pct");
GraphicsImporterDrawer ip = new GraphicsImporterDrawer(new QTFile(shipFile));
QDRect r = new QDRect(ip.getDescription().getWidth(), ip.getDescription().getHeight());
ImageSpec si =
ImageUtil.makeTransparent(
ip, QDColor.blue, new QDGraphics(QDGraphics.kDefaultPixelFormat, r));
Matrix matrix3 = new Matrix();
matrix3.setTx(50);
matrix3.setTy(50);
TwoDSprite s3 =
new TwoDSprite(si, matrix3, true, 8, new GraphicsMode(QDConstants.blend, QDColor.green));
sh.addMember(s3);
// Add Dragger (DEPRECATED CODE)
/* Dragger dragger = new Dragger (InputEvent.SHIFT_MASK);
SWController controller = new SWController (dragger, true);
sh.addController (controller);*/
QTMouseTargetController shipController = new QTMouseTargetController(true);
shipController.addQTMouseListener(
new DragAction(new TranslateMatrix()) {
// only activates when the shift modifier is pressed
public boolean matchModifierFilter(int mods) {
if ((mods & 0xF) == QTConstants.kJavaShiftMask) return true;
return false;
}
});
sh.addController(shipController);
// Add Controllers
// Build ActionList
SimpleActionList al = new SimpleActionList();
ImageSequencer is = new ImageSequencer(seq);
is.setLooping(ImageSequencer.kLoopForwards);
al.addMember(new NextImageAction(10, 1, is, s1));
al.addMember(new BounceAction(5, 1, sh, s1, 3, 2));
ImageSequencer is2 = new ImageSequencer(seq);
is2.setLooping(ImageSequencer.kLoopForwards);
al.addMember(new NextImageAction(20, 1, is2, s2));
al.addMember(new BounceAction(20, 1, sh, s2, 4, 3));
sh.addController(al);
}
/**
* Compute the label's screen position from its geographic position.
*
* @param dc Current draw context.
*/
protected void computeGeometry(DrawContext dc) {
// Project the label position onto the viewport
Position pos = this.getPosition();
if (pos == null) return;
this.placePoint = dc.computeTerrainPoint(pos.getLatitude(), pos.getLongitude(), 0);
this.screenPlacePoint = dc.getView().project(this.placePoint);
this.eyeDistance = this.placePoint.distanceTo3(dc.getView().getEyePoint());
boolean orientationReversed = false;
if (this.orientationPosition != null) {
// Project the orientation point onto the screen
Vec4 orientationPlacePoint =
dc.computeTerrainPoint(
this.orientationPosition.getLatitude(), this.orientationPosition.getLongitude(), 0);
Vec4 orientationScreenPoint = dc.getView().project(orientationPlacePoint);
this.rotation = this.computeRotation(this.screenPlacePoint, orientationScreenPoint);
// The orientation is reversed if the orientation point falls to the right of the screen
// point. Text is
// never drawn upside down, so when the orientation is reversed the text flips vertically to
// keep the text
// right side up.
orientationReversed = (orientationScreenPoint.x <= this.screenPlacePoint.x);
}
this.computeBoundsIfNeeded(dc);
Offset offset = this.getOffset();
Point2D offsetPoint =
offset.computeOffset(this.bounds.getWidth(), this.bounds.getHeight(), null, null);
// If a rotation is applied to the text, then rotate the offset as well. An offset in the x
// direction
// will move the text along the orientation line, and a offset in the y direction will move the
// text
// perpendicular to the orientation line.
if (this.rotation != null) {
double dy = offsetPoint.getY();
// If the orientation is reversed we need to adjust the vertical offset to compensate for the
// flipped
// text. For example, if the offset normally aligns the top of the text with the place point
// then without
// this adjustment the bottom of the text would align with the place point when the
// orientation is
// reversed.
if (orientationReversed) {
dy = -(dy + this.bounds.getHeight());
}
Vec4 pOffset = new Vec4(offsetPoint.getX(), dy);
Matrix rot = Matrix.fromRotationZ(this.rotation.multiply(-1));
pOffset = pOffset.transformBy3(rot);
offsetPoint = new Point((int) pOffset.getX(), (int) pOffset.getY());
}
int x = (int) (this.screenPlacePoint.x + offsetPoint.getX());
int y = (int) (this.screenPlacePoint.y - offsetPoint.getY());
this.screenPoint = new Point(x, y);
this.screenExtent = this.computeTextExtent(x, y, this.rotation);
}
/**
* Constructor
*
* @param f1 FPoint2
* @param f2 FPoint2
* @param pt FPoint2, or null for bisector
*/
private void construct(FPoint2 f1, FPoint2 f2, FPoint2 pt) {
// userData[LEFT] = new DArray();
// userData[RIGHT] =new DArray();
final boolean db = false;
if (db) {
System.out.println("Hyperbola constructor\n f1=" + f1 + "\n f2=" + f2 + "\n pt=" + pt);
}
boolean bisector = (pt == null);
initializeVisibleSegments();
// if point on arm is closer to f2 than f1, swap f1 & f2.
if (!bisector && FPoint2.distanceSquared(f1, pt) > FPoint2.distanceSquared(f2, pt)) {
flipped = true;
}
this.foci[RIGHT] = new FPoint2(f1);
this.foci[LEFT] = new FPoint2(f2);
if (!bisector) {
this.pt = new FPoint2(pt);
}
double fociDist = FPoint2.distance(f1, f2);
if (fociDist == 0) {
throw new FPError("Hyperbola foci are same point");
}
c = fociDist * .5;
// calculate the translation of the hyperbola away from
// standard position.
FPoint2 rFocus = getFocus(0), lFocus = getFocus(1);
origin = new FPoint2(.5 * (rFocus.x + lFocus.x), .5 * (rFocus.y + lFocus.y));
// calculate the angle of rotation of the hyperbola away
// from the standard position.
double theta = Math.atan2(rFocus.y - lFocus.y, rFocus.x - lFocus.x);
Matrix fromCenterInW = Matrix.getTranslate(origin, true);
Matrix rotToE = Matrix.getRotate(-theta);
toE2 = rotToE;
Matrix.mult(toE2, fromCenterInW, toE2);
// calculate inverse
toW2 = toE2.invert(null);
// Matrix toCenterInW = Matrix.translationMatrix(origin, false);
// Matrix rotToW = Matrix.getRotate2D(theta);
//
// toW2 = toCenterInW;
// Matrix.mult(toW2, rotToW, toW2);
// Tools.warn("just invert matrix here");
//
if (bisector) {
valid = true;
} else {
// get the arm point in hyperbola space.
FPoint2 workPt = toE2.apply(pt, null);
double xs = workPt.x * workPt.x;
double cs = c * c;
Polyn q = new Polyn(1, -(cs + xs + workPt.y * workPt.y), cs * xs);
if (db) {
System.out.println("a2 quadratic:\n" + q);
}
final DArray qsoln = new DArray();
q.solve(qsoln);
if (db) {
Streams.out.println(qsoln);
}
double val = q.c(1) * -.5;
int ql = qsoln.size();
if (ql >= 1) {
val = qsoln.getDouble(0);
}
// choose the root that is less than c*c.
if (ql == 2) {
if (val > qsoln.getDouble(1)) {
val = qsoln.getDouble(1);
if (db) {
System.out.println(" two roots, choosing smaller.");
}
}
}
if (db) {
System.out.println(" root chosen=" + val);
}
a = Polyn.sqrt(val);
A = a * a;
B = A / (c * c - A);
}
valid = true;
if (db) {
System.out.println(" ==> " + this);
}
}
/**
* ************************************************************* Official Method for setting the
* zoom and location for heatmap DO NOT IMPLEMENT A NEW FUNCTION Make the necessary
* customizations, then call this function
* *************************************************************
*
* @param newZoom
* @param genomeX
* @param genomeY
* @param scaleFactor (pass -1 if scaleFactor should be calculated)
* @return
*/
public boolean unsafeActuallySetZoomAndLocation(
String chrXName,
String chrYName,
HiCZoom newZoom,
int genomeX,
int genomeY,
double scaleFactor,
boolean resetZoom,
ZoomCallType zoomCallType,
boolean allowLocationBroadcast) {
if (dataset == null) return false; // No data in view
// Check this zoom operation is possible, if not, fail it here:
// if (superAdapter.testNewZoom(newZoom))
// {
// return false;
// }
// String chr1OriginalName = xContext.getChromosome().getName();
// String chr2OriginalName = yContext.getChromosome().getName();
if (chrXName.length() > 0 && chrYName.length() > 0) {
setChromosomesFromBroadcast(chrXName, chrYName);
// We might end with All->All view, make sure normalization state is updates accordingly...
superAdapter.getMainViewPanel().setNormalizationDisplayState(superAdapter.getHiC());
}
if (newZoom == null) {
System.err.println("Invalid zoom " + newZoom);
}
Chromosome chr1 = xContext.getChromosome();
Chromosome chr2 = yContext.getChromosome();
final Matrix matrix = dataset.getMatrix(chr1, chr2);
if (matrix == null) {
superAdapter.launchGenericMessageDialog(
"Sorry, this region is not available", "Matrix unavailable", JOptionPane.WARNING_MESSAGE);
return false;
}
MatrixZoomData newZD = matrix.getZoomData(newZoom);
if (HiCFileTools.isAllChromosome(chr1)) {
newZD = matrix.getFirstZoomData(Unit.BP);
}
if (newZD == null) {
superAdapter.launchGenericMessageDialog(
"Sorry, this zoom is not available", "Zoom unavailable", JOptionPane.WARNING_MESSAGE);
return false;
}
/* TODO Undo Zoom implementation mss2 _UZI
if(currentZoom != null) {
tempZoomState = new ZoomState(chr1OriginalName, chr2OriginalName, currentZoom.clone(), (int) xContext.getBinOrigin(),
(int) yContext.getBinOrigin(), getScaleFactor(), resetZoom, ZoomCallType.GOTO);
}
*/
currentZoom = newZoom;
xContext.setZoom(currentZoom);
yContext.setZoom(currentZoom);
if (scaleFactor > 0) {
setScaleFactor(scaleFactor);
} else {
int maxBinCount =
Math.max(newZD.getXGridAxis().getBinCount(), newZD.getYGridAxis().getBinCount());
double defaultScaleFactor =
Math.max(
1.0, (double) superAdapter.getHeatmapPanel().getMinimumDimension() / maxBinCount);
setScaleFactor(defaultScaleFactor);
}
int binX = newZD.getXGridAxis().getBinNumberForGenomicPosition(genomeX);
int binY = newZD.getYGridAxis().getBinNumberForGenomicPosition(genomeY);
switch (zoomCallType) {
case INITIAL:
case STANDARD:
center(binX, binY);
break;
case DRAG:
xContext.setBinOrigin(binX);
yContext.setBinOrigin(binY);
break;
case DIRECT:
xContext.setBinOrigin(genomeX);
yContext.setBinOrigin(genomeY);
break;
}
// Notify HeatmapPanel render that zoom has changed. Render should update zoom slider once with
// previous range values
setZoomChanged();
if (resetZoom) {
superAdapter.updateAndResetZoom(newZoom);
} else {
superAdapter.updateZoom(newZoom);
}
superAdapter.refresh();
if (linkedMode && allowLocationBroadcast) {
broadcastLocation();
}
/*
TODO Undo Zoom implementation mss2 _UZI
if(zoomCallType == ZoomCallType.INITIAL || tempZoomState == null || chrXName.equals(Globals.CHR_ALL) || chrYName.equals(Globals.CHR_ALL)
|| tempZoomState.chr1Name.equals(Globals.CHR_ALL) || tempZoomState.chr2Name.equals(Globals.CHR_ALL)){
canRedoZoomChange = false;
canUndoZoomChange = false;
}
else {
// defauts for a normal zoom operation
canRedoZoomChange = false;
canUndoZoomChange = true;
previousZoomState = tempZoomState;
}
*/
return true;
}