public MatrixZoomData getControlZd() {
Matrix matrix = getControlMatrix();
if (matrix == null || currentZoom == null) {
return null;
} else {
return matrix.getZoomData(currentZoom);
}
}
public Matrix matrixAbjoint() { // 求伴随矩阵
int i, j;
Matrix matrix = new Matrix();
matrix = Matrix.matrixCopy(this);
matrix = matrix.matrixReverse().matrixNumMultiply(matrix.determinantValue());
return matrix;
}
public Matrix matrixNumMultiply(double x) { // 矩阵乘以一个数
int i, j;
Matrix matrix = new Matrix(this);
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) matrix.setElement(i, j, x * matrix.getElement(i, j));
return matrix;
}
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 static Matrix panelToMatrix(JTextField[] jtfMatrix, int line, int row, double accuracy) {
int i, j;
Matrix matrix = new Matrix(line, row, accuracy);
for (i = 0; i < line; i++)
for (j = 0; j < row; j++) {
if (jtfMatrix[i * row + j].getText().equals("")) return null;
matrix.setElement(i, j, Double.parseDouble(jtfMatrix[i * row + j].getText()));
}
return matrix;
}
public static void matrixToPanel(JTextField[] jtfMatrix, Matrix matrix) {
int i, j;
DecimalFormat df = new DecimalFormat(String.valueOf(matrix.getAccuracy()).replace('1', '0'));
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) {
jtfMatrix[i * matrix.getRow() + j].setText(
String.valueOf(df.format(matrix.getElement(i, j))));
}
}
public Matrix matrixTranspose() { // 矩阵转置
int i, j;
Matrix trans_matrix = new Matrix();
for (i = 0; i < getLine(); i++)
for (j = 0; j < getRow(); j++) trans_matrix.setElement(j, i, this.getElement(i, j));
trans_matrix.setLine(getLine());
trans_matrix.setRow(getRow());
trans_matrix.setAccuracy(getAccuracy());
return trans_matrix;
}
public int matrixRank() // 矩阵的秩
{
int rank = 0, i, j;
Matrix matrix = new Matrix();
matrix = matrixLineSimplify();
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++)
if (Math.abs(matrix.getElement(i, j)) > matrix.getAccuracy()) {
rank++;
break;
}
return rank;
}
public Matrix(double[][] matrixArray, int line, int row, double accuracy, String name) {
this.matrixArray = Matrix.matrixArrayCopy(matrixArray);
this.line = line;
this.row = row;
this.accuracy = accuracy;
this.name = name;
}
public Matrix matrixPower(int n) { // 矩阵的幂
int i;
Matrix matrix = new Matrix(this);
for (i = 2; i <= n; i++) matrix = Matrix.matrixMultiply(matrix, this);
return matrix;
}
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 Matrix matrixAccuralize() { // 精确化矩阵
int i, j;
Matrix matrix = new Matrix(this);
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++)
if (Math.abs(matrix.getElement(i, j)) <= matrix.getAccuracy()) matrix.setElement(i, j, 0.0);
return matrix;
}
public static Matrix scanMatrix() { // 输入矩阵
int i, j;
Matrix matrix = new Matrix();
Scanner scanner = new Scanner(System.in);
matrix.setLine(scanner.nextInt());
matrix.setRow(scanner.nextInt());
matrix.setAccuracy(scanner.nextDouble());
for (i = 0; i < matrix.getLine(); i++) {
for (j = 0; j < matrix.getRow(); j++) matrix.setElement(i, j, scanner.nextDouble());
}
return matrix;
}
public void setMatrixArray(double[][] array) {
this.matrixArray = Matrix.matrixArrayCopy(array);
}
public Matrix(Matrix matrix) {
this.matrixArray = Matrix.matrixArrayCopy(matrix.getMatrixArray());
this.line = matrix.getLine();
this.row = matrix.getRow();
this.accuracy = matrix.getAccuracy();
}
/**
* ************************************************************* 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;
}
public Matrix(double[][] matrixArray, int line, int row) {
this.matrixArray = Matrix.matrixArrayCopy(matrixArray);
this.line = line;
this.row = row;
}
public static Matrix matrixCopy(Matrix matrix) { // 矩阵复制
int i, j;
Matrix matrix_copy = new Matrix();
matrix_copy.setLine(matrix.getLine());
matrix_copy.setRow(matrix.getRow());
matrix_copy.setAccuracy(matrix.getAccuracy());
matrix_copy.setName(matrix.getName());
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) matrix_copy.setMatrixArray(matrix.getMatrixArray());
return matrix_copy;
}
public double determinantValue() // 计算行列式
{
int i, j, k, p = 0;
double change, value = 1.0;
Matrix matrix = new Matrix(this);
for (i = 0; i < matrix.getLine(); i++) {
for (j = i + 1; j < matrix.getLine(); j++)
for (; p < matrix.getLine(); p++) {
if (matrix.getElement(i, p) == 0 && matrix.getElement(j, p) != 0)
for (k = p; k < matrix.getRow(); k++)
matrix.setElement(i, k, matrix.getElement(i, k) + matrix.getElement(j, k));
else if (matrix.getElement(i, p) == 0 && matrix.getElement(j, p) == 0) {
for (; j < matrix.getLine() && matrix.getElement(j, p) == 0; j++) ;
if (j == matrix.getLine()) {
j = i + 1;
continue;
} else {
for (k = p; k < matrix.getRow(); k++)
matrix.setElement(i, k, matrix.getElement(i, k) + matrix.getElement(j, k));
}
} else if (matrix.getElement(i, p) != 0 && matrix.getElement(j, p) == 0) break;
change = matrix.getElement(j, p) / matrix.getElement(i, p);
for (k = p; k < matrix.getRow(); k++)
matrix.setElement(j, k, matrix.getElement(j, k) - matrix.getElement(i, k) * change);
break;
}
p = i;
}
for (i = 0; i < matrix.getLine(); i++) value *= matrix.getElement(i, i);
return value;
}
public static Matrix matrixMinus(Matrix matrix1, Matrix matrix2) { // 矩阵减法
int i, j;
Matrix matrix = new Matrix();
for (i = 0; i < matrix1.getLine(); i++)
for (j = 0; j < matrix1.getRow(); j++)
matrix.setElement(i, j, matrix1.getElement(i, j) - matrix2.getElement(i, j));
matrix.setLine(matrix1.getLine());
matrix.setRow(matrix1.getRow());
matrix.setAccuracy(matrix1.getAccuracy());
return matrix;
}
public Matrix matrixReverse() { // 求矩阵的逆
int i, j, k;
double change;
Matrix matrix_reverse = new Matrix(this);
for (i = 0; i < matrix_reverse.getLine(); i++)
for (j = matrix_reverse.getRow(); j < 2 * matrix_reverse.getRow(); j++)
matrix_reverse.setElement(i, j, (j == matrix_reverse.getRow() + i) ? 1 : 0);
matrix_reverse.setRow(2 * matrix_reverse.getRow());
matrix_reverse = matrix_reverse.matrixLineSimplify();
/*将矩阵的左半边化为单位阵*/
for (i = 0; i < matrix_reverse.getLine() - 1; i++)
for (j = i + 1; j < matrix_reverse.getRow() / 2; j++) {
if (matrix_reverse.getElement(i, j) == 0) continue;
if (matrix_reverse.getElement(i, j) < 0)
for (k = 0; k < matrix_reverse.getRow(); k++)
matrix_reverse.setElement(i, k, -matrix_reverse.getElement(i, k));
if (matrix_reverse.getElement(j, j) < 0)
for (k = 0; k < matrix_reverse.getRow(); k++)
matrix_reverse.setElement(j, k, -matrix_reverse.getElement(j, k));
change = matrix_reverse.getElement(i, j) / matrix_reverse.getElement(j, j);
for (k = 0; k < matrix_reverse.getRow(); k++)
matrix_reverse.setElement(
i, k, matrix_reverse.getElement(i, k) - matrix_reverse.getElement(j, k) * change);
}
matrix_reverse.setRow(matrix_reverse.getRow() / 2);
for (i = 0; i < matrix_reverse.getLine(); i++)
for (j = 0; j < matrix_reverse.getRow(); j++)
matrix_reverse.setElement(i, j, matrix_reverse.getElement(i, j + matrix_reverse.getRow()));
return matrix_reverse;
}
public Matrix matrixLineSimplify() { // 矩阵的行简化
int i, j, k, p = 0;
double change, first_of_line;
Matrix matrix0 = new Matrix(this);
for (i = 0; i < matrix0.getLine(); i++) {
for (j = i + 1; j < matrix0.getLine(); j++)
for (; p < matrix0.getRow(); p++) {
if (matrix0.getElement(i, p) == 0 && matrix0.getElement(j, p) != 0)
for (k = 0; k < matrix0.getRow(); k++)
matrix0.setElement(i, k, matrix0.getElement(i, k) + matrix0.getElement(j, k));
else if (matrix0.getElement(i, p) == 0 && matrix0.getElement(j, p) == 0) {
for (; j < matrix0.getLine() && matrix0.getElement(j, p) == 0; j++) ;
if (j == matrix0.getLine()) {
j = i + 1;
continue;
} else {
for (k = p; k < matrix0.getRow(); k++)
matrix0.setElement(i, k, matrix0.getElement(i, k) + matrix0.getElement(j, k));
}
} else if (matrix0.getElement(i, p) != 0 && matrix0.getElement(j, p) == 0) break;
if (matrix0.getElement(i, p) < 0)
for (k = p; k < matrix0.getRow(); k++)
matrix0.setElement(i, k, -matrix0.getElement(i, k));
if (matrix0.getElement(j, p) < 0)
for (k = p; k < matrix0.getRow(); k++)
matrix0.setElement(j, k, -matrix0.getElement(j, k));
change = matrix0.getElement(j, p) / matrix0.getElement(i, p);
for (k = p; k < matrix0.getRow(); k++)
matrix0.setElement(j, k, matrix0.getElement(j, k) - matrix0.getElement(i, k) * change);
break;
}
p = i;
}
// 将每一行最简化
matrix0 = matrix0.matrixAccuralize();
for (i = 0; i < matrix0.getLine(); i++) {
for (j = 0; j < matrix0.getRow() && matrix0.getElement(i, j) == 0; j++) ;
first_of_line = matrix0.getElement(i, j);
if (j == matrix0.getRow()) continue;
for (; j < matrix0.getRow(); j++)
matrix0.setElement(i, j, matrix0.getElement(i, j) / first_of_line);
}
return matrix0;
}
public static Matrix matrixMultiply(Matrix matrix1, Matrix matrix2) { // 矩阵乘法
int i, j, k;
Matrix matrix = new Matrix();
matrix.setLine(matrix1.getLine());
matrix.setRow(matrix2.getRow());
matrix.setAccuracy(matrix1.getAccuracy());
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++) matrix.setElement(i, j, 0.0);
for (i = 0; i < matrix.getLine(); i++)
for (j = 0; j < matrix.getRow(); j++)
for (k = 0; k < matrix1.getRow(); k++)
matrix.setElement(
i, j, matrix.getElement(i, j) + matrix1.getElement(i, k) * matrix2.getElement(k, j));
return matrix;
}