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umcg.genetica.math.matrix.DoubleMatrixDatasetRA Maven / Gradle / Ivy
/*
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* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import java.io.*;
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
*
* @author lude, juha
*/
@Deprecated
public class DoubleMatrixDatasetRA extends DoubleMatrixDatasetAC {
private static final Logger LOGGER = Logger.getLogger(DoubleMatrixDatasetRA.class.getName());
public int nrColsTotal = 0;
public Set rowsToInclude = null;
public Set colsToInclude = null;
public String fileName = null;
private RandomAccessFile raf;
private int[] rowIndexToRawRowIndex;
private int[] colIndexToRawColIndex;
public DoubleMatrixDatasetRA(String fileName) throws IOException {
this(fileName, LoadLabels.LOAD_BOTH);
}
public DoubleMatrixDatasetRA(String fileName, LoadLabels ll) throws IOException {
LOGGER.log(Level.INFO, "Loading dataset: {0}", fileName);
if (fileName.endsWith(".binary")) {
try {
loadExpressionDataInBinaryFormat(fileName, ll);
} catch (ClassNotFoundException ex) {
throw new IOException(ex); // for backward compatibility we don't throw ClassNotFoundExceptions :I
}
} else {
throw new IOException("Only .binary format supported for random access! Given file: " + fileName);
}
}
public DoubleMatrixDatasetRA(String fileName, Set rowsToInclude) throws IOException {
this(fileName, rowsToInclude, LoadLabels.LOAD_BOTH);
}
public DoubleMatrixDatasetRA(String fileName, Set rowsToInclude, LoadLabels ll) throws IOException {
this.rowsToInclude = rowsToInclude;
LOGGER.log(Level.INFO, "Loading dataset: {0}", fileName);
if (fileName.endsWith(".binary")) {
try {
loadExpressionDataInBinaryFormat(fileName, ll);
} catch (ClassNotFoundException ex) {
throw new IOException(ex); // for backward compatibility we don't throw ClassNotFoundExceptions :I
}
} else {
throw new IOException("Only .binary format supported for random access! Given file: " + fileName);
}
}
public DoubleMatrixDatasetRA(String fileName, Set rowsToInclude, Set colsToInclude) throws IOException {
this(fileName, rowsToInclude, colsToInclude, LoadLabels.LOAD_BOTH);
}
public DoubleMatrixDatasetRA(String fileName, Set rowsToInclude, Set colsToInclude, LoadLabels ll) throws IOException {
this.rowsToInclude = rowsToInclude;
this.colsToInclude = colsToInclude;
LOGGER.log(Level.INFO, "Loading dataset: {0}", fileName);
if (fileName.endsWith(".binary")) {
try {
loadExpressionDataInBinaryFormat(fileName, ll);
} catch (ClassNotFoundException ex) {
throw new IOException(ex);
}
} else {
throw new IOException("Only .binary format supported for random access! Given file: " + fileName);
}
}
private void loadExpressionDataInBinaryFormat(String fileName, LoadLabels ll) throws IOException, ClassNotFoundException {
//First load the raw binary data:
this.fileName = fileName;
File fileBinary = new File(fileName + ".dat");
int nrRowsThisBinaryFile = -1;
int nrColsThisBinaryFile = -1;
this.raf = new RandomAccessFile(fileBinary, "r");
raf.seek(0);
byte[] bytes = new byte[4];
raf.read(bytes, 0, 4);
nrRowsThisBinaryFile = byteArrayToInt(bytes);
raf.read(bytes, 0, 4);
nrColsThisBinaryFile = byteArrayToInt(bytes);
if (rowsToInclude == null && colsToInclude == null) {
//We want to load all the data:
nrRows = nrRowsThisBinaryFile;
nrCols = nrColsThisBinaryFile;
//Now load the row and column identifiers from files
switch (ll) {
case LOAD_BOTH:
loadRowObjects(fileName, nrRows);
loadColumnObjects(fileName, nrCols);
break;
case LOAD_ROWS:
loadRowObjects(fileName, nrRows);
break;
case LOAD_COLUMNS:
loadColumnObjects(fileName, nrCols);
break;
}
nrColsTotal = nrCols;
} else {
//We want to confine the set of probes and samples to a subset. Deal with this in a different way.
loadRowObjects(fileName, nrRowsThisBinaryFile);
loadColumnObjects(fileName, nrColsThisBinaryFile);
nrColsTotal = nrColsThisBinaryFile;
}
recalculateHashMaps();
LOGGER.log(Level.INFO, "Access to binary file:\t{0}\tok, nrRows:\t{1}\tnrCols:\t{2}", new Object[]{fileName, nrRows, nrCols});
}
public static List getRowObjectsOnly(String fileName) throws FileNotFoundException, IOException, ClassNotFoundException {
File fileRows = new File(fileName + ".rows.ser");
List objects = new ArrayList();
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(fileRows));
ObjectInputStream ois = new ObjectInputStream(bis);
while (bis.available() > 0) {
objects.add(ois.readObject());
}
bis.close();
ois.close();
return objects;
}
public static List getColumnObjectsOnly(String fileName) throws FileNotFoundException, IOException, ClassNotFoundException {
File fileCols = new File(fileName + ".columns.ser");
List objects = new ArrayList();
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(fileCols));
ObjectInputStream ois = new ObjectInputStream(bis);
while (bis.available() > 0) {
objects.add(ois.readObject());
}
bis.close();
ois.close();
return objects;
}
private void loadRowObjects(String fileName, int nrRowsThisBinaryFile) throws FileNotFoundException, IOException, ClassNotFoundException {
int[] rowSubsetIndex = new int[nrRowsThisBinaryFile];
for (int r = 0; r < rowSubsetIndex.length; r++) {
rowSubsetIndex[r] = -1;
}
File fileRows = new File(fileName + ".rows.ser");
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(fileRows));
ObjectInputStream ois = new ObjectInputStream(bis);
int rowIndex = 0;
rowObjects = new ArrayList();//rowsToInclude.size());
HashMap hashRowsPresentAndRequested = new HashMap();
while (bis.available() > 0) {
T rowObject = (T) ois.readObject();
if (rowsToInclude == null || rowsToInclude.contains(rowObject)) {
rowSubsetIndex[rowIndex] = hashRowsPresentAndRequested.size();
hashRowsPresentAndRequested.put(rowObject, rowIndex);
rowObjects.add(rowObject);
}
rowIndex++;
}
bis.close();
ois.close();
nrRows = hashRowsPresentAndRequested.size();
rowIndexToRawRowIndex = new int[nrRows];
bis = new BufferedInputStream(new FileInputStream(fileRows));
ois = new ObjectInputStream(bis);
int rowCounter = 0;
rowIndex = 0;
while (bis.available() > 0) {
T rowObject = (T) ois.readObject();
if (rowsToInclude == null || rowsToInclude.contains(rowObject)) {
rowIndexToRawRowIndex[rowCounter] = rowIndex;
rowCounter++;
}
rowIndex++;
}
bis.close();
ois.close();
}
private void loadColumnObjects(String fileName, int nrColsThisBinaryFile) throws FileNotFoundException, IOException, ClassNotFoundException {
int[] colSubsetIndex = new int[nrColsThisBinaryFile];
for (int c = 0; c < colSubsetIndex.length; c++) {
colSubsetIndex[c] = -1;
}
File fileCols = new File(fileName + ".columns.ser");
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(fileCols));
ObjectInputStream ois = new ObjectInputStream(bis);
int colIndex = 0;
colObjects = new ArrayList();//colsToInclude.size());
HashMap hashColsPresentAndRequested = new HashMap();
while (bis.available() > 0) {
U colObject = (U) ois.readObject();
if (colsToInclude == null || colsToInclude.contains(colObject)) {
colSubsetIndex[colIndex] = hashColsPresentAndRequested.size();
hashColsPresentAndRequested.put(colObject, colIndex);
colObjects.add(colObject);
}
colIndex++;
}
bis.close();
ois.close();
nrCols = hashColsPresentAndRequested.size();
colIndexToRawColIndex = new int[nrCols];
bis = new BufferedInputStream(new FileInputStream(fileCols));
ois = new ObjectInputStream(bis);
int colCounter = 0;
colIndex = 0;
while (bis.available() > 0) {
U colObject = (U) ois.readObject();
if (colsToInclude == null || colsToInclude.contains(colObject)) {
colIndexToRawColIndex[colCounter] = colIndex;
colCounter++;
}
colIndex++;
}
bis.close();
ois.close();
}
public double[] getNextRow() {
if (nrCols != nrColsTotal) {
throw new IllegalStateException("Not applicable to datasets with not all columns included. (Columns in file: " + nrColsTotal + ", columns included: " + nrCols + ")");
}
double[] values = new double[nrCols];
int col = 0;
try {
for (col = 0; col < nrColsTotal; col++) {
values[col] = raf.readDouble();
}
} catch (IOException e) {
System.err.println("Can't get element at column " + col + ": " + e.getMessage());
}
return values;
}
@Override
public synchronized double[] get(int x) {
if (nrCols != nrColsTotal) {
throw new IllegalStateException("Not applicable to datasets with not all columns included. (Columns in file: " + nrColsTotal + ", columns included: " + nrCols + ")");
}
int rawRowIndex = x;
if (rowIndexToRawRowIndex != null) {
rawRowIndex = rowIndexToRawRowIndex[x];
}
double[] values = new double[nrCols];
int col = 0;
try {
raf.seek(8 + (rawRowIndex * (long) nrColsTotal) * 8);
for (col = 0; col < nrColsTotal; col++) {
values[col] = raf.readDouble();
}
} catch (IOException e) {
System.err.println("Can't get element (" + rawRowIndex + ", " + col + "): " + e.getMessage());
}
return values;
}
@Override
public synchronized double get(int x, int y) {
int rawRowIndex = x;
if (rowIndexToRawRowIndex != null) {
rawRowIndex = rowIndexToRawRowIndex[x];
}
int rawColIndex = y;
if (colIndexToRawColIndex != null) {
rawColIndex = colIndexToRawColIndex[y];
}
double value = Double.NaN;
try {
raf.seek(8 + (rawRowIndex * (long) nrColsTotal + rawColIndex) * 8);
value = raf.readDouble();
} catch (IOException e) {
System.err.println("Can't get element (" + rawRowIndex + ", " + rawColIndex + "): " + e.getMessage());
}
return value;
}
@Override
public void recalculateHashMaps() {
if (rowObjects != null) {
hashRows.clear();
for (int probeItr = 0; probeItr < nrRows; probeItr++) {
hashRows.put(rowObjects.get(probeItr), probeItr);
}
}
if (colObjects != null) {
hashCols.clear();
for (int sampleItr = 0; sampleItr < nrCols; sampleItr++) {
hashCols.put(colObjects.get(sampleItr), sampleItr);
}
}
}
//TODO ByteBuffer
private byte[] intToByteArray(int value) {
return new byte[]{(byte) (value >>> 24),
(byte) (value >>> 16),
(byte) (value >>> 8),
(byte) value};
}
private int byteArrayToInt(byte[] b) {
return (b[0] << 24)
+ ((b[1] & 0xff) << 16)
+ ((b[2] & 0xff) << 8)
+ (b[3] & 0xff);
}
}
