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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package com.actelion.research.util;
import com.actelion.research.calc.Matrix;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.StringTokenizer;
/**
*
*
* MatrixSparse
* @author Modest von Korff
* @version 1.0
* 2008 MvK: Start implementation
*/
public class MatrixSparse {
private static final int BUFFER_SIZE = 10000;
private static final int READ_BUFFER_SIZE = 10^7;
private LinkedHashMap> hmIndex_hmIndex;
private double [] data;
private int position;
private int rows;
private int cols;
public MatrixSparse(File fi) throws Exception{
init();
read(fi);
}
public MatrixSparse(File fi, int rows) throws Exception{
init();
read(fi, rows);
}
public MatrixSparse(int rows, int cols){
init();
this.rows=rows;
this.cols=cols;
}
public void init(){
hmIndex_hmIndex = new LinkedHashMap>();
data = new double [BUFFER_SIZE];
position = -1;
}
public void set(int row, int col, double v){
if(row >= rows){
String m = "Row index " + row + " out of bounds " + rows + ".";
throw new IndexOutOfBoundsException(m);
} else if(col >= cols){
String m = "Col index " + col + " out of bounds " + cols + ".";
throw new IndexOutOfBoundsException(m);
}
position++;
if(position == data.length){
resizeArray(position+1);
}
data[position]=v;
LinkedHashMap lhmRow = hmIndex_hmIndex.get(row);
if(lhmRow == null){
lhmRow = new LinkedHashMap();
hmIndex_hmIndex.put(row, lhmRow);
}
lhmRow.put(col, position);
}
/**
*
* @param row
* @param col
* @return NaN if the value was not set.
*/
public double get(int row, int col){
if(hmIndex_hmIndex.containsKey(row)){
if(hmIndex_hmIndex.get(row).containsKey(col)){
int pos = hmIndex_hmIndex.get(row).get(col);
return data[pos];
}
}
return Double.NaN;
}
public double [] getArray(){
return data;
}
public Matrix getMatrixK(){
Matrix ma = new Matrix(rows(), cols());
for (int i = 0; i < rows(); i++) {
for (int j = 0; j < cols(); j++) {
ma.set(i,j, get(i,j));
}
}
return ma;
}
public int cols(){
return cols;
}
public int rows(){
return rows;
}
private void read(File file) throws IOException {
FileInputStream iStr = new FileInputStream(file);
FileChannel fc = iStr.getChannel();
ByteBuffer buf = ByteBuffer.allocate(READ_BUFFER_SIZE);
StringBuilder sb = new StringBuilder();
boolean bEOF=false;
while (!bEOF){
buf.position(0);
int size = fc.read(buf);
if(size==-1){
break;
}
for (int i = 0; i < size; i++) {
int c = buf.get(i);
if(c==-1) {
bEOF=true;
} else {
if(c=='\n') {
read(sb.toString());
sb.delete(0, sb.length());
} else {
sb.append((char)c);
}
}
}
}
fc.close();
}
private void read(File file, int rows) throws IOException {
FileInputStream iStr = new FileInputStream(file);
FileChannel fc = iStr.getChannel();
ByteBuffer buf = ByteBuffer.allocate(READ_BUFFER_SIZE);
StringBuilder sb = new StringBuilder();
boolean bEOF=false;
int cc=0;
while (!bEOF){
buf.position(0);
int size = fc.read(buf);
if(size==-1){
break;
}
for (int i = 0; i < size; i++) {
int c = buf.get(i);
if(c==-1) {
bEOF=true;
} else {
if(c=='\n') {
read(sb.toString());
sb.delete(0, sb.length());
cc++;
if(cc==rows){
bEOF = true;
break;
}
} else {
sb.append((char)c);
}
}
}
}
fc.close();
}
private void read(String line){
StringTokenizer st = new StringTokenizer(line);
int row = Integer.parseInt(st.nextToken());
int col = Integer.parseInt(st.nextToken());
double v = Double.parseDouble(st.nextToken());
if(row>=rows)
rows = row + 1;
if(col>=cols)
cols = col + 1;
set(row, col, v);
}
private void resizeArray(int newsize){
if(data.length < newsize){
int si = data.length;
while(si < newsize) {
si += BUFFER_SIZE;
}
double [] dataTmp = new double [si];
int length = Math.min(position, newsize);
System.arraycopy(data, 0, dataTmp, 0, length);
data = dataTmp;
}
}
public String toStringRow(int row, NumberFormat nf) {
StringBuilder sb = new StringBuilder();
if(hmIndex_hmIndex.get(row)!=null){
List liCol = new ArrayList(hmIndex_hmIndex.get(row).keySet());
for (Integer col : liCol) {
double v = data[hmIndex_hmIndex.get(row).get(col)];
String s = row + " " + col + " " + nf.format(v) + "\n";
sb.append(s);
}
}
return sb.toString();
}
public String toString(NumberFormat nf) {
StringBuilder sb = new StringBuilder();
List liRow = new ArrayList(hmIndex_hmIndex.keySet());
for (Integer row : liRow) {
List liCol = new ArrayList(hmIndex_hmIndex.get(row).keySet());
for (Integer col : liCol) {
double v = data[hmIndex_hmIndex.get(row).get(col)];
String s = row + " " + col + " " + nf.format(v) + "\n";
sb.append(s);
}
}
return sb.toString();
}
public String toString() {
NumberFormat nf = new DecimalFormat("0.############");
return toString(nf);
}
}