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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.datamodel;
import java.io.IOException;
import java.io.InputStream;
import java.io.Serializable;
import java.text.DecimalFormat;
import java.util.*;
import com.actelion.research.util.ArrayUtils;
import com.actelion.research.util.BurtleHasher;
public class IntArray implements Serializable {
private static final int START_CAPACITY = 32;
private static final int MAX_DELTA_CAPACITY = (int)Math.pow(2, 20);
private int [] data;
private int size;
private int delta_capacity;
private int hash;
public IntArray() {
init(START_CAPACITY);
}
public IntArray(int capacity) {
init(capacity);
}
/**
* Shallow constructor.
* @param a
*/
public IntArray(int [] a) {
data = a;
size = data.length;
delta_capacity = size/2;
calculateHashCode();
}
/**
* Deep constructor.
* @param ia
*/
public IntArray(IntArray ia) {
init(ia.data.length);
System.arraycopy(ia.data, 0, data, 0, ia.size);
size = ia.size;
delta_capacity = ia.delta_capacity;
hash = ia.hash;
}
private void init(int capacity){
data = new int[capacity];
delta_capacity = capacity/2;
size = 0;
hash = -1;
}
public void calculateHashCode(){
int h = BurtleHasher.hashlittle(data, 13, size);
hash = h;
}
public int getCapacity(){
return data.length;
}
/**
* Computational expensive operation!
* @param value
*/
public void removeValue(int value){
int ccFound=0;
for (int i = 0; i < size; i++) {
if(data[i]==value){
ccFound++;
}
}
if(ccFound==0){
return;
}
int newlen = size-ccFound;
int [] arr = new int [newlen];
int cc=0;
for (int i = 0; i < size; i++) {
if(data[i]!=value){
arr[cc++]=data[i];
}
}
data=arr;
size = newlen;
}
public boolean equals(Object o) {
IntArray ia = (IntArray)o;
boolean eq = true;
if(length() != ia.length()){
return false;
}
for (int i = 0; i < size; i++) {
if(data[i] != ia.data[i]) {
eq = false;
break;
}
}
return eq;
}
public int hashCode() {
return hash;
}
public int get(int i){
return data[i];
}
/**
*
* @return shallow copy.
*/
public int [] get(){
resize(size);
return data;
}
public int add(int v){
facultativeResize();
data[size]=v;
int index = size;
size++;
hash = -1;
return index;
}
public int max(){
int max = Integer.MIN_VALUE;
for (int i = 0; i < size; i++) {
if(data[i]>max){
max=data[i];
}
}
return max;
}
private void facultativeResize(){
if(size == data.length){
long newsize = (long)data.length + (long)delta_capacity;
resize(newsize);
if(delta_capacity data.length){
resize(newsize);
}
System.arraycopy(a, 0, data, size, a.length);
size = newsize;
hash = -1;
}
public void add(List li){
for (int v : li) {
add(v);
}
calculateHashCode();
}
public void add(byte [] a){
for (int i = 0; i < a.length; i++) {
add(a[i]);
}
}
/**
*
* @return number of occupied fields.
*/
public int length(){
return size;
}
/**
*
* @return last value in the array and removes it.
*/
public int removeLast(){
int last = get(size-1);
size--;
return last;
}
private void resize(long newlen){
if(data.length == newlen){
return;
}
int intNewlen = 0;
long max = Integer.MAX_VALUE;
if(newlen >= max) {
intNewlen = Integer.MAX_VALUE;
new RuntimeException("Warning! Maximum length of integer array reached.").printStackTrace();
} else {
intNewlen = (int)newlen;
}
int [] arr = new int [intNewlen];
System.arraycopy(data, 0, arr, 0, Math.min(data.length, intNewlen));
data = arr;
}
public void set(int index, int value){
data[index]=value;
}
public List toList() {
List li = new ArrayList(length());
for (int i = 0; i < length(); i++) {
li.add(get(i));
}
return li;
}
public void clear(){
reset();
}
public void reset(){
size=0;
}
public String toString() {
StringBuilder sb = new StringBuilder();
DecimalFormat nf = new DecimalFormat("0");
for (int i = 0; i < size; i++) {
sb.append(nf.format(data[i]) + " ");
}
return sb.toString();
}
public String toString(String seperator) {
int types = length();
StringBuilder sb = new StringBuilder();
for (int i = 0; i < types; i++) {
sb.append(get(i));
if(i < types-1){
sb.append(seperator);
}
}
return sb.toString();
}
public static IntArray read(InputStream s) throws IOException{
int size = parseInteger(s);
int delta_capacity = parseInteger(s);
int hash = parseInteger(s);
int [] a = new int [size];
for (int i = 0; i < size; i++) {
a[i] = parseInteger(s);
}
IntArray ia = new IntArray();
ia.data = a;
ia.size = size;
ia.delta_capacity = delta_capacity;
ia.hash = hash;
return ia;
}
public String write2String() throws IOException{
StringBuilder sb = new StringBuilder();
sb.append(size);
sb.append(" ");
sb.append(delta_capacity);
sb.append(" ");
sb.append(hash);
sb.append(" ");
sb.append(toString());
return sb.toString();
}
public static int parseInteger(InputStream s) throws IOException{
int i = -1;
StringBuilder sb = new StringBuilder();
while(' ' != (i=s.read())){
if(i==-1){
break;
}
sb.append((char)i);
}
int val = Integer.parseInt(sb.toString());
return val;
}
public void sort(){
resize(size);
Arrays.sort(data);
}
public static void shuffle(IntArray arr){
Random rnd = new Random();
int cycles = 7;
int size = arr.length();
for (int i = 0; i < cycles; i++) {
for (int j = 0; j < size; j++) {
int dest = rnd.nextInt(size);
if(dest==j){
continue;
}
int v = arr.get(j);
arr.set(j, arr.get(dest));
arr.set(dest, v);
}
}
}
public static IntArray read(String l){
IntArray ia = new IntArray();
StringTokenizer st = new StringTokenizer(l, ", ;");
while(st.hasMoreTokens()){
String t = st.nextToken().trim();
int i = Integer.parseInt(t);
ia.add(i);
}
return ia;
}
public static boolean equals(int [] a, int [] b){
boolean eq = true;
if(a.length != b.length){
return false;
}
for (int i = 0; i < a.length; i++) {
if(a[i] != b[i]) {
eq = false;
break;
}
}
return eq;
}
public static List toList(int [] a) {
List li = new ArrayList<>(a.length);
for (int i = 0; i < a.length; i++) {
li.add(a[i]);
}
return li;
}
public static int [] resize(int [] data, int newlen){
int [] arr = null;
if(data.length == newlen){
return arr;
}
int intNewlen = 0;
long max = Integer.MAX_VALUE;
if(newlen >= max) {
intNewlen = Integer.MAX_VALUE;
new RuntimeException("Warning! Maximum length of integer array reached.").printStackTrace();
} else {
intNewlen = newlen;
}
arr = new int [intNewlen];
System.arraycopy(data, 0, arr, 0, Math.min(data.length, intNewlen));
return arr;
}
}