package jalview.ext.android; /* * Copyright (C) 2006 The Android Open Source Project * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ /** * SparseIntArrays map integers to integers. Unlike a normal array of integers, * there can be gaps in the indices. It is intended to be more memory efficient * than using a HashMap to map Integers to Integers, both because it avoids * auto-boxing keys and values and its data structure doesn't rely on an extra * entry object for each mapping. * *

* Note that this container keeps its mappings in an array data structure, using * a binary search to find keys. The implementation is not intended to be * appropriate for data structures that may contain large numbers of items. It * is generally slower than a traditional HashMap, since lookups require a * binary search and adds and removes require inserting and deleting entries in * the array. For containers holding up to hundreds of items, the performance * difference is not significant, less than 50%. *

* *

* It is possible to iterate over the items in this container using * {@link #keyAt(int)} and {@link #valueAt(int)}. Iterating over the keys using * keyAt(int) with ascending values of the index will return the * keys in ascending order, or the values corresponding to the keys in ascending * order in the case of valueAt(int). *

*/ /* * Imported into Jalview September 2016 * Change log: * Sep 2016 method add(int, int) added for more efficient increment of counts * (a single binary search, rather than one on read and one on write) */ public class SparseIntArray implements Cloneable { private int[] mKeys; private int[] mValues; private int mSize; /** * Creates a new SparseIntArray containing no mappings. */ public SparseIntArray() { this(10); } /** * Creates a new SparseIntArray containing no mappings that will not require * any additional memory allocation to store the specified number of mappings. * If you supply an initial capacity of 0, the sparse array will be * initialized with a light-weight representation not requiring any additional * array allocations. */ public SparseIntArray(int initialCapacity) { if (initialCapacity == 0) { mKeys = ContainerHelpers.EMPTY_INTS; mValues = ContainerHelpers.EMPTY_INTS; } else { initialCapacity = idealIntArraySize(initialCapacity); mKeys = new int[initialCapacity]; mValues = new int[initialCapacity]; } mSize = 0; } @Override public SparseIntArray clone() { SparseIntArray clone = null; try { clone = (SparseIntArray) super.clone(); clone.mKeys = mKeys.clone(); clone.mValues = mValues.clone(); } catch (CloneNotSupportedException cnse) { /* ignore */ } return clone; } /** * Gets the int mapped from the specified key, or 0 if no such * mapping has been made. */ public int get(int key) { return get(key, 0); } /** * Gets the int mapped from the specified key, or the specified value if no * such mapping has been made. */ public int get(int key, int valueIfKeyNotFound) { int i = ContainerHelpers.binarySearch(mKeys, mSize, key); if (i < 0) { return valueIfKeyNotFound; } else { return mValues[i]; } } /** * Removes the mapping from the specified key, if there was any. */ public void delete(int key) { int i = ContainerHelpers.binarySearch(mKeys, mSize, key); if (i >= 0) { removeAt(i); } } /** * Removes the mapping at the given index. */ public void removeAt(int index) { System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1)); System.arraycopy(mValues, index + 1, mValues, index, mSize - (index + 1)); mSize--; } /** * Adds a mapping from the specified key to the specified value, replacing the * previous mapping from the specified key if there was one. */ public void put(int key, int value) { int i = ContainerHelpers.binarySearch(mKeys, mSize, key); if (i >= 0) { mValues[i] = value; } else { i = ~i; if (mSize >= mKeys.length) { int n = idealIntArraySize(mSize + 1); int[] nkeys = new int[n]; int[] nvalues = new int[n]; // Log.e("SparseIntArray", "grow " + mKeys.length + " to " + n); System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length); System.arraycopy(mValues, 0, nvalues, 0, mValues.length); mKeys = nkeys; mValues = nvalues; } if (mSize - i != 0) { // Log.e("SparseIntArray", "move " + (mSize - i)); System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i); System.arraycopy(mValues, i, mValues, i + 1, mSize - i); } mKeys[i] = key; mValues[i] = value; mSize++; } } /** * Returns the number of key-value mappings that this SparseIntArray currently * stores. */ public int size() { return mSize; } /** * Given an index in the range 0...size()-1, returns the key from * the indexth key-value mapping that this SparseIntArray stores. * *

* The keys corresponding to indices in ascending order are guaranteed to be * in ascending order, e.g., keyAt(0) will return the smallest * key and keyAt(size()-1) will return the largest key. *

*/ public int keyAt(int index) { return mKeys[index]; } /** * Given an index in the range 0...size()-1, returns the value * from the indexth key-value mapping that this SparseIntArray * stores. * *

* The values corresponding to indices in ascending order are guaranteed to be * associated with keys in ascending order, e.g., valueAt(0) will * return the value associated with the smallest key and * valueAt(size()-1) will return the value associated with the * largest key. *

*/ public int valueAt(int index) { return mValues[index]; } /** * Returns the index for which {@link #keyAt} would return the specified key, * or a negative number if the specified key is not mapped. */ public int indexOfKey(int key) { return ContainerHelpers.binarySearch(mKeys, mSize, key); } /** * Returns an index for which {@link #valueAt} would return the specified key, * or a negative number if no keys map to the specified value. Beware that * this is a linear search, unlike lookups by key, and that multiple keys can * map to the same value and this will find only one of them. */ public int indexOfValue(int value) { for (int i = 0; i < mSize; i++) { if (mValues[i] == value) { return i; } } return -1; } /** * Removes all key-value mappings from this SparseIntArray. */ public void clear() { mSize = 0; } /** * Puts a key/value pair into the array, optimizing for the case where the key * is greater than all existing keys in the array. */ public void append(int key, int value) { if (mSize != 0 && key <= mKeys[mSize - 1]) { put(key, value); return; } int pos = mSize; if (pos >= mKeys.length) { int n = idealIntArraySize(pos + 1); int[] nkeys = new int[n]; int[] nvalues = new int[n]; // Log.e("SparseIntArray", "grow " + mKeys.length + " to " + n); System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length); System.arraycopy(mValues, 0, nvalues, 0, mValues.length); mKeys = nkeys; mValues = nvalues; } mKeys[pos] = key; mValues[pos] = value; mSize = pos + 1; } /** * Inlined here by copying from com.android.internal.util.ArrayUtils * * @param i * @return */ public static int idealIntArraySize(int need) { return idealByteArraySize(need * 4) / 4; } /** * Inlined here by copying from com.android.internal.util.ArrayUtils * * @param i * @return */ public static int idealByteArraySize(int need) { for (int i = 4; i < 32; i++) { if (need <= (1 << i) - 12) { return (1 << i) - 12; } } return need; } /** * {@inheritDoc} * *

* This implementation composes a string by iterating over its mappings. */ @Override public String toString() { if (size() <= 0) { return "{}"; } StringBuilder buffer = new StringBuilder(mSize * 28); buffer.append('{'); for (int i = 0; i < mSize; i++) { if (i > 0) { buffer.append(", "); } int key = keyAt(i); buffer.append(key); buffer.append('='); int value = valueAt(i); buffer.append(value); } buffer.append('}'); return buffer.toString(); } /** * Method (copied from put) added for Jalview to efficiently increment a key's * value if present, else add it with the given value. This avoids a double * binary search (once to get the value, again to put the updated value). * * @param key * @oparam toAdd * @return the new value of the count for the key * @throw ArithmeticException if the result would exceed the maximum value of * an int */ public int add(int key, int toAdd) { int newValue = toAdd; int i = ContainerHelpers.binarySearch(mKeys, mSize, key); if (i >= 0) { checkOverflow(mValues[i], toAdd); mValues[i] += toAdd; newValue = mValues[i]; } else { i = ~i; if (mSize >= mKeys.length) { int n = idealIntArraySize(mSize + 1); int[] nkeys = new int[n]; int[] nvalues = new int[n]; System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length); System.arraycopy(mValues, 0, nvalues, 0, mValues.length); mKeys = nkeys; mValues = nvalues; } if (mSize - i != 0) { System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i); System.arraycopy(mValues, i, mValues, i + 1, mSize - i); } mKeys[i] = key; mValues[i] = toAdd; mSize++; } return newValue; } /** * Throws ArithmeticException if adding addend to value would exceed the range * of int * * @param value * @param addend */ static void checkOverflow(int value, int addend) { /* * test cases being careful to avoid overflow while testing! */ if (addend > 0) { if (value > 0 && Integer.MAX_VALUE - value < addend) { throw new ArithmeticException("Integer overflow adding " + addend + " to " + value); } } else if (addend < 0) { if (value < 0 && Integer.MIN_VALUE - value > addend) { throw new ArithmeticException("Integer underflow adding " + addend + " to " + value); } } } }