/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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. */ /** * SparseShortArrays map shorts to shorts. Unlike a normal array of shorts, * there can be gaps in the indices. It is intended to be more memory efficient * than using a HashMap to map Shorts to Shorts, 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). *

*/ /* * Added to Jalview September 2016. A copy of SparseIntArray designed to store * short values (to minimise space usage). *

* Note that operations append, put, add throw ArithmeticException if either the * key or the resulting value overflows the range of a short. Calling code * should trap and handle this, for example by switching to using a * SparseIntArray instead. */ public class SparseShortArray implements Cloneable { private short[] mKeys; private short[] mValues; private int mSize; /** * Creates a new SparseShortArray containing no mappings. */ public SparseShortArray() { this(10); } /** * Creates a new SparseShortArray 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 SparseShortArray(int initialCapacity) { if (initialCapacity == 0) { mKeys = new short[0]; mValues = new short[0]; } else { initialCapacity = idealShortArraySize(initialCapacity); mKeys = new short[initialCapacity]; mValues = new short[initialCapacity]; } mSize = 0; } @Override public SparseShortArray clone() { SparseShortArray clone = null; try { clone = (SparseShortArray) 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. * * @throws ArithmeticException * if key is outside the range of a short value */ public int get(int key, int valueIfKeyNotFound) { checkOverflow(key); int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key); if (i < 0) { return valueIfKeyNotFound; } else { return mValues[i]; } } /** * Removes the mapping from the specified key, if there was any. * * @throws ArithmeticException * if key is outside the range of a short value */ public void delete(int key) { checkOverflow(key); int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) 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. * * @throws ArithmeticException * if either argument is outside the range of a short value */ public void put(int key, int value) { checkOverflow(key); checkOverflow(value); int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key); if (i >= 0) { mValues[i] = (short) value; } else { i = ~i; if (mSize >= mKeys.length) { int n = idealShortArraySize(mSize + 1); short[] nkeys = new short[n]; short[] nvalues = new short[n]; // Log.e("SparseShortArray", "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("SparseShortArray", "move " + (mSize - i)); System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i); System.arraycopy(mValues, i, mValues, i + 1, mSize - i); } mKeys[i] = (short) key; mValues[i] = (short) value; mSize++; } } /** * Returns the number of key-value mappings that this SparseShortArray * 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 SparseShortArray * 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 short 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 SparseShortArray * 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 short 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. * * @throws ArithmeticException * if key is outside the range of a short value */ public int indexOfKey(int key) { checkOverflow(key); return ContainerHelpers.binarySearch(mKeys, mSize, (short) 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 SparseShortArray. */ 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 = idealShortArraySize(pos + 1); short[] nkeys = new short[n]; short[] nvalues = new short[n]; // Log.e("SparseShortArray", "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; } checkOverflow(key); checkOverflow(value); mKeys[pos] = (short) key; mValues[pos] = (short) value; mSize = pos + 1; } /** * Throws an exception if the value is outside the range of a short. * * @param value * @throws ArithmeticException */ public static void checkOverflow(int value) { if (value > Short.MAX_VALUE || value < Short.MIN_VALUE) { throw new ArithmeticException(String.valueOf(value)); } } /** * Inlined here by copying from com.android.internal.util.ArrayUtils * * @param i * @return */ public static int idealShortArraySize(int need) { return idealByteArraySize(need * 2) / 2; } /** * 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 * @throws ArithmeticException * if key, or result of adding toAdd, is outside the range of a * short value */ public int add(int key, int toAdd) { int newValue = toAdd; checkOverflow(key); int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key); if (i >= 0) { checkOverflow(toAdd + mValues[i]); mValues[i] += (short) toAdd; newValue = mValues[i]; } else { checkOverflow(toAdd); i = ~i; if (mSize >= mKeys.length) { int n = idealShortArraySize(mSize + 1); short[] nkeys = new short[n]; short[] nvalues = new short[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] = (short) key; mValues[i] = (short) toAdd; mSize++; } return newValue; } }