--- /dev/null
+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.
+ */
+/**
+ * SparseDoubleArray map integers to doubles. 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 Integer to Double, both because it avoids
+ * auto-boxing keys and values and its data structure doesn't rely on an extra
+ * entry object for each mapping.
+ *
+ * <p>
+ * 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%.
+ * </p>
+ *
+ * <p>
+ * It is possible to iterate over the items in this container using
+ * {@link #keyAt(int)} and {@link #valueAt(int)}. Iterating over the keys using
+ * <code>keyAt(int)</code> 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 <code>valueAt(int)<code>.
+ * </p>
+ */
+
+/*
+ * Change log:
+ * Jan 2017 cloned from SparseIntArray for Jalview to support SparseMatrix
+ * - SparseDoubleArray(double[]) constructor added
+ * - multiply() added for more efficient multiply (or divide) of a value
+ */
+public class SparseDoubleArray implements Cloneable
+{
+ private int[] mKeys;
+
+ private double[] mValues;
+
+ private int mSize;
+
+ /**
+ * Creates a new SparseDoubleArray containing no mappings.
+ */
+ public SparseDoubleArray()
+ {
+ this(10);
+ }
+
+ /**
+ * Creates a new SparseDoubleArray 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 SparseDoubleArray(int initialCapacity)
+ {
+ if (initialCapacity == 0)
+ {
+ mKeys = ContainerHelpers.EMPTY_INTS;
+ mValues = ContainerHelpers.EMPTY_DOUBLES;
+ }
+ else
+ {
+ initialCapacity = idealDoubleArraySize(initialCapacity);
+ mKeys = new int[initialCapacity];
+ mValues = new double[initialCapacity];
+ }
+ mSize = 0;
+ }
+
+ /**
+ * Constructor given an array of double values; stores the non-zero values
+ *
+ * @param row
+ */
+ public SparseDoubleArray(double[] row)
+ {
+ this();
+ for (int i = 0; i < row.length; i++)
+ {
+ if (row[i] != 0d)
+ {
+ put(i, row[i]);
+ }
+ }
+ }
+
+ @Override
+ public SparseDoubleArray clone()
+ {
+ SparseDoubleArray clone = null;
+ try
+ {
+ clone = (SparseDoubleArray) super.clone();
+ clone.mKeys = mKeys.clone();
+ clone.mValues = mValues.clone();
+ } catch (CloneNotSupportedException cnse)
+ {
+ /* ignore */
+ }
+ return clone;
+ }
+
+ /**
+ * Gets the value mapped from the specified key, or <code>0</code> if no such
+ * mapping has been made.
+ */
+ public double get(int key)
+ {
+ return get(key, 0d);
+ }
+
+ /**
+ * Gets the int mapped from the specified key, or the specified value if no
+ * such mapping has been made.
+ */
+ public double get(int key, double 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, double value)
+ {
+ int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+ if (i >= 0)
+ {
+ mValues[i] = value;
+ }
+ else
+ {
+ i = ~i;
+ if (mSize >= mKeys.length)
+ {
+ int n = idealDoubleArraySize(mSize + 1);
+ int[] nkeys = new int[n];
+ double[] nvalues = new double[n];
+ // Log.e("SparseDoubleArray", "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("SparseDoubleArray", "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 SparseDoubleArray
+ * currently stores.
+ */
+ public int size()
+ {
+ return mSize;
+ }
+
+ /**
+ * Given an index in the range <code>0...size()-1</code>, returns the key from
+ * the <code>index</code>th key-value mapping that this SparseDoubleArray
+ * stores.
+ *
+ * <p>
+ * The keys corresponding to indices in ascending order are guaranteed to be
+ * in ascending order, e.g., <code>keyAt(0)</code> will return the smallest
+ * key and <code>keyAt(size()-1)</code> will return the largest key.
+ * </p>
+ */
+ public int keyAt(int index)
+ {
+ return mKeys[index];
+ }
+
+ /**
+ * Given an index in the range <code>0...size()-1</code>, returns the value
+ * from the <code>index</code>th key-value mapping that this SparseDoubleArray
+ * stores.
+ *
+ * <p>
+ * The values corresponding to indices in ascending order are guaranteed to be
+ * associated with keys in ascending order, e.g., <code>valueAt(0)</code> will
+ * return the value associated with the smallest key and
+ * <code>valueAt(size()-1)</code> will return the value associated with the
+ * largest key.
+ * </p>
+ */
+ public double 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(double value)
+ {
+ for (int i = 0; i < mSize; i++)
+ {
+ if (mValues[i] == value)
+ {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ /**
+ * Removes all key-value mappings from this SparseDoubleArray.
+ */
+ 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, double value)
+ {
+ if (mSize != 0 && key <= mKeys[mSize - 1])
+ {
+ put(key, value);
+ return;
+ }
+ int pos = mSize;
+ if (pos >= mKeys.length)
+ {
+ int n = idealDoubleArraySize(pos + 1);
+ int[] nkeys = new int[n];
+ double[] nvalues = new double[n];
+ // Log.e("SparseDoubleArray", "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;
+ }
+
+ /**
+ * Created by analogy with
+ * com.android.internal.util.ArrayUtils#idealLongArraySize
+ *
+ * @param i
+ * @return
+ */
+ public static int idealDoubleArraySize(int need)
+ {
+ return idealByteArraySize(need * 8) / 8;
+ }
+
+ /**
+ * 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}
+ *
+ * <p>
+ * 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('=');
+ double 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 for the key
+ */
+ public double add(int key, double toAdd)
+ {
+ double newValue = toAdd;
+ int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+ if (i >= 0)
+ {
+ mValues[i] += toAdd;
+ newValue = mValues[i];
+ }
+ else
+ {
+ i = ~i;
+ if (mSize >= mKeys.length)
+ {
+ int n = idealDoubleArraySize(mSize + 1);
+ int[] nkeys = new int[n];
+ double[] nvalues = new double[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;
+ }
+
+ /**
+ * Method added for Jalview to efficiently multiply a key's value if present,
+ * else do nothing. 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 for the key
+ */
+ public double multiply(int key, double d)
+ {
+ double newValue = 0d;
+ int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+ if (i >= 0)
+ {
+ mValues[i] *= d;
+ newValue = mValues[i];
+ }
+ return newValue;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff