*/
package jalview.util;
+import java.util.Arrays;
+import java.util.Comparator;
+
+/**
+ * A class to perform efficient sorting of arrays of objects based on arrays of
+ * scores or other attributes. For example, residues by percentage frequency.
+ *
+ * @author gmcarstairs
+ *
+ */
public class QuickSort
{
+ static class FloatComparator implements Comparator<Integer>
+ {
+
+ private final float[] values;
+
+ FloatComparator(float[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Float.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ static class IntComparator implements Comparator<Integer>
+ {
+
+ private final int[] values;
+
+ IntComparator(int[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Integer.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(int[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(float[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(double[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to descending order of the items in the
+ * first array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(String[] arr, Object[] s)
{
stringSort(arr, 0, arr.length - 1, s);
}
- public static void stringSort(String[] arr, int p, int r, Object[] s)
+ static void stringSort(String[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(float[] arr, int p, int r, Object[] s)
+ static void sort(float[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(double[] arr, int p, int r, Object[] s)
+ static void sort(double[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(int[] arr, int p, int r, Object[] s)
+ static void sort(int[] arr, int p, int r, Object[] s)
{
int q;
}
}
- private static int partition(float[] arr, int p, int r, Object[] s)
+ static int partition(float[] arr, int p, int r, Object[] s)
{
float x = arr[p];
int i = p - 1;
}
}
- private static int partition(int[] arr, int p, int r, Object[] s)
+ static int partition(float[] arr, int p, int r, char[] s)
+ {
+ float x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ float tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ char tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int partition(int[] arr, int p, int r, Object[] s)
{
int x = arr[p];
int i = p - 1;
}
}
- private static int partition(double[] arr, int p, int r, Object[] s)
+ static int partition(double[] arr, int p, int r, Object[] s)
{
double x = arr[p];
int i = p - 1;
}
}
- private static int stringPartition(String[] arr, int p, int r, Object[] s)
+ static int stringPartition(String[] arr, int p, int r, Object[] s)
{
String x = arr[p];
int i = p - 1;
}
}
}
+
+ /**
+ * Sorts both arrays to give ascending order in the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(float[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ float[] f1 = new float[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ float val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * Copy zero values back to original arrays
+ */
+ System.arraycopy(f1, 0, arr, 0, nextZeroValue);
+ System.arraycopy(s1, 0, s, 0, nextZeroValue);
+
+ if (nextZeroValue == arr.length)
+ {
+ return; // all zero
+ }
+ /*
+ * Sort the non-zero values
+ */
+ float[] nonZeroFloats = Arrays
+ .copyOfRange(f1, nextZeroValue, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
+ externalSort(nonZeroFloats, nonZeroChars);
+ // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroFloats, 0, arr, nextZeroValue,
+ nonZeroFloats.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort by making an array of indices, and sorting it using a comparator that
+ * refers to the float values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ */
+ protected static void externalSort(float[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new FloatComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ float[] sortedFloats = new float[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedFloats[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedFloats, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
+
+ /**
+ * Make an array whose values are 0...length.
+ *
+ * @param length
+ * @return
+ */
+ protected static Integer[] makeIndexArray(final int length)
+ {
+ Integer[] indices = new Integer[length];
+ for (int i = 0; i < length; i++)
+ {
+ indices[i] = i;
+ }
+ return indices;
+ }
+
+ static void sort(float[] arr, int p, int r, char[] s)
+ {
+ int q;
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, s);
+ }
+ }
+
+ /**
+ * Sorts both arrays to give ascending order in the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(int[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ int[] f1 = new int[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ int val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * Copy zero values back to original arrays
+ */
+ System.arraycopy(f1, 0, arr, 0, nextZeroValue);
+ System.arraycopy(s1, 0, s, 0, nextZeroValue);
+
+ if (nextZeroValue == arr.length)
+ {
+ return; // all zero
+ }
+ /*
+ * Sort the non-zero values
+ */
+ int[] nonZeroInts = Arrays
+ .copyOfRange(f1, nextZeroValue, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
+ externalSort(nonZeroInts, nonZeroChars);
+ // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort by making an array of indices, and sorting it using a comparator that
+ * refers to the float values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ */
+ protected static void externalSort(int[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new IntComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ int[] sortedInts = new int[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedInts[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedInts, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
}
git://source.jalview.org / jalview.git / blobdiff