X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fjavajs%2Futil%2FAU.java;fp=unused%2Fjavajs%2Futil%2FAU.java;h=25acbfcded148e9fe46e8f1cd68c2adc94b4ee01;hb=65740880573a48adc758bec3939ece9d9ae104dd;hp=0000000000000000000000000000000000000000;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477;p=jalview.git

diff --git a/unused/javajs/util/AU.java b/unused/javajs/util/AU.java
new file mode 100644
index 0000000..25acbfc
--- /dev/null
+++ b/unused/javajs/util/AU.java
@@ -0,0 +1,551 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2005-11-10 09:52:44 -0600 (Thu, 10 Nov 2005) $
+ * $Revision: 4255 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005  The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 2.1 of the License, or (at your option) any later version.
+ *
+ *  This library 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
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public
+ *  License along with this library; if not, write to the Free Software
+ *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package javajs.util;
+
+// 4/23/15 BH getComponentType fix
+
+import java.lang.reflect.Array;
+
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Map;
+
+
+final public class AU {
+
+  /**
+   * Very important that this not be used with Int32Array or Float32Array,
+   * because it is not initialize to all zeros in MSIE 9. 
+   * 
+   * @param array
+   * @param minimumLength
+   * @return array
+   */
+  public static Object ensureLength(Object array, int minimumLength) {
+    return (array != null && getLength(array) >= minimumLength ? array 
+        : arrayCopyObject(array, minimumLength));
+  }
+
+  public static String[] ensureLengthS(String[] array, int minimumLength) {
+    return (array != null && array.length >= minimumLength ? array
+        : arrayCopyS(array, minimumLength));
+  }
+
+  public static float[] ensureLengthA(float[] array, int minimumLength) {
+   return (array != null && array.length >= minimumLength ? array: arrayCopyF(array, minimumLength));
+  }
+
+  public static int[] ensureLengthI(int[] array, int minimumLength) {
+    return (array != null && array.length >= minimumLength ? array : arrayCopyI(array, minimumLength));
+  }
+
+  public static short[] ensureLengthShort(short[] array, int minimumLength) {
+    return (array != null && array.length >= minimumLength ? array : arrayCopyShort(array, minimumLength));
+  }
+
+  public static byte[] ensureLengthByte(byte[] array, int minimumLength) {
+    return (array != null && array.length >= minimumLength ? array : arrayCopyByte(array, minimumLength));
+  }
+
+  /**
+   * Very important that this not be used with Int32Array or Float32Array,
+   * because it is not initialized to all zeros in MSIE 9.
+   * 
+   * @param array
+   * @return array
+   */
+  public static Object doubleLength(Object array) {
+    return arrayCopyObject(array, (array == null ? 16 : 2 * getLength(array)));
+  }
+
+  public static String[] doubleLengthS(String[] array) {
+    return arrayCopyS(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static float[] doubleLengthF(float[] array) {
+    return arrayCopyF(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static int[] doubleLengthI(int[] array) {
+    return arrayCopyI(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static short[] doubleLengthShort(short[] array) {
+    return arrayCopyShort(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static byte[] doubleLengthByte(byte[] array) {
+    return arrayCopyByte(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static boolean[] doubleLengthBool(boolean[] array) {
+    return arrayCopyBool(array, (array == null ? 16 : 2 * array.length));
+  }
+
+  public static Object deleteElements(Object array, int firstElement,
+                                     int nElements) {
+    if (nElements == 0 || array == null)
+      return array;
+    int oldLength = getLength(array);
+    if (firstElement >= oldLength)
+      return array;
+    int n = oldLength - (firstElement + nElements);
+    if (n < 0)
+      n = 0;
+    Object t = newInstanceO(array, firstElement + n);
+    if (firstElement > 0)
+      System.arraycopy(array, 0, t, 0, firstElement);
+    if (n > 0)
+      System.arraycopy(array, firstElement + nElements, t, firstElement, n);
+    return t;
+  }
+
+  /**
+   * note -- cannot copy if array is null! does not copy if length is unchanged
+   * 
+   * @param array
+   * @param newLength
+   * @return array
+   */
+  public static Object arrayCopyObject(Object array, int newLength) {  
+    int oldLength = (array == null ? -1 : getLength(array));
+    if (newLength < 0) newLength = oldLength;
+    if (newLength == oldLength)
+     return array;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    Object t = newInstanceO(array, newLength);
+    if (oldLength > 0)
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+        : newLength);
+    return t;
+
+  }
+
+  /**
+   * Very important that this not be used with Int32Array or Float32Array,
+   * because those need to be initialized to all zeros in MSIE 9, and
+   * MSIE 9 cannot distinguish Int32Array or Float32Array from Array.
+   * 
+   * @param array
+   * @param n
+   * @return array
+   */
+  private static Object newInstanceO(Object array, int n) {
+    return Array.newInstance(array.getClass().getComponentType(), n);
+  }
+
+  public static int getLength(Object array) {
+    /**
+     * @j2sNative
+     * 
+     *  return array.length
+     *   
+     */
+    {
+      return Array.getLength(array);
+    }
+  }
+
+  public static String[] arrayCopyS(String[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    String[] t = new String[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static int[][] arrayCopyII(int[][] array, int newLength) {
+    int[][] t = newInt2(newLength);
+    if (array != null) {
+      int oldLength = array.length;
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static T3[] arrayCopyPt(T3[] array, int newLength) {
+    if (newLength < 0)
+      newLength = array.length;
+    T3[] t = new T3[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static float[] arrayCopyF(float[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    float[] t = new float[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static int[] arrayCopyI(int[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    int[] t = new int[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  /**
+   * a specialized method that allows copying from a starting point either
+   * to the end or to the middle (color schemes, especially)
+   * @param array
+   * @param i0
+   * @param n
+   * @return array or null
+   */
+  public static int[] arrayCopyRangeI(int[] array, int i0, int n) {
+    if (array == null)
+      return null;
+    int oldLength = array.length;
+    if (n == -1) n = oldLength;
+    if (n == -2) n = oldLength / 2;
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.array(-1, array, i0, n);
+     * 
+     */
+    {
+        n -= i0;
+        int[] t = new int[n];
+        System.arraycopy(array, i0, t, 0, n);
+        return t;
+    }
+  }
+
+  public static int[] arrayCopyRangeRevI(int[] array, int i0, int n) {
+    if (array == null)
+      return null;
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.array(-1, array, i0, n).reverse();
+     */
+    {
+        int[] t = arrayCopyRangeI(array, i0, n);
+        if (n < 0)
+          n = array.length;
+        for (int i = n / 2; --i >= 0;)
+          swapInt(t, i, n - 1 - i);
+        return t;
+    }
+  }
+
+  public static short[] arrayCopyShort(short[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    short[] t = new short[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static byte[] arrayCopyByte(byte[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    byte[] t = new byte[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static boolean[] arrayCopyBool(boolean[] array, int newLength) {
+    int oldLength = (array == null ? -1 : array.length);
+    if (newLength < 0) newLength = oldLength;
+    /**
+     * @j2sNative
+     * 
+     *     if (newLength < oldLength) return Clazz.array(-1, array, 0, newLength);
+     */
+    {}
+    boolean[] t = new boolean[newLength];
+    if (array != null) {
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static void swapInt(int[] array, int indexA, int indexB) {
+    int t = array[indexA];
+    array[indexA] = array[indexB];
+    array[indexB] = t;
+  }
+
+  /*
+  public static void swap(short[] array, int indexA, int indexB) {
+    short t = array[indexA];
+    array[indexA] = array[indexB];
+    array[indexB] = t;
+  }
+
+  public static void swap(float[] array, int indexA, int indexB) {
+    float t = array[indexA];
+    array[indexA] = array[indexB];
+    array[indexB] = t;
+  }
+  */
+  
+  public static String dumpArray(String msg, float[][] A, int x1, int x2, int y1, int y2) {
+    String s = "dumpArray: " + msg + "\n";
+    for (int x = x1; x <= x2; x++)
+      s += "\t*" + x + "*";
+    for (int y = y2; y >= y1; y--) {
+      s += "\n*" + y + "*";
+      for (int x = x1; x <= x2; x++)
+        s += "\t" + (x < A.length && y < A[x].length ? A[x][y] : Float.NaN);
+    }
+    return s;
+  }
+
+  public static String dumpIntArray(int[] A, int n) {
+    String str = "";
+    for (int i = 0; i < n; i++)
+      str += " " + A[i];
+    return str;
+  }
+
+  public static String sortedItem(Lst<String> v, int n) {
+    if (v.size() == 0)
+      return null;
+    if (v.size() == 1)
+      return v.get(0);
+    String[] keys = v.toArray(new String[v.size()]);
+    Arrays.sort(keys);
+    return keys[n % keys.length];
+  }
+
+  /**
+   * Helper method for creating a List<Tx>[] without warnings.
+   * 
+   * @param <type> Type of objects in the list.
+   * @param size Array size.
+   * @return Array of List<type>
+   */
+  @SuppressWarnings("unchecked")
+  public static <type> Lst<type>[] createArrayOfArrayList(int size) {
+    return new Lst[size];
+  }
+
+  /**
+   * Helper method for creating a Map<K, V>[] without warnings.
+   * 
+   * @param <K> Type of object for the keys in the map.
+   * @param <V> Type of object for the values in the map.
+   * @param size Array size.
+   * @return Array of Map<K, V>
+   */
+  @SuppressWarnings("unchecked")
+  public static <K, V> Map<K, V>[] createArrayOfHashtable(int size) {
+    return new Hashtable[size];
+  }
+
+  public static void swap(Object[] o, int i, int j) {
+    Object oi = o[i];
+    o[i] = o[j];
+    o[j] = oi;
+  }
+
+  public static float[][] newFloat2(int n) {
+    return new float[n][];
+  }
+
+	public static boolean[][] newBool2(int n) {
+	return new boolean[n][];
+	}
+
+  public static int[][] newInt2(int n) {
+    return new int[n][];
+  }
+
+  public static int[][][] newInt3(int nx, int ny) {
+    return (ny < 0 ? new int[nx][][] : new int[nx][ny][]);
+  }
+
+  public static float[][][] newFloat3(int nx, int ny) {
+    return (ny < 0 ? new float[nx][][] : new float[nx][ny][]);
+  }
+
+  public static int[][][][] newInt4(int n) {
+    return new int[n][][][];
+  }
+
+  public static short[][] newShort2(int n) {
+    return new short[n][];
+  }
+
+  public static byte[][] newByte2(int n) {
+    return new byte[n][];
+  }
+
+  public static double[][] newDouble2(int n) {
+    return new double[n][];
+  }
+
+  /**
+   * remove all keys from a map that start with given root
+   * @param map
+   * @param root
+   * @return number removed
+   */
+  public static int removeMapKeys(Map<String, ?> map, String root) {
+    Lst<String> list = new Lst<String>();
+    for (String key: map.keySet())
+      if (key.startsWith(root))
+        list.addLast(key);
+    for (int i = list.size(); --i >= 0;)
+      map.remove(list.get(i));
+    return list.size();
+  }
+
+	public static boolean isAS(Object x) {
+		return x instanceof String[];
+	}
+
+	public static boolean isASS(Object x) {
+		return x instanceof String[][];
+	}
+
+	public static boolean isAP(Object x) {
+		return x instanceof T3[];
+	}
+
+	public static boolean isAF(Object x) {
+	  return x instanceof float[];
+	}
+
+	public static boolean isAFloat(Object x) {
+	  return x instanceof Float[];
+	}
+
+	public static boolean isAD(Object x) {
+	  return x instanceof double[];
+	}
+
+	public static boolean isADD(Object x) {
+	  return x instanceof double[][];
+	}
+
+	public static boolean isAB(Object x) {
+	  return x instanceof byte[];
+	}
+
+	public static boolean isAI(Object x) {
+	  return x instanceof int[];
+	}
+
+	public static boolean isAII(Object x) {
+	  return (x instanceof int[][]);
+	}
+
+	public static boolean isAFF(Object x) {
+	  return x instanceof float[][];
+	}
+
+	public static boolean isAFFF(Object x) {
+	  return x instanceof float[][][];
+	}
+	
+	/**
+	 * Ensure that we have signed and not unsigned bytes coming out of any
+	 * process, but particularly out of file reading.
+	 * 
+	 * @param b
+	 * @return b
+	 */
+	public static byte[] ensureSignedBytes(byte[] b) {
+		if (b != null) {
+			/**
+			 * @j2sNative
+			 * 
+			 * 			for (var i = b.length; --i >= 0;) { var j = b[i] &
+			 *            0xFF; if (j >= 0x80) j -= 0x100; b[i] = j; }
+			 * 
+			 */
+			{
+			}
+		}
+		return b;
+	}
+
+
+}