X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=src%2Fjavajs%2Futil%2FAU.java;fp=src%2Fjavajs%2Futil%2FAU.java;h=50c591249941f8fe492419c9bfddf28e7e0e39ae;hp=1fca3da88f99209ff6e966662356b8878246f32f;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/src/javajs/util/AU.java b/src/javajs/util/AU.java
index 1fca3da..50c5912 100644
--- a/src/javajs/util/AU.java
+++ b/src/javajs/util/AU.java
@@ -1,655 +1,655 @@
-/* $RCSfile$
- * $Author: egonw $
- * $Date: 2005-11-10 09:52:44 -0600 (Thu, 10 Nov 2005) $
- * $Revision: 4255 $
- *
- * 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 initialized to all zeros in MSIE 9.
-   * 
-   * @param array
-   * @param minimumLength
-   * @return array
-   */
-  public static Object ensureLength(Object array, int minimumLength) {
-    if (array != null && getLength(array) >= minimumLength)
-      return array;
-    return arrayCopyObject(array, minimumLength);
-  }
-
-  public static String[] ensureLengthS(String[] array, int minimumLength) {
-    if (array != null && array.length >= minimumLength)
-      return array;
-    return arrayCopyS(array, minimumLength);
-  }
-
-  public static float[] ensureLengthA(float[] array, int minimumLength) {
-    if (array != null && array.length >= minimumLength)
-      return array;
-    return arrayCopyF(array, minimumLength);
-  }
-
-  public static int[] ensureLengthI(int[] array, int minimumLength) {
-    if (array != null && array.length >= minimumLength)
-      return array;
-    return arrayCopyI(array, minimumLength);
-  }
-
-  public static short[] ensureLengthShort(short[] array, int minimumLength) {
-    if (array != null && array.length >= minimumLength)
-      return array;
-    return arrayCopyShort(array, minimumLength);
-  }
-
-  public static byte[] ensureLengthByte(byte[] array, int minimumLength) {
-    if (array != null && array.length >= minimumLength)
-      return array;
-    return 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!
-   * 
-   * @param array
-   * @param newLength
-   * @return array
-   */
-  public static Object arrayCopyObject(Object array, int newLength) {
-    //System.out.println("ArrayUtil.copy " + newLength + " " + array + "  ");
-    if (array == null) {
-      return null; // We can't allocate since we don't know the type of array
-    }
-    int oldLength = getLength(array);
-    if (newLength == oldLength)
-      return array;
-    Object t = newInstanceO(array, newLength);
-    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) {
-    /**
-     * @j2sNative
-     * 
-     * if (!array.getClass().getComponentType)
-     * 	 return new Array(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) {
-    if (newLength < 0)
-      newLength = array.length;
-    String[] t = new String[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      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) {
-    if (newLength < 0)
-      newLength = array.length;
-    float[] t = new float[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
-          : newLength);
-    }
-    return t;
-  }
-
-  public static int[] arrayCopyI(int[] array, int newLength) {
-    if (newLength < 0)
-      newLength = array.length;
-    int[] t = new int[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      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;
-    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;
-    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) {
-    if (newLength < 0)
-      newLength = array.length;
-    short[] t = new short[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
-          : newLength);
-    }
-    return t;
-  }
-
-  public static byte[] arrayCopyByte(byte[] array, int newLength) {
-    if (newLength < 0)
-      newLength = array.length;
-    byte[] t = new byte[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
-          : newLength);
-    }
-    return t;
-  }
-
-  public static boolean[] arrayCopyBool(boolean[] array, int newLength) {
-    if (newLength < 0)
-      newLength = array.length;
-    boolean[] t = new boolean[newLength];
-    if (array != null) {
-      int oldLength = array.length;
-      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) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    return new float[n][];
-    }
-  }
-
-  public static int[][] newInt2(int n) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    return new int[n][];
-    }
-  }
-
-  public static int[][][] newInt3(int nx, int ny) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(nx, null);
-     * 
-     */
-    {
-      return (ny < 0 ? new int[nx][][] : new int[nx][ny][]);
-    }
-  }
-
-  public static float[][][] newFloat3(int nx, int ny) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(nx, null);
-     * 
-     */
-    {
-      return (ny < 0 ? new float[nx][][] : new float[nx][ny][]);
-    }
-  }
-
-  public static int[][][][] newInt4(int n) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    return new int[n][][][];
-    }
-  }
-
-  public static short[][] newShort2(int n) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    return new short[n][];
-    }
-  }
-
-  public static byte[][] newByte2(int n) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    return new byte[n][];
-    }
-  }
-
-  public static double[][] newDouble2(int n) {
-    /**
-     * @j2sNative
-     * 
-     * return Clazz.newArray(n, null);
-     * 
-     */
-    {
-    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) {
-	  /**
-	   * 
-	   * look also for array with first null element
-	   * so untypable -- just call it a String[]
-	   * (group3Lists, created in ModelLoader)
-	   * 
-	   * @j2sNative
-	   *  return Clazz.isAS(x);
-	   */
-	  {
-	  return x instanceof String[];
-	  }
-	}
-
-	public static boolean isASS(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isASS(x);
-	   */
-	  {
-	  return x instanceof String[][];
-	  }
-	}
-
-	public static boolean isAP(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAP(x);
-	   */
-	  {
-	  return x instanceof T3[];
-	  }
-	}
-
-	public static boolean isAF(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAF(x);
-	   */
-	  {
-	  return x instanceof float[];
-	  }
-	}
-
-	public static boolean isAFloat(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAFloat(x);
-	   */
-	  {
-	  return x instanceof Float[];
-	  }
-	}
-
-	public static boolean isAD(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAF(x);
-	   */
-	  {
-	  return x instanceof double[];
-	  }
-	}
-
-	public static boolean isADD(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAFF(x);
-	   */
-	  {
-	  return x instanceof double[][];
-	  }
-	}
-
-	public static boolean isAB(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAI(x);
-	   */
-	  {
-	  return x instanceof byte[];
-	  }
-	}
-
-	public static boolean isAI(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAI(x);
-	   */
-	  {
-	  return x instanceof int[];
-	  }
-	}
-
-	public static boolean isAII(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAII(x);
-	   */
-	  {
-	  return (x instanceof int[][]);
-	  }
-	}
-
-	public static boolean isAFF(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAFF(x);
-	   */
-	  {
-	  return x instanceof float[][];
-	  }
-	}
-
-	public static boolean isAFFF(Object x) {
-	  /**
-	   * @j2sNative
-	   *  return Clazz.isAFFF(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
-	 */
-	public static void ensureSignedBytes(byte[] b) {
-	  /**
-	   * @j2sNative
-	   * 
-	   * for (var i = b.length; --i >= 0;) {
-	   *   var j = b[i] & 0xFF;
-	   *   if (j >= 0x80) j -= 0x100;
-	   *   b[i] = j;
-	   * }
-	   * 
-	   */
-	  {
-	  }
-	}
-
-
-}
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2005-11-10 09:52:44 -0600 (Thu, 10 Nov 2005) $
+ * $Revision: 4255 $
+ *
+ * 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 initialized to all zeros in MSIE 9.
+   * 
+   * @param array
+   * @param minimumLength
+   * @return array
+   */
+  public static Object ensureLength(Object array, int minimumLength) {
+    if (array != null && getLength(array) >= minimumLength)
+      return array;
+    return arrayCopyObject(array, minimumLength);
+  }
+
+  public static String[] ensureLengthS(String[] array, int minimumLength) {
+    if (array != null && array.length >= minimumLength)
+      return array;
+    return arrayCopyS(array, minimumLength);
+  }
+
+  public static float[] ensureLengthA(float[] array, int minimumLength) {
+    if (array != null && array.length >= minimumLength)
+      return array;
+    return arrayCopyF(array, minimumLength);
+  }
+
+  public static int[] ensureLengthI(int[] array, int minimumLength) {
+    if (array != null && array.length >= minimumLength)
+      return array;
+    return arrayCopyI(array, minimumLength);
+  }
+
+  public static short[] ensureLengthShort(short[] array, int minimumLength) {
+    if (array != null && array.length >= minimumLength)
+      return array;
+    return arrayCopyShort(array, minimumLength);
+  }
+
+  public static byte[] ensureLengthByte(byte[] array, int minimumLength) {
+    if (array != null && array.length >= minimumLength)
+      return array;
+    return 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!
+   * 
+   * @param array
+   * @param newLength
+   * @return array
+   */
+  public static Object arrayCopyObject(Object array, int newLength) {
+    //System.out.println("ArrayUtil.copy " + newLength + " " + array + "  ");
+    if (array == null) {
+      return null; // We can't allocate since we don't know the type of array
+    }
+    int oldLength = getLength(array);
+    if (newLength == oldLength)
+      return array;
+    Object t = newInstanceO(array, newLength);
+    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) {
+    /**
+     * @j2sNative
+     * 
+     * if (!array.getClass().getComponentType)
+     * 	 return new Array(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) {
+    if (newLength < 0)
+      newLength = array.length;
+    String[] t = new String[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      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) {
+    if (newLength < 0)
+      newLength = array.length;
+    float[] t = new float[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static int[] arrayCopyI(int[] array, int newLength) {
+    if (newLength < 0)
+      newLength = array.length;
+    int[] t = new int[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      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;
+    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;
+    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) {
+    if (newLength < 0)
+      newLength = array.length;
+    short[] t = new short[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static byte[] arrayCopyByte(byte[] array, int newLength) {
+    if (newLength < 0)
+      newLength = array.length;
+    byte[] t = new byte[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+          : newLength);
+    }
+    return t;
+  }
+
+  public static boolean[] arrayCopyBool(boolean[] array, int newLength) {
+    if (newLength < 0)
+      newLength = array.length;
+    boolean[] t = new boolean[newLength];
+    if (array != null) {
+      int oldLength = array.length;
+      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) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    return new float[n][];
+    }
+  }
+
+  public static int[][] newInt2(int n) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    return new int[n][];
+    }
+  }
+
+  public static int[][][] newInt3(int nx, int ny) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(nx, null);
+     * 
+     */
+    {
+      return (ny < 0 ? new int[nx][][] : new int[nx][ny][]);
+    }
+  }
+
+  public static float[][][] newFloat3(int nx, int ny) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(nx, null);
+     * 
+     */
+    {
+      return (ny < 0 ? new float[nx][][] : new float[nx][ny][]);
+    }
+  }
+
+  public static int[][][][] newInt4(int n) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    return new int[n][][][];
+    }
+  }
+
+  public static short[][] newShort2(int n) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    return new short[n][];
+    }
+  }
+
+  public static byte[][] newByte2(int n) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    return new byte[n][];
+    }
+  }
+
+  public static double[][] newDouble2(int n) {
+    /**
+     * @j2sNative
+     * 
+     * return Clazz.newArray(n, null);
+     * 
+     */
+    {
+    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) {
+	  /**
+	   * 
+	   * look also for array with first null element
+	   * so untypable -- just call it a String[]
+	   * (group3Lists, created in ModelLoader)
+	   * 
+	   * @j2sNative
+	   *  return Clazz.isAS(x);
+	   */
+	  {
+	  return x instanceof String[];
+	  }
+	}
+
+	public static boolean isASS(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isASS(x);
+	   */
+	  {
+	  return x instanceof String[][];
+	  }
+	}
+
+	public static boolean isAP(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAP(x);
+	   */
+	  {
+	  return x instanceof T3[];
+	  }
+	}
+
+	public static boolean isAF(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAF(x);
+	   */
+	  {
+	  return x instanceof float[];
+	  }
+	}
+
+	public static boolean isAFloat(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAFloat(x);
+	   */
+	  {
+	  return x instanceof Float[];
+	  }
+	}
+
+	public static boolean isAD(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAF(x);
+	   */
+	  {
+	  return x instanceof double[];
+	  }
+	}
+
+	public static boolean isADD(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAFF(x);
+	   */
+	  {
+	  return x instanceof double[][];
+	  }
+	}
+
+	public static boolean isAB(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAI(x);
+	   */
+	  {
+	  return x instanceof byte[];
+	  }
+	}
+
+	public static boolean isAI(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAI(x);
+	   */
+	  {
+	  return x instanceof int[];
+	  }
+	}
+
+	public static boolean isAII(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAII(x);
+	   */
+	  {
+	  return (x instanceof int[][]);
+	  }
+	}
+
+	public static boolean isAFF(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAFF(x);
+	   */
+	  {
+	  return x instanceof float[][];
+	  }
+	}
+
+	public static boolean isAFFF(Object x) {
+	  /**
+	   * @j2sNative
+	   *  return Clazz.isAFFF(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
+	 */
+	public static void ensureSignedBytes(byte[] b) {
+	  /**
+	   * @j2sNative
+	   * 
+	   * for (var i = b.length; --i >= 0;) {
+	   *   var j = b[i] & 0xFF;
+	   *   if (j >= 0x80) j -= 0x100;
+	   *   b[i] = j;
+	   * }
+	   * 
+	   */
+	  {
+	  }
+	}
+
+
+}