--- /dev/null
+package javajs.util;
+
+import java.io.BufferedInputStream;
+import java.io.InputStream;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.api.GenericBinaryDocumentReader;
+
+/**
+ * A simple MessagePack reader. See https://github.com/msgpack/msgpack/blob/master/spec.md
+ * with very few dependencies.
+ *
+ * Nuances:
+ *
+ * Does not implement unsigned int32 or int64 (delivers simple integers in all cases).
+ * Does not use doubles; just floats
+ *
+ * Note:
+ *
+ * homogeneousArrays == true will deliver null for empty array.
+ *
+ *
+ * Use in MMTF:
+ *
+ *
+ * BufferedInputStream bs = [whatever]
+ *
+ * GenericBinaryDocument binaryDoc = new javajs.util.BinaryDocument();
+ *
+ * binaryDoc.setStream(bs, true);
+ *
+ *
+ * map = (new MessagePackReader(binaryDoc, true)).readMap();
+ *
+ * entities = (Object[]) map.get("entityList");
+ *
+ * float[] x = (float[]) decode((byte[]) map.get("xCoordList"))
+ *
+ *
+ * @author Bob Hanson hansonr@stolaf.edu
+ */
+
+public class MessagePackReader {
+
+ private GenericBinaryDocumentReader doc;
+
+ private boolean isHomo;// homogeneous arrays -- use int[] not Integer
+
+ // these maps must be checked for the specific number of bits, in the following order:
+ private final static int POSITIVEFIXINT_x80 = 0x80; //0xxxxxxx
+ private final static int FIXMAP_xF0 = 0x80; //1000xxxx
+// private final static int FIXARRAY_xF0 = 0x90; //1001xxxx
+ private final static int FIXSTR_xE0 = 0xa0; //101xxxxx
+ private final static int NEGATIVEFIXINT_xE0 = 0xe0; //111xxxxx
+ private final static int DEFINITE_xE0 = 0xc0; //110xxxxx
+
+ private final static int NIL = 0xc0;
+// private final static int (NEVERUSED) = 0xc1;
+ private final static int FALSE = 0xc2;
+ private final static int TRUE = 0xc3;
+ private final static int BIN8 = 0xc4;
+ private final static int BIN16 = 0xc5;
+ private final static int BIN32 = 0xc6;
+ private final static int EXT8 = 0xc7;
+ private final static int EXT16 = 0xc8;
+ private final static int EXT32 = 0xc9;
+ private final static int FLOAT32 = 0xca;
+ private final static int FLOAT64 = 0xcb;
+ private final static int UINT8 = 0xcc;
+ private final static int UINT16 = 0xcd;
+ private final static int UINT32 = 0xce;
+ private final static int UINT64 = 0xcf;
+ private final static int INT8 = 0xd0;
+ private final static int INT16 = 0xd1;
+ private final static int INT32 = 0xd2;
+ private final static int INT64 = 0xd3;
+ private final static int FIXEXT1 = 0xd4;
+ private final static int FIXEXT2 = 0xd5;
+ private final static int FIXEXT4 = 0xd6;
+ private final static int FIXEXT8 = 0xd7;
+ private final static int FIXEXT16 = 0xd8;
+ private final static int STR8 = 0xd9;
+ private final static int STR16 = 0xda;
+ private final static int STR32 = 0xdb;
+ private final static int ARRAY16 = 0xdc;
+ private final static int ARRAY32 = 0xdd;
+ private final static int MAP16 = 0xde;
+ private final static int MAP32 = 0xdf;
+
+ public MessagePackReader(GenericBinaryDocumentReader binaryDoc, boolean isHomogeneousArrays) {
+ isHomo = isHomogeneousArrays;
+ doc = binaryDoc;
+ }
+
+ public MessagePackReader() {
+ // for reflection
+ }
+
+ public Map<String, Object> getMapForStream(BufferedInputStream is) throws Exception {
+ doc = new BinaryDocument().setStream(is, true);
+ Map<String, Object> map = readMap();
+ is.close();
+ return map;
+ }
+
+ @SuppressWarnings("unchecked")
+ public Map<String, Object> readMap() throws Exception {
+ return (Map<String, Object>) getNext(null, 0);
+ }
+
+ public Object getNext(Object array, int pt) throws Exception {
+ int b = doc.readByte() & 0xFF;
+ int be0 = b & 0xE0;
+ if ((b & POSITIVEFIXINT_x80) == 0) {
+ if (array != null) {
+ ((int[]) array)[pt] = b;
+ return null;
+ }
+ return Integer.valueOf(b);
+ }
+ switch (be0) {
+ case NEGATIVEFIXINT_xE0:
+ b = BC.intToSignedInt(b | 0xFFFFFF00);
+ if (array != null) {
+ ((int[]) array)[pt] = b;
+ return null;
+ }
+ return Integer.valueOf(b);
+ case FIXSTR_xE0: {
+ String s = doc.readString(b & 0x1F);
+ if (array != null) {
+ ((String[]) array)[pt] = s;
+ return null;
+ }
+ return s;
+ }
+ case FIXMAP_xF0:
+ return ((b & 0xF0) == FIXMAP_xF0 ? getMap(b & 0x0F) : getArray(b & 0x0F));
+ case DEFINITE_xE0:
+ switch (b) {
+ case NIL:
+ return null;
+ case FALSE:
+ return Boolean.FALSE;
+ case TRUE:
+ return Boolean.TRUE;
+ case EXT8:
+ return getObject(doc.readUInt8());
+ case EXT16:
+ return getObject(doc.readUnsignedShort());
+ case EXT32:
+ return getObject(doc.readInt()); // should be unsigned int
+ case FIXEXT1:
+ return getObject(1);
+ case FIXEXT2:
+ return getObject(2);
+ case FIXEXT4:
+ return getObject(4);
+ case FIXEXT8:
+ return getObject(8);
+ case FIXEXT16:
+ return getObject(16);
+ case ARRAY16:
+ return getArray(doc.readUnsignedShort());
+ case ARRAY32:
+ return getArray(doc.readInt());
+ case MAP16:
+ return getMap(doc.readUnsignedShort());
+ case MAP32:
+ return getMap(doc.readInt());
+
+ // binary arrays:
+
+ case BIN8:
+ return doc.readBytes(doc.readUInt8());
+ case BIN16:
+ return doc.readBytes(doc.readUnsignedShort());
+ case BIN32:
+ return doc.readBytes(doc.readInt());
+ }
+ if (array == null) {
+ switch (b) {
+ case FLOAT32:
+ return Float.valueOf(doc.readFloat());
+ case FLOAT64:
+ return Float.valueOf((float) doc.readDouble());
+ case UINT8:
+ return Integer.valueOf(doc.readUInt8());
+ case UINT16:
+ return Integer.valueOf(doc.readUnsignedShort());
+ case UINT32:
+ return Integer.valueOf(doc.readInt()); // technically should be UInt32
+ case UINT64:
+ return Long.valueOf(doc.readLong()); // should be unsigned long; incompatible with JavaScript!
+ case INT8:
+ return Integer.valueOf(doc.readByte());
+ case INT16:
+ return Integer.valueOf(doc.readShort());
+ case INT32:
+ return Integer.valueOf(doc.readInt()); // should be Unsigned Int here
+ case INT64:
+ return Long.valueOf(doc.readLong());
+ case STR8:
+ return doc.readString(doc.readUInt8());
+ case STR16:
+ return doc.readString(doc.readShort());
+ case STR32:
+ return doc.readString(doc.readInt());
+ }
+ } else {
+ switch (b) {
+ case FLOAT32:
+ ((float[]) array)[pt] = doc.readFloat();
+ break;
+ case FLOAT64:
+ ((float[]) array)[pt] = (float) doc.readDouble();
+ break;
+ case UINT8:
+ ((int[]) array)[pt] = doc.readUInt8();
+ break;
+ case UINT16:
+ ((int[]) array)[pt] = doc.readUnsignedShort();
+ break;
+ case UINT32:
+ ((int[]) array)[pt] = doc.readInt(); // should be unsigned int
+ break;
+ case UINT64:
+ ((int[]) array)[pt] = (int) doc.readLong(); // should be unsigned long; incompatible with JavaScript!
+ break;
+ case INT8:
+ ((int[]) array)[pt] = doc.readByte();
+ break;
+ case INT16:
+ ((int[]) array)[pt] = doc.readShort();
+ break;
+ case INT32:
+ ((int[]) array)[pt] = doc.readInt(); // should be Unsigned Int here
+ break;
+ case INT64:
+ ((int[]) array)[pt] = (int) doc.readLong();
+ break;
+ case STR8:
+ ((String[]) array)[pt] = doc.readString(doc.readUInt8());
+ break;
+ case STR16:
+ ((String[]) array)[pt] = doc.readString(doc.readShort());
+ break;
+ case STR32:
+ ((String[]) array)[pt] = doc.readString(doc.readInt());
+ break;
+ }
+ }
+ }
+ return null;
+ }
+
+ private Object getObject(int n) throws Exception {
+ return new Object[] { Integer.valueOf(doc.readUInt8()), doc.readBytes(n) };
+ }
+
+ private Object getArray(int n) throws Exception {
+ if (isHomo) {
+ if (n == 0)
+ return null;
+ Object v = getNext(null, 0);
+ if (v instanceof Integer) {
+ int[] a = new int[n];
+ a[0] = ((Integer) v).intValue();
+ v = a;
+ } else if (v instanceof Float) {
+ float[] a = new float[n];
+ a[0] = ((Float) v).floatValue();
+ v = a;
+ } else if (v instanceof String) {
+ String[] a = new String[n];
+ a[0] = (String) v;
+ v = a;
+ } else {
+ Object[] o = new Object[n];
+ o[0] = v;
+ for (int i = 1; i < n; i++)
+ o[i] = getNext(null, 0);
+ return o;
+ }
+ for (int i = 1; i < n; i++)
+ getNext(v, i);
+ return v;
+ }
+ Object[] o = new Object[n];
+ for (int i = 0; i < n; i++)
+ o[i] = getNext(null, 0);
+ return o;
+ }
+
+ private Object getMap(int n) throws Exception {
+ Map<String, Object> map = new Hashtable<String, Object>();
+ for (int i = 0; i < n; i++) {
+ String key = getNext(null, 0).toString();
+ //Logger.info(key);
+
+ Object value = getNext(null, 0);
+ if (value == null) {
+ //Logger.info("null value for " + key);
+ } else {
+ map.put(key, value);
+ }
+ }
+ return map;
+ }
+
+ /////////////// MMTF MessagePack decoding ///////////////
+
+ /**
+ * This single method takes care of all MMTF needs.
+ *
+ * See https://github.com/rcsb/mmtf/blob/master/spec.md
+ *
+ * @param b
+ *
+ * @return array of int, char, or float, depending upon the type
+ */
+ public static Object decode(byte[] b) {
+ int type = BC.bytesToInt(b, 0, true);
+ int n = BC.bytesToInt(b, 4, true);
+ int param = BC.bytesToInt(b, 8, true);
+ switch (type) {
+ case 1:
+ return getFloats(b, n, 1);
+ case 2: // 1-byte
+ case 3: // 2-byte
+ case 4: // 4-byte
+ return getInts(b, n);
+ case 5:
+ return rldecode32ToStr(b);
+ case 6:
+ return rldecode32ToChar(b, n);
+ case 7:
+ return rldecode32(b, n);
+ case 8:
+ return rldecode32Delta(b, n);
+ case 9:
+ return rldecodef(b, n, param);
+ case 10:
+ return unpack16Deltaf(b, n, param);
+ case 11:
+ return getFloats(b, n, param);
+ case 12: // two-byte
+ case 13: // one-byte
+ return unpackf(b, 14 - type, n, param);
+ case 14: // two-byte
+ case 15: // one-byte
+ return unpack(b, 16 - type, n);
+ default:
+ System.out.println("MMTF type " + type + " not found!");
+ return null;
+ }
+ }
+
+ /**
+ * mmtf type 1 and 11
+ *
+ * byte[4] to float32
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] getFloats(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] a = new float[n];
+ try {
+ switch ((b.length - 12) / n) {
+ case 2:
+ for (int i = 0, j = 12; i < n; i++, j += 2)
+ a[i] = BC.bytesToShort(b, j, false) / divisor;
+ break;
+ case 4:
+ for (int i = 0, j = 12; i < n; i++, j += 4)
+ a[i] = BC.bytesToFloat(b, j, false);
+ break;
+ }
+ } catch (Exception e) {
+ }
+ return a;
+ }
+
+ /**
+ * mmtf types 2-4
+ *
+ * Decode a byte array into a byte, short, or int array.
+ *
+ * @param b
+ * @param n
+ *
+ * @return array of integers
+ */
+ public static int[] getInts(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] a = new int[n];
+ switch ((b.length - 12) / n) {
+ case 1:
+ for (int i = 0, j = 12; i < n; i++, j++)
+ a[i] = b[j];
+ break;
+ case 2:
+ for (int i = 0, j = 12; i < n; i++, j += 2)
+ a[i] = BC.bytesToShort(b, j, true);
+ break;
+ case 4:
+ for (int i = 0, j = 12; i < n; i++, j += 4)
+ a[i] = BC.bytesToInt(b, j, true);
+ break;
+ }
+ return a;
+ }
+
+ /**
+ * mmtf type 5
+ *
+ * Decode each four bytes as a 1- to 4-character string label where a 0 byte
+ * indicates end-of-string.
+ *
+ * @param b
+ * a byte array
+ * @return String[]
+ */
+ public static String[] rldecode32ToStr(byte[] b) {
+ String[] id = new String[(b.length - 12) / 4];
+ out: for (int i = 0, len = id.length, pt = 12; i < len; i++) {
+ SB sb = new SB();
+ for (int j = 0; j < 4; j++) {
+ switch (b[pt]) {
+ case 0:
+ id[i] = sb.toString();
+ pt += 4 - j;
+ continue out;
+ default:
+ sb.appendC((char) b[pt++]);
+ if (j == 3)
+ id[i] = sb.toString();
+ continue;
+ }
+ }
+ }
+ return id;
+ }
+
+ /**
+ * mmtf type 6
+ *
+ * Decode an array of int32 using run-length decoding to one char per int.
+ *
+ * @param b
+ * @param n
+ * @return array of characters
+ */
+ public static char[] rldecode32ToChar(byte[] b, int n) {
+ if (b == null)
+ return null;
+ char[] ret = new char[n];
+ for (int i = 0, pt = 3; i < n;) {
+ char val = (char) b[((pt++) << 2) + 3];
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val;
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 7
+ *
+ * Decode an array of int32 using run-length decoding.
+ *
+ * @param b
+ * @param n
+ * @return array of integers
+ */
+ public static int[] rldecode32(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ for (int i = 0, pt = 3; i < n;) {
+ int val = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val;
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 8
+ *
+ * Decode an array of int32 using run-length decoding of a difference array.
+ *
+ * @param b
+ * @param n
+ * @return array of integers
+ */
+ public static int[] rldecode32Delta(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ for (int i = 0, pt = 3, val = 0; i < n;) {
+ int diff = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = (val = val + diff);
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 9
+ *
+ * Decode an array of int32 using run-length decoding and divide by a divisor
+ * to give a float32.
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] rldecodef(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ for (int i = 0, pt = 3; i < n;) {
+ int val = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val / divisor;
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 10
+ *
+ * Decode an array of int16 using run-length decoding of a difference array.
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] unpack16Deltaf(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ for (int i = 0, pt = 6, val = 0, buf = 0; i < n;) {
+ int diff = BC.bytesToShort(b, (pt++) << 1, true);
+ if (diff == Short.MAX_VALUE || diff == Short.MIN_VALUE) {
+ buf += diff;
+ } else {
+ ret[i++] = (val = val + diff + buf) / divisor;
+ buf = 0;
+ }
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 12 and 13
+ *
+ * Unpack an array of int8 or int16 to int32 and divide to give a float32.
+ *
+ * untested
+ *
+ * @param b
+ * @param nBytes
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] unpackf(byte[] b, int nBytes, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ switch (nBytes) {
+ case 1:
+ for (int i = 0, pt = 12, offset = 0; i < n;) {
+ int val = b[pt++];
+ if (val == Byte.MAX_VALUE || val == Byte.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = (val + offset) / divisor;
+ offset = 0;
+ }
+ }
+ break;
+ case 2:
+ for (int i = 0, pt = 6, offset = 0; i < n;) {
+ int val = BC.bytesToShort(b, (pt++) << 1, true);
+ if (val == Short.MAX_VALUE || val == Short.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = (val + offset) / divisor;
+ offset = 0;
+ }
+ }
+ break;
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 14 and 15
+ *
+ * Unpack an array of int8 or int16 to int32.
+ *
+ * untested
+ *
+ * @param b
+ * @param nBytes
+ * @param n
+ * @return array of integers
+ */
+ public static int[] unpack(byte[] b, int nBytes, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ switch (nBytes) {
+ case 1:
+ for (int i = 0, pt = 12, offset = 0; i < n;) {
+ int val = b[pt++];
+ if (val == Byte.MAX_VALUE || val == Byte.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = val + offset;
+ offset = 0;
+ }
+ }
+ break;
+ case 2:
+ for (int i = 0, pt = 6, offset = 0; i < n;) {
+ int val = BC.bytesToShort(b, (pt++) << 1, true);
+ if (val == Short.MAX_VALUE || val == Short.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = val + offset;
+ offset = 0;
+ }
+ }
+ break;
+ }
+ return ret;
+ }
+
+ ///**
+ //* Decode an array of int16 using run-length decoding
+ //* of a difference array.
+ //*
+ //* @param b
+ //* @param n
+ //* @param i0
+ //* @return array of integers
+ //*/
+ //public static int[] rldecode16Delta(byte[] b, int n, int i0) {
+ //if (b == null)
+ //return null;
+ //int[] ret = new int[n];
+ //for (int i = 0, pt = i0 / 2, val = 0; i < n;) {
+ //int diff = BC.bytesToShort(b, (pt++) << 1, true);
+ //for (int j = BC.bytesToShort(b, (pt++) << 1, true); --j >= 0;)
+ //ret[i++] = (val = val + diff);
+ //}
+ //return ret;
+ //}
+
+ ///**
+ //* Do a split delta to a float[] array
+ //* @param xyz label "x", "y", "z", or "bFactor"
+ //* @param factor for dividing in the end -- 1000f or 100f
+ //* @return float[]
+ //*
+ //*/
+ //public static float[] getFloatsSplit(String xyz, float factor) {
+ //byte[] big = (byte[]) map.get(xyz + "Big");
+ //return (big == null ? null : splitDelta(big,
+ //(byte[]) map.get(xyz + "Small"), fileAtomCount, factor));
+ //}
+
+ ///**
+ //* Do a split delta to a float[] array
+ //*
+ //* @param big
+ //* [n m n m n m...] where n is a "big delta" and m is a number of
+ //* "small deltas
+ //* @param small
+ //* array containing the small deltas
+ //* @param n
+ //* the size of the final array
+ //* @param factor
+ //* to divide the final result by -- 1000f or 100f here
+ //* @return float[]
+ //*/
+ //public static float[] splitDelta(byte[] big, byte[] small, int n, float factor) {
+ //float[] ret = new float[n];
+ //for (int i = 0, smallpt = 0, val = 0, datapt = 0, len = big.length >> 2; i < len; i++) {
+ //ret[datapt++] = (val = val + BC.bytesToInt(big, i << 2, true)) / factor;
+ //if (++i < len)
+ //for (int j = BC.bytesToInt(big, i << 2, true); --j >= 0; smallpt++)
+ //ret[datapt++] = (val = val + BC.bytesToShort(small, smallpt << 1, true))
+ // / factor;
+ //}
+ //return ret;
+ //}
+ //
+
+
+}
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