/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you 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.
 */

package org.apache.uima.cas.impl;

import java.io.DataOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;

import org.apache.uima.UimaSerializable;
import org.apache.uima.cas.CASRuntimeException;
import org.apache.uima.cas.CommonArrayFS;
import org.apache.uima.cas.Marker;
import org.apache.uima.cas.impl.CASImpl.FsChange;
import org.apache.uima.cas.impl.SlotKinds.SlotKind;
import org.apache.uima.internal.util.Misc;
import org.apache.uima.internal.util.Obj2IntIdentityHashMap;
import org.apache.uima.internal.util.function.Consumer_T_withIOException;
import org.apache.uima.jcas.cas.BooleanArray;
import org.apache.uima.jcas.cas.ByteArray;
import org.apache.uima.jcas.cas.DoubleArray;
import org.apache.uima.jcas.cas.FSArray;
import org.apache.uima.jcas.cas.FloatArray;
import org.apache.uima.jcas.cas.IntegerArray;
import org.apache.uima.jcas.cas.LongArray;
import org.apache.uima.jcas.cas.ShortArray;
import org.apache.uima.jcas.cas.StringArray;
import org.apache.uima.jcas.cas.TOP;
import org.apache.uima.util.CasIOUtils;

// @formatter:off
/**
 * This object has 2 purposes.
 *   - it can hold a collection of individually Java-object-serializable objects representing a CAS +
 *     the list of FS's indexed in the CAS
 *     
 *   - it has special methods (versions of addCAS) to do a custom binary serialization (no compression) of a CAS + lists
 *     of its indexed FSs.  
 * 
 * One use of this class follows this form:
 * 
 * 1) create an instance of this class
 * 2) add a Cas to it (via addCAS methods)
 * 3) use the instance of this class as the argument to anObjectOutputStream.writeObject(anInstanceOfThisClass)
 *    In UIMA this is done in the SerializationUtils class; it appears to be used for Vinci service adapters.
 * 
 * There are also custom serialization methods that serialize to outputStreams.
 * 
 * The format of the serialized data is in one of several formats:
 *   normal Java object serialization / custom binary serialization
 *
 *   The custom binary serialization is in several formats:
 *     full / delta:
 *       full - the entire cas
 *       delta - only differences from a previous "mark" are serialized
 *       
 *   This class only does uncompressed forms of custom binary serialization.    
 *     
 * This class is for internal use.  Some of the serialized formats are readable by the C++
 * implementation, and used for efficiently transferring CASes between Java frameworks and other ones.
 * Others are used with Vinci to communicate to remote annotators.
 * 
 * To serialize the type definition and index specifications for a CAS
 * 
 * @see org.apache.uima.cas.impl.CASMgrSerializer
 */
// @formatter:on
public class CASSerializer implements Serializable {

  static final long serialVersionUID = -7972011651957420295L;

  static class AddrPlusValue {
    final int addr; // heap or aux heap addr
    final long value; // boolean, byte, short, long, double value

    AddrPlusValue(int addr, long value) {
      this.addr = addr;
      this.value = value;
    }
  }

  // The heap itself.
  public int[] heapArray = null;

  // Heap metadata. This is not strictly required, the heap can be
  // deserialized
  // without. Must be null if not used.
  public int[] heapMetaData = null;

  // The string table for strings that are feature structure values. Note that
  // the 0th position in the string table should be null and will be ignored.
  public String[] stringTable;

  // Special encoding of fs pseudo-addrs and counts by view incl. sofa and view counts
  public int[] fsIndex;

  public byte[] byteHeapArray;

  public short[] shortHeapArray;

  public long[] longHeapArray;

  /**
   * Constructor for CASSerializer.
   */
  public CASSerializer() {
  }

  /**
   * Serialize CAS data without heap-internal meta data. Currently used for serialization to C++.
   * 
   * @param casImpl
   *          The CAS to be serialized.
   */
  public void addNoMetaData(CASImpl casImpl) {
    addCAS(casImpl, false);
  }

  /**
   * Add the CAS to be serialized. Note that we need the implementation here, the interface is not
   * enough.
   * 
   * @param cas
   *          The CAS to be serialized.
   */
  public void addCAS(CASImpl cas) {
    addCAS(cas, true);
  }

  /**
   * Add the CAS to be serialized.
   * 
   * @param cas
   *          The CAS to be serialized.
   * @param addMetaData
   *          - true to include metadata
   */
  public void addCAS(CASImpl cas, boolean addMetaData) {
    synchronized (cas.svd) {
      BinaryCasSerDes bcsd = cas.getBinaryCasSerDes();
      // next call runs the setup, which scans all the reachables
      final CommonSerDesSequential csds = BinaryCasSerDes4.getCsds(cas.getBaseCAS(), false); // saves
                                                                                             // the
                                                                                             // csds
                                                                                             // in
                                                                                             // the
                                                                                             // cas
      bcsd.scanAllFSsForBinarySerialization(null, csds); // no mark
      this.fsIndex = bcsd.getIndexedFSs(csds.fs2addr); // must follow scanAll...

      if (addMetaData) {
        // some details about current main-heap specifications
        // not required to deserialize
        // not sent for C++
        // is 7 words long
        // not serialized by custom serializers, only by Java object serialization
        int heapsz = bcsd.heap.getCellsUsed();
        this.heapMetaData = new int[] { Heap.getRoundedSize(heapsz), // a bit more than the size of
                                                                     // the used heap
            heapsz, // the position of the next (unused) slot in the heap
            heapsz, 0, 0, 1024, // initial size
            0 };
      }
      copyHeapsToArrays(bcsd);
    }
  }

  private void outputStringHeap(DataOutputStream dos, CASImpl cas,
          StringHeapDeserializationHelper shdh, BinaryCasSerDes bcsd) throws IOException {
    // output the strings

    // compute the number of total size of data in stringHeap
    // total size = char buffer length + length of strings in the string list;
    int stringHeapLength = shdh.charHeapPos;
    int stringListLength = 0;
    for (int i = 0; i < shdh.refHeap.length; i += 3) {
      int ref = shdh.refHeap[i + StringHeapDeserializationHelper.STRING_LIST_ADDR_OFFSET];
      // this is a string in the string list
      // get length and add to total string heap length
      if (ref != 0) {
        // terminate each string with a null
        stringListLength += 1 + bcsd.stringHeap.getStringForCode(ref).length();
      }
    }

    int stringTotalLength = stringHeapLength + stringListLength;
    if (stringHeapLength == 0 && stringListLength > 0) {
      // nothing from stringHeap
      // add 1 for the null at the beginning
      stringTotalLength += 1;
    }
    dos.writeInt(stringTotalLength);

    // write the data in the stringheap, if there is any
    if (stringTotalLength > 0) {
      if (shdh.charHeapPos > 0) {
        dos.writeChars(String.valueOf(shdh.charHeap, 0, shdh.charHeapPos));
      } else {
        // no stringheap data
        // if there is data in the string lists, write a leading 0
        if (stringListLength > 0) {
          dos.writeChar(0);
        }
      }

      // word alignment
      if (stringTotalLength % 2 != 0) {
        dos.writeChar(0);
      }
    }

    // write out the string ref heap
    // each reference consist of a offset into stringheap and a length
    int refheapsz = ((shdh.refHeap.length - StringHeapDeserializationHelper.FIRST_CELL_REF)
            / StringHeapDeserializationHelper.REF_HEAP_CELL_SIZE) * 2;
    refheapsz++;
    dos.writeInt(refheapsz);
    dos.writeInt(0);
    for (int i = StringHeapDeserializationHelper.FIRST_CELL_REF; i < shdh.refHeap.length; i += 3) {
      dos.writeInt(shdh.refHeap[i + StringHeapDeserializationHelper.CHAR_HEAP_POINTER_OFFSET]);
      dos.writeInt(shdh.refHeap[i + StringHeapDeserializationHelper.CHAR_HEAP_STRLEN_OFFSET]);
    }
  }

  void addTsiCAS(CASImpl cas, OutputStream ostream) {

  }

  // @formatter:off
  /**
   * Serializes the CAS data and writes it to the output stream.
   * ---------------------------------------------------------------------
   * Blob         Format    Element 
   * Size         Number of Description 
   * (bytes)      Elements 
   * ------------ --------- -------------------------------- 
   * 4            1         Blob key = "UIMA" in utf-8 
   * 4            1         Version (currently = 1) 
   * 4            1         size of 32-bit FS Heap array = s32H 
   * 4            s32H      32-bit FS heap array 
   * 4            1         size of 16-bit string Heap array = sSH  
   * 2            sSH       16-bit string heap array 
   * 4            1         size of string Ref Heap zrray = sSRH 
   * 4            2*sSRH    string ref offsets and lengths 
   * 4            1         size of FS index array = sFSI 
   * 4            sFSI      FS index array
   * 4            1         size of 8-bit Heap array = s8H  
   * 1            s8H       8-bit Heap array 
   * 4            1         size of 16-bit Heap array = s16H 
   * 2            s16H      16-bit Heap array 
   * 4            1         size of 64-bit Heap array = s64H 
   * 8            s64H      64-bit Heap array
   * ---------------------------------------------------------------------
   * 
   * @param cas
   *          The CAS to be serialized. ostream The output stream.
   * @param ostream
   *          -
   */
  // @formatter:on
  public void addCAS(CASImpl cas, OutputStream ostream) {
    addCAS(cas, ostream, false);
  }

  public void addCAS(CASImpl cas, OutputStream ostream, boolean includeTsi) {
    synchronized (cas.svd) {
      final BinaryCasSerDes bcsd = cas.getBinaryCasSerDes();

      // next call runs the setup, which scans all the reachables
      // these may have changed since this was previously computed due to updates in the CAS
      final CommonSerDesSequential csds = BinaryCasSerDes4.getCsds(cas.getBaseCAS(), false); // saves
                                                                                             // the
                                                                                             // csds
                                                                                             // in
                                                                                             // the
                                                                                             // cas,
                                                                                             // used
                                                                                             // for
                                                                                             // possible
                                                                                             // future
                                                                                             // delta
                                                                                             // deser
      bcsd.scanAllFSsForBinarySerialization(null, csds); // no mark

      try {

        DataOutputStream dos = new DataOutputStream(ostream);

        // get the indexed FSs for all views
        this.fsIndex = bcsd.getIndexedFSs(csds.fs2addr);

        // output the key and version number
        CommonSerDes.createHeader().seqVer(2) // 0 original, 1 UIMA-4743 2 for uima v3
                .typeSystemIndexDefIncluded(includeTsi).v3().write(dos);

        if (includeTsi) {
          CasIOUtils.writeTypeSystem(cas, ostream, true);
        }

        // output the FS heap
        final int heapSize = bcsd.heap.getCellsUsed();
        dos.writeInt(heapSize);
        // writing the 0th (null) element, because that's what V2 did
        final int[] vs = bcsd.heap.heap;
        for (int i = 0; i < heapSize; i++) {
          dos.writeInt(vs[i]);
        }

        // output the strings
        StringHeapDeserializationHelper shdh = bcsd.stringHeap.serialize();

        outputStringHeap(dos, cas, shdh, bcsd);
        // // compute the number of total size of data in stringHeap
        // // total size = char buffer length + length of strings in the string list;
        // int stringHeapLength = shdh.charHeapPos;
        // int stringListLength = 0;
        // for (int i = 0; i < shdh.refHeap.length; i += 3) {
        // int ref = shdh.refHeap[i + StringHeapDeserializationHelper.STRING_LIST_ADDR_OFFSET];
        // // this is a string in the string list
        // // get length and add to total string heap length
        // if (ref != 0) {
        // // terminate each string with a null
        // stringListLength += 1 + cas.getStringHeap().getStringForCode(ref).length();
        // }
        // }
        //
        // int stringTotalLength = stringHeapLength + stringListLength;
        // if (stringHeapLength == 0 && stringListLength > 0) {
        // // nothing from stringHeap
        // // add 1 for the null at the beginning
        // stringTotalLength += 1;
        // }
        // dos.writeInt(stringTotalLength);
        //
        // // write the data in the stringheap, if there is any
        // if (stringTotalLength > 0) {
        // if (shdh.charHeapPos > 0) {
        // dos.writeChars(String.valueOf(shdh.charHeap, 0, shdh.charHeapPos));
        // } else {
        // // no stringheap data
        // // if there is data in the string lists, write a leading 0
        // if (stringListLength > 0) {
        // dos.writeChar(0);
        // }
        // }
        //
        // // word alignment
        // if (stringTotalLength % 2 != 0) {
        // dos.writeChar(0);
        // }
        // }
        //
        // // write out the string ref heap
        // // each reference consist of a offset into stringheap and a length
        // int refheapsz = ((shdh.refHeap.length - StringHeapDeserializationHelper.FIRST_CELL_REF) /
        // StringHeapDeserializationHelper.REF_HEAP_CELL_SIZE) * 2;
        // refheapsz++;
        // dos.writeInt(refheapsz);
        // dos.writeInt(0);
        // for (int i = StringHeapDeserializationHelper.FIRST_CELL_REF; i < shdh.refHeap.length; i
        // += 3) {
        // dos.writeInt(shdh.refHeap[i + StringHeapDeserializationHelper.CHAR_HEAP_POINTER_OFFSET]);
        // dos.writeInt(shdh.refHeap[i + StringHeapDeserializationHelper.CHAR_HEAP_STRLEN_OFFSET]);
        // }

        // output the index FSs
        dos.writeInt(this.fsIndex.length);
        for (int i = 0; i < this.fsIndex.length; i++) {
          dos.writeInt(this.fsIndex[i]);
        }

        // 8bit heap
        final int byteheapsz = bcsd.byteHeap.getSize();
        dos.writeInt(byteheapsz);
        dos.write(bcsd.byteHeap.heap, 0, byteheapsz);

        // word alignment
        int align = (4 - (byteheapsz % 4)) % 4;
        for (int i = 0; i < align; i++) {
          dos.writeByte(0);
        }

        // 16bit heap
        final int shortheapsz = bcsd.shortHeap.getSize();
        dos.writeInt(shortheapsz);
        final short[] sh = bcsd.shortHeap.heap;
        for (int i = 0; i < shortheapsz; i++) {
          dos.writeShort(sh[i]);
        }

        // word alignment
        if (shortheapsz % 2 != 0) {
          dos.writeShort(0);
        }

        // 64bit heap
        int longheapsz = bcsd.longHeap.getSize();
        dos.writeInt(longheapsz);
        final long[] lh = bcsd.longHeap.heap;
        for (int i = 0; i < longheapsz; i++) {
          dos.writeLong(lh[i]);
        }
      } catch (IOException e) {
        throw new CASRuntimeException(CASRuntimeException.BLOB_SERIALIZATION, e.getMessage());
      }

      bcsd.setHeapExtents();
      // non delta serialization
      csds.setHeapEnd(bcsd.nextHeapAddrAfterMark);
    }
  }

  // @formatter:off
  /**
   * Serializes only new and modified FS and index operations made after the tracking mark is
   * created. Serializes CAS data in binary Delta format described below and writes it to the output
   * stream.
   * 
   * ElementSize NumberOfElements Description
   * ----------- ---------------- ---------------------------------------------------------
   * 4				   1				        Blob key = "UIMA" in utf-8 (byte order flag)
   * 4				   1				        Version (1 = complete cas, 2 = delta cas)
   * 4				   1				        size of 32-bit heap array = s32H
   * 4           s32H             32-bit FS heap array (new elements) 
   * 4           1 				        size of 16-bit string Heap array = sSH 
   * 2 			     sSH 				      16-bit string heap array (new strings)
   * 4 				   1 				        size of string Ref Heap array = sSRH 
   * 4 			     2*sSRH				    string ref offsets and lengths (for new strings)
   * 4           1        				number of modified, preexisting 32-bit modified FS heap elements = sM32H
   * 4			     2*sM32H          32-bit heap offset and value (preexisting cells modified)	 
   * 4 	         1 	        			size of FS index array = sFSI 
   * 4		       sFSI 	    			FS index array in Delta format
   * 4 		 	  	 1 			        	size of 8-bit Heap array = s8H 
   * 1 			     s8H 			      	8-bit Heap array (new elements)
   * 4 			  	 1 			        	size of 16-bit Heap array = s16H
   * 2 			     s16H 				    16-bit Heap array (new elements) 
   * 4 			  	 1 			        	size of 64-bit Heap array = s64H 
   * 8 			     s64H 				    64-bit Heap array (new elements)
   * 4				   1			        	number of modified, preexisting 8-bit heap elements = sM8H
   * 4			     sM8H             8-bit heap offsets (preexisting cells modified)
   * 1			     sM8H             8-bit heap values  (preexisting cells modified)
   * 4			  	 1				        number of modified, preexisting 16-bit heap elements = sM16H
   * 4			     sM16H            16-bit heap offsets (preexisting cells modified)
   * 2			     sM16H            16-bit heap values  (preexisting cells modified)
   * 4			  	 1				        number of modified, preexisting 64-bit heap elements = sM64H
   * 4			     sM64H            64-bit heap offsets (preexisting cells modified)
   * 2			     sM64H            64-bit heap values  (preexisting cells modified)
   * 
   * 
   * @param cas
   *          -
   * @param ostream
   *          -
   * @param trackingMark
   *          -
   */
  // @formatter:on
  public void addCAS(CASImpl cas, OutputStream ostream, Marker trackingMark) {
    if (!trackingMark.isValid()) {
      throw new CASRuntimeException(CASRuntimeException.INVALID_MARKER, "Invalid Marker.");
    }
    MarkerImpl mark = (MarkerImpl) trackingMark;
    synchronized (cas.svd) {
      final BinaryCasSerDes bcsd = cas.getBinaryCasSerDes();
      // next call runs the setup, which scans all the reachables
      final CommonSerDesSequential csds = BinaryCasSerDes4.getCsds(cas.getBaseCAS(), true); // saves
                                                                                            // the
                                                                                            // csds
                                                                                            // in
                                                                                            // the
                                                                                            // cas
      // because the output is only the new elements, this populates the arrays with only the new
      // elements
      // Note: all heaps reserve slot 0 for null, real data starts at position 1
      List<TOP> all = bcsd.scanAllFSsForBinarySerialization(mark, csds);

      // if (csds.getHeapEnd() == 0) {
      // System.out.println("debug");
      // }
      final Obj2IntIdentityHashMap<TOP> fs2auxOffset = new Obj2IntIdentityHashMap<>(TOP.class,
              TOP._singleton);

      int byteOffset = 1;
      int shortOffset = 1;
      int longOffset = 1;

      // scan all below mark and set up maps from aux array FSs to the offset to where the array
      // starts in the modelled aux heap
      for (TOP fs : all) {
        if (trackingMark.isNew(fs)) {
          break;
        }
        if (fs instanceof CommonArrayFS) {
          CommonArrayFS ca = (CommonArrayFS) fs;
          SlotKind kind = fs._getTypeImpl().getComponentSlotKind();
          switch (kind) {
            case Slot_BooleanRef:
            case Slot_ByteRef:
              fs2auxOffset.put(fs, byteOffset);
              byteOffset += ca.size();
              break;
            case Slot_ShortRef:
              fs2auxOffset.put(fs, shortOffset);
              shortOffset += ca.size();
              break;
            case Slot_LongRef:
            case Slot_DoubleRef:
              fs2auxOffset.put(fs, longOffset);
              longOffset += ca.size();
              break;
            default:
          } // end of switch
        } // end of if commonarray
        else { // fs has feature slots
          // model long and double refs which use up the long aux heap for 1 cell
          TypeImpl ti = fs._getTypeImpl();
          longOffset += ti.getNbrOfLongOrDoubleFeatures();
        }
      } // end of for

      try {
        DataOutputStream dos = new DataOutputStream(ostream);

        // get the indexed FSs
        this.fsIndex = bcsd.getDeltaIndexedFSs(mark, csds.fs2addr);

        CommonSerDes.createHeader().delta().seqVer(2) // 1 for UIMA-4743 2 for uima v3
                .v3().write(dos);

        // output the new FS heap cells

        final int heapSize = bcsd.heap.getCellsUsed() - 1; // first entry (null) is not written

        // Write heap - either the entire heap, or for delta, just the new part

        dos.writeInt(heapSize);
        final int[] vs = bcsd.heap.heap;
        for (int i = 1; i <= heapSize; i++) { // <= because heapsize is 1 less than cells used, but
                                              // we start at index 1
          dos.writeInt(vs[i]);
        }

        // convert v3 change-logging to v2 form, setting the chgXX-addr and chgXX-values lists.
        // we do this before the strings or aux arrays are written out, because this
        // could make additions to those.

        // addresses are in terms of modeled v2 arrays, as absolute addr in the aux arrays, and
        // values
        List<AddrPlusValue> chgMainAvs = new ArrayList<>();
        List<AddrPlusValue> chgByteAvs = new ArrayList<>();
        List<AddrPlusValue> chgShortAvs = new ArrayList<>();
        List<AddrPlusValue> chgLongAvs = new ArrayList<>();

        scanModifications(bcsd, csds, cas.getModifiedFSList(), fs2auxOffset, chgMainAvs, chgByteAvs,
                chgShortAvs, chgLongAvs);

        // output the new strings
        StringHeapDeserializationHelper shdh = bcsd.stringHeap.serialize(1);

        outputStringHeap(dos, cas, shdh, bcsd);

        // output modified FS Heap cells
        // this is output in a way that is the total number of slots changed ==
        // the sum over all fsChanges of
        // for each fsChange, the number of slots (heap-sited-array or feature) modified
        final int modHeapSize = chgMainAvs.size();
        dos.writeInt(modHeapSize); // num modified
        for (AddrPlusValue av : chgMainAvs) {
          dos.writeInt(av.addr);
          dos.writeInt((int) av.value);
        }

        // output the index FSs
        dos.writeInt(this.fsIndex.length);
        for (int i = 0; i < this.fsIndex.length; i++) {
          dos.writeInt(this.fsIndex[i]);
        }

        // 8bit heap new
        int byteheapsz = bcsd.byteHeap.getSize() - 1;
        dos.writeInt(byteheapsz);
        dos.write(bcsd.byteHeap.heap, 1, byteheapsz); // byte 0 not used

        // word alignment
        int align = (4 - (byteheapsz % 4)) % 4;
        for (int i = 0; i < align; i++) {
          dos.writeByte(0);
        }

        // 16bit heap new
        int shortheapsz = bcsd.shortHeap.getSize() - 1;
        dos.writeInt(shortheapsz);
        for (int i = 1; i <= shortheapsz; i++) { // <= in test because we're starting at 1
          dos.writeShort(bcsd.shortHeap.heap[i]);
        }

        // word alignment
        if (shortheapsz % 2 != 0) {
          dos.writeShort(0);
        }

        // 64bit heap new
        int longheapsz = bcsd.longHeap.getSize() - 1;
        dos.writeInt(longheapsz);
        for (int i = 1; i <= longheapsz; i++) {
          dos.writeLong(bcsd.longHeap.heap[i]);
        }

        // 8bit heap modified cells
        writeMods(chgByteAvs, dos, av -> dos.writeByte((byte) av.value));

        // word alignment
        align = (4 - (chgByteAvs.size() % 4)) % 4;
        for (int i = 0; i < align; i++) {
          dos.writeByte(0);
        }

        // 16bit heap modified cells
        writeMods(chgShortAvs, dos, av -> dos.writeShort((short) av.value));

        // word alignment
        if (chgShortAvs.size() % 2 != 0) {
          dos.writeShort(0);
        }

        // 64bit heap modified cells
        writeMods(chgLongAvs, dos, av -> dos.writeLong(av.value));

      } catch (IOException e) {
        throw new CASRuntimeException(CASRuntimeException.BLOB_SERIALIZATION, e.getMessage());
      }
    }
  }

  private void writeMods(List<AddrPlusValue> avs, DataOutputStream dos,
          Consumer_T_withIOException<AddrPlusValue> writeValue) throws IOException {
    int size = avs.size();
    dos.writeInt(size);
    for (AddrPlusValue av : avs) {
      dos.writeInt(av.addr);
    }
    for (AddrPlusValue av : avs) {
      writeValue.accept(av);
    }
  }

  /**
   * The offset in the modeled heaps:
   * 
   * @param index
   *          the 0-based index into the array
   * @param fs
   *          the feature structure representing the array
   * @return the addr into an aux array or main heap
   */
  private static int convertArrayIndexToAuxHeapAddr(BinaryCasSerDes bcsd, int index, TOP fs,
          Obj2IntIdentityHashMap<TOP> fs2auxOffset) {
    int offset = fs2auxOffset.get(fs);
    assert offset > 0;
    return offset;
  }

  private static int convertArrayIndexToMainHeapAddr(int index, TOP fs,
          Obj2IntIdentityHashMap<TOP> fs2addr) {
    return fs2addr.get(fs) + 2 + index;
  }

  /**
   * Scan the v3 fsChange info and produce v2 style info into chgXxxAddr, chgXxxValue
   * 
   * A prescan approach is needed in order to write the number of modifications preceding the write
   * of the values (which unfortunately were written to the same stream in V2).
   * 
   * @param bcsd
   *          holds the model needed for v2 aux arrays
   * @param cas
   *          the cas to use for the delta serialization
   * @param chgMainHeapAddr
   *          an ordered collection of changed addresses as an array for the main heap
   * @param chgByteAddr
   *          an ordered collection of changed addresses as an array for the aux byte heap
   * @param chgShortAddr
   *          an ordered collection of changed addresses as an array for the aus short heap
   * @param chgLongAddr
   *          an ordered collection of changed addresses as an array for the aux long heap
   * 
   * @param chgMainHeapValue
   *          corresponding values
   */
  static void scanModifications(BinaryCasSerDes bcsd, CommonSerDesSequential csds,
          FsChange[] fssModified, Obj2IntIdentityHashMap<TOP> fs2auxOffset,
          List<AddrPlusValue> chgMainAvs, List<AddrPlusValue> chgByteAvs,
          List<AddrPlusValue> chgShortAvs, List<AddrPlusValue> chgLongAvs) {

    // scan the sorted mods to precompute the various change items:
    // changed main heap: addr and new slot value
    // for aux heaps: new values.
    // Note: the changed main heap values point to these (and also to new string values)
    // -- for byte (and boolean), short, long
    // for aux heaps: changed (updated) values: the addr(s) followed by the values
    final Obj2IntIdentityHashMap<TOP> fs2addr = csds.fs2addr;
    for (FsChange fsChange : fssModified) {
      final TOP fs = fsChange.fs;
      final TypeImpl type = fs._getTypeImpl();
      if (fsChange.arrayUpdates != null) {
        switch (type.getComponentSlotKind()) {

          case Slot_BooleanRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgByteAvs.add(new AddrPlusValue(
                      convertArrayIndexToAuxHeapAddr(bcsd, index, fs, fs2auxOffset),
                      ((BooleanArray) fs).get(index) ? 1 : 0));
            });
            break;

          case Slot_ByteRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgByteAvs.add(new AddrPlusValue(
                      convertArrayIndexToAuxHeapAddr(bcsd, index, fs, fs2auxOffset),
                      ((ByteArray) fs).get(index)));
            });
            break;

          case Slot_ShortRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgShortAvs.add(new AddrPlusValue(
                      convertArrayIndexToAuxHeapAddr(bcsd, index, fs, fs2auxOffset),
                      ((ShortArray) fs).get(index)));
            });
            break;

          case Slot_LongRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgLongAvs.add(new AddrPlusValue(
                      convertArrayIndexToAuxHeapAddr(bcsd, index, fs, fs2auxOffset),
                      ((LongArray) fs).get(index)));
            });
            break;

          case Slot_DoubleRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgLongAvs.add(new AddrPlusValue(
                      convertArrayIndexToAuxHeapAddr(bcsd, index, fs, fs2auxOffset),
                      CASImpl.double2long(((DoubleArray) fs).get(index))));
            });
            break;

          // heap stored arrays
          case Slot_Int:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgMainAvs.add(new AddrPlusValue(convertArrayIndexToMainHeapAddr(index, fs, fs2addr),
                      ((IntegerArray) fs).get(index)));
            });
            break;

          case Slot_Float:
            fsChange.arrayUpdates.forAllInts(index -> {
              chgMainAvs.add(new AddrPlusValue(convertArrayIndexToMainHeapAddr(index, fs, fs2addr),
                      CASImpl.float2int(((FloatArray) fs).get(index))));
            });
            break;

          case Slot_StrRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              int v = bcsd.nextStringHeapAddrAfterMark
                      + bcsd.stringHeap.addString(((StringArray) fs).get(index));
              chgMainAvs.add(
                      new AddrPlusValue(convertArrayIndexToMainHeapAddr(index, fs, fs2addr), v));
            });
            break;

          case Slot_HeapRef:
            fsChange.arrayUpdates.forAllInts(index -> {
              TOP tgtFs = (TOP) ((FSArray) fs).get(index);
              chgMainAvs.add(new AddrPlusValue(convertArrayIndexToMainHeapAddr(index, fs, fs2addr),
                      fs2addr.get(tgtFs)));
            });
            break;

          default:
            Misc.internalError();
        } // end of switch
      } else { // end of if-array
        // 1 or more features modified
        if (fs instanceof UimaSerializable) {
          ((UimaSerializable) fs)._save_to_cas_data();
        }
        BitSet fm = fsChange.featuresModified;
        int offset = fm.nextSetBit(0);
        while (offset >= 0) {
          int addr = csds.fs2addr.get(fs) + offset + 1; // skip over type code);
          int value = 0;

          FeatureImpl feat = type.getFeatureImpls()[offset];

          switch (feat.getSlotKind()) {
            case Slot_Boolean:
              value = fs._getBooleanValueNc(feat) ? 1 : 0;
              break;

            case Slot_Byte:
              value = fs._getByteValueNc(feat);
              break;
            case Slot_Short:
              value = fs._getShortValueNc(feat);
              break;
            case Slot_Int:
              value = fs._getIntValueNc(feat);
              break;
            case Slot_Float:
              value = CASImpl.float2int(fs._getFloatValueNc(feat));
              break;
            case Slot_LongRef: {
              value = bcsd.nextLongHeapAddrAfterMark
                      + bcsd.longHeap.addLong(fs._getLongValueNc(feat));
              break;
            }
            case Slot_DoubleRef: {
              value = bcsd.nextLongHeapAddrAfterMark
                      + bcsd.longHeap.addLong(CASImpl.double2long(fs._getDoubleValueNc(feat)));
              break;
            }
            case Slot_StrRef: {
              value = bcsd.nextStringHeapAddrAfterMark
                      + bcsd.stringHeap.addString(fs._getStringValueNc(feat));
              break;
            }
            case Slot_HeapRef:
              value = fs2addr.get(fs._getFeatureValueNc(feat));
              break;
            default:
              Misc.internalError();
          } // end of switch

          chgMainAvs.add(new AddrPlusValue(addr, value));

          offset = fm.nextSetBit(offset + 1);
        } // loop over changed feature offsets
      } // end of features-modified case
    } // end of for all fsChanges
  }

  // /**
  // * Serialize with compression
  // * Target is not constrained to the C++ format
  // * For non delta serialization, pass marker with 0 as values
  // * @throws IOException
  // */
  //
  // public void serialize(CASImpl cas, OutputStream ostream, Marker marker) throws IOException {
  // if (marker != null && !marker.isValid() ) {
  // CASRuntimeException exception = new CASRuntimeException(
  // CASRuntimeException.INVALID_MARKER, new String[] { "Invalid Marker." });
  // throw exception;
  // }
  // MarkerImpl mark = (MarkerImpl) marker;
  // DataOutputStream dos = new DataOutputStream(ostream);
  //
  // this.fsIndex = cas.getDeltaIndexedFSs(mark);
  // outputVersion(3 , dos);
  //
  // // output the new FS heap cells
  // final int heapSize = cas.getHeap().getCellsUsed() - mark.nextFSId);
  // compressHeapOut(dos, cas, heapSize, mark)
  //
  // // output the new strings
  //
  // }

  int[] getHeapMetadata() {
    return this.heapMetaData;
  }

  int[] getHeapArray() {
    return this.heapArray;
  }

  String[] getStringTable() {
    return this.stringTable;
  }

  int[] getFSIndex() {
    return this.fsIndex;
  }

  byte[] getByteArray() {
    return this.byteHeapArray;
  }

  short[] getShortArray() {
    return this.shortHeapArray;
  }

  long[] getLongArray() {
    return this.longHeapArray;
  }

  private void copyHeapsToArrays(BinaryCasSerDes bcsd) {
    this.heapArray = bcsd.heap.toArray();
    this.byteHeapArray = bcsd.byteHeap.toArray();
    this.shortHeapArray = bcsd.shortHeap.toArray();
    this.longHeapArray = bcsd.longHeap.toArray();
    this.stringTable = bcsd.stringHeap.toArray();
  }
}
