content: /*
   * [The "BSD licence"]
   * Copyright (c) 2010 Ben Gruver (JesusFreke)
   * All rights reserved.
   *
   * Redistribution and use in source and binary forms, with or without
   * modification, are permitted provided that the following conditions
   * are met:
   * 1. Redistributions of source code must retain the above copyright
   *    notice, this list of conditions and the following disclaimer.
   * 2. Redistributions in binary form must reproduce the above copyright
   *    notice, this list of conditions and the following disclaimer in the
   *    documentation and/or other materials provided with the distribution.
   * 3. The name of the author may not be used to endorse or promote products
   *    derived from this software without specific prior written permission.
   *
   * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
   * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
   * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
   * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
   * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
   * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
   * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
   * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
   * INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
   * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   */
  
  package org.jf.dexlib;
  
  import org.jf.dexlib.Util.*;
  
  import java.io.*;
  import java.security.DigestException;
  import java.security.MessageDigest;
  import java.security.NoSuchAlgorithmException;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.zip.Adler32;
  import java.util.zip.ZipEntry;
  import java.util.zip.ZipFile;
  
  /**
   * <h3>Main use cases</h3>
   *
   * <p>These are the main use cases that drove the design of this library</p>
   *
   * <ol>
   * <li><p><b>Annotate an existing dex file</b> - In this case, the intent is to document the structure of
   *    an existing dex file. We want to be able to read in the dex file, and then write out a dex file
   *    that is exactly the same (while adding annotation information to an AnnotatedOutput object)</p></li>
   *
   * <li><p><b>Canonicalize an existing dex file</b> - In this case, the intent is to rewrite an existing dex file
   *    so that it is in a canonical form. There is a certain amount of leeway in how various types of
   *    tems in a dex file are ordered or represented. It is sometimes useful to be able to easily
   *    compare a disassebled and reassembled dex file with the original dex file. If both dex-files are
   *    written canonically, they "should" match exactly, barring any explicit changes to the reassembled
   *    file.</p>
   *
   *    <p>Currently, there are a couple of pieces of information that probably won't match exactly
   *    <ul>
   *    <li>the order of exception handlers in the <code>EncodedCatchHandlerList</code> for a method</li>
   *    <li>the ordering of some of the debug info in the <code>{@link org.jf.dexlib.DebugInfoItem}</code> for a method</li>
   *    </ul></p>
   *
   *
   *    <p>Note that the above discrepancies should typically only be "intra-item" differences. They
   *    shouldn't change the size of the item, or affect how anything else is placed or laid out</p></li>
   *
   * <li><p><b>Creating a dex file from scratch</b> - In this case, a blank dex file is created and then classes
   *    are added to it incrementally by calling the {@link org.jf.dexlib.Section#intern intern} method of
   *    {@link DexFile#ClassDefsSection}, which will add all the information necessary to represent the given
   *    class. For example, when assembling a dex file from a set of assembly text files.</p>
   *
   *    <p>In this case, we can choose to write  the dex file in a canonical form or not. It is somewhat
   *    slower to write it in a canonical format, due to the extra sorting and calculations that are
   *    required.</p></li>
   *
   *
   * <li><p><b>Reading in the dex file</b> - In this case, the intent is to read in a dex file and expose all the
   *    data to the calling application. For example, when disassembling a dex file into a text based
   *    assembly format, or doing other misc processing of the dex file.</p></li>
   *
   *
   * <h3>Other use cases</h3>
   *
   * <p>These are other use cases that are possible, but did not drive the design of the library.
   * No effort was made to test these use cases or ensure that they work. Some of these could
   * probably be better achieved with a disassemble - modify - reassemble type process, using
   * smali/baksmali or another assembler/disassembler pair that are compatible with each other</p>
   *
   * <ul>
   * <li>deleting classes/methods/etc. from a dex file</li>
   * <li>merging 2 dex files</li>
   * <li>splitting a dex file</li>
   * <li>moving classes from 1 dex file to another</li>
   * <li>removing the debug information from a dex file</li>
   * <li>obfustication of a dex file</li>
   * </ul>
   */
  public class DexFile
  {
      /**
       * A mapping from ItemType to the section that contains items of the given type
       */
      private final Section[] sectionsByType;
  
      /**
       * Ordered lists of the indexed and offsetted sections. The order of these lists specifies the order
       * that the sections will be written in
       */
      private final IndexedSection[] indexedSections;
      private final OffsettedSection[] offsettedSections;
  
      /**
       * dalvik had a bug where it wrote the registers for certain types of debug info in a signed leb
       * format, instead of an unsigned leb format. There are no negative registers of course, but
       * certain positive values have a different encoding depending on whether they are encoded as
       * an unsigned leb128 or a signed leb128. Specifically, the signed leb128 is 1 byte longer in some cases.
       *
       * This determine whether we should keep any signed registers as signed, or force all register to
       * unsigned. By default we don't keep track of whether they were signed or not, and write them back
       * out as unsigned. This option only has an effect when reading an existing dex file. It has no
       * effect when a dex file is created from scratch
       *
       * The 2 main use-cases in play are
       * 1. Annotate an existing dex file - In this case, preserveSignedRegisters should be false, so that we keep
       * track of any signed registers and write them back out as signed Leb128 values.
       *
       * 2. Canonicalize an existing dex file - In this case, fixRegisters should be true, so that all
       * registers in the debug info are written as unsigned Leb128 values regardless of how they were
       * originally encoded
       */
      private final boolean preserveSignedRegisters;
  
      /**
       * When true, any instructions in a code item are skipped over instead of being read in. This is useful when
       * you only need the information about the classes and their methods, for example, when loading the BOOTCLASSPATH
       * jars in order to analyze a dex file
       */
      private final boolean skipInstructions;
  
      /**
       * When true, this prevents any sorting of the items during placement of the dex file. This
       * should *only* be set to true when this dex file was read in from an existing (valid) dex file,
       * and no modifications were made (i.e. no items added or deleted). Otherwise it is likely that
       * an invalid dex file will be generated.
       *
       * This is useful for the first use case (annotating an existing dex file). This ensures the items
       * retain the same order as in the original dex file.
       */
      private boolean inplace = false;
  
      /**
       * When true, this imposes an full ordering on all the items, to force them into a (possibly
       * arbitrary) canonical order. When false, only the items that the dex format specifies
       * an order for are sorted. The rest of the items are not ordered.
       *
       * This is useful for the second use case (canonicalizing an existing dex file) or possibly for
       * the third use case (creating a dex file from scratch), if there is a need to write the new
       * dex file in a canonical form.
       */
      private boolean sortAllItems = false;
  
  
      /**
       * this is used to access the dex file from within inner classes, when they declare fields or
       * variable that hide fields on this object
       */
      private final DexFile dexFile = this;
  
      /**
       * Is this file an odex file? This is only set when reading in an odex file
       */
      private boolean isOdex = false;
  
      private OdexHeader odexHeader;
      private OdexDependencies odexDependencies;
  
      private int dataOffset;
      private int dataSize;
      private int fileSize;
  
      /**
       * A private constructor containing common code to initialize the section maps and lists
       * @param preserveSignedRegisters If true, keep track of any registers in the debug information
       * @param skipInstructions If true, skip the instructions in any code item.
       * that are signed, so they will be written in the same format. See
       * <code>getPreserveSignedRegisters()</code>
       */
      private DexFile(boolean preserveSignedRegisters, boolean skipInstructions) {
          this.preserveSignedRegisters = preserveSignedRegisters;
          this.skipInstructions = skipInstructions;
  
          sectionsByType = new Section[] {
              StringIdsSection,
                  TypeIdsSection,
                  ProtoIdsSection,
                  FieldIdsSection,
                  MethodIdsSection,
                  ClassDefsSection,
                  TypeListsSection,
                  AnnotationSetRefListsSection,
                  AnnotationSetsSection,
                  ClassDataSection,
                  CodeItemsSection,
                  AnnotationDirectoriesSection,
                  StringDataSection,
                  DebugInfoItemsSection,
                  AnnotationsSection,
                  EncodedArraysSection,
                  null,
                  null
          };
  
          indexedSections = new IndexedSection[] {
              StringIdsSection,
                  TypeIdsSection,
                  ProtoIdsSection,
                  FieldIdsSection,
                  MethodIdsSection,
                  ClassDefsSection
          };
  
          offsettedSections = new OffsettedSection[] {
              AnnotationSetRefListsSection,
                  AnnotationSetsSection,
                  CodeItemsSection,
                  AnnotationDirectoriesSection,
                  TypeListsSection,
                  StringDataSection,
                  AnnotationsSection,
                  EncodedArraysSection,
                  ClassDataSection,
                  DebugInfoItemsSection
          };
      }
  
  
      /**
       * Construct a new DexFile instance by reading in the given dex file.
       * @param file The dex file to read in
       * @throws IOException if an IOException occurs
       */
      public DexFile(String file)
          throws IOException {
          this(new File(file), true, false);
      }
  
      /**
       * Construct a new DexFile instance by reading in the given dex file,
       * and optionally keep track of any registers in the debug information that are signed,
       * so they will be written in the same format.
       * @param file The dex file to read in
       * @param preserveSignedRegisters If true, keep track of any registers in the debug information
       * that are signed, so they will be written in the same format. See
       * @param skipInstructions If true, skip the instructions in any code item.
       * <code>getPreserveSignedRegisters()</code>
       * @throws IOException if an IOException occurs
       */
      public DexFile(String file, boolean preserveSignedRegisters, boolean skipInstructions)
          throws IOException {
          this(new File(file), preserveSignedRegisters, skipInstructions);
      }
  
      /**
       * Construct a new DexFile instance by reading in the given dex file.
       * @param file The dex file to read in
       * @throws IOException if an IOException occurs
       */
      public DexFile(File file)
          throws IOException {
          this(file, true, false);
      }
  
      /**
       * Construct a new DexFile instance by reading in the given dex file,
       * and optionally keep track of any registers in the debug information that are signed,
       * so they will be written in the same format.
       * @param file The dex file to read in
       * @param preserveSignedRegisters If true, keep track of any registers in the debug information
       * that are signed, so they will be written in the same format.
       * @param skipInstructions If true, skip the instructions in any code item.
       * @see #getPreserveSignedRegisters
       * @throws IOException if an IOException occurs
       */
      public DexFile(File file, boolean preserveSignedRegisters, boolean skipInstructions)
          throws IOException {
          this(preserveSignedRegisters, skipInstructions);
  
          long fileLength;
          byte[] magic = FileUtils.readFile(file, 0, 8);
  
          InputStream inputStream = null;
          Input in = null;
          ZipFile zipFile = null;
  
          try {
              //do we have a zip file?
              if (magic[0] == 0x50 && magic[1] == 0x4B) {
                  zipFile = new ZipFile(file);
                  ZipEntry zipEntry = zipFile.getEntry("classes.dex");
                  if (zipEntry == null) {
                      throw new NoClassesDexException("zip file " + file.getName() + " does not contain a classes.dex " +
                              "file");
                  }
                  fileLength = zipEntry.getSize();
                  if (fileLength < 40) {
                      throw new RuntimeException("The classes.dex file in " + file.getName() + " is too small to be a" +
                              " valid dex file");
                  } else if (fileLength > Integer.MAX_VALUE) {
                      throw new RuntimeException("The classes.dex file in " + file.getName() + " is too large to read in");
                  }
                  inputStream = new BufferedInputStream(zipFile.getInputStream(zipEntry));
  
                  inputStream.mark(8);
                  for (int i=0; i<8; i++) {
                      magic[i] = (byte)inputStream.read();
                  }
                  inputStream.reset();
              } else {
                  fileLength = file.length();
                  if (fileLength < 40) {
                      throw new RuntimeException(file.getName() + " is too small to be a valid dex file");
                  }
                  if (fileLength < 40) {
                      throw new RuntimeException(file.getName() + " is too small to be a valid dex file");
                  } else if (fileLength > Integer.MAX_VALUE) {
                      throw new RuntimeException(file.getName() + " is too large to read in");
                  }
                  inputStream = new FileInputStream(file);
              }
  
              byte[] dexMagic, odexMagic;
              boolean isDex = false;
              this.isOdex = false;
  
              if (Arrays.equals(magic, HeaderItem.MAGIC)) {
                  isDex = true;
              } else if (Arrays.equals(magic, OdexHeader.MAGIC_35)) {
                  isOdex = true;
              } else if (Arrays.equals(magic, OdexHeader.MAGIC_36)) {
                  isOdex = true;
              }
  
              if (isOdex) {
                  byte[] odexHeaderBytes = FileUtils.readStream(inputStream, 40);
                  Input odexHeaderIn = new ByteArrayInput(odexHeaderBytes);
                  odexHeader = new OdexHeader(odexHeaderIn);
  
                  int dependencySkip = odexHeader.depsOffset - odexHeader.dexOffset - odexHeader.dexLength;
                  if (dependencySkip < 0) {
                      throw new ExceptionWithContext("Unexpected placement of the odex dependency data");
                  }
  
                  if (odexHeader.dexOffset > 40) {
                      FileUtils.readStream(inputStream, odexHeader.dexOffset - 40);
                  }
  
                  in = new ByteArrayInput(FileUtils.readStream(inputStream, odexHeader.dexLength));
  
                  if (dependencySkip > 0) {
                      FileUtils.readStream(inputStream, dependencySkip);
                  }
  
                  odexDependencies = new OdexDependencies(
                          new ByteArrayInput(FileUtils.readStream(inputStream, odexHeader.depsLength)));
              } else if (isDex) {
                  in = new ByteArrayInput(FileUtils.readStream(inputStream, (int)fileLength));
              } else {
                  StringBuffer sb = new StringBuffer("bad magic value:");
                  for (int i=0; i<8; i++) {
                      sb.append(" ");
                      sb.append(Hex.u1(magic[i]));
                  }
                  throw new RuntimeException(sb.toString());
              }
          } finally {
              if (inputStream != null) {
                  inputStream.close();
              }
              if (zipFile != null) {
                  zipFile.close();
              }
          }
  
          ReadContext readContext = new ReadContext();
  
          HeaderItem.readFrom(in, 0, readContext);
  
          //the map offset was set while reading in the header item
          int mapOffset = readContext.getSectionOffset(ItemType.TYPE_MAP_LIST);
  
          in.setCursor(mapOffset);
          MapItem.readFrom(in, 0, readContext);
  
          //the sections are ordered in such a way that the item types
          Section sections[] = new Section[] {
              StringDataSection,
                  StringIdsSection,
                  TypeIdsSection,
                  TypeListsSection,
                  ProtoIdsSection,
                  FieldIdsSection,
                  MethodIdsSection,
                  AnnotationsSection,
                  AnnotationSetsSection,
                  AnnotationSetRefListsSection,
                  AnnotationDirectoriesSection,
                  DebugInfoItemsSection,
                  CodeItemsSection,
                  ClassDataSection,
                  EncodedArraysSection,
                  ClassDefsSection
          };
  
          for (Section section: sections) {
              if (section == null) {
                  continue;
              }
  
              if (skipInstructions && (section == CodeItemsSection || section == DebugInfoItemsSection)) {
                  continue;
              }
  
              int sectionOffset = readContext.getSectionOffset(section.ItemType);
              if (sectionOffset > 0) {
                  int sectionSize = readContext.getSectionSize(section.ItemType);
                  in.setCursor(sectionOffset);
                  section.readFrom(sectionSize, in, readContext);
              }
          }
      }
  
      public DexFile(byte[] input, boolean preserveSignedRegisters, boolean skipInstructions) {
          this(preserveSignedRegisters, skipInstructions);
  
          long fileLength;
          byte[] magic = new byte[8];
          System.arraycopy(input,0,magic,0,8);
  
          Input in = null;
          fileLength = input.length;
          if (fileLength < 40) {
              throw new RuntimeException( " is too small to be a valid dex file");
          } else if (fileLength > Integer.MAX_VALUE) {
              throw new RuntimeException( " is too large to read in");
          }
  
  
          if (Arrays.equals(magic, HeaderItem.MAGIC)) {
              in = new ByteArrayInput(input);
          } else {
              StringBuffer sb = new StringBuffer("bad magic value:");
              for (int i=0; i<8; i++) {
                  sb.append(" ");
                  sb.append(Hex.u1(magic[i]));
              }
              throw new RuntimeException(sb.toString());
          }
  
          ReadContext readContext = new ReadContext();
  
          HeaderItem.readFrom(in, 0, readContext);
  
          //the map offset was set while reading in the header item
          int mapOffset = readContext.getSectionOffset(ItemType.TYPE_MAP_LIST);
  
          in.setCursor(mapOffset);
          MapItem.readFrom(in, 0, readContext);
  
          //the sections are ordered in such a way that the item types
          Section sections[] = new Section[] {
              StringDataSection,
                  StringIdsSection,
                  TypeIdsSection,
                  TypeListsSection,
                  ProtoIdsSection,
                  FieldIdsSection,
                  MethodIdsSection,
                  AnnotationsSection,
                  AnnotationSetsSection,
                  AnnotationSetRefListsSection,
                  AnnotationDirectoriesSection,
                  DebugInfoItemsSection,
                  CodeItemsSection,
                  ClassDataSection,
                  EncodedArraysSection,
                  ClassDefsSection
          };
  
          for (Section section: sections) {
              if (section == null) {
                  continue;
              }
  
              if (skipInstructions && (section == CodeItemsSection || section == DebugInfoItemsSection)) {
                  continue;
              }
  
              int sectionOffset = readContext.getSectionOffset(section.ItemType);
              if (sectionOffset > 0) {
                  int sectionSize = readContext.getSectionSize(section.ItemType);
                  in.setCursor(sectionOffset);
                  section.readFrom(sectionSize, in, readContext);
              }
          }
      }
  
      public DexFile(byte[] in) {
          this(in,true, false);
      }
  
  
  
  
      /**
       * Constructs a new, blank dex file. Classes can be added to this dex file by calling
       * the <code>Section.intern()</code> method of <code>ClassDefsSection</code>
       */
      public DexFile() {
          this(true, false);
      }
  
      /**
       * Get the <code>Section</code> containing items of the same type as the given item
       * @param item Get the <code>Section</code> that contains items of this type
       * @param <T> The specific item subclass - inferred from the passed item
       * @return the <code>Section</code> containing items of the same type as the given item
       */
      public <T extends Item> Section<T> getSectionForItem(T item) {
          return (Section<T>)sectionsByType[item.getItemType().SectionIndex];
      }
  
      /**
       * Get the <code>Section</code> containing items of the given type
       * @param itemType the type of item
       * @return the <code>Section</code> containing items of the given type
       */
      public Section getSectionForType(ItemType itemType) {
          return sectionsByType[itemType.SectionIndex];
      }
  
      /**
       * Get a boolean value indicating whether this dex file preserved any signed
       * registers in the debug info as it read the dex file in. By default, the dex file
       * doesn't check whether the registers are encoded as unsigned or signed values.
       *
       * This does *not* affect the actual register value that is read in. The value is
       * read correctly regardless
       *
       * This does affect whether any signed registers will retain the same encoding or be
       * forced to the (correct) unsigned encoding when the dex file is written back out.
       *
       * See the discussion about signed register values in the documentation for
       * <code>DexFile</code>
       * @return a boolean indicating whether this dex file preserved any signed registers
       * as it was read in
       */
      public boolean getPreserveSignedRegisters() {
          return preserveSignedRegisters;
      }
  
      /**
       * Get a boolean value indicating whether to skip any instructions in a code item while reading in the dex file.
       * This is useful when  you only need the information about the classes and their methods, for example, when
       * loading the BOOTCLASSPATH jars in order to analyze a dex file
       * @return a boolean value indicating whether to skip any instructions in a code item
       */
      public boolean skipInstructions() {
          return skipInstructions;
      }
  
      /**
       * Get a boolean value indicating whether all items should be placed into a
       * (possibly arbitrary) "canonical" ordering. If false, then only the items
       * that must be ordered per the dex specification are sorted.
       *
       * When true, writing the dex file involves somewhat more overhead
       *
       * If both SortAllItems and Inplace are true, Inplace takes precedence
       * @return a boolean value indicating whether all items should be sorted
       */
      public boolean getSortAllItems() {
          return this.sortAllItems;
      }
  
      /**
       * Set a boolean value indicating whether all items should be placed into a
       * (possibly arbitrary) "canonical" ordering. If false, then only the items
       * that must be ordered per the dex specification are sorted.
       *
       * When true, writing the dex file involves somewhat more overhead
       *
       * If both SortAllItems and Inplace are true, Inplace takes precedence
       * @param value a boolean value indicating whether all items should be sorted
       */
      public void setSortAllItems(boolean value) {
          this.sortAllItems = value;
      }
  
      /**
       * @return a boolean value indicating whether this dex file was created by reading in an odex file
       */
      public boolean isOdex() {
          return this.isOdex;
      }
  
      /**
       * @return an OdexDependencies object that contains the dependencies for this odex, or null if this
       * DexFile represents a dex file instead of an odex file
       */
      public OdexDependencies getOdexDependencies() {
          return odexDependencies;
      }
  
      /**
       * @return An OdexHeader object containing the information from the odex header in this dex file, or null if there
       * is no odex header
       */
      public OdexHeader getOdexHeader() {
          return odexHeader;
      }
  
      /**
       * Get a boolean value indicating whether items in this dex file should be
       * written back out "in-place", or whether the normal layout logic should be
       * applied.
       *
       * This should only be used for a dex file that has been read from an existing
       * dex file, and no modifications have been made to the dex file. Otherwise,
       * there is a good chance that the resulting dex file will be invalid due to
       * items that aren't placed correctly
       *
       * If both SortAllItems and Inplace are true, Inplace takes precedence
       * @return a boolean value indicating whether items in this dex file should be
       * written back out in-place.
       */
      public boolean getInplace() {
          return this.inplace;
      }
  
      /**
       * @return the size of the file, in bytes
       */
      public int getFileSize() {
          return fileSize;
      }
  
      /**
       * @return the size of the data section, in bytes
       */
      public int getDataSize() {
          return dataSize;
      }
  
      /**
       * @return the offset where the data section begins
       */
      public int getDataOffset() {
          return dataOffset;
      }
  
      /**
       * Set a boolean value indicating whether items in this dex file should be
       * written back out "in-place", or whether the normal layout logic should be
       * applied.
       *
       * This should only be used for a dex file that has been read from an existing
       * dex file, and no modifications have been made to the dex file. Otherwise,
       * there is a good chance that the resulting dex file will be invalid due to
       * items that aren't placed correctly
       *
       * If both SortAllItems and Inplace are true, Inplace takes precedence
       * @param value a boolean value indicating whether items in this dex file should be
       * written back out in-place.
       */
      public void setInplace(boolean value) {
          this.inplace = value;
      }
  
      /**
       * Get an array of Section objects that are sorted by offset.
       * @return an array of Section objects that are sorted by offset.
       */
      protected Section[] getOrderedSections() {
          int sectionCount = 0;
  
          for (Section section: sectionsByType) {
              if (section != null && section.getItems().size() > 0) {
                  sectionCount++;
              }
          }
  
          Section[] sections = new Section[sectionCount];
          sectionCount = 0;
          for (Section section: sectionsByType) {
              if (section != null && section.getItems().size() > 0) {
                  sections[sectionCount++] = section;
              }
          }
  
          Arrays.sort(sections, new Comparator<Section>() {
              public int compare(Section a, Section b) {
                  return a.getOffset() - b.getOffset();
              }
          });
  
          return sections;
      }
  
      /**
       * This method should be called before writing a dex file. It sorts the sections
       * as needed or as indicated by <code>getSortAllItems()</code> and <code>getInplace()</code>,
       * and then performs a pass through all of the items, finalizing the position (i.e.
       * index and/or offset) of each item in the dex file.
       *
       * This step is needed primarily so that the indexes and offsets of all indexed and
       * offsetted items are available when writing references to those items elsewhere.
       */
      public void place() {
          int offset = HeaderItem.placeAt(0, 0);
  
          int sectionsPosition = 0;
          Section[] sections;
          if (this.inplace) {
              sections = this.getOrderedSections();
          } else {
              sections = new Section[indexedSections.length + offsettedSections.length];
              System.arraycopy(indexedSections, 0, sections, 0, indexedSections.length);
              System.arraycopy(offsettedSections, 0, sections, indexedSections.length,  offsettedSections.length);
          }
  
          while (sectionsPosition < sections.length && sections[sectionsPosition].ItemType.isIndexedItem()) {
              Section section = sections[sectionsPosition];
              if (!this.inplace) {
                  section.sortSection();
              }
  
              offset = section.placeAt(offset);
  
              sectionsPosition++;
          }
  
          dataOffset = offset;
  
          while (sectionsPosition < sections.length) {
              Section section = sections[sectionsPosition];
              if (this.sortAllItems && !this.inplace) {
                  section.sortSection();
              }
              offset = section.placeAt(offset);
  
              sectionsPosition++;
          }
  
          offset = AlignmentUtils.alignOffset(offset, ItemType.TYPE_MAP_LIST.ItemAlignment);
          offset = MapItem.placeAt(offset, 0);
  
          fileSize = offset;
          dataSize = offset - dataOffset;
      }
  
      /**
       * Writes the dex file to the give <code>AnnotatedOutput</code> object. If
       * <code>out.Annotates()</code> is true, then annotations that document the format
       * of the dex file are written.
       *
       * You must call <code>place()</code> on this dex file, before calling this method
       * @param out the AnnotatedOutput object to write the dex file and annotations to
       *
       * After calling this method, you should call <code>calcSignature()</code> and
       * then <code>calcChecksum()</code> on the resulting byte array, to calculate the
       * signature and checksum in the header
       */
      public void writeTo(AnnotatedOutput out) {
  
          out.annotate(0, "-----------------------------");
          out.annotate(0, "header item");
          out.annotate(0, "-----------------------------");
          out.annotate(0, " ");
          HeaderItem.writeTo(out);
  
          out.annotate(0, " ");
  
          int sectionsPosition = 0;
          Section[] sections;
          if (this.inplace) {
              sections = this.getOrderedSections();
          } else {
              sections = new Section[indexedSections.length + offsettedSections.length];
              System.arraycopy(indexedSections, 0, sections, 0, indexedSections.length);
              System.arraycopy(offsettedSections, 0, sections, indexedSections.length,  offsettedSections.length);
          }
  
          while (sectionsPosition < sections.length) {
              sections[sectionsPosition].writeTo(out);
              sectionsPosition++;
          }
  
          out.alignTo(MapItem.getItemType().ItemAlignment);
  
          out.annotate(0, " ");
          out.annotate(0, "-----------------------------");
          out.annotate(0, "map item");
          out.annotate(0, "-----------------------------");
          out.annotate(0, " ");
          MapItem.writeTo(out);
      }
  
      public final HeaderItem HeaderItem = new HeaderItem(this);
      public final MapItem MapItem = new MapItem(this);
  
      /**
       * The <code>IndexedSection</code> containing <code>StringIdItem</code> items
       */
      public final IndexedSection<StringIdItem> StringIdsSection =
          new IndexedSection<StringIdItem>(this, ItemType.TYPE_STRING_ID_ITEM);
  
      /**
       * The <code>IndexedSection</code> containing <code>TypeIdItem</code> items
       */
      public final IndexedSection<TypeIdItem> TypeIdsSection =
          new IndexedSection<TypeIdItem>(this, ItemType.TYPE_TYPE_ID_ITEM);
  
      /**
       * The <code>IndexedSection</code> containing <code>ProtoIdItem</code> items
       */
      public final IndexedSection<ProtoIdItem> ProtoIdsSection =
          new IndexedSection<ProtoIdItem>(this, ItemType.TYPE_PROTO_ID_ITEM);
  
      /**
       * The <code>IndexedSection</code> containing <code>FieldIdItem</code> items
       */
      public final IndexedSection<FieldIdItem> FieldIdsSection =
          new IndexedSection<FieldIdItem>(this, ItemType.TYPE_FIELD_ID_ITEM);
  
      /**
       * The <code>IndexedSection</code> containing <code>MethodIdItem</code> items
       */
      public final IndexedSection<MethodIdItem> MethodIdsSection =
          new IndexedSection<MethodIdItem>(this, ItemType.TYPE_METHOD_ID_ITEM);
  
      /**
       * The <code>IndexedSection</code> containing <code>ClassDefItem</code> items
       */
      public final IndexedSection<ClassDefItem> ClassDefsSection =
          new IndexedSection<ClassDefItem>(this, ItemType.TYPE_CLASS_DEF_ITEM) {
  
              public int placeAt(int offset) {
                  if (dexFile.getInplace()) {
                      return super.placeAt(offset);
                  }
  
                  int ret = ClassDefItem.placeClassDefItems(this, offset);
  
                  Collections.sort(this.items, new Comparator<ClassDefItem>() {
  
                      public int compare(ClassDefItem a, ClassDefItem b) {
                          return a.getOffset() - b.getOffset();
                      }
                  });
  
                  this.offset = items.get(0).getOffset();
                  return ret;
              }
          };
  
      /**
       * The <code>OffsettedSection</code> containing <code>TypeListItem</code> items
       */
      public final OffsettedSection<TypeListItem> TypeListsSection =
          new OffsettedSection<TypeListItem>(this, ItemType.TYPE_TYPE_LIST);
  
      /**
       * The <code>OffsettedSection</code> containing <code>AnnotationSetRefList</code> items
       */
      public final OffsettedSection<AnnotationSetRefList> AnnotationSetRefListsSection =
          new OffsettedSection<AnnotationSetRefList>(this, ItemType.TYPE_ANNOTATION_SET_REF_LIST);
  
      /**
       * The <code>OffsettedSection</code> containing <code>AnnotationSetItem</code> items
       */
      public final OffsettedSection<AnnotationSetItem> AnnotationSetsSection =
          new OffsettedSection<AnnotationSetItem>(this, ItemType.TYPE_ANNOTATION_SET_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>ClassDataItem</code> items
       */
      public final OffsettedSection<ClassDataItem> ClassDataSection =
          new OffsettedSection<ClassDataItem>(this, ItemType.TYPE_CLASS_DATA_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>CodeItem</code> items
       */
      public final OffsettedSection<CodeItem> CodeItemsSection =
          new OffsettedSection<CodeItem>(this, ItemType.TYPE_CODE_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>StringDataItem</code> items
       */
      public final OffsettedSection<StringDataItem> StringDataSection =
          new OffsettedSection<StringDataItem>(this, ItemType.TYPE_STRING_DATA_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>DebugInfoItem</code> items
       */
      public final OffsettedSection<DebugInfoItem> DebugInfoItemsSection =
          new OffsettedSection<DebugInfoItem>(this, ItemType.TYPE_DEBUG_INFO_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>AnnotationItem</code> items
       */
      public final OffsettedSection<AnnotationItem> AnnotationsSection =
          new OffsettedSection<AnnotationItem>(this, ItemType.TYPE_ANNOTATION_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>EncodedArrayItem</code> items
       */
      public final OffsettedSection<EncodedArrayItem> EncodedArraysSection =
          new OffsettedSection<EncodedArrayItem>(this, ItemType.TYPE_ENCODED_ARRAY_ITEM);
  
      /**
       * The <code>OffsettedSection</code> containing <code>AnnotationDirectoryItem</code> items
       */
      public final OffsettedSection<AnnotationDirectoryItem> AnnotationDirectoriesSection =
          new OffsettedSection<AnnotationDirectoryItem>(this, ItemType.TYPE_ANNOTATIONS_DIRECTORY_ITEM);
  
  
      /**
       * Calculates the signature for the dex file in the given byte array,
       * and then writes the signature to the appropriate location in the header
       * containing in the array
       *
       * @param bytes non-null; the bytes of the file
       */
      public static void calcSignature(byte[] bytes) {
          MessageDigest md;
  
          try {
              md = MessageDigest.getInstance("SHA-1");
          } catch (NoSuchAlgorithmException ex) {
              throw new RuntimeException(ex);
          }
  
          md.update(bytes, 32, bytes.length - 32);
  
          try {
              int amt = md.digest(bytes, 12, 20);
              if (amt != 20) {
                  throw new RuntimeException("unexpected digest write: " + amt +
                          " bytes");
              }
          } catch (DigestException ex) {
              throw new RuntimeException(ex);
          }
      }
  
      /**
       * Calculates the checksum for the <code>.dex</code> file in the
       * given array, and modify the array to contain it.
       *
       * @param bytes non-null; the bytes of the file
       */
      public static void calcChecksum(byte[] bytes) {
          Adler32 a32 = new Adler32();
  
          a32.update(bytes, 12, bytes.length - 12);
  
          int sum = (int) a32.getValue();
  
          bytes[8]  = (byte) sum;
          bytes[9]  = (byte) (sum >> 8);
          bytes[10] = (byte) (sum >> 16);
          bytes[11] = (byte) (sum >> 24);
      }
  
      public static class NoClassesDexException extends ExceptionWithContext {
          public NoClassesDexException(String message) {
              super(message);
          }
      }
  }
  