package org.apache.maven.jxr;
   
   /*
    * CodeViewer.java
    * CoolServlets.com
    * March 2000
    *
    * Copyright (C) 2000 CoolServlets.com
    *
   * 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) Neither the name CoolServlets.com nor the names of its contributors may be
   *   used to endorse or promote products derived from this software without
   *   specific prior written permission.
   *
   * THIS SOFTWARE IS PROVIDED BY COOLSERVLETS.COM AND CONTRIBUTORS ``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 COOLSERVLETS.COM OR CONTRIBUTORS 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.
   */
  
  import org.apache.commons.lang3.StringUtils;
  import org.apache.maven.jxr.pacman.ClassType;
  import org.apache.maven.jxr.pacman.FileManager;
  import org.apache.maven.jxr.pacman.ImportType;
  import org.apache.maven.jxr.pacman.JavaFile;
  import org.apache.maven.jxr.pacman.PackageManager;
  import org.apache.maven.jxr.pacman.PackageType;
  import org.apache.maven.jxr.util.SimpleWordTokenizer;
  import org.apache.maven.jxr.util.StringEntry;
  
  import java.io.BufferedReader;
  import java.io.FileInputStream;
  import java.io.FileOutputStream;
  import java.io.FileReader;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.io.InputStreamReader;
  import java.io.ObjectInputStream;
  import java.io.ObjectOutputStream;
  import java.io.OutputStreamWriter;
  import java.io.PrintWriter;
  import java.io.Reader;
  import java.io.Serializable;
  import java.io.Writer;
  import java.nio.file.Files;
  import java.nio.file.Path;
  import java.util.Collections;
  import java.util.HashSet;
  import java.util.Hashtable;
  import java.util.List;
  import java.util.Locale;
  import java.util.Map;
  import java.util.Set;
  
  /**
   * Syntax highlights java by turning it into html. A codeviewer object is created and then keeps state as lines are
   * passed in. Each line passed in as java test, is returned as syntax highlighted html text. Users of the class can set
   * how the java code will be highlighted with setter methods. Only valid java lines should be passed in since the object
   * maintains state and may not handle illegal code gracefully. The actual system is implemented as a series of filters
   * that deal with specific portions of the java code. The filters are as follows:
   *
   * <pre>
   *  htmlFilter
   *    |__
   *      ongoingMultiLineCommentFilter -&gt; uriFilter
   *        |__
   *          inlineCommentFilter
   *            |__
   *              beginMultiLineCommentFilter -&gt; ongoingMultiLineCommentFilter
   *                |__
   *                  stringFilter
   *                    |__
   *                      keywordFilter
   *                        |__
   *                          uriFilter
   *                            |__
   *                              jxrFilter
   *                                |__
   *                                  importFilter
   * </pre>
   */
  public class JavaCodeTransform
      implements Serializable
  {
      // ----------------------------------------------------------------------
      // public fields
      // ----------------------------------------------------------------------
 
     /**
      * show line numbers
      */
     private static final boolean LINE_NUMBERS = true;
 
     /**
      * start comment delimiter
      */
     private static final String COMMENT_START = "<em class=\"jxr_comment\">";
 
     /**
      * end comment delimiter
      */
     private static final String COMMENT_END = "</em>";
 
     /**
      * start javadoc comment delimiter
      */
     private static final String JAVADOC_COMMENT_START = "<em class=\"jxr_javadoccomment\">";
 
     /**
      * end javadoc comment delimiter
      */
     private static final String JAVADOC_COMMENT_END = "</em>";
 
     /**
      * start String delimiter
      */
     private static final String STRING_START = "<span class=\"jxr_string\">";
 
     /**
      * end String delimiter
      */
     private static final String STRING_END = "</span>";
 
     /**
      * start reserved word delimiter
      */
     private static final String RESERVED_WORD_START = "<strong class=\"jxr_keyword\">";
 
     /**
      * end reserved word delimiter
      */
     private static final String RESERVED_WORD_END = "</strong>";
 
     /**
      * stylesheet file name
      */
     private static final String STYLESHEET_FILENAME = "stylesheet.css";
 
     /**
      * Description of the Field
      */
     private static final String[] VALID_URI_SCHEMES = { "http://", "https://", "mailto:" };
 
     /**
      * Specify the only characters that are allowed in a URI besides alpha and numeric characters. Refer RFC2396 -
      * http://www.ietf.org/rfc/rfc2396.txt
      */
     private static final char[] VALID_URI_CHARS = { '?', '+', '%', '&', ':', '/', '.', '@', '_', ';', '=', '$', ',',
         '-', '!', '~', '*', '\'', '(', ')' };
 
     // ----------------------------------------------------------------------
     // private fields
     // ----------------------------------------------------------------------
 
     /**
      * HashTable containing java reserved words
      */
     private Map<String, String> reservedWords = new Hashtable<>();
 
     /**
      * flag set to true when a multi-line comment is started
      */
     private boolean inMultiLineComment = false;
 
     /**
      * flag set to true when a javadoc comment is started
      */
     private boolean inJavadocComment = false;
 
     /**
      * Set the filename that is currently being processed.
      */
     private Path currentFilename = null;
 
     /**
      * The current CVS revision of the currently transformed document
      */
     private String revision = null;
 
     /**
      * The output encoding
      */
     private String outputEncoding = null;
 
     /**
      * The wanted locale
      */
     private Locale locale = null;
 
     /**
      * Relative path to javadocs, suitable for hyperlinking
      */
     private Path javadocLinkDir;
 
     /**
      * Package Manager for this project.
      */
     private final PackageManager packageManager;
 
     /**
      * current file manager
      */
     private final FileManager fileManager;
 
     {
         reservedWords.put( "abstract", "abstract" );
         reservedWords.put( "do", "do" );
         reservedWords.put( "inner", "inner" );
         reservedWords.put( "public", "public" );
         reservedWords.put( "var", "var" );
         reservedWords.put( "boolean", "boolean" );
         reservedWords.put( "continue", "continue" );
         reservedWords.put( "int", "int" );
         reservedWords.put( "return", "return" );
         reservedWords.put( "void", "void" );
         reservedWords.put( "break", "break" );
         reservedWords.put( "else", "else" );
         reservedWords.put( "interface", "interface" );
         reservedWords.put( "short", "short" );
         reservedWords.put( "volatile", "volatile" );
         reservedWords.put( "byvalue", "byvalue" );
         reservedWords.put( "extends", "extends" );
         reservedWords.put( "long", "long" );
         reservedWords.put( "static", "static" );
         reservedWords.put( "while", "while" );
         reservedWords.put( "case", "case" );
         reservedWords.put( "final", "final" );
         reservedWords.put( "native", "native" );
         reservedWords.put( "super", "super" );
         reservedWords.put( "transient", "transient" );
         reservedWords.put( "cast", "cast" );
         reservedWords.put( "float", "float" );
         reservedWords.put( "new", "new" );
         reservedWords.put( "rest", "rest" );
         reservedWords.put( "catch", "catch" );
         reservedWords.put( "for", "for" );
         reservedWords.put( "null", "null" );
         reservedWords.put( "synchronized", "synchronized" );
         reservedWords.put( "char", "char" );
         reservedWords.put( "finally", "finally" );
         reservedWords.put( "operator", "operator" );
         reservedWords.put( "this", "this" );
         reservedWords.put( "class", "class" );
         reservedWords.put( "generic", "generic" );
         reservedWords.put( "outer", "outer" );
         reservedWords.put( "switch", "switch" );
         reservedWords.put( "const", "const" );
         reservedWords.put( "goto", "goto" );
         reservedWords.put( "package", "package" );
         reservedWords.put( "throw", "throw" );
         reservedWords.put( "double", "double" );
         reservedWords.put( "if", "if" );
         reservedWords.put( "private", "private" );
         reservedWords.put( "true", "true" );
         reservedWords.put( "default", "default" );
         reservedWords.put( "import", "import" );
         reservedWords.put( "protected", "protected" );
         reservedWords.put( "try", "try" );
         reservedWords.put( "throws", "throws" );
         reservedWords.put( "implements", "implements" );
     }
 
     public JavaCodeTransform( PackageManager packageManager, FileManager fileManager )
     {
         this.packageManager = packageManager;
         this.fileManager = fileManager;
     }
 
     // ----------------------------------------------------------------------
     // public methods
     // ----------------------------------------------------------------------
 
     /**
      * Now different method of seeing if at end of input stream, closes inputs stream at end.
      *
      * @param line String
      * @return filtered line of code
      */
     private String syntaxHighlight( String line )
     {
         return htmlFilter( line );
     }
 
     /**
      * Gets the header attribute of the JavaCodeTransform object
      *
      * @param out the writer where the header is appended to
      * @return String
      */
     private void appendHeader( PrintWriter out )
     {
         String outputEncoding = this.outputEncoding;
         if ( outputEncoding == null )
         {
             outputEncoding = "ISO-8859-1";
         }
 
         // header
         out.println( "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" "
             + "\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">" );
         out.print( "<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"" );
         out.print( locale );
         out.print( "\" lang=\"" );
         out.print( locale );
         out.println( "\">" );
         out.print( "<head>" );
         out.print( "<meta http-equiv=\"content-type\" content=\"text/html; charset=" );
         out.print( outputEncoding );
         out.println( "\" />" );
 
         // title ("classname xref")
         out.print( "<title>" );
         try
         {
             JavaFile javaFile = fileManager.getFile( this.getCurrentFilename() );
             // Use the name of the file instead of the class to handle inner classes properly
             if ( javaFile.getClassType() != null && javaFile.getClassType().getFilename() != null )
             {
                 out.print( javaFile.getClassType().getFilename() );
             }
             else
             {
                 out.print( this.getCurrentFilename() );
             }
             out.print( ' ' );
         }
         catch ( IOException e )
         {
             e.printStackTrace();
         }
         finally
         {
             out.println( "xref</title>" );
         }
 
         // stylesheet link
         out.print( "<link type=\"text/css\" rel=\"stylesheet\" href=\"" );
         out.print( this.getPackageRoot() );
         out.print( STYLESHEET_FILENAME );
         out.println( "\" />" );
 
         out.println( "</head>" );
         out.println( "<body>" );
         out.print( this.getFileOverview() );
 
         // start code section
         out.println( "<pre>" );
     }
 
     /**
      * Gets the footer attribute of the JavaCodeTransform object
      *
      * @param out the writer where the header is appended to
      * @param bottom the bottom text
      * @return String
      */
     private void appendFooter( PrintWriter out, String bottom )
     {
         out.println( "</pre>" );
         out.println( "<hr/>" );
         out.print( "<div id=\"footer\">" );
         out.print( bottom );
         out.println( "</div>" );
         out.println( "</body>" );
         out.println( "</html>" );
     }
 
     /**
      * This is the public method for doing all transforms of code.
      *
      * @param sourceReader Reader
      * @param destWriter Writer
      * @param locale String
      * @param outputEncoding String
      * @param javadocLinkDir String
      * @param revision String
      * @param bottom string
      * @throws IOException
      */
     private void transform( Reader sourceReader, Writer destWriter, Locale locale,
                                  String outputEncoding, Path javadocLinkDir, String revision, String bottom )
         throws IOException
     {
         this.locale = locale;
         this.outputEncoding = outputEncoding;
         this.javadocLinkDir = javadocLinkDir;
         this.revision = revision;
 
         BufferedReader in = new BufferedReader( sourceReader );
 
         PrintWriter out = new PrintWriter( destWriter );
 
         String line;
 
         appendHeader( out );
 
         int linenumber = 1;
         while ( ( line = in.readLine() ) != null )
         {
             if ( LINE_NUMBERS )
             {
                 out.print( "<a class=\"jxr_linenumber\" name=\"L" + linenumber + "\" " + "href=\"#L" + linenumber
                     + "\">" + linenumber + "</a>" + getLineWidth( linenumber ) );
             }
 
             out.println( this.syntaxHighlight( line ) );
 
             ++linenumber;
         }
 
         appendFooter( out, bottom );
 
         out.flush();
     }
 
     /**
      * This is the public method for doing all transforms of code.
      *
      * @param sourcefile String
      * @param destfile String
      * @param locale String
      * @param inputEncoding String
      * @param outputEncoding String
      * @param javadocLinkDir String
      * @param revision String
      * @param bottom TODO
      * @throws IOException
      */
     public final void transform( Path sourcefile, Path destfile, Locale locale, String inputEncoding,
                                  String outputEncoding, Path javadocLinkDir, String revision, String bottom )
         throws IOException
     {
         this.setCurrentFilename( sourcefile );
 
         // make sure that the parent directories exist...
         Files.createDirectories( destfile.getParent() );
 
         try ( Reader fr = getReader( sourcefile, inputEncoding ); Writer fw = getWriter( destfile, outputEncoding ) )
         {
             transform( fr, fw, locale, outputEncoding, javadocLinkDir, revision, bottom );
         }
         catch ( RuntimeException e )
         {
             System.out.println( "Unable to processPath " + sourcefile + " => " + destfile );
             throw e;
         }
     }
 
     private Writer getWriter( Path destfile, String outputEncoding )
         throws IOException
     {
         Writer fw;
         if ( outputEncoding != null )
         {
             fw = new OutputStreamWriter( new FileOutputStream( destfile.toFile() ), outputEncoding );
         }
         else
         {
             fw = new FileWriter( destfile.toFile() );
         }
         return fw;
     }
 
     private Reader getReader( Path sourcefile, String inputEncoding )
         throws IOException
     {
         Reader fr;
         if ( inputEncoding != null )
         {
             fr = new InputStreamReader( new FileInputStream( sourcefile.toFile() ), inputEncoding );
         }
         else
         {
             fr = new FileReader( sourcefile.toFile() );
         }
         return fr;
     }
 
     /**
      * Get the current filename
      *
      * @return String
      */
     private Path getCurrentFilename()
     {
         return this.currentFilename;
     }
 
     /**
      * Set the current filename
      *
      * @param filename String
      */
     private void setCurrentFilename( Path filename )
     {
         this.currentFilename = filename;
     }
 
     /**
      * From the current file, determine the package root based on the current path.
      *
      * @return String
      */
     private String getPackageRoot()
     {
         StringBuilder buff = new StringBuilder();
 
         JavaFile jf;
 
         try
         {
             jf = fileManager.getFile( this.getCurrentFilename() );
         }
         catch ( IOException e )
         {
             e.printStackTrace();
             return null;
         }
 
         String current = jf.getPackageType().getName();
 
         int count = this.getPackageCount( current );
 
         for ( int i = 0; i < count; ++i )
         {
             buff.append( "../" );
         }
 
         return buff.toString();
     }
 
     /**
      * Given a line of text, search for URIs and make href's out of them
      *
      * @param line String
      * @return String
      */
     private String uriFilter( String line )
     {
         for ( String scheme : VALID_URI_SCHEMES )
         {
             int index = line.indexOf( scheme );
 
             if ( index != -1 )
             {
                 int start = index;
                 int end = -1;
 
                 for ( int j = start; j < line.length(); ++j )
                 {
                     char current = line.charAt( j );
 
                     if ( !Character.isLetterOrDigit( current ) && isInvalidURICharacter( current ) )
                     {
                         end = j;
                         break;
                     }
 
                     end = j;
                 }
 
                 // now you should have the full URI so you can replace this
                 // in the current buffer
 
                 if ( end != -1 )
                 {
                     String uri = ( end + 1 == line.length() ) ? line.substring( start ) : line.substring( start, end );
 
                     line =
                         StringUtils.replace( line, uri, "<a href=\"" + uri + "\" target=\"alexandria_uri\">" + uri
                             + "</a>" );
                 }
             }
         }
 
         // if we are in a multiline comment we should not call JXR here.
         if ( !inMultiLineComment && !inJavadocComment )
         {
             return jxrFilter( line );
         }
 
         return line;
     }
 
     /**
      * The current revision of the CVS module
      *
      * @return String
      */
     public final String getRevision()
     {
         return this.revision;
     }
 
     /**
      * Cross Reference the given line with JXR returning the new content.
      *
      * @param line String
      * @param packageName String
      * @param classType ClassType
      * @return String
      */
     private String xrLine( String line, String packageName, ClassType classType )
     {
         StringBuilder buff = new StringBuilder( line );
 
         String link;
         String find;
         String href;
 
         if ( classType != null )
         {
             href = this.getHREF( packageName, classType );
             find = classType.getName();
 
             // build out what the link would be.
             link = "<a name=\"" + find + "\" href=\"" + href + "\">" + find + "</a>";
         }
         else
         {
             href = this.getHREF( packageName );
             find = packageName;
 
             // build out what the link would be.
             link = "<a href=\"" + href + "\">" + find + "</a>";
         }
 
         // use the SimpleWordTokenizer to find all entries
         // that match word. Then replace these with the link
 
         // now replace the word in the buffer with the link
 
         String replace = link;
         List<StringEntry> tokens = SimpleWordTokenizer.tokenize( buff.toString(), find );
 
         // JXR-141: If there are more than 1 tokens to be replaced,
         // then the start+end values are out of order during the
         // buff.replace.
         // Reversing the list solves it
         Collections.reverse( tokens );
 
         for ( StringEntry token : tokens )
         {
             int start = token.getIndex();
             int end = token.getIndex() + find.length();
 
             buff.replace( start, end, replace );
 
         }
 
         return buff.toString();
     }
 
     // ----------------------------------------------------------------------
     // private methods
     // ----------------------------------------------------------------------
 
     /**
      * Filter html tags into more benign text.
      *
      * @param line String
      * @return html encoded line
      */
     private String htmlFilter( String line )
     {
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
         line = line.replace( "&", "&amp;" )
                     .replace( "<", "&lt;" )
                     .replace( ">", "&gt;" )
                     .replace( "\\\\", "&#92;&#92;" )
                     .replace( "\\\"", "\\&quot;" )
                     .replace( "'\"'", "'&quot;'" );
         return ongoingMultiLineCommentFilter( line );
     }
 
     /**
      * Handle ongoing multi-line comments, detecting ends if present. State is maintained in private boolean members,
      * one each for javadoc and (normal) multiline comments.
      *
      * @param line String
      * @return String
      */
     private String ongoingMultiLineCommentFilter( String line )
     {
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
         final String[] tags =
             inJavadocComment ? new String[] { JAVADOC_COMMENT_START, JAVADOC_COMMENT_END }
                             : inMultiLineComment ? new String[] { COMMENT_START, COMMENT_END } : null;
 
         if ( tags == null )
         {
             // pass the line down to the next filter for processing.
             return inlineCommentFilter( line );
         }
 
         int index = line.indexOf( "*/" );
         // only filter the portion without the end-of-comment,
         // since * and / seem to be valid URI characters
         String comment = uriFilter( index < 0 ? line : line.substring( 0, index ) );
         if ( index >= 0 )
         {
             inJavadocComment = false;
             inMultiLineComment = false;
         }
         StringBuilder buf = new StringBuilder( tags[0] ).append( comment );
 
         if ( index >= 0 )
         {
             buf.append( "*/" );
         }
         buf.append( tags[1] );
 
         if ( index >= 0 && line.length() > index + 2 )
         {
             buf.append( inlineCommentFilter( line.substring( index + 2 ) ) );
         }
         return buf.toString();
     }
 
     /**
      * Filter inline comments from a line and formats them properly. One problem we'll have to solve here: comments
      * contained in a string should be ignored... this is also true of the multi-line comments. So, we could either
      * ignore the problem, or implement a function called something like isInsideString(line, index) where index points
      * to some point in the line that we need to check... started doing this function below.
      *
      * @param line String
      * @return String
      */
     private String inlineCommentFilter( String line )
     {
         // assert !inJavadocComment;
         // assert !inMultiLineComment;
 
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
         int index = line.indexOf( "//" );
         if ( ( index >= 0 ) && !isInsideString( line, index ) )
         {
             return new StringBuilder( beginMultiLineCommentFilter( line.substring( 0, index ) ) ).append( COMMENT_START ).append( line.substring( index ) ).append( COMMENT_END ).toString();
         }
 
         return beginMultiLineCommentFilter( line );
     }
 
     /**
      * Detect and handle the start of multiLine comments. State is maintained in private boolean members one each for
      * javadoc and (normal) multiline comments.
      *
      * @param line String
      * @return String
      */
     private String beginMultiLineCommentFilter( String line )
     {
         // assert !inJavadocComment;
         // assert !inMultiLineComment;
 
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
 
         int index = line.indexOf( "/*" );
         // check to see if a multi-line comment starts on this line:
         if ( ( index > -1 ) && !isInsideString( line, index ) )
         {
             String fromIndex = line.substring( index );
             if ( fromIndex.startsWith( "/**" ) && !( fromIndex.startsWith( "/**/" ) ) )
             {
                 inJavadocComment = true;
             }
             else
             {
                 inMultiLineComment = true;
             }
             // Return result of other filters + everything after the start
             // of the multiline comment. We need to pass the through the
             // to the ongoing multiLineComment filter again in case the comment
             // ends on the same line.
             return new StringBuilder( stringFilter( line.substring( 0, index ) ) ).append( ongoingMultiLineCommentFilter( fromIndex ) ).toString();
         }
 
         // Otherwise, no useful multi-line comment information was found so
         // pass the line down to the next filter for processesing.
         else
         {
             return stringFilter( line );
         }
     }
 
     /**
      * Filters strings from a line of text and formats them properly.
      *
      * @param line String
      * @return String
      */
     private String stringFilter( String line )
     {
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
         StringBuilder buf = new StringBuilder();
         if ( line.indexOf( '"' ) <= -1 )
         {
             return keywordFilter( line );
         }
         int start = 0;
         int startStringIndex = -1;
         int endStringIndex = -1;
         int tempIndex;
         // Keep moving through String characters until we want to stop...
         while ( ( tempIndex = line.indexOf( '"' ) ) > -1 )
         {
             // We found the beginning of a string
             if ( startStringIndex == -1 )
             {
                 startStringIndex = 0;
                 buf.append( stringFilter( line.substring( start, tempIndex ) ) );
                 buf.append( STRING_START ).append( '"' );
                 line = line.substring( tempIndex + 1 );
             }
             // Must be at the end
             else
             {
                 startStringIndex = -1;
                 endStringIndex = tempIndex;
                 buf.append( line, 0, endStringIndex + 1 );
                 buf.append( STRING_END );
                 line = line.substring( endStringIndex + 1 );
             }
         }
 
         buf.append( keywordFilter( line ) );
 
         return buf.toString();
     }
 
     /**
      * Filters keywords from a line of text and formats them properly.
      *
      * @param line String
      * @return String
      */
     private String keywordFilter( String line )
     {
         final String classKeyword = "class";
 
         if ( line == null || line.equals( "" ) )
         {
             return "";
         }
         StringBuilder buf = new StringBuilder();
         int i = 0;
         char ch;
         StringBuilder temp = new StringBuilder();
         while ( i < line.length() )
         {
             temp.setLength( 0 );
             ch = line.charAt( i );
             while ( i < line.length() && ( ( ch >= 'a' && ch <= 'z' ) || ( ch >= 'A' && ch <= 'Z' ) ) )
             {
                 temp.append( ch );
                 i++;
                 if ( i < line.length() )
                 {
                     ch = line.charAt( i );
                 }
             }
             String tempString = temp.toString();
 
             // Special handling of css style class definitions
             if ( classKeyword.equals( tempString ) && ch == '=' )
             {
                 i++;
             }
             else if ( reservedWords.containsKey( tempString ) )
             {
                 StringBuilder newLine = new StringBuilder( line.substring( 0, i - tempString.length() ) );
                 newLine.append( RESERVED_WORD_START );
                 newLine.append( tempString );
                 newLine.append( RESERVED_WORD_END );
                 newLine.append( line.substring( i ) );
                 line = newLine.toString();
                 i += ( RESERVED_WORD_START.length() + RESERVED_WORD_END.length() );
             }
             else
             {
                 i++;
             }
         }
         buf.append( line );
 
         return uriFilter( buf.toString() );
     }
 
     /**
      * Checks to see if some position in a line is between String start and ending characters. Not yet used in code or
      * fully working :)
      *
      * @param line String
      * @param position int
      * @return boolean
      */
     private boolean isInsideString( String line, int position )
     {
         if ( line.indexOf( '"' ) < 0 )
         {
             return false;
         }
         int index;
         String left = line.substring( 0, position );
         String right = line.substring( position );
         int leftCount = 0;
         int rightCount = 0;
         while ( ( index = left.indexOf( '"' ) ) > -1 )
         {
             leftCount++;
             left = left.substring( index + 1 );
         }
         while ( ( index = right.indexOf( '"' ) ) > -1 )
         {
             rightCount++;
             right = right.substring( index + 1 );
         }
         return ( rightCount % 2 != 0 && leftCount % 2 != 0 );
     }
 
     /**
      * Description of the Method
      *
      * @param oos ObjectOutputStream
      * @throws IOException
      */
     final void writeObject( ObjectOutputStream oos )
         throws IOException
     {
         oos.defaultWriteObject();
     }
 
     /**
      * Description of the Method
      *
      * @param ois ObjectInputStream
      * @throws ClassNotFoundException
      * @throws IOException
      */
     final void readObject( ObjectInputStream ois )
         throws ClassNotFoundException, IOException
     {
         ois.defaultReadObject();
     }
 
     /**
      * Get an overview header for this file.
      *
      * @return String
      */
     private String getFileOverview()
     {
         StringBuilder overview = new StringBuilder();
 
         // only add the header if javadocs are present
         if ( javadocLinkDir != null )
         {
             overview.append( "<div id=\"overview\">" );
             // get the URI to get Javadoc info.
             Path javadocURI = javadocLinkDir;
 
             try
             {
                 JavaFile jf = fileManager.getFile( this.getCurrentFilename() );
 
                 javadocURI = javadocLinkDir.resolve( jf.getPackageType().getName().replace( '.', '/' ) )
                                 ;
                 // Use the name of the file instead of the class to handle inner classes properly
                 if ( jf.getClassType() != null && jf.getClassType().getFilename() != null )
                 {
                     javadocURI = javadocURI.resolve( jf.getClassType().getFilename() + ".html" );
                 }
 
                 String javadocHREF = "<a href=\"" + javadocURI.toString().replace( '\\', '/' ) + "\">View Javadoc</a>";
 
                 // get the generation time...
                 overview.append( javadocHREF );
             }
             catch ( IOException e )
             {
                 e.printStackTrace();
             }
 
             overview.append( "</div>" );
         }
 
         return overview.toString();
     }
 
     /**
      * Handles line width which may need to change depending on which line number you are on.
      *
      * @param linenumber int
      * @return String
      */
     private String getLineWidth( int linenumber )
     {
         if ( linenumber < 10 )
         {
             return "   ";
         }
         else if ( linenumber < 100 )
         {
             return "  ";
         }
         else
         {
             return " ";
         }
     }
 
     /**
      * Handles finding classes based on the current filename and then makes HREFs for you to link to them with.
      *
      * @param line String
      * @return String
      */
     private String jxrFilter( String line )
     {
         JavaFile jf;
 
         try
         {
             // if the current file isn't set then just return
             if ( this.getCurrentFilename() == null )
             {
                 return line;
             }
 
             jf = fileManager.getFile( this.getCurrentFilename() );
         }
         catch ( IOException e )
         {
             e.printStackTrace();
             return line;
         }
 
         Set<String> packages = new HashSet<>();
 
         // get the imported packages
         for ( ImportType importType : jf.getImportTypes() )
         {
             packages.add( importType.getPackage() );
         }
 
         // add the current package.
         packages.add( jf.getPackageType().getName() );
 
         List<StringEntry> words = SimpleWordTokenizer.tokenize( line );
 
         // go through each word and then match them to the correct class if necessary.
         for ( StringEntry word : words )
         {
             for ( String pkg : packages )
             {
                 // get the package from the PackageManager because this will hold
                 // the version with the classes also.
 
                 PackageType currentImport = packageManager.getPackageType( pkg );
 
                 // the package here might in fact be null because it wasn't parsed out
                 // this might be something that is either not included or is part
                 // of another package and wasn't parsed out.
 
                 if ( currentImport == null )
                 {
                     continue;
                 }
 
                 // see if the current word is within the package
 
                 // at this point the word could be a fully qualified package name
                 // (FQPN) or an imported package name.
 
                 String wordName = word.toString();
 
                 if ( wordName.indexOf( '.' ) != -1 )
                 {
                     // if there is a "." in the string then we have to assume
                     // it is a package.
 
                     String fqpnPackage = wordName.substring( 0, wordName.lastIndexOf( '.' ) );
                     String fqpnClass = wordName.substring( wordName.lastIndexOf( '.' ) + 1 );
 
                     // note. since this is a reference to a full package then
                     // it doesn't have to be explicitly imported so this information
                     // is useless. Instead just see if it was parsed out.
 
                     PackageType pt = packageManager.getPackageType( fqpnPackage );
 
                     if ( pt != null )
                     {
                         ClassType ct = pt.getClassType( fqpnClass );
 
                         if ( ct != null )
                         {
                             // OK. the user specified a full package to be imported
                             // that is in the package manager so it is time to
                             // link to it.
 
                             line = xrLine( line, pt.getName(), ct );
                         }
                     }
 
                     if ( fqpnPackage.equals( currentImport.getName() )
                         && currentImport.getClassType( fqpnClass ) != null )
                     {
                         // then the package we are currently in is the one specified in the string
                         // and the import class is correct.
                         line = xrLine( line, pkg, currentImport.getClassType( fqpnClass ) );
                     }
                 }
                 else if ( currentImport.getClassType( wordName ) != null )
                 {
                     line = xrLine( line, pkg, currentImport.getClassType( wordName ) );
                 }
             }
         }
 
         return importFilter( line );
     }
 
     /**
      * Given the current package, get an HREF to the package and class given
      *
      * @param dest String
      * @param jc ClassType
      * @return String
      */
     private String getHREF( String dest, ClassType jc )
     {
         StringBuilder href = new StringBuilder();
 
         // find out how to go back to the root
         href.append( this.getPackageRoot() );
 
         // now find out how to get to the dest package
         dest = StringUtils.replace( dest, ".*", "" ).replace( '.', '/' );
 
         href.append( dest );
 
         // Now append filename.html
         if ( jc != null )
         {
             href.append( '/' );
             href.append( jc.getFilename() );
             href.append( ".html" );
             href.append( '#' );
             href.append( jc.getName() );
         }
 
         return href.toString();
     }
 
     /**
      * Based on the destination package, get the HREF.
      *
      * @param dest String
      * @return String
      */
     private String getHREF( String dest )
     {
         return getHREF( dest, null );
     }
 
     /**
      * <p>
      * Given the name of a package... get the number of subdirectories/subpackages there would be.
      * </p>
      * <p>
      * EX: <code>org.apache.maven == 3</code>
      * </p>
      *
      * @param packageName String
      * @return int
      */
     private int getPackageCount( String packageName )
     {
         if ( packageName == null )
         {
             return 0;
         }
 
         int count = 0;
         int index = 0;
 
         while ( true )
         {
             index = packageName.indexOf( '.', index );
 
             if ( index == -1 )
             {
                 break;
             }
             ++index;
             ++count;
         }
 
         // need to increment this by one
         ++count;
 
         return count;
     }
 
     /**
      * Parse out the current link and look for package/import statements and then create HREFs for them
      *
      * @param line String
      * @return String
      */
     private String importFilter( String line )
     {
         int start = -1;
 
         /*
          * Used for determining if this is a package declaration. If it is then we can make some additional assumptions:
          * - that this isn't a Class import so the full String is valid - that it WILL be on the disk since this is
          * based on the current - file.
          */
         boolean isPackage = line.trim().startsWith( "package " );
         boolean isImport = line.trim().startsWith( "import " );
 
         if ( isImport || isPackage )
         {
             start = line.trim().indexOf( ' ' );
         }
 
         if ( start != -1 )
         {
             // filter out this packagename...
             String pkg = line.substring( start ).trim();
 
             // specify the classname of this import if any.
             String classname = null;
 
             if (pkg.contains(".*"))
             {
                 pkg = StringUtils.replace( pkg, ".*", "" );
             }
             else if ( !isPackage )
             {
                 // this is an explicit Class import
 
                 String packageLine = pkg;
 
                 // This catches a boundary problem where you have something like:
                 //
                 // Foo foo = FooMaster.getFooInstance().
                 // danceLittleFoo();
                 //
                 // This breaks Jxr and won't be a problem when we hook
                 // in the real parser.
 
                 int a = packageLine.lastIndexOf( '.' ) + 1;
                 int b = packageLine.length() - 1;
 
                 if ( a > b + 1 )
                 {
                     classname = packageLine.substring( packageLine.lastIndexOf( '.' ) + 1, packageLine.length() - 1 );
 
                     int end = pkg.lastIndexOf( '.' );
                     if ( end == -1 )
                     {
                         end = pkg.length() - 1;
                     }
 
                     pkg = pkg.substring( 0, end );
                 }
             }
 
             pkg = StringUtils.replace( pkg, ";", "" );
             String pkgHREF = getHREF( pkg );
             // if this package is within the PackageManager then you can create an HREF for it.
 
             if ( packageManager.getPackageType( pkg ) != null || isPackage )
             {
                 // Create an HREF for explicit classname imports
                 if ( classname != null )
                 {
                     line =
                         StringUtils.replace( line, classname, "<a href=\"" + pkgHREF + '/' + classname + ".html"
                             + "\">" + classname + "</a>" );
                 }
 
                 // now replace the given package with a href
                 line =
                     StringUtils.replace( line, pkg, "<a href=\"" + pkgHREF + '/' + DirectoryIndexer.INDEX + "\">" + pkg
                         + "</a>" );
             }
 
         }
 
         return line;
     }
 
     /**
      * if the given char is not one of the following in VALID_URI_CHARS then return true
      *
      * @param c char to check against VALID_URI_CHARS list
      * @return <code>true</code> if c is a valid URI char
      */
     private boolean isInvalidURICharacter( char c )
     {
         for ( char validUriChar : VALID_URI_CHARS )
         {
             if ( validUriChar == c )
             {
                 return false;
             }
         }
 
         return true;
     }
 }