Convert a jar to an optional package

Here's the code I promised I would post to convert a jar pulled out of a Maven repository into an optional package. Note here that jars pulled out of a Maven repository have the following example syntax: examplelib-1.0.0.jar. Given this syntax, the following code manipulates the Manifest of the jar to make the jar compatible with the JEE optional package specifications:

 ZipFile oldZipFile = new ZipFile(new File(fileName));
 Enumeration entries = oldZipFile.entries();

   ZipOutputStream out = new ZipOutputStream(new FileOutputStream(
           outFile));
   
   // Loop through entries in the existing jar file 
   while (entries.hasMoreElements())
   {
    ZipEntry entry = entries.nextElement();
    // Put all other files besides the manifest into the converted jar as is
    if (entry.getName().indexOf("MANIFEST") == -1)
    {
     out.putNextEntry(entry);

     InputStream inStream = oldZipFile.getInputStream(entry);
     // Transfer bytes from the ZIP file to the output file
     byte[] buf = new byte[1024];
     int len;
     while ((len = inStream.read(buf)) > 0)
      out.write(buf, 0, len);

     inStream.close();
    } 
    else
    {
     manifest = new OptManifest();
     manifest.setExtName(trueFileName);
     
     // Read the manifest
     InputStream inStream = oldZipFile.getInputStream(entry);
     BufferedReader in = new BufferedReader(
             new InputStreamReader(inStream));
     StringBuffer buffer = new StringBuffer();

     // Read each line of the manifest file to determine its state
     boolean extnNameFound = false;
     boolean specVerFound = false;
     boolean implVerFound = false;
     
     String line = null;
     while ((line = in.readLine()) != null)
     {
      if ( !specVerFound )
       specVerFound = ( line.toLowerCase().indexOf("specification-version")!=-1? true: false ); 

      if ( !implVerFound )
       implVerFound = ( line.toLowerCase().indexOf("implementation-version")!=-1? true: false ); 
            
      if ( !extnNameFound )
       extnNameFound = (line.toLowerCase().indexOf("extension-name")!=-1? true: false);
      
      boolean hasOptPkgParam = ( specVerFound || implVerFound || extnNameFound? true : false );
      
      // Add lines that are not optional package parameters
      if ( line!=null && !line.equals("") && !hasOptPkgParam )
       buffer.append(line + "\n");
     }
     
     // Add Optional package information to the manifest
     String versionToUse = determineVersion(fileName);
     if ( versionToUse!=null && !versionToUse.equals("") )
     {
      // Assign cleaned up specification version 
      String specVersionToUse = getSpecificationVersion(versionToUse);      
      buffer.append("Specification-Version: " + specVersionToUse + "\n");
      manifest.setExtSpecVersion(specVersionToUse);
      
      // Assign cleaned up implementation version
      String implVersionToUse = getImplementationVersion(versionToUse);
      buffer.append("Implementation-Version: " + implVersionToUse + "\n");
      manifest.setExtImplVersion(implVersionToUse);
     }     
     
     inStream.close();
     in.close();

     ZipEntry newManifestEntry = new ZipEntry(entry.getName());
     out.putNextEntry(newManifestEntry);

     // Transfer bytes from the file to the ZIP file
     out.write(buffer.toString().getBytes());
    }

    // Close the new entry in the new zip file
    out.closeEntry();
   }
   out.close();

Here's how your can derive the specification and implementation versions:

 private String getSpecificationVersion(String versionToUse)
 {
  StringBuffer specVersionToUse = new StringBuffer();
  // Regex expression that only allows digits and periods, and a digit cannot
  // be preceded by an underscore
  String regex = "(?<!_| )[\\.?[0-9]*]";
  Pattern pattern = Pattern.compile(regex);
  Matcher m = pattern.matcher(versionToUse);
  while ( m.find() )
   specVersionToUse.append(m.group());
  
  if ( specVersionToUse.charAt(0)=='.')
   specVersionToUse = specVersionToUse.replace(0, 1, "");
  
  if ( specVersionToUse.charAt(specVersionToUse.length()-1)=='.')
   specVersionToUse = specVersionToUse.replace(specVersionToUse.length()-1, specVersionToUse.length(), "");

  return specVersionToUse.toString();
 }

 private String getImplementationVersion(String versionToUse)
 {
  String implVersion = versionToUse;
  int versionIndex = versionToUse.indexOf('-');
  
  // Get the version starting from the hyphen prior to a digit
  String regexPattern = "[0-9]";
  while ( versionIndex!=-1 )
  {
   char charAtIndex = versionToUse.charAt(versionIndex+1);  
   if ( !Pattern.matches(regexPattern, String.valueOf(charAtIndex)) )
    versionIndex = versionToUse.indexOf('-', versionIndex+1);
   else
   {
    implVersion = versionToUse.substring(versionIndex+1);
    break;
   }
  }
  return implVersion;
 }