reference.java

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         if (resolver == null) {
            Object exArgs[] = { URI };

            throw new ReferenceNotInitializedException(
               "signature.Verification.Reference.NoInput", exArgs);
         }

         resolver.addProperties(this._manifest._resolverProperties);

         XMLSignatureInput input = resolver.resolve(URIAttr, this._baseURI);
                  

         return input;
      }  catch (ResourceResolverException ex) {
         throw new ReferenceNotInitializedException("empty", ex);
      } catch (XMLSecurityException ex) {
         throw new ReferenceNotInitializedException("empty", ex);
      }
   }

   /**
    * Returns the data which is referenced by the URI attribute. This method
    * only works works after a call to verify.
    * @return a XMLSignature with a byte array.
    * @throws ReferenceNotInitializedException
    *
    * @deprecated use getContentsBeforeTransformation
    */
   public XMLSignatureInput getTransformsInput() throws ReferenceNotInitializedException   
	{  
   		XMLSignatureInput input=getContentsBeforeTransformation();
   		XMLSignatureInput result;
		try {
			result = new XMLSignatureInput(input.getBytes());
		} catch (CanonicalizationException ex) {
			 throw new ReferenceNotInitializedException("empty", ex);
		} catch (IOException ex) {
			 throw new ReferenceNotInitializedException("empty", ex);
		}
		result.setSourceURI(input.getSourceURI());   
		return result;
	
   }

   private XMLSignatureInput getContentsAfterTransformation(XMLSignatureInput input, OutputStream os)
           throws XMLSignatureException {

      try {
         Transforms transforms = this.getTransforms();
         XMLSignatureInput output = null;

         if (transforms != null) {
            output = transforms.performTransforms(input,os);
            this._transformsOutput = output;//new XMLSignatureInput(output.getBytes());

            //this._transformsOutput.setSourceURI(output.getSourceURI());
         } else {
            output = input;
         }

         return output;
      } catch (ResourceResolverException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (CanonicalizationException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (InvalidCanonicalizerException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (TransformationException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (XMLSecurityException ex) {
         throw new XMLSignatureException("empty", ex);
      }
   }

   /**
    * Returns the XMLSignatureInput which is the result of the Transforms.
    * @return a XMLSignatureInput with all transformations applied.
    * @throws XMLSignatureException
    */
   public XMLSignatureInput getContentsAfterTransformation()
           throws XMLSignatureException {

      XMLSignatureInput input = this.getContentsBeforeTransformation();

      return this.getContentsAfterTransformation(input, null);
   }

   /**
    * This method returns the XMLSignatureInput which represents the node set before
    * some kind of canonicalization is applied for the first time.
    * @return Gets a the node doing everything till the first c14n is needed
    *
    * @throws XMLSignatureException
    */
   public XMLSignatureInput getNodesetBeforeFirstCanonicalization()
           throws XMLSignatureException {

      try {
         XMLSignatureInput input = this.getContentsBeforeTransformation();
         XMLSignatureInput output = input;
         Transforms transforms = this.getTransforms();

         if (transforms != null) {
            doTransforms: for (int i = 0; i < transforms.getLength(); i++) {
               Transform t = transforms.item(i);
               String URI = t.getURI();

               if (URI.equals(Transforms
                       .TRANSFORM_C14N_EXCL_OMIT_COMMENTS) || URI
                          .equals(Transforms
                             .TRANSFORM_C14N_EXCL_WITH_COMMENTS) || URI
                                .equals(Transforms
                                   .TRANSFORM_C14N_OMIT_COMMENTS) || URI
                                      .equals(Transforms
                                         .TRANSFORM_C14N_WITH_COMMENTS)) {

                  break doTransforms;
               }

               output = t.performTransform(output, null);
            }

            output.setSourceURI(input.getSourceURI());
         }
         return output;
      } catch (IOException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (ResourceResolverException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (CanonicalizationException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (InvalidCanonicalizerException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (TransformationException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (XMLSecurityException ex) {
         throw new XMLSignatureException("empty", ex);
      }
   }

   /**
    * Method getHTMLRepresentation
    * @return The HTML of the transformation
    * @throws XMLSignatureException
    */
   public String getHTMLRepresentation() throws XMLSignatureException {

      try {
         XMLSignatureInput nodes = this.getNodesetBeforeFirstCanonicalization();
         Set inclusiveNamespaces = new HashSet();

         {
            Transforms transforms = this.getTransforms();
            Transform c14nTransform = null;

            if (transforms != null) {
               doTransforms: for (int i = 0; i < transforms.getLength(); i++) {
                  Transform t = transforms.item(i);
                  String URI = t.getURI();

                  if (URI.equals(Transforms.TRANSFORM_C14N_EXCL_OMIT_COMMENTS)
                          || URI.equals(
                             Transforms.TRANSFORM_C14N_EXCL_WITH_COMMENTS)) {
                     c14nTransform = t;

                     break doTransforms;
                  }
               }
            }

            if (c14nTransform != null) {

               if (c14nTransform
                       .length(InclusiveNamespaces
                          .ExclusiveCanonicalizationNamespace, InclusiveNamespaces
                          ._TAG_EC_INCLUSIVENAMESPACES) == 1) {

                  // there is one InclusiveNamespaces element
                  InclusiveNamespaces in = new InclusiveNamespaces(
                        XMLUtils.selectNode(
                        c14nTransform.getElement().getFirstChild(),
						InclusiveNamespaces.ExclusiveCanonicalizationNamespace, 
                        InclusiveNamespaces._TAG_EC_INCLUSIVENAMESPACES,0), this.getBaseURI());

                  inclusiveNamespaces = InclusiveNamespaces.prefixStr2Set(
                     in.getInclusiveNamespaces());
               }
            }
         }

         return nodes.getHTMLRepresentation(inclusiveNamespaces);
      } catch (TransformationException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (InvalidTransformException ex) {
         throw new XMLSignatureException("empty", ex);
      } catch (XMLSecurityException ex) {
         throw new XMLSignatureException("empty", ex);
      }
   }

   /**
    * This method only works works after a call to verify.
    * @return the transformed output(i.e. what is going to be digested).
    */
   public XMLSignatureInput getTransformsOutput() {
      return this._transformsOutput;
   }

   /**
    * This method returns the {@link XMLSignatureInput} which is referenced by the
    * <CODE>URI</CODE> Attribute.
    * @param os where to write the transformation can be null.
    * @return the element to digest
    *
    * @throws XMLSignatureException
    * @see Manifest#verifyReferences()
    */
   protected XMLSignatureInput dereferenceURIandPerformTransforms(OutputStream os)
           throws XMLSignatureException {

      try {
         XMLSignatureInput input = this.getContentsBeforeTransformation();
         XMLSignatureInput output = this.getContentsAfterTransformation(input, os);

         /* at this stage, this._transformsInput and this._transformsOutput
          * contain a huge amount of nodes. When we do not cache these nodes
          * but only preserve the octets, the memory footprint is dramatically
          * reduced.
          */

         this._transformsOutput = output;

         return output;
      } catch (XMLSecurityException ex) {
         throw new ReferenceNotInitializedException("empty", ex);
      }
   }

   /**
    * Method getTransforms
    *
    * @return The transforms that applied this reference.
    * @throws InvalidTransformException
    * @throws TransformationException
    * @throws XMLSecurityException
    * @throws XMLSignatureException
    */
   public Transforms getTransforms()
           throws XMLSignatureException, InvalidTransformException,
                  TransformationException, XMLSecurityException {

      Element transformsElement = XMLUtils.selectDsNode(this._constructionElement.getFirstChild(),
            Constants._TAG_TRANSFORMS,0);

      if (transformsElement != null) {
         Transforms transforms = new Transforms(transformsElement,
                                                this._baseURI);

         return transforms;
      } 
       return null;      
   }

   /**
    * Method getReferencedBytes
    * 
    * @return the bytes that will be used to generated digest.
    * @throws ReferenceNotInitializedException
    * @throws XMLSignatureException
    */
   public byte[] getReferencedBytes()
           throws ReferenceNotInitializedException, XMLSignatureException {
    try {
        XMLSignatureInput output=this.dereferenceURIandPerformTransforms(null);

        byte[] signedBytes = output.getBytes();

        return signedBytes;
     } catch (IOException ex) {
        throw new ReferenceNotInitializedException("empty", ex);
     } catch (CanonicalizationException ex) {
        throw new ReferenceNotInitializedException("empty", ex);
     } 

   }


   /**
    * Method resolverResult
    *
    * @return reference Calculate the digest of this reference.
    * @throws ReferenceNotInitializedException
    * @throws XMLSignatureException
    */
   private byte[] calculateDigest()
           throws ReferenceNotInitializedException, XMLSignatureException {

      try {
         
         MessageDigestAlgorithm mda = this.getMessageDigestAlgorithm();

         mda.reset();
         DigesterOutputStream diOs=new DigesterOutputStream(mda);
         OutputStream os=new UnsyncBufferedOutputStream(diOs);
         XMLSignatureInput output=this.dereferenceURIandPerformTransforms(os);         
         output.updateOutputStream(os);
         os.flush();
         //this.getReferencedBytes(diOs);
         //mda.update(data);

         return diOs.getDigestValue();
      } catch (XMLSecurityException ex) {
         throw new ReferenceNotInitializedException("empty", ex);
      } catch (IOException ex) {
      	 throw new ReferenceNotInitializedException("empty", ex);
	}
   }

   /**
    * Returns the digest value.
    *
    * @return the digest value.
    * @throws Base64DecodingException if Reference contains no proper base64 encoded data.
	* @throws XMLSecurityException if the Reference does not contain a DigestValue element
    */
   public byte[] getDigestValue() throws Base64DecodingException, XMLSecurityException {
      Element digestValueElem = XMLUtils.selectDsNode(this._constructionElement.getFirstChild()
            ,Constants._TAG_DIGESTVALUE,0);
	  if (digestValueElem == null) {
		  // The required element is not in the XML!
		  Object[] exArgs ={ Constants._TAG_DIGESTVALUE, 
							 Constants.SignatureSpecNS };
		  throw new XMLSecurityException(
					"signature.Verification.NoSignatureElement", 
					exArgs);
	  }
      byte[] elemDig = Base64.decode(digestValueElem);
      return elemDig;
   }


   /**
    * Tests reference valdiation is success or false
    *
    * @return true if reference valdiation is success, otherwise false
    * @throws ReferenceNotInitializedException
    * @throws XMLSecurityException
    */
   public boolean verify()
           throws ReferenceNotInitializedException, XMLSecurityException {

      byte[] elemDig = this.getDigestValue();
      byte[] calcDig = this.calculateDigest();
      boolean equal = MessageDigestAlgorithm.isEqual(elemDig, calcDig);

      if (!equal) {
         log.log(java.util.logging.Level.WARNING, "Verification failed for URI \"" + this.getURI() + "\"");
      } else {
         if (log.isLoggable(java.util.logging.Level.INFO))                                  log.log(java.util.logging.Level.INFO, "Verification successful for URI \"" + this.getURI() + "\"");
      }

      return equal;
   }

   /**
    * Method getBaseLocalName
    * @inheritDoc
    *
    */
   public String getBaseLocalName() {
      return Constants._TAG_REFERENCE;
   }
}