Added IO option to disable generator of XML declaration statements in…

… the output CML.

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>

src/main/nu/xom/CustomSerializer.java

@@ -0,0 +1,74 @@
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (C) 2009  Egon Willighagen <egonw@users.sf.net>
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package nu.xom;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.UnsupportedEncodingException;
+
+/**
+ * Custom {@link Serializer} with the sole purpose and functionality to not
+ * output the XML declaration. Needs to be in the <code>nu.xom</code> package
+ * to allow overwriting of the writeXMLDeclaration method.
+ * 
+ * @author     egonw
+ * @cdk.module libiocml
+ */
+public class CustomSerializer extends Serializer {
+
+    /**
+     * Instantiates a new {@link CustomSerializer} using the matching
+     * {@link Serializer#Serializer(OutputStream)}.
+     * 
+     * @param out the output stream to write the document on
+     */
+    public CustomSerializer(OutputStream out) {
+        super(out);
+    }
+
+    /**
+     * Instantiates a new {@link CustomSerializer} using the matching
+     * {@link Serializer#Serializer(OutputStream, String)}.
+     * 
+     * @param out      the output stream to write the document on
+     * @param encoding the character encoding for the serialization
+     */
+    public CustomSerializer(OutputStream out, String encoding)
+            throws UnsupportedEncodingException {
+        super(out, encoding);
+    }
+
+    /**
+     * Overwrite the {@link Serializer#writeXMLDeclaration()} method, and have
+     * it not output the XML declaration.
+     */
+    protected void writeXMLDeclaration() throws IOException {
+        // do nothing
+    }
+
+}
+
+
+

src/main/org/openscience/cdk/io/CMLWriter.java

@@ -36,6 +36,7 @@
 import java.util.List;
 
 import nu.xom.Attribute;
+import nu.xom.CustomSerializer;
 import nu.xom.Document;
 import nu.xom.Element;
 import nu.xom.Serializer;
@@ -119,6 +120,7 @@ public class CMLWriter extends DefaultChemObjectWriter {
     private BooleanIOSetting schemaInstanceOutput;
     private StringIOSetting instanceLocation;
     private BooleanIOSetting indent;
+    private BooleanIOSetting xmlDeclaration;
 
     private LoggingTool logger;
 
@@ -268,7 +270,12 @@ public void write(IChemObject object) throws CDKException {
 
         Document doc = new Document(root);
         try {
-            Serializer serializer = new Serializer(output, "ISO-8859-1");
+            Serializer serializer = null;
+            if (xmlDeclaration.isSet()) {
+                serializer = new Serializer(output, "ISO-8859-1");
+            } else {
+                serializer = new CustomSerializer(output, "ISO-8859-1");
+            }
             if (indent.isSet()) {
                 logger.info("Indenting XML output");
                 serializer.setIndent(2);
@@ -313,6 +320,10 @@ private void initIOSettings() {
         indent = new BooleanIOSetting("Indenting", IOSetting.LOW,
           "Should the output be indented?", 
           "true");
+
+        xmlDeclaration = new BooleanIOSetting("XMLDeclaration", IOSetting.LOW,
+                "Should the output contain an XML declaration?",
+                "true");
     }
 
     private void customizeJob() {
@@ -326,16 +337,18 @@ private void customizeJob() {
             fireIOSettingQuestion(instanceLocation);
         }
         fireIOSettingQuestion(indent);
+        fireIOSettingQuestion(xmlDeclaration);
     }
 
     public IOSetting[] getIOSettings() {
-        IOSetting[] settings = new IOSetting[6];
+        IOSetting[] settings = new IOSetting[7];
         settings[0] = cmlIds;
         settings[1] = namespacedOutput;
         settings[2] = namespacePrefix;
         settings[3] = schemaInstanceOutput;
         settings[4] = instanceLocation;
         settings[5] = indent;
+        settings[6] = xmlDeclaration;
         return settings;
     }