[Cml-cvs] jumbo4.6/cifdom/src/uk/co/demon/ursus/cif/apps ActaReader.java,1.2,1.3 CIFSAXExample.java,1.2,1.3 CIFToDom.java,1.1,1.2

[billyfish <bil...@us...>]

Update of /cvsroot/cml/jumbo4.6/cifdom/src/uk/co/demon/ursus/cif/apps
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20406/cifdom/src/uk/co/demon/ursus/cif/apps

Modified Files:
	ActaReader.java CIFSAXExample.java CIFToDom.java 
Log Message:
changed the underlying dom to xom

Index: CIFSAXExample.java
===================================================================
RCS file: /cvsroot/cml/jumbo4.6/cifdom/src/uk/co/demon/ursus/cif/apps/CIFSAXExample.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** CIFSAXExample.java	2 Mar 2005 23:41:05 -0000	1.2
--- CIFSAXExample.java	22 Mar 2005 22:20:23 -0000	1.3
***************
*** 79,84 ****
      public void addItem(CIFItem item) throws CIFException {
  //        System.out.println("Adding item: "+item.getName()+"/"+item.getValue());
!         String name = item.getName();
!         String value = item.getValue();
          if (name.equalsIgnoreCase("_cell_length_a")) {
              System.out.println("a: "+value);
--- 79,84 ----
      public void addItem(CIFItem item) throws CIFException {
  //        System.out.println("Adding item: "+item.getName()+"/"+item.getValue());
!         String name = item.getItemName();
!         String value = item.getItemValue();
          if (name.equalsIgnoreCase("_cell_length_a")) {
              System.out.println("a: "+value);

Index: ActaReader.java
===================================================================
RCS file: /cvsroot/cml/jumbo4.6/cifdom/src/uk/co/demon/ursus/cif/apps/ActaReader.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ActaReader.java	2 Mar 2005 23:41:05 -0000	1.2
--- ActaReader.java	22 Mar 2005 22:20:23 -0000	1.3
***************
*** 4,7 ****
--- 4,9 ----
  import java.io.File;
  import java.io.FileInputStream;
+ import java.io.FileNotFoundException;
+ import java.io.FileOutputStream;
  import java.io.FileReader;
  import java.io.FileWriter;
***************
*** 9,12 ****
--- 11,15 ----
  import java.io.InputStreamReader;
  import java.io.IOException;
+ import java.io.OutputStream;
  import java.io.Reader;
  
***************
*** 17,24 ****
--- 20,40 ----
  import java.util.Properties;
  
+ /*
  import org.w3c.dom.Document;
  import org.w3c.dom.Element;
  import org.w3c.dom.Node;
  import org.w3c.dom.NodeList;
+ */
+ 
+ import nu.xom.Attribute;
+ import nu.xom.Builder;
+ import nu.xom.Document;
+ import nu.xom.Element;
+ import nu.xom.Elements;
+ import nu.xom.Node;
+ import nu.xom.ParentNode;
+ import nu.xom.Serializer;
+ import nu.xom.Text;
+ 
  
  //import org.w3c.tidy.Tidy;
***************
*** 26,30 ****
  import javax.xml.parsers.DocumentBuilderFactory;
  
- import org.xml.sax.InputSource;
  
  import uk.co.demon.ursus.cif.CIFDocument;
--- 42,45 ----
***************
*** 78,81 ****
--- 93,119 ----
      }
  
+     public void serializeDoc (String filename, Document doc) throws FileNotFoundException, IOException {
+         FileOutputStream stm = new FileOutputStream (filename);
+         serializeDoc (stm, doc);
+     }
+ 
+     public void serializeDoc (OutputStream stm, Document doc) throws IOException {
+         Serializer serializer = new Serializer(stm, "ISO-8859-1");
+         serializer.setIndent(4);
+         serializer.setMaxLength(64);
+         serializer.write(doc);
+     }
+ 
+     public void serializeElement (String filename, Element e) throws FileNotFoundException, IOException {
+         FileOutputStream stm = new FileOutputStream (filename);
+         Document d = new Document (e);
+         serializeDoc (stm, d);
+     }
+ 
+     public void serializeElement (OutputStream stm, Element e) throws IOException {
+         Document d = new Document (e);
+         serializeDoc (stm, d);
+     }
+ 
      public void set2DDir(String d) {
          dir2d = d;
***************
*** 298,320 ****
    </div>
  --*/
!         try {
!             xmlTocDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
!         } catch (Exception e) {
!             System.out.println("BUG: "+e);
!         }
!         Element xmlTop = xmlTocDoc.createElement("html");
!         xmlTocDoc.appendChild(xmlTop);
!         NodeList divList = tocDoc.getElementsByTagName("div");
!         for (int i = 0; i < divList.getLength(); i++) {
!             Element divNode = (Element) divList.item(i);
!             NodeList pList = divNode.getElementsByTagName("p");
!             Element pNode = (Element) pList.item(0);
!             NodeList aList = pNode.getElementsByTagName("a");
!             String id = ((Element)aList.item(0)).getAttribute("name");
!             Element a = xmlTocDoc.createElement("a");
!             a.setAttribute("name", id);
              xmlTop.appendChild(a);
!             String absRef = ((Element)aList.item(3)).getAttribute("href");
!             String cifRef = ((Element)aList.item(4)).getAttribute("href");
              try {
                  Document absDoc = readAbstract(getUrlRoot()+absRef);
--- 336,354 ----
    </div>
  --*/
!         Element xmlTop = new Element("html");
!         xmlTocDoc = new Document (xmlTop);
!         Elements divElems = tocDoc.getRootElement ().getChildElements("div");
!         final int numElems = divElems.size ();
!         for (int i = 0; i < numElems; i++) {
!             Element divNode = divElems.get(i);
!             Elements pList = divNode.getChildElements ("p");
!             Element pNode = pList.get (0);
!             Elements aList = pNode.getChildElements("a");
!             String id = aList.get (0).getAttributeValue("name");
!             Element a = new Element("a");
!             a.addAttribute (new Attribute ("name", id));
              xmlTop.appendChild(a);
!             String absRef = aList.get(3).getAttributeValue ("href");
!             String cifRef = aList.get(4).getAttributeValue ("href");
              try {
                  Document absDoc = readAbstract(getUrlRoot()+absRef);
***************
*** 336,342 ****
              count++;
          }
!         FileWriter fw = new FileWriter(xmlToc);
!         PMRDOMUtil.output(xmlTocDoc, fw);
!         fw.close();
      }
  
--- 370,375 ----
              count++;
          }
! 
!         serializeDoc (xmlToc, xmlTocDoc);
      }
  
***************
*** 344,349 ****
          Document abstractDoc = null;
          System.out.println("reading abstract: "+abstractx);
          try {
!             abstractDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(new InputStreamReader(new URL(abstractx).openStream())));
          } catch (Exception e) {
              throw new CIFException(""+e);
--- 377,384 ----
          Document abstractDoc = null;
          System.out.println("reading abstract: "+abstractx);
+         Builder b = new Builder ();
+ 
          try {
!             abstractDoc = b.build (new URL(abstractx).openStream());
          } catch (Exception e) {
              throw new CIFException(""+e);
***************
*** 354,371 ****
      public void writeAbstract(Document absDoc, String file) throws IOException {
          System.out.println("Writing abstract: "+file);
!         FileWriter fw = new FileWriter(file);
!         PMRDOMUtil.output(absDoc, fw);
!         fw.close();
      }
  
      public void readToc() throws CIFException, IOException {
          System.out.println("reading toc: "+toc);
          try {
!             tocDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(new FileReader(toc)));
!         } catch (IOException ioe) {
!             ioe.printStackTrace();
!             throw ioe;
          } catch (Exception e) {
-             e.printStackTrace();
              throw new CIFException(""+e);
          }
--- 389,404 ----
      public void writeAbstract(Document absDoc, String file) throws IOException {
          System.out.println("Writing abstract: "+file);
! 
! 		serializeDoc (file, absDoc);
      }
  
      public void readToc() throws CIFException, IOException {
          System.out.println("reading toc: "+toc);
+ 
+         Builder b = new Builder ();
+ 
          try {
!             tocDoc = b.build (new FileInputStream (toc));
          } catch (Exception e) {
              throw new CIFException(""+e);
          }
***************
*** 374,380 ****
      public void writeToc() throws IOException {
          System.out.println("Writing toc: "+toc);
!         FileWriter fw = new FileWriter(toc);
!         PMRDOMUtil.output(tocDoc, fw);
!         fw.close();
      }
  
--- 407,412 ----
      public void writeToc() throws IOException {
          System.out.println("Writing toc: "+toc);
! 
!         serializeDoc (toc, tocDoc);
      }
  
***************
*** 444,449 ****
  
      public void makeHtml() throws IOException, CIFException {
          try {
!             xmlTocDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(new FileReader(xmlToc)));
          } catch (Exception e) {
  //            System.out.println("xmlToc error: "+e);
--- 476,483 ----
  
      public void makeHtml() throws IOException, CIFException {
+ 		Builder b = new Builder ();
+ 
          try {
! 			xmlTocDoc = b.build (new FileInputStream (toc));
          } catch (Exception e) {
  //            System.out.println("xmlToc error: "+e);
***************
*** 451,471 ****
          }
  // make menu
!         Document menuDoc = null;
!         try {
!             menuDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
!         } catch (Exception e) {
!             throw new CIFException(""+e);
!         }
!         Element menuRoot = menuDoc.createElement("html");
          menuDoc.appendChild(menuRoot);
!         Element ul = menuDoc.createElement("ul");
          menuRoot.appendChild(ul);
  
!         NodeList aList = xmlTocDoc.getElementsByTagName("a");
  
!         for (int i = 0; i < aList.getLength(); i++) {
!             String id = ((Element) aList.item(i)).getAttribute("name");
              try {
!                 currentCifDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(new FileReader(cmlDir+File.separator+id+".cml")));
              } catch (IOException ioe) {
                  System.err.println("Unexpected IO error: "+ioe);
--- 485,502 ----
          }
  // make menu
! 
! 		Element menuRoot = new Element("html");
! 		Document menuDoc = new Document (menuRoot);
! 
          menuDoc.appendChild(menuRoot);
!         Element ul = new Element("ul");
          menuRoot.appendChild(ul);
  
!         Elements aList = xmlTocDoc.getRootElement ().getChildElements ("a");
  
!         for (int i = 0; i < aList.size(); i++) {
!             String id = aList.get(i).getAttributeValue("name");
              try {
! 				currentCifDoc = b.build (new FileInputStream (cmlDir+File.separator+id+".cml"));
              } catch (IOException ioe) {
                  System.err.println("Unexpected IO error: "+ioe);
***************
*** 474,511 ****
                  throw new CIFException(""+e);
              }
!             Element li = menuDoc.createElement("li");
              ul.appendChild(li);
!             Element a = menuDoc.createElement("a");
              li.appendChild(a);
!             a.setAttribute("href", htmlRoot+File.separator+id+"top.html");
!             a.setAttribute("target", "main");
!             a.appendChild(menuDoc.createTextNode(id));
              Element[] mol2s = make2DCml(id);
              makeTop(mol2s, id);
          }
!         FileWriter fw = new FileWriter(rootDir+File.separator+"menu.html");
!         PMRDOMUtil.output(menuDoc, fw);
!         fw.close();
      }
  
      void makeTop(Element[] mol2s, String id) throws IOException, CIFException {
!         Document topDoc = null;
!         try {
!             topDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
!         } catch (Exception e) {
!             throw new CIFException(""+e);
!         }
  
  // add links
!         Element ul = topDoc.createElement("ul");
          topDoc.appendChild(ul);
          Element li;
          Element a;
!         li = topDoc.createElement("li");
          ul.appendChild(li);
!         a = topDoc.createElement("a");
          li.appendChild(a);
!         a.setAttribute("href", ".."+File.separator+cmlRoot+File.separator+id+".cml");
!         a.appendChild(topDoc.createTextNode("3Db"));
  
  // add abstract
--- 505,537 ----
                  throw new CIFException(""+e);
              }
!             Element li = new Element("li");
              ul.appendChild(li);
!             Element a = new Element("a");
              li.appendChild(a);
!             a.addAttribute(new Attribute ("href", htmlRoot+File.separator+id+"top.html"));
!             a.addAttribute(new Attribute ("target", "main"));
!             a.appendChild(new Text (id));
              Element[] mol2s = make2DCml(id);
              makeTop(mol2s, id);
          }
!         serializeDoc (rootDir+File.separator+"menu.html", menuDoc);
      }
  
      void makeTop(Element[] mol2s, String id) throws IOException, CIFException {
! 		Element ul = new Element("ul");
! 		Document topDoc = new Document (ul);
! 
  
  // add links
! 
          topDoc.appendChild(ul);
          Element li;
          Element a;
!         li = new Element("li");
          ul.appendChild(li);
!         a = new Element("a");
          li.appendChild(a);
!         a.addAttribute(new Attribute ("href", ".."+File.separator+cmlRoot+File.separator+id+".cml"));
!         a.appendChild(new Text ("3Db"));
  
  // add abstract
***************
*** 515,519 ****
          System.out.println("Reading abstract: "+file);
          try {
!             absDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(new FileReader(file)));
              absDoc = trimAbs(absDoc);
          } catch (IOException ioe) {
--- 541,546 ----
          System.out.println("Reading abstract: "+file);
          try {
!             Builder b = new Builder ();
! 			absDoc = b.build (new FileInputStream (file));
              absDoc = trimAbs(absDoc);
          } catch (IOException ioe) {
***************
*** 524,562 ****
          }
  
!         FileWriter fw = new FileWriter(htmlDir+File.separator+id+"top.html");
!         fw.write("<html>");
!         fw.write("<h1>"+id+"</h1>");
!         PMRDOMUtil.output(absDoc, fw);
!         PMRDOMUtil.output(topDoc, fw);
!         make2DHtml(fw, id, mol2s);
!         make3DHtml(fw, id);
!         fw.write("</html>");
!         fw.close();
      }
  
      private Document trimAbs(Document absDoc) {
!         NodeList aList = absDoc.getElementsByTagName("a");
!         int l = aList.getLength();
          for (int i = l-1; i >= 0; i--) {
!             Node a = aList.item(i);
!             Node parent = a.getParentNode();
              if (parent != null) {
                  parent.removeChild(a);
              }
          }
!         NodeList pList = absDoc.getElementsByTagName("p");
!         l = pList.getLength();
          for (int i = l-1; i >= 0; i--) {
!             Node p = pList.item(i);
!             Node parent = p.getParentNode();
              if ((i == 3 || i == 2) && parent != null) {
                  parent.removeChild(p);
              }
          }
!         NodeList iList = absDoc.getElementsByTagName("img");
!         l = iList.getLength();
          for (int i = l-1; i >= 0; i--) {
!             Node ii = iList.item(i);
!             Node parent = ii.getParentNode();
              parent.removeChild(ii);
          }
--- 551,597 ----
          }
  
! 		FileOutputStream stm = new FileOutputStream (htmlDir+File.separator+id+"top.html");
! 		StringBuffer sb = new StringBuffer ("<html>\n");
! 
! 		sb.append ("<h1>");
! 		sb.append (id);
! 		sb.append ("<h1>");
! 
!  		stm.write (sb.toString ().getBytes ());
!         sb.delete (0, sb.length ());
! 
!         serializeDoc (stm, absDoc);
!         serializeDoc (stm, topDoc);
! 
!         make2DHtml(stm, id, mol2s);
!         make3DHtml(stm, id);
! 
!        	stm.write ("</html>".getBytes ());
      }
  
      private Document trimAbs(Document absDoc) {
!         Elements aList = absDoc.getRootElement ().getChildElements ("a");
!         int l = aList.size();
          for (int i = l-1; i >= 0; i--) {
!             Element a = aList.get(i);
!             ParentNode parent = a.getParent();
              if (parent != null) {
                  parent.removeChild(a);
              }
          }
!         Elements pList = absDoc.getRootElement ().getChildElements ("p");
!         l = pList.size();
          for (int i = l-1; i >= 0; i--) {
!             Element p = pList.get(i);
!             ParentNode parent = p.getParent ();
              if ((i == 3 || i == 2) && parent != null) {
                  parent.removeChild(p);
              }
          }
!         Elements iList = absDoc.getRootElement ().getChildElements ("img");
!         l = iList.size();
          for (int i = l-1; i >= 0; i--) {
!             Element ii = iList.get(i);
!             ParentNode parent = ii.getParent ();
              parent.removeChild(ii);
          }
***************
*** 565,618 ****
      }
  
!     public void make2DHtml(FileWriter fw, String id, Element[] mol2s) throws IOException {
          for (int i = 0; i < mol2s.length; i++) {
              if (i % 3 == 0) {
!                 fw.write("<tr>\n");
              }
!             fw.write("<td>\n");
!             fw.write("<script LANGUAGE=\"JavaScript1.1\" SRC=\"../marvin.js\"></script>\n");
!             fw.write("<script LANGUAGE=\"JavaScript1.1\">\n");
!             fw.write("<!--\n");
!             fw.write("marvin_jvm = \"builtin\";\n");
!             fw.write("marvin_gui = \"swing\";\n");
!             fw.write("mview_begin(\"..\", 300, 300);\n");
!             fw.write("mview_param(\"implicitH\", \"off\");\n");
!             fw.write("mview_param(\"explicitH\", \"true\");\n");
!             fw.write("mview_param(\"editable\", \"0\");\n");
!             fw.write("mview_param(\"detachable\", \"false\");\n");
              // requires slash, not File.separator
!             fw.write("mview_param(\"mol\", \".."+"/"+root2d+"/"+id+"."+(i+1)+".cml\");\n");
!             fw.write("mview_end();\n");
!             fw.write("//-->\n");
!             fw.write("</script>\n");
!             fw.write("</td>\n");
              if (i % 3 == 2) {
!                 fw.write("</tr>\n");
              }
          }
          if ((mol2s.length-1) % 3 != 2) {
!             fw.write("</tr>\n");
          }
      }
  
      public Element[] make2DCml(String id) throws IOException {
!         NodeList mols = currentCifDoc.getElementsByTagName("molecule");
!         Element molecule0 = (Element) mols.item(0);
  // remove 3D attributes
!         NodeList atomList = molecule0.getElementsByTagName("atom");
!         for (int i = 0; i < atomList.getLength(); i++) {
!             Element atom = (Element) atomList.item(i);
!             atom.removeAttribute("x3");
!             atom.removeAttribute("y3");
!             atom.removeAttribute("z3");
!             atom.removeAttribute("xFract");
!             atom.removeAttribute("yFract");
!             atom.removeAttribute("zFract");
          }
          removeDuplicateAtomsAndBonds(molecule0);
  
  // split molecules and write each
!         NodeList childMols = molecule0.getElementsByTagName("molecule");
!         Element[] molecules = new Element[childMols.getLength()];
  // no child molecules, take complete DOM
          if (molecules.length == 0) {
--- 600,675 ----
      }
  
!     public void make2DHtml(FileOutputStream stm, String id, Element[] mol2s) throws IOException {
! 
          for (int i = 0; i < mol2s.length; i++) {
              if (i % 3 == 0) {
!                 stm.write("<tr>\n".getBytes ());
              }
!             stm.write("<td>\n".getBytes ());
!             stm.write("<script LANGUAGE=\"JavaScript1.1\" SRC=\"../marvin.js\"></script>\n".getBytes ());
!             stm.write("<script LANGUAGE=\"JavaScript1.1\">\n".getBytes ());
!             stm.write("<!--\n".getBytes ());
!             stm.write("marvin_jvm = \"builtin\";\n".getBytes ());
!             stm.write("marvin_gui = \"swing\";\n".getBytes ());
!             stm.write("mview_begin(\"..\", 300, 300);\n".getBytes ());
!             stm.write("mview_param(\"implicitH\", \"off\".getBytes ());\n".getBytes ());
!             stm.write("mview_param(\"explicitH\", \"true\".getBytes ());\n".getBytes ());
!             stm.write("mview_param(\"editable\", \"0\".getBytes ());\n".getBytes ());
!             stm.write("mview_param(\"detachable\", \"false\".getBytes ());\n".getBytes ());
              // requires slash, not File.separator
!             String s ="mview_param(\"mol\", \".."+"/"+root2d+"/"+id+"."+(i+1)+".cml\"\n";
!             stm.write (s.getBytes ());
!             stm.write("mview_end();\n".getBytes ());
!             stm.write("//-->\n".getBytes ());
!             stm.write("</script>\n".getBytes ());
!             stm.write("</td>\n".getBytes ());
              if (i % 3 == 2) {
!                 stm.write("</tr>\n".getBytes ());
              }
          }
          if ((mol2s.length-1) % 3 != 2) {
!             stm.write("</tr>\n".getBytes ());
          }
      }
  
      public Element[] make2DCml(String id) throws IOException {
!         Elements mols = currentCifDoc.getRootElement ().getChildElements ("molecule");
!         Element molecule0 = mols.get (0);
  // remove 3D attributes
!         Elements atomList = molecule0.getChildElements ("atom");
!         Attribute a = null;
! 
!         for (int i = 0; i < atomList.size(); i++) {
!             Element atom = atomList.get(i);
! 
! 			if ((a = atom.getAttribute ("x3")) != null) {
! 				atom.removeAttribute (a);
! 			}
! 
!  			if ((a = atom.getAttribute ("y3")) != null) {
!  				atom.removeAttribute (a);
! 			}
! 
!  			if ((a = atom.getAttribute ("z3")) != null) {
!  				atom.removeAttribute (a);
! 			}
! 
! 			if ((a = atom.getAttribute ("xFract")) != null) {
! 				atom.removeAttribute (a);
! 			}
! 
!  			if ((a = atom.getAttribute ("yFract")) != null) {
!  				atom.removeAttribute (a);
! 			}
! 
!  			if ((a = atom.getAttribute ("zFract")) != null) {
!  				atom.removeAttribute (a);
! 			}
          }
          removeDuplicateAtomsAndBonds(molecule0);
  
  // split molecules and write each
!         Elements childMols = molecule0.getChildElements ("molecule");
!         Element[] molecules = new Element[childMols.size()];
  // no child molecules, take complete DOM
          if (molecules.length == 0) {
***************
*** 622,633 ****
  // else split child molecules
              for (int i = 0; i < molecules.length; i++) {
!                 molecules[i] = (Element) childMols.item(i);
              }
          }
  //output molecules
          for (int i = 0; i < molecules.length; i++) {
!             FileWriter fw = new FileWriter(dir2d+File.separator+id+"."+(i+1)+".cml");
!             PMRDOMUtil.output(molecules[i], fw);
!             fw.close();
          }
          return molecules;
--- 679,689 ----
  // else split child molecules
              for (int i = 0; i < molecules.length; i++) {
!                 molecules[i] = childMols.get(i);
              }
          }
  //output molecules
          for (int i = 0; i < molecules.length; i++) {
!             FileOutputStream stm = new FileOutputStream (dir2d+File.separator+id+"."+(i+1)+".cml");
!             serializeElement (stm, molecules [i]);
          }
          return molecules;
***************
*** 636,659 ****
  // remove duplicate atoms and bonds (symmetry bug)
      private void removeDuplicateAtomsAndBonds(Element molecule) {
!         NodeList atomList = molecule.getElementsByTagName("atom");
          HashMap atomMap = new HashMap();
!         int natoms = atomList.getLength();
          for (int i = natoms-1; i >= 0; i--) {
!             Element atom = (Element) atomList.item(i);
!             String id = atom.getAttribute("id");
              if (atomMap.containsKey(id)) {
!                 atom.getParentNode().removeChild(atom);
              } else {
                  atomMap.put(id, atom);
              }
          }
!         NodeList bondList = molecule.getElementsByTagName("bond");
          HashMap bondMap = new HashMap();
!         int nbonds = bondList.getLength();
          for (int i = nbonds-1; i >= 0; i--) {
!             Element bond = (Element) bondList.item(i);
!             String id = bond.getAttribute("id");
              if (bondMap.containsKey(id)) {
!                 bond.getParentNode().removeChild(bond);
              } else {
                  bondMap.put(id, bond);
--- 692,715 ----
  // remove duplicate atoms and bonds (symmetry bug)
      private void removeDuplicateAtomsAndBonds(Element molecule) {
!         Elements atomList = molecule.getChildElements("atom");
          HashMap atomMap = new HashMap();
!         int natoms = atomList.size();
          for (int i = natoms-1; i >= 0; i--) {
!             Element atom = atomList.get(i);
!             String id = atom.getAttributeValue("id");
              if (atomMap.containsKey(id)) {
!                 atom.getParent ().removeChild(atom);
              } else {
                  atomMap.put(id, atom);
              }
          }
!         Elements bondList = molecule.getChildElements("bond");
          HashMap bondMap = new HashMap();
!         int nbonds = bondList.size();
          for (int i = nbonds-1; i >= 0; i--) {
!             Element bond = bondList.get(i);
!             String id = bond.getAttributeValue("id");
              if (bondMap.containsKey(id)) {
!                 bond.getParent ().removeChild(bond);
              } else {
                  bondMap.put(id, bond);
***************
*** 663,672 ****
  
  
!     public void make3DHtml(FileWriter fw, String id) throws IOException {
!         fw.write("    <APPLET code=\"JmolApplet\" width=\"400\" height=\"400\" codebase=\".\"  ARCHIVE=\"../JmolApplet.jar\">\n");
!         fw.write("        <param name=\"load\" value=\".."+File.separator+root3d+File.separator+id+"sup1.cml\">\n");
!         fw.write("        </param>\n");
!         fw.write("    You have to enable Java and JavaScript on your machine !\n");
!         fw.write("    </APPLET>\n");
      }
      static void usage() {
--- 719,729 ----
  
  
!     public void make3DHtml(FileOutputStream stm, String id) throws IOException {
!         stm.write("    <APPLET code=\"JmolApplet\" width=\"400\" height=\"400\" codebase=\".\"  ARCHIVE=\"../JmolApplet.jar\">\n".getBytes ());
!         String s = "        <param name=\"load\" value=\".."+File.separator+root3d+File.separator+id+"sup1.cml\">\n";
!         stm.write(s.getBytes ());
!         stm.write("        </param>\n".getBytes ());
!         stm.write("    You have to enable Java and JavaScript on your machine !\n".getBytes ());
!         stm.write("    </APPLET>\n".getBytes ());
      }
      static void usage() {

Index: CIFToDom.java
===================================================================
RCS file: /cvsroot/cml/jumbo4.6/cifdom/src/uk/co/demon/ursus/cif/apps/CIFToDom.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** CIFToDom.java	16 Feb 2005 18:35:32 -0000	1.1
--- CIFToDom.java	22 Mar 2005 22:20:23 -0000	1.2
***************
*** 27,31 ****
  import uk.co.demon.ursus.cif.CIFParserFactory;
  
- import jumbo.xml.util.PMRDOMUtil;
  
  /**
--- 27,30 ----
***************
*** 246,250 ****
  						if (bw != null) {
  							try {
! 								PMRDOMUtil.output (doc, bw);
  							} catch (IOException ioe) {
  								System.err.println ("Couldn't output document to file.");
--- 245,249 ----
  						if (bw != null) {
  							try {
! 								bw.write (doc.toXML ());
  							} catch (IOException ioe) {
  								System.err.println ("Couldn't output document to file.");