[Cml-cvs] jumbo50/src/org/xmlcml/cml/element CMLAtom.java-1,NONE,1.1 CMLAttributeList.java,NONE,1.1 CMLNodeFactory.java,NONE,1.1 CMLTypeList.java,NONE,1.1 CMLReaction.java,1.15,1.16 ProductReactant.java,1.1,NONE ProductReactantList.java,1.2,NONE

[Peter Murray-R. <pe...@us...>]

Update of /cvsroot/cml/jumbo50/src/org/xmlcml/cml/element
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20453/src/org/xmlcml/cml/element

Modified Files:
	CMLReaction.java 
Added Files:
	CMLAtom.java-1 CMLAttributeList.java CMLNodeFactory.java 
	CMLTypeList.java 
Removed Files:
	ProductReactant.java ProductReactantList.java 
Log Message:
refactored reactions and forward references from elements to tools

--- NEW FILE: CMLAttributeList.java ---
package org.xmlcml.cml.element;

import java.util.Map;
import java.util.HashMap;
import java.util.logging.Logger;
import org.xmlcml.cml.base.CMLException;
import org.xmlcml.cml.base.CMLAttribute;
import org.xmlcml.cml.base.StringAttribute;
import org.xmlcml.cml.base.StringArrayAttribute;
import org.xmlcml.cml.base.IntAttribute;
import org.xmlcml.cml.base.IntArrayAttribute;
import org.xmlcml.cml.base.DoubleAttribute;
import org.xmlcml.cml.base.DoubleArrayAttribute;
import nu.xom.Attribute;

/** user-modifiable class supporting CMLAttributeList.
*
* autogenerated from schema
* use as a shell which can be edited
[...1747 lines suppressed...]
    * @return Attribute
    */
    public static Attribute makeAttributeFromGroupName(String attributeGroupName, String value, String URI) throws CMLException {
        CMLAttribute attribute =  CMLAttribute.createSubclassedAttribute(CMLAttributeList.getAttribute(attributeGroupName), value);
        if (attribute != null) {
            attribute.setCMLValue(value);
        }

        return attribute;

    }
    /** get summary.
    *
    * @return String
    */
    public String getSummary() {
        return "";

    }
}

--- NEW FILE: CMLAtom.java-1 ---
package org.xmlcml.cml.element;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;

import jumbo.euclid.Angle;
import jumbo.euclid.EuclidException;
import jumbo.euclid.Point3;
import jumbo.euclid.Real2;
import jumbo.euclid.Transform2;
import jumbo.euclid.Transform3;
import jumbo.euclid.Vector2;
import jumbo.euclid.Vector3;
import nu.xom.Element;
import nu.xom.Node;

[...1810 lines suppressed...]
			newLigands[count++] = heaviestAtom;
			newLigandVector.remove(heaviest);
		}
		return newLigands;
	}
	
	private int getHeaviestAtom(List<CMLAtom> newAtomVector) {
		int heaviestAtNum = -1;
		int heaviest = -1;
		for (int i = 0; i < newAtomVector.size(); i++) {
			CMLAtom atom = newAtomVector.get(i);
			int atnum = atom.getAtomicNumber();
			if (atnum > heaviestAtNum) {
				heaviest = i;
				heaviestAtNum = atnum;
			}
		}
		return heaviest;
	}
}
--- ProductReactant.java DELETED ---

--- ProductReactantList.java DELETED ---

--- NEW FILE: CMLTypeList.java ---
package org.xmlcml.cml.element;

import java.util.Map;
import java.util.HashMap;
import java.util.logging.Logger;
import org.xmlcml.cml.base.CMLException;
import org.xmlcml.cml.base.CMLType;

/** NON-modifiable class supporting CMLTypeList.
*
* autogenerated from schema
* DO  NOT EDIT!!

*/
public class CMLTypeList {

// fields;
    // map of types by type name
    public static Map<String, CMLType> typeMap = new HashMap<String, CMLType>();
[...1002 lines suppressed...]
        st.setBase("xsd:string");
        st.setId("st.elementTypeArrayType");
        st.setSummary("An array of elementTypes.");
        st.setDescription("Instances of this type will be used in array-style representation of atoms.");
        st.setIsList(true);
        typeMap.put("elementTypeArrayType", st);
        //----type-------maxType----------
        st = new CMLType();
        namex = "maxType";
        st.setName(namex);
        st.setBase("xsd:string");
        st.setId("st.maxType");
        st.setSummary("The maximum INCLUSIVE value of a quantity.");
        st.setDescription("\n The maximum INCLUSIVE value of a sortable quantity such as\n numeric, date or string. It should be ignored for dataTypes such as URL. \nThe use of min and\n max attributes can be used to give a range for the quantity.\n The statistical basis of this range is not defined. The value of max \nis usually an observed \nquantity (or calculated from observations). To restrict a value, the \nmaxExclusive type in a dictionary should be used.\n The type of the maximum is the same as the quantity to which it refers - numeric,\n date and string are currently allowed");
        typeMap.put("maxType", st);
        } catch (CMLException e) {
            logger.severe("bug"+e);
        }
    };
}

Index: CMLReaction.java
===================================================================
RCS file: /cvsroot/cml/jumbo50/src/org/xmlcml/cml/element/CMLReaction.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** CMLReaction.java	29 Nov 2005 08:41:04 -0000	1.15
--- CMLReaction.java	30 Nov 2005 15:51:14 -0000	1.16
***************
*** 1,7 ****
  package org.xmlcml.cml.element;
  
- import java.io.IOException;
- import java.io.StringWriter;
- import java.io.Writer;
  import java.util.ArrayList;
  import java.util.List;
--- 1,4 ----
***************
*** 117,203 ****
  
  	/**
- 	 * output and analyse aggregate formula for products and reactants.
- 	 * 
- 	 * 
- 	 * @param w
- 	 *            the output writer
- 	 * @throws CMLException
- 	 * @throws IOException
- 	 */
- 	public void outputBalance(Writer w) throws CMLException, IOException {
- 		CMLReactantList reactantList = (CMLReactantList) this
- 				.getFirstCMLChild(CMLReactantList.TAG);
- 		CMLFormula reactantFormula = null;
- 		if (reactantList != null) {
- 			reactantFormula = ProductReactantList.getAggregateFormula(reactantList);
- 			w.write(reactantFormula.getFormattedString());
- 		} else {
- 			w.write("Null reactantList");
- 		}
- 		w.write(" = ");
- 
- 		CMLProductList productList = (CMLProductList) this
- 				.getFirstCMLChild(CMLProductList.TAG);
- 		if (productList != null) {
- 			CMLFormula productFormula = ProductReactantList.getAggregateFormula(productList);
- 			w.write(productFormula.getFormattedString());
- 
- 			w.write(" ; difference: ");
- 
- 			String differenceFormula = reactantFormula
- 					.getDifference(productFormula);
- 			w.write(differenceFormula);
- 		} else {
- 			w.write("Null productList");
- 		}
- 	}
- 
- 	/**
- 	 * output simple inline version of reaction.
- 	 * 
- 	 * of form "C2H4 + H2O = C2H6O" without newline
- 	 * 
- 	 * @param w
- 	 *            the output writer
- 	 * @throws CMLException
- 	 * @throws IOException
- 	 */
- 	public void outputReaction(Writer w) throws CMLException, IOException {
- 		CMLReactantList reactantList = (CMLReactantList) this.getFirstCMLChild(CMLReactantList.TAG);
- 		if (reactantList != null) {
- 			int reactantCount = reactantList.getCMLChildCount(CMLReactant.TAG);
- 			for (int i = 0; i < reactantCount; i++) {
- 				CMLReactant reactant = (CMLReactant) reactantList.getChildCMLElement(CMLReactant.TAG, i);
- 				if (reactant == null) {
- 					w.write("Null reactant");
- 				} else {
- 					CMLFormula reactantFormula = ProductReactant.getFormula(reactant);
- 					w.write(((i > 0) ? " + " : S_EMPTY)
- 							+ reactantFormula.getFormattedString());
- 				}
- 			}
- 		} else {
- 			w.write("Null reactantList");
- 		}
- 		w.write(" = ");
- 		CMLProductList productList = (CMLProductList) this.getFirstCMLChild(CMLProductList.TAG);
- 		if (productList != null) {
- 			int productCount = productList.getCMLChildCount(CMLProduct.TAG);
- 			for (int i = 0; i < productCount; i++) {
- 				CMLProduct product = (CMLProduct) productList.getChildCMLElement(CMLProduct.TAG, i);
- 				if (product == null) {
- 					w.write("Null product");
- 				} else {
- 					CMLFormula productFormula = ProductReactant.getFormula(product);
- 					w.write(((i > 0) ? " + " : S_EMPTY)
- 							+ productFormula.getFormattedString());
- 				}
- 			}
- 		} else {
- 			w.write("Null productList");
- 		}
- 	}
- 
- 	/**
  	 * merge productLists into single productList.
  	 * 
--- 114,117 ----
***************
*** 339,372 ****
  	}
  
- 	/**
- 	 * get all molecules on reactant or product side. includes cmlSpectator
- 	 * 
- 	 * @param reactantProduct
- 	 *            CMLSpectator.REACTANT or CMLSpectator.PRODUCT
- 	 * @return all molecules
- 	 */
- 	public List<CMLMolecule> getMoleculesIncludingSpectators(String reactantProduct) {
- 		List<CMLMolecule> moleculeList = new ArrayList<CMLMolecule>();
- 		if (reactantProduct.equals(CMLReactant.TAG)) {
- 			CMLReactantList reactantList = (CMLReactantList) this.getFirstCMLChild(CMLReactantList.TAG);
- 			if (reactantList != null) {
- 				moleculeList = ProductReactantList.getMolecules(reactantList);
- 			}
- 		} else if (reactantProduct.equals(CMLProduct.TAG)) {
- 			CMLProductList productList = (CMLProductList) this.getFirstCMLChild(CMLProductList.TAG);
- 			if (productList != null) {
- 				moleculeList = ProductReactantList.getMolecules(productList);
- 			}
- 		}
- 		CMLSpectatorList spectatorList = (CMLSpectatorList) this.getFirstCMLChild(CMLSpectatorList.TAG);
- 		if (spectatorList != null) {
- 			List<CMLMolecule> moleculex = spectatorList.getSpectatorMolecules(reactantProduct);
- 			for (int i = 0; i < moleculex.size(); i++) {
- 				moleculeList.add(moleculex.get(i));
- 			}
- 		}
- 		return moleculeList;
- 	}
- 
  	public List<CMLMolecule> concat(Elements moleculeNodes1, List<CMLMolecule> m2) {
  		List<CMLMolecule> m = new ArrayList <CMLMolecule>();
--- 253,256 ----
***************
*** 486,509 ****
  		}
  	}
- 
- 	/**
- 	 * output the reaction analysis to a string.
- 	 * 
- 	 * @return the string
- 	 * @throws CMLException
- 	 */
- 	public String analyzeReaction() throws CMLException {
- 		StringWriter w = new StringWriter();
- 		try {
- 			this.outputReaction(w);
- 			w.write(S_NL);
- 			this.outputBalance(w);
- 			w.write(S_NL);
- 			w.close();
- 		} catch (IOException ioe) {
- 			logger.severe("BUG " + ioe);
- 		}
- 		return w.toString();
- 	}
- 
  }
--- 370,372 ----

--- NEW FILE: CMLNodeFactory.java ---
package org.xmlcml.cml.element;

import java.util.Stack;
import nu.xom.Attribute;
import nu.xom.Element;
import nu.xom.NodeFactory;
import nu.xom.Nodes;
import nu.xom.Text;
import org.xmlcml.cml.base.CMLElement;
import org.xmlcml.cml.base.CMLException;
import org.xmlcml.cml.base.CMLRuntime;

/** user-modifiable class supporting CMLNodeFactory.
*
* autogenerated from schema
* use as a shell which can be edited

*/
public class CMLNodeFactory extends NodeFactory {

// fields;
    // current of current node
    public Element current;
    // current element stack
    public Stack<Element> stack = new Stack<Element>();
    /** must give simple documentation.
    *
    */
    public CMLNodeFactory() {
    }

    /** callback from element start tag.
    *
    * @param name element name
    * @param namespace namespace of element
    * @return Element
    */
    public Element startMakingElement(String name, String namespace) {
// fields;
        // new element
        Element newElement;
        if (false) {
        } else if(name.equals("symmetry")) {
            newElement = CMLSymmetry.makeElementInContext(current);
        } else if(name.equals("peakList")) {
            newElement = CMLPeakList.makeElementInContext(current);
        } else if(name.equals("product")) {
            newElement = CMLProduct.makeElementInContext(current);
        } else if(name.equals("region")) {
            newElement = CMLRegion.makeElementInContext(current);
        } else if(name.equals("point3")) {
            newElement = CMLPoint3.makeElementInContext(current);
        } else if(name.equals("expression")) {
            newElement = CMLExpression.makeElementInContext(current);
        } else if(name.equals("reactantList")) {
            newElement = CMLReactantList.makeElementInContext(current);
        } else if(name.equals("actionList")) {
            newElement = CMLActionList.makeElementInContext(current);
        } else if(name.equals("alternative")) {
            newElement = CMLAlternative.makeElementInContext(current);
        } else if(name.equals("object")) {
            newElement = CMLObject.makeElementInContext(current);
        } else if(name.equals("string")) {
            newElement = CMLString.makeElementInContext(current);
        } else if(name.equals("parameter")) {
            newElement = CMLParameter.makeElementInContext(current);
        } else if(name.equals("reactionStep")) {
            newElement = CMLReactionStep.makeElementInContext(current);
        } else if(name.equals("spectrumList")) {
            newElement = CMLSpectrumList.makeElementInContext(current);
        } else if(name.equals("bondStereo")) {
            newElement = CMLBondStereo.makeElementInContext(current);
        } else if(name.equals("peakStructure")) {
            newElement = CMLPeakStructure.makeElementInContext(current);
        } else if(name.equals("atomParity")) {
            newElement = CMLAtomParity.makeElementInContext(current);
        } else if(name.equals("mechanismComponent")) {
            newElement = CMLMechanismComponent.makeElementInContext(current);
        } else if(name.equals("operator")) {
            newElement = CMLOperator.makeElementInContext(current);
        } else if(name.equals("array")) {
            newElement = CMLArray.makeElementInContext(current);
        } else if(name.equals("scalar")) {
            newElement = CMLScalar.makeElementInContext(current);
        } else if(name.equals("stringArray")) {
            newElement = CMLStringArray.makeElementInContext(current);
        } else if(name.equals("peakGroup")) {
            newElement = CMLPeakGroup.makeElementInContext(current);
        } else if(name.equals("unitList")) {
            newElement = CMLUnitList.makeElementInContext(current);
        } else if(name.equals("angle")) {
            newElement = CMLAngle.makeElementInContext(current);
        } else if(name.equals("torsion")) {
            newElement = CMLTorsion.makeElementInContext(current);
        } else if(name.equals("spectatorList")) {
            newElement = CMLSpectatorList.makeElementInContext(current);
        } else if(name.equals("latticeVector")) {
            newElement = CMLLatticeVector.makeElementInContext(current);
        } else if(name.equals("module")) {
            newElement = CMLModule.makeElementInContext(current);
        } else if(name.equals("line3")) {
            newElement = CMLLine3.makeElementInContext(current);
        } else if(name.equals("integerArray")) {
            newElement = CMLIntegerArray.makeElementInContext(current);
        } else if(name.equals("zMatrix")) {
            newElement = CMLZMatrix.makeElementInContext(current);
        } else if(name.equals("observation")) {
            newElement = CMLObservation.makeElementInContext(current);
        } else if(name.equals("enumeration")) {
            newElement = CMLEnumeration.makeElementInContext(current);
        } else if(name.equals("potentialForm")) {
            newElement = CMLPotentialForm.makeElementInContext(current);
        } else if(name.equals("system")) {
            newElement = CMLSystem.makeElementInContext(current);
        } else if(name.equals("name")) {
            newElement = CMLName.makeElementInContext(current);
        } else if(name.equals("bondTypeList")) {
            newElement = CMLBondTypeList.makeElementInContext(current);
        } else if(name.equals("action")) {
            newElement = CMLAction.makeElementInContext(current);
        } else if(name.equals("vector3")) {
            newElement = CMLVector3.makeElementInContext(current);
        } else if(name.equals("atomicBasisFunction")) {
            newElement = CMLAtomicBasisFunction.makeElementInContext(current);
        } else if(name.equals("metadataList")) {
            newElement = CMLMetadataList.makeElementInContext(current);
        } else if(name.equals("unit")) {
            newElement = CMLUnit.makeElementInContext(current);
        } else if(name.equals("length")) {
            newElement = CMLLength.makeElementInContext(current);
        } else if(name.equals("definition")) {
            newElement = CMLDefinition.makeElementInContext(current);
        } else if(name.equals("link")) {
            newElement = CMLLink.makeElementInContext(current);
        } else if(name.equals("reactiveCentre")) {
            newElement = CMLReactiveCentre.makeElementInContext(current);
        } else if(name.equals("relatedEntry")) {
            newElement = CMLRelatedEntry.makeElementInContext(current);
        } else if(name.equals("isotopeList")) {
            newElement = CMLIsotopeList.makeElementInContext(current);
        } else if(name.equals("transitionState")) {
            newElement = CMLTransitionState.makeElementInContext(current);
        } else if(name.equals("documentation")) {
            newElement = CMLDocumentation.makeElementInContext(current);
        } else if(name.equals("plane3")) {
            newElement = CMLPlane3.makeElementInContext(current);
        } else if(name.equals("atomSet")) {
            newElement = CMLAtomSet.makeElementInContext(current);
        } else if(name.equals("spectator")) {
            newElement = CMLSpectator.makeElementInContext(current);
        } else if(name.equals("identifier")) {
            newElement = CMLIdentifier.makeElementInContext(current);
        } else if(name.equals("bondArray")) {
            newElement = CMLBondArray.makeElementInContext(current);
        } else if(name.equals("floatArray")) {
            newElement = CMLFloatArray.makeElementInContext(current);
        } else if(name.equals("lattice")) {
            newElement = CMLLattice.makeElementInContext(current);
        } else if(name.equals("table")) {
            newElement = CMLTable.makeElementInContext(current);
        } else if(name.equals("arg")) {
            newElement = CMLArg.makeElementInContext(current);
        } else if(name.equals("potential")) {
            newElement = CMLPotential.makeElementInContext(current);
        } else if(name.equals("reactionStepList")) {
            newElement = CMLReactionStepList.makeElementInContext(current);
        } else if(name.equals("xaxis")) {
            newElement = CMLXaxis.makeElementInContext(current);
        } else if(name.equals("mechanism")) {
            newElement = CMLMechanism.makeElementInContext(current);
        } else if(name.equals("atom")) {
            newElement = CMLAtom.makeElementInContext(current);
        } else if(name.equals("spectrumData")) {
            newElement = CMLSpectrumData.makeElementInContext(current);
        } else if(name.equals("potentialList")) {
            newElement = CMLPotentialList.makeElementInContext(current);
        } else if(name.equals("electron")) {
            newElement = CMLElectron.makeElementInContext(current);
        } else if(name.equals("eigen")) {
            newElement = CMLEigen.makeElementInContext(current);
        } else if(name.equals("parameterList")) {
            newElement = CMLParameterList.makeElementInContext(current);
        } else if(name.equals("reactionScheme")) {
            newElement = CMLReactionScheme.makeElementInContext(current);
        } else if(name.equals("float")) {
            newElement = CMLFloat.makeElementInContext(current);
        } else if(name.equals("reactant")) {
            newElement = CMLReactant.makeElementInContext(current);
        } else if(name.equals("yaxis")) {
            newElement = CMLYaxis.makeElementInContext(current);
        } else if(name.equals("integer")) {
            newElement = CMLInteger.makeElementInContext(current);
        } else if(name.equals("stmml")) {
            newElement = CMLStmml.makeElementInContext(current);
        } else if(name.equals("property")) {
            newElement = CMLProperty.makeElementInContext(current);
        } else if(name.equals("appinfo")) {
            newElement = CMLAppinfo.makeElementInContext(current);
        } else if(name.equals("bond")) {
            newElement = CMLBond.makeElementInContext(current);
        } else if(name.equals("formula")) {
            newElement = CMLFormula.makeElementInContext(current);
        } else if(name.equals("particle")) {
            newElement = CMLParticle.makeElementInContext(current);
        } else if(name.equals("substanceList")) {
            newElement = CMLSubstanceList.makeElementInContext(current);
        } else if(name.equals("unitType")) {
            newElement = CMLUnitType.makeElementInContext(current);
        } else if(name.equals("bondType")) {
            newElement = CMLBondType.makeElementInContext(current);
        } else if(name.equals("reaction")) {
            newElement = CMLReaction.makeElementInContext(current);
        } else if(name.equals("bondSet")) {
            newElement = CMLBondSet.makeElementInContext(current);
        } else if(name.equals("map")) {
            newElement = CMLMap.makeElementInContext(current);
        } else if(name.equals("productList")) {
            newElement = CMLProductList.makeElementInContext(current);
        } else if(name.equals("substance")) {
            newElement = CMLSubstance.makeElementInContext(current);
        } else if(name.equals("dimension")) {
            newElement = CMLDimension.makeElementInContext(current);
        } else if(name.equals("metadata")) {
            newElement = CMLMetadata.makeElementInContext(current);
        } else if(name.equals("sample")) {
            newElement = CMLSample.makeElementInContext(current);
        } else if(name.equals("propertyList")) {
            newElement = CMLPropertyList.makeElementInContext(current);
        } else if(name.equals("atomArray")) {
            newElement = CMLAtomArray.makeElementInContext(current);
        } else if(name.equals("molecule")) {
            newElement = CMLMolecule.makeElementInContext(current);
        } else if(name.equals("reactionList")) {
            newElement = CMLReactionList.makeElementInContext(current);
        } else if(name.equals("peak")) {
            newElement = CMLPeak.makeElementInContext(current);
        } else if(name.equals("annotation")) {
            newElement = CMLAnnotation.makeElementInContext(current);
        } else if(name.equals("atomType")) {
            newElement = CMLAtomType.makeElementInContext(current);
        } else if(name.equals("entry")) {
            newElement = CMLEntry.makeElementInContext(current);
        } else if(name.equals("atomTypeList")) {
            newElement = CMLAtomTypeList.makeElementInContext(current);
        } else if(name.equals("band")) {
            newElement = CMLBand.makeElementInContext(current);
        } else if(name.equals("cml")) {
            newElement = CMLCml.makeElementInContext(current);
        } else if(name.equals("gradient")) {
            newElement = CMLGradient.makeElementInContext(current);
        } else if(name.equals("list")) {
            newElement = CMLList.makeElementInContext(current);
        } else if(name.equals("sphere3")) {
            newElement = CMLSphere3.makeElementInContext(current);
        } else if(name.equals("transform3")) {
            newElement = CMLTransform3.makeElementInContext(current);
        } else if(name.equals("basisSet")) {
            newElement = CMLBasisSet.makeElementInContext(current);
        } else if(name.equals("spectrum")) {
            newElement = CMLSpectrum.makeElementInContext(current);
        } else if(name.equals("crystal")) {
            newElement = CMLCrystal.makeElementInContext(current);
        } else if(name.equals("amount")) {
            newElement = CMLAmount.makeElementInContext(current);
        } else if(name.equals("isotope")) {
            newElement = CMLIsotope.makeElementInContext(current);
        } else if(name.equals("conditionList")) {
            newElement = CMLConditionList.makeElementInContext(current);
        } else if(name.equals("abundance")) {
            newElement = CMLAbundance.makeElementInContext(current);
        } else if(name.equals("matrix")) {
            newElement = CMLMatrix.makeElementInContext(current);
        } else if(name.equals("label")) {
            newElement = CMLLabel.makeElementInContext(current);
        } else if(name.equals("dictionary")) {
            newElement = CMLDictionary.makeElementInContext(current);
        } else if(name.equals("description")) {
            newElement = CMLDescription.makeElementInContext(current);
        } else if(name.equals("bandList")) {
            newElement = CMLBandList.makeElementInContext(current);
        } else if (namespace != null && namespace.trim().length() != 0) {
            newElement = new Element(name, namespace);
        } else {
            newElement = new Element(name);
        }
        stack.push(current);
        current = newElement;
        return newElement;
    }
    /** callback from element end tag.
    *
    * @param element the context element
    * @return Nodes
    */
    public Nodes finishMakingElement(Element element) {
        Element parent = stack.pop();
        if (current instanceof CMLElement) {
            ((CMLElement) current).finishMakingElement(parent);
        }
        current = parent;
        Nodes nodes = new Nodes();
        nodes.append(element);
        return nodes;
    }
    /** callback from each attribute.
    *
    * @param name attribute name
    * @param URI attribute namespace
    * @param value attribute value
    * @param type attribute type (ignored)
    * @return Nodes
    */
    public Nodes makeAttribute(String name, String URI, String value, Attribute.Type type) {
        Nodes nodes = new Nodes();
        Attribute attribute = null;
        try {
            int prefixLoc = name.indexOf(":");
            if (URI != null && URI.trim().length() != 0 && prefixLoc != -1) {
        // namespaced non-cml attribute is allowed
                attribute = new Attribute(name, value, URI);
            } else if (current instanceof CMLElement) {
                CMLElement currentCML = (CMLElement) current;
                String attributeGroupName = currentCML.getAttributeGroupName(name);
                if (attributeGroupName == null) {
                    throw new CMLRuntime("+unknown attribute: "+name);
                }
                attribute = CMLAttributeList.makeAttributeFromGroupName(attributeGroupName, value, URI);
            } else if (prefixLoc == -1) {
        // non-prefixed non-cml element
                attribute = new Attribute(name, value);
            } else if (prefixLoc != -1) {
        // prefixed non-cml element
                attribute = new Attribute(name, value, URI);
            }
        } catch (CMLException e) {
            throw new CMLRuntime(""+e);
        }
        nodes.append(attribute);
        return nodes;
    }
    /** FIXME text - needs to trap/check values.
    *
    * @param text String content
    * @return Nodes
    */
    public Nodes makeText(String text) {
        Nodes nodes = new Nodes();
        nodes.append(new Text(text));
        return nodes;
    }
    /** no-op.
    *
    * @param text String content

    */
    public static void main(String text) {
    }
}