Re: [cml/ccml-discuss] CML trouble in Bioclipse

[peter murray-r. <pm...@ca...>]

At 17:12 12/03/2006, Egon Willighagen wrote:

>Hi all,
>
>I did some more digging, and decided to workaround the CMLBuilder, and used
>the XOM Builder in combination with the CMLNodeFactory...
>
>In all cases, this is the CML fragment:
>
><cml:molecule xmlns:cml="http://www.xml-cml.org/schema">
><cml:atomArray atomID="a1 a2 a3 a4" elementType="C C O O" formalCharge="0 0 0
>0" />
><cml:bondArray atomRef1="a1 a2 a2" atomRef2="a2 a3 a4" order="1 2 1" />
></cml:molecule>

I found this in a piece of Xerces code. Seems to make sense:

/**
    * Determine whether a scheme conforms to the rules for a scheme name.
    * A scheme is conformant if it starts with an alphanumeric, and
    * contains only alphanumerics, '+','-' and '.'.
    *
    * @return true if the scheme is conformant, false otherwise
    */
    public static boolean isConformantSchemeName(String p_scheme) {
      if (p_scheme == null || p_scheme.trim().length() == 0) {
        return false;
      }
      if (!isAlpha(p_scheme.charAt(0))) {
        return false;
      }
      char testChar;
      for (int i = 1; i < p_scheme.length(); i++) {
        testChar = p_scheme.charAt(i);
        if (!isAlphanum(testChar) &&
            SCHEME_CHARACTERS.indexOf(testChar) == -1) {
          return false;
        }
      }
      return true;
    }

it seems very unlikely that this is the real problem, so perhaps the 
namespace being passed has got lost, become null or empty or got 
corrupted. Is there any way of printing it out?

P.



Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069