Example usage for org.dom4j Node numberValueOf

Introduction

In this page you can find the example usage for org.dom4j Node numberValueOf.

Prototype

Number numberValueOf(String xpathExpression);

Source Link

Document

numberValueOf evaluates an XPath expression and returns the numeric value of the XPath expression if the XPath expression results in a number, or null if the result is not a number.

Usage

From source file:com.adobe.ac.maven.ncss.NumericNodeComparator.java

License:Apache License

/**
 * {@inheritDoc}// w w w  .j av a2  s .c o m
 */
public int compare(final Object object1, final Object object2) {
    final Node node1 = (Node) object1;
    final Node node2 = (Node) object2;
    return node2.numberValueOf(tagProperty).intValue() - node1.numberValueOf(tagProperty).intValue();
}

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From source file:com.adobe.ac.pmd.metrics.maven.utils.NumericNodeComparator.java

License:Apache License

/**
 * {@inheritDoc}//from w w w . ja v  a 2  s .  c o  m
 */
public int compare(final Node node1, final Node node2) {
    return node2.numberValueOf(tagProperty).intValue() - node1.numberValueOf(tagProperty).intValue();
}

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From source file:nl.ru.cmbi.pisa.wrapper.PisaCachedWebDao.java

License:Apache License

/**
 * Gets the 3D rotation-translation biomolecule matrices from PISA.
 * <p>//from  w w w.  j  a v a2 s . c o m
 * These matrices detail how chains in the specified PDB entry should be manipulated to obtain desired the PISA
 * assembly.
 * 
 * @param rawPdbId
 *            the 4-letter PDB code we want the assembly of (e.g. "1crn")
 * @param setNr
 *            the PISA assembly set. "1" is most stable in solution, higher numbers increasingly unstable.
 * @param assemblyNr
 *            the substructure within an assembly. Note that structurally identical substructures get the
 *            same assemblyNr. This DAO ignores all but the first substructure. Ignored chains (those chains not
 *            needed to make this assembly) are listed in the {@link MatricesResult#ignoredChains} property of the
 *            returned result.
 * @return A compound result of the transformation matrices to apply and the ignored chains (I.E. those
 *         chains whose transformation lead to an identical substructure to the one returned). This result may be
 *         empty.
 * @throws IOException
 *             when web-fetching fails.
 */
@SuppressWarnings("unchecked")
public MatricesResult getMatrices(final String rawPdbId, final int setNr, final int assemblyNr)
        throws IOException {

    final String pdbId = rawPdbId.trim().toLowerCase();
    Document mmrInfo;
    try {
        mmrInfo = parseDocumentOf(getRawMultimerInfoSingle(pdbId));
    } catch (final DocumentException docex) {
        log.error("Problem parsing Pisa raw multimer info for {}, see debug level for details", pdbId);
        log.debug("Exception: ", docex);
        throw new IOException("Problem parsing multimer XML document", docex);
    }

    final List<ChainTransform> output = new ArrayList<ChainTransform>();
    final Set<String> ignoredChainIds = new HashSet<String>();

    try {
        // Unfortunately, multiple assemblies share the same <ID> subnode if they are structurally identical
        // So, we need indexing ("[1]") to get only the first of an identical set of assemblies
        // ('identical' meaning "structurally identical except for ChainIDs")
        // Sigh... reusing IDs for different things!
        final String matricesXpath = String.format(
                "(/pisa_multimers/pdb_entry[ pdb_code='%s' ]/asm_set[ ser_no=%d ]/assembly[ id=%d ])[1]/molecule",
                pdbId, setNr, assemblyNr);

        final List<Node> matrices = mmrInfo.selectNodes(matricesXpath);

        for (final Node node : matrices) {
            final ChainTransform ct = new ChainTransform(node.valueOf("chain_id"),
                    // X-row
                    (Double) node.numberValueOf("rxx"), (Double) node.numberValueOf("rxy"),
                    (Double) node.numberValueOf("rxz"), (Double) node.numberValueOf("tx"),
                    // Y-row
                    (Double) node.numberValueOf("ryx"), (Double) node.numberValueOf("ryy"),
                    (Double) node.numberValueOf("ryz"), (Double) node.numberValueOf("ty"),
                    // Z-row
                    (Double) node.numberValueOf("rzx"), (Double) node.numberValueOf("rzy"),
                    (Double) node.numberValueOf("rzz"), (Double) node.numberValueOf("tz"));
            if (ct.isUnity() && ct.isStationary()) {
                ct.setDuplication(false);
            } else {
                ct.setDuplication(true);
            }

            output.add(ct);
        }

        final String ignoredMatricesXpath = String.format(
                "(/pisa_multimers/pdb_entry[ pdb_code='%s' ]/asm_set[ ser_no=%d ]/assembly[ id=%d ])[position() > 1]/molecule/chain_id",
                pdbId, setNr, assemblyNr);
        final List<Node> ignoredChains = mmrInfo.selectNodes(ignoredMatricesXpath);

        for (final Node ignoredChain : ignoredChains) {
            ignoredChainIds.add(ignoredChain.getText());
        }

    } catch (final ClassCastException ccex) {
        log.error(
                "malformed XML response from PISA when getting matrices for assembly {}:{}.{}: expected list of matrix nodes, but obtained something else",
                new Object[] { pdbId, setNr, assemblyNr });
        throw new IOException("malformed XML response from PISA when getting matrices for assembly of " + pdbId
                + ": expected list of matrix nodes, but obtained something else", ccex);
    }

    return new MatricesResult(output, ignoredChainIds);
}

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From source file:org.codehaus.mojo.javancss.NumericNodeComparator.java

License:Apache License

/**
 * {@inheritDoc}/*from w ww .j a va 2s.  com*/
 */
public int compare(Object object1, Object object2) {
    Node node1 = (Node) object1;
    Node node2 = (Node) object2;
    return node2.numberValueOf(tagProperty).intValue() - node1.numberValueOf(tagProperty).intValue();
}

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