Re: [xsl] Instance construction and use of a java.util.ArrayList

[Michael Kay <mike@xxxxxxxxxxxx>]

In Saxon, if you don't use a variable then its initializer is never 
evaluated. So declaring a variable in the hope that its initializer will 
cause side-effects is not a good strategy.

Using xsl:value-of to evaluate the side-effecting method is better, but 
of course it gives you a problem when the method (as here) returns a 
result. The way to deal with this is to filter away the result with a 
predicate that always returns false, for example

<xsl:value-of select="ArrayList.add(...)[string(.)='never']"/>

Product-specific questions are best asked on a forum specific to that 
product. For Saxon, please use the forums at dev.saxonica.com.

Michael Kay
Saxonica


On 17/08/2012 16:02, Roger Martin wrote:
> Hi,
>
> I'm using saxonb9-1-0-8j with jdk1.7.0_05 on Unbuntu 12.04 (64 bit) 
> and Windows 7 (Home Premium 64 bit)
>
> Attempting to use a java.util.ArrayList for going to another class 
> needing a Java array. But first:
>
> ...in namespace area...
> xmlns:KabschAlignment="java:org.openscience.cdk.geometry.alignment.KabschAlignment"
>                  xmlns:cdkatom="java:org.openscience.cdk.Atom"
>                  xmlns:Point3d="java:javax.vecmath.Point3d"
>                  xmlns:ArrayList="java:java.util.ArrayList"
>                  xmlns:date="java:java.util.Date"
> .......
> further along
>
> .......
> <xsl:variable name="primary-atom-list" select="ArrayList:new()"/>
> <xsl:for-each select="./cml:molecule/cml:molecule/cml:atomArray/*">
> <xsl:variable name="add" select="ArrayList:add($primary-atom-list, 
> cdkatom:new(@elementType, Point3d:new(@x3, @y3, @z3)))"/>
> </xsl:for-each>
> <xsl:comment>
> <xsl:text> primary atoms: </xsl:text>
> <xsl:value-of select="$number-of-atoms"/>
> <xsl:text> size: </xsl:text>
> <xsl:value-of select="ArrayList:size($primary-atom-list)"/>
> </xsl:comment>
> .......
> the size as printed in the comment is zero.  I've tried simpler 
> content for ArrayList and same zero.  Also if the
>
> ....
> <xsl:variable name="add" select="ArrayList:add($primary-atom-list, 
> cdkatom:new(@elementType, Point3d:new(@x3, @y3, @z3)))"/>
> ....
> is changed to
>
> ....
> <xsl:value-of select="ArrayList:add($primary-atom-list, 
> cdkatom:new(@elementType, Point3d:new(@x3, @y3, @z3)))"/>
> ....
> a bunch of truetruetrue's arrive in output.
>
> ......
> <xsl:variable name="primary-atom-list" select="ArrayList:new()"/>
> <xsl:for-each select="./cml:molecule/cml:molecule/cml:atomArray/*">
> <xsl:variable name="add" select="ArrayList:add($primary-atom-list, 
> 'test with string')"/>
> </xsl:for-each>
> <xsl:comment>
> <xsl:text> primary atoms: </xsl:text>
> <xsl:value-of select="$number-of-atoms"/>
> <xsl:text> size: </xsl:text>
> <xsl:value-of select="ArrayList:size($primary-atom-list)"/>
> </xsl:comment>
> .......
> leads to zero size as well.  Tried a few add's in a row instead of the 
> for-each loop and got zero size too.
>
> Compiles and runs just fine.  No errors or exceptions.  The rest of 
> the xsl works and completes.
>
> Any ideas?  Do I need to make a custom class to do the work?
>
> The idea is to send two atom arrays into the KabschAlignment (which is 
> a big algorithm not fitting xsl readily) to check for rmsd match of 
> two chemicals or not:
>
> --------
> .<?xml version="1.0"?>
> <!-- Collates nmr values to the starting chemical definition by 
> selecting comparable candidate from the nmr cml document.
> -->
> <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"; 
> xmlns:xlink="http://www.w3.org/1999/xlink";
> xmlns:divcon="http://quantumbioinc.com/schema/divcon";
> xmlns:molecularmechanics="http://quantumbioinc.com/schema/molecularmechanics";
> xmlns:cml="http://www.xml-cml.org/schema/cml2/core";
>                  xmlns:ocml="http://www.xml-cml.org/schema";
>                  xmlns:functx="http://www.functx.com";
>                  xmlns:xs="http://www.w3.org/2001/XMLSchema";
>                  xmlns:saxon="http://saxon.sf.net";
> xmlns:KabschAlignment="java:org.openscience.cdk.geometry.alignment.KabschAlignment"
>                  xmlns:cdkatom="java:org.openscience.cdk.Atom"
>                  xmlns:Point3d="java:javax.vecmath.Point3d"
>                  xmlns:ArrayList="java:java.util.ArrayList"
>                  xmlns:date="java:java.util.Date"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
> xsi:schemaLocation="http://quantumbioinc.com/schema/divcon 
> ../schemas/divcon.xsd"
>                  version="2.0" extension-element-prefixes="saxon">
> <xsl:output method="xml" encoding="UTF-8" indent="yes"/>
> <!--xsl:strip-space elements="*"/-->
> <xsl:param name="file-path" select="."/>
>
> <xsl:function name="functx:is-value-in-sequence" as="xs:boolean"
>               xmlns:functx="http://www.functx.com"; >
> <xsl:param name="value" as="xs:anyAtomicType?"/>
> <xsl:param name="seq" as="xs:anyAtomicType*"/>
>
> <xsl:sequence select="
>    $value = $seq
>  "/>
>
> </xsl:function>
>
> <xsl:template match="/">
> <xsl:apply-templates select="./divcon:divcon"/>
> </xsl:template>
>
> <xsl:template match="divcon:divcon">
> <xsl:element name="divcon:divcon" inherit-namespaces="yes">
> <xsl:copy-of select="@*"/>
> <xsl:namespace name="cml" 
> select="'http://www.xml-cml.org/schema/cml2/core'"/>
> <xsl:namespace name="xlink" select="'http://www.w3.org/1999/xlink'"/>
> <xsl:copy-of select="./divcon:general-quantum-mechanics"/>
> <xsl:copy-of select="./divcon:Hamiltonian"/>
> <xsl:copy-of select="./divcon:geometry-optimization"/>
> <xsl:copy-of select="./divcon:outputs"/>
> <xsl:copy-of select="./divcon:charges"/>
> <xsl:copy-of select="./divcon:heat-of-formation"/>
> <xsl:copy-of select="./divcon:solvation-free-energy"/>
> <xsl:copy-of select="./divcon:ionization-potential"/>
> <xsl:copy-of select="./divcon:dipole-moment"/>
> <xsl:copy-of select="./divcon:subsettings"/>
> <xsl:copy-of select="./divcon:divcon/self-consistent-reaction-field"/>
> <xsl:copy-of select="./divcon:divcon/nuclear-magnetic-resonance"/>
> <xsl:apply-templates select="./cml:cml"/>
> <xsl:apply-templates select="./divcon:benchmark-set"/>
> <xsl:apply-templates select="./divcon:experimental-reference-set"/>
> <xsl:copy-of select="./divcon:energyArray"/>
> <xsl:copy-of select="./divcon:partial-chargeArray"/>
> <xsl:copy-of select="./divcon:score-set"/>
> <xsl:copy-of select="./divcon:computation-status"/>
> </xsl:element>
> </xsl:template>
>
> <xsl:template match="cml:cml">
> <xsl:variable name="number-of-atoms" 
> select="count(./cml:molecule/cml:molecule/cml:atomArray/*)"/>
> <xsl:variable name="primary-atom-list" select="ArrayList:new()"/>
> <xsl:for-each select="./cml:molecule/cml:molecule/cml:atomArray/*">
> <xsl:variable name="add" select="ArrayList:add($primary-atom-list, 
> cdkatom:new(@elementType, Point3d:new(@x3, @y3, @z3)))"/>
> </xsl:for-each>
> <xsl:comment>
> <xsl:text> primary atoms: </xsl:text>
> <xsl:value-of select="$number-of-atoms"/>
> <xsl:text> size: </xsl:text>
> <xsl:value-of select="ArrayList:size($primary-atom-list)"/>
> </xsl:comment>
> <xsl:variable name="atom-array" 
> select="document($file-path)/ocml:cml/ocml:molecule/*"/>
> <xsl:for-each-group select="$atom-array" group-by="count(./atom) = 
> $number-of-atoms">
> <xsl:comment>
> <xsl:if test="function-available('date:to-string') and
>                           function-available('date:new')">
> <p><xsl:value-of select="date:to-string(date:new())"/></p>
> <xsl:text>
>
> </xsl:text>
> </xsl:if>
> <xsl:value-of select="local-name(.)"/>
> <xsl:text>: group </xsl:text>
> <xsl:value-of select="count(./*)"/>
> <xsl:text> name: </xsl:text>
> <xsl:value-of select="name(./*[1])"/>
> </xsl:comment>
> <xsl:variable name="atom-list" select="ArrayList:new()"/>
> <xsl:for-each select="./*">
> <xsl:variable name="add" select="ArrayList:add($atom-list, 
> cdkatom:new(@elementType, Point3d:new(@x3, @y3, @z3)))"/>
> </xsl:for-each>
> <xsl:variable name="kabsch-alignment" 
> select="KabschAlignment:new(ArrayList:to-array($primary-atom-list), 
> ArrayList:to-array($atom-list))"/>
> <xsl:variable name="align" 
> select="KabschAlignment:align($kabsch-alignment)"/>
> <xsl:variable name="rmsd" 
> select="KabschAlignment:get-RMSD($kabsch-alignment)"/>
> <xsl:comment>
> <xsl:text> cdk atoms: </xsl:text>
> <xsl:value-of select="count($atom-list)"/>
> <xsl:text> size: </xsl:text>
> <xsl:value-of select="ArrayList:size($atom-list)"/>
> <xsl:text> rmsd: </xsl:text>
> <xsl:value-of select="$rmsd"/>
> </xsl:comment>
> </xsl:for-each-group>
> </xsl:template>
>
> <xsl:template match="divcon:benchmark-set">
> <xsl:element name="divcon:benchmark-set" inherit-namespaces="yes">
> <xsl:copy-of select="./divcon:reference-mark"/>
> <xsl:copy-of select="./divcon:heat-of-formation"/>
> <xsl:copy-of select="./divcon:solvation-free-energy"/>
> <xsl:copy-of select="./divcon:ionization-potential"/>
> <xsl:copy-of select="./divcon:dipole-moment"/>
> </xsl:element>
> </xsl:template>
>
> <xsl:template match="divcon:experimental-reference-set">
> <xsl:element name="divcon:experimental-reference-set" 
> inherit-namespaces="yes">
> <xsl:copy-of select="./divcon:heat-of-formation"/>
> <xsl:copy-of select="./divcon:solvation-free-energy"/>
> <xsl:copy-of select="./divcon:ionization-potential"/>
> <xsl:copy-of select="./divcon:dipole-moment"/>
> </xsl:element>
> </xsl:template>
>
> </xsl:stylesheet>
> -------