#!/bin/sh

XSLTPROC=/usr/bin/xsltproc
MKTEMP=/usr/bin/mktemp
if [ ! -x $XSLTPROC ]; then
  echo "Error: could not find xsltproc"
  exit 1
elif [ ! -x $MKTEMP ]; then
  echo "Error: could not find mktemp"
  exit 1
elif [ $# -ne 1 ]; then
  echo "Error: need exactly one argument"
  exit 1
fi
TMPXSLTDIR=
trap 'rm -rf $TMPXSLTDIR; exit' 0 1 2 3 15
TMPXSLTDIR=$(mktemp -d)
cat > $TMPXSLTDIR/finishXML.py << "EOF"
#!/usr/bin/env python

import sys
from xml.parsers import expat

def finishXMLFile(filename):
    """
This function will read in a file which is a truncated well-formed XML file,
and fix it up at the end so that it is well-formed. 

What it does *not* do:
1) Cope with ill-formed files (ie files that could not be transformed into
   a well-formed file simply by appending characters)
2) Make any guarantees of the validitiy of the output file.

Known bugs:
1) If the file hasn't got a root element - or the root element opening
   tag is incomplete - this will not create one, so the result will
   be ill-formed. Probably this should throw an exception.
2) I think it's possible that where the file is Unicode, and the
   truncation happens halfway through a Unicode character, that the
   result will not be well-formed.
3) No checking is made that the input file is actually correct in its
   nearly-well-formedness.

Warning: this *overwrites* the file which is given to it (Done this
         way to save space since I am dealing with several-hundred
         megabyte files ...
"""

    tagStack = []
    def start(name, attributes): tagStack.append(name)
    def end(name): tagStack.pop()

    p = expat.ParserCreate()
    p.StartElementHandler = start
    p.EndElementHandler = end

    e = None
    fIn = open(filename,'r+')
    try:
        p.ParseFile(fIn)
    except expat.ExpatError, e:
        pass

    if not e: return

    fIn.seek(0, 0)

    for i in range(e.lineno-1): fIn.readline()
    lastLine = fIn.readline()

    fIn.seek(-len(lastLine), 1)
    fIn.truncate()

    lastLine = lastLine.rstrip() # for some reason python appends a newline
    if e.message.startswith("no element found"):
        # We're in a text section, carry on
        pass
    elif e.message.startswith("unclosed token"):
        # throw away the final token and finish
        lastLine = lastLine[:e.offset]
    elif e.message.startswith("unclosed CDATA section"):
        lastLine = lastLine + u']]>'
    elif e.message.startswith("not well-formed (invalid token)"):
        # We need to worry about where we are. These
        # are the possibilities
        if (lastLine[-1] == u'/'):
            # We have "<tagName /"
            lastLine = lastLine + u'>'
        elif (lastLine[-1] == u'<'):
            # We have simply "<"
            lastLine = lastLine[:-1]
        elif (lastLine[-1] == u'<'): 
            # We have "</t" with offset before the "<"
            lastLine = lastLine[:e.offset]
        elif (lastLine[-1] == u'!'):
            # We have "<!"
            lastLine = lastLine[:-2]
        elif (lastLine[-1] == u'-'):
             if (lastLine[-3:] == u'<!-'):
                 lastLine = lastLine[:-3]
             elif (lastLine[-4:] == u'<!--'):
                 lastLine = lastLine[:-4]
             else:
                 # We have "<!-- blah --"
                 lastLine = lastLine + u'>'
        elif (lastLine[-1] == u"A"):
            # We have "<![CDATA"
            lastLine = lastLine[:-8]
        elif (lastLine[-1] == u"?"):
            # We have "<?"
            lastLine = lastLine[:-2]

    fIn.write(lastLine)

    tagStack.reverse()
    for tag in tagStack:
       fIn.write("</"+tag+">")
    fIn.close()

if __name__ == '__main__':
    finishXMLFile(sys.argv[1])
EOF
cat > $TMPXSLTDIR/array.xsl << "EOF"
<?xml version="1.0"?>
<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:str="http://exslt.org/strings"
        xmlns="http://www.w3.org/1999/xhtml"
        xmlns:cml="http://www.xml-cml.org/schema"
        extension-element-prefixes="str">

  <xsl:import href="loop.xsl"/>

  <xsl:template match="cml:kpoint" mode="eigen">
    <div><i><xsl:text>k</xsl:text></i><xsl:text>-point at: (</xsl:text>
    <xsl:for-each select="str:tokenize(@coords)">
      <xsl:value-of select="format-number(., '0.0000')"/>
      <xsl:if test="position()!=last()">
	<xsl:text>,</xsl:text>
      </xsl:if>
    </xsl:for-each>
    <xsl:text>) with weight </xsl:text><xsl:value-of select="@weight"/></div>
  </xsl:template>

  <xsl:template match="cml:property" mode="eigen">
    <table><tr>
      <xsl:call-template name="rows-for-loop">
	<xsl:with-param name="i" select="1"/>
	<xsl:with-param name="increment" select="1"/>
	<xsl:with-param name="testValue" select="ceiling(cml:array/@size div 8)"/>
	<xsl:with-param name="innerTestValue" select="8"/>
	<xsl:with-param name="outputString" select="concat(normalize-space(cml:array/text()),' ')"/>
      </xsl:call-template>
      </tr></table>
  </xsl:template>

  <xsl:template match="cml:array">
    <xsl:variable name="delimiter">
      <xsl:choose>
        <xsl:when test="@delimiter">
          <xsl:value-of select="@delimiter"/>
        </xsl:when>
        <xsl:otherwise>
          <xsl:value-of select="' '"/>
        </xsl:otherwise>
      </xsl:choose>
    </xsl:variable>
    <p><br/></p>
    <table class="prop2">
      <tr>
        <xsl:for-each select="str:tokenize(text(),$delimiter)">
	  <td>
	    <xsl:choose>
              <xsl:when test="ceiling(.) = floor(.) and not(contains(.,'.'))">
	        <xsl:value-of select="."/>
	      </xsl:when>
	      <xsl:when test="string(number(.)) != 'NaN'">
	        <xsl:value-of select="format-number(., '0.0000')"/>
	      </xsl:when>
	      <xsl:otherwise>
	        <xsl:value-of select="."/>
              </xsl:otherwise>
            </xsl:choose>	        
	  </td>
        </xsl:for-each>
      </tr>
    </table>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/averageVolume.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>
<xsl:stylesheet version="1.0"
   xmlns:cml="http://www.xml-cml.org/schema"
   xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
   xmlns:tohw="http://www.uszla.me.uk/xsl/1.0/functions"
   xmlns:g="http://www.uszla.me.uk/xsl/1.0/graph"
   extension-element-prefixes="tohw"
>

<xsl:import href="graphfuncs.xsl"/>

<xsl:output method="xml"/>

<xsl:param name="fileList"/>

<xsl:template match="/">
  <g:graphSet>
    <g:pointList>
      <xsl:apply-templates select="*"/>
    </g:pointList>
  </g:graphSet>
</xsl:template>

<xsl:template match="file">
  <xsl:element name="point" namespace="http://www.uszla.me.uk/xsl/1.0/graph">
    <xsl:attribute name="x">
      <xsl:value-of select="document(.)//cml:parameterList[@title='control parameters']/cml:parameter[@dictRef='dl_poly:pressure']/cml:scalar"/>
    </xsl:attribute>
    <xsl:attribute name="y">
      <xsl:value-of select="sum(document(.)//cml:step/cml:propertyList[@title='instantaneous']/cml:property[@dictRef='dl_poly:volume']/cml:scalar) div count(document(.)//cml:step/cml:propertyList[@title='instantaneous']/cml:property[@dictRef='dl_poly:volume']/cml:scalar)"/>
    </xsl:attribute>
  </xsl:element>
</xsl:template>


</xsl:stylesheet>

EOF
cat > $TMPXSLTDIR/bandList.xsl << "EOF"
<!--===================== BANDS =========================-->

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:str="http://exslt.org/strings"
        xmlns="http://www.w3.org/1999/xhtml"
        xmlns:cml="http://www.xml-cml.org/schema"
        extension-element-prefixes="str">
	
<!-- bandList -->
  <xsl:template match="cml:bandList">
    <xsl:if test="title"><H3><xsl:value-of select="@title"/></H3></xsl:if>
<!--    <H3>Eigenvalues</H3>  -->
    <table>
      <xsl:apply-templates select="cml:band"/>
    </table>
  </xsl:template>
  
<!-- band -->
  <xsl:template match="cml:band">
    <xsl:param name="mouseoverString">
      <xsl:for-each select="str:tokenize(@kpoint,' ')">
        <xsl:value-of select="format-number(., '0.000')"/>
      </xsl:for-each>
      <xsl:text> (</xsl:text>
      <xsl:value-of select="format-number(@weight, '0.000')"/>
      <xsl:text>)</xsl:text>
    </xsl:param>

    <tr>
      <th align="left">
	<span>
	  <xsl:attribute name="title">
	    <xsl:value-of select="$mouseoverString"/>
	  </xsl:attribute>
	  <i>k</i>-point
	  <xsl:value-of select="position()"/>
	</span>
      </th>
    </tr>
    <tr>
      <td>
        <table>
	<xsl:for-each select="str:tokenize(normalize-space(.), ' ')">
	  <xsl:if test="(position()-1) mod 10 = 0">
           <xsl:variable name="pos" select="position()"/>
           <tr>
            <td class="eigen"><xsl:value-of select="../token[$pos+0]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+1]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+2]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+3]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+4]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+5]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+6]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+7]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+8]"/></td>
            <td class="eigen"><xsl:value-of select="../token[$pos+9]"/></td>
          </tr>
         </xsl:if>
	</xsl:for-each>
        </table>
      </td>
    </tr>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/dict2frag.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:cml="http://www.xml-cml.org/schema"
        xmlns="http://www.w3.org/1999/xhtml"
        exclude-result-prefixes="xsl cml"
        >

  <xsl:template name="addDict">
    <xsl:variable name="unique-dictRefs" select="//cml:*[@dictRef and (generate-id(.)=generate-id(key('dictRef-keys',  concat(namespace::*[name()=substring-before(../@dictRef,':')], '#', substring-after(@dictRef, ':')))[1]))]"/>
    <!-- Muenchian grouping -->

    <xsl:for-each select="$unique-dictRefs">
      <xsl:sort select="translate(substring-after(@dictRef, ':'), 'abcdefghijklmnopqrstuvwxyz','ABCDEFGHIJKLMNOPQRSTUVWXYZ')"/>
      <xsl:variable name="dictRef" select="@dictRef"/>
      <xsl:variable name="dictURI"
		    select="namespace::*[name()=substring-before($dictRef,':')]"/>
      <xsl:variable name="dictEntry" select="substring-after($dictRef, ':')"/>
      <xsl:choose>
	<xsl:when test="$dictURI!='' and document('dictionaries.xml')//cml:dictionary[@namespace=$dictURI]/cml:entry[@id=$dictEntry]">
	  <xsl:apply-templates select="document('dictionaries.xml')//cml:dictionary[@namespace=$dictURI]/cml:entry[@id=$dictEntry]"/> 
	</xsl:when>
	<xsl:otherwise>
	  <xsl:call-template name="empty-entry">
	    <xsl:with-param name="id" select="$dictEntry"/>
	  </xsl:call-template>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:for-each>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/dict2html.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:stm="http://www.xml-cml.org/schema/stmml"
        xmlns="http://www.w3.org/1999/xhtml"
        >

  <xsl:import href="dictcommon.xsl"/>

  <xsl:output method="xml" version="1.0" encoding="UTF-8" 
    omit-xml-declaration="no" standalone="yes"
    doctype-public="-//W3C//DTD XHTML 1.0 Strict//EN"
    doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"
    indent="yes" media-type="application/xhtml+xml"/>

  <xsl:template match="/">
    <html>
      <head>
	<title><xsl:value-of select="/stm:dictionary/@title"/></title>
      </head>
    <body>
      <h1><xsl:value-of select="/stm:dictionary/@title"/></h1>
      <hr></hr>
      <xsl:apply-templates select="/stm:dictionary/stm:entry">
	<!-- need translate below to prevent separating upper & lower case entries -->
        <xsl:sort data-type="text" order="ascending" 
		  select="translate(@term,'abcdefghijklmnopqrstuvwxyz','ABCDEFGHIJKLMNOPQRSTUVWXYZ')"/>
      </xsl:apply-templates>
    </body>
  </html>
</xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/dict2xsl.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:stm="http://www.xml-cml.org/schema/stmml"
        xmlns="http://www.w3.org/1999/xhtml"
        >

  <xsl:import href="dictcommon.xsl"/>

  <xsl:output method="xml" version="1.0" encoding="UTF-8" 
    omit-xml-declaration="no" standalone="yes"
    indent="yes" media-type="text/xsl"/>

  <xsl:template match="/">
    <xsl:element name="xsl:stylesheet" namespace="http://www.w3.org/1999/XSL/Transform">
      <xsl:attribute name="version">1.0</xsl:attribute>
 <!--      <xsl:attribute name="xmlns">http://www.w3.org/1999/xhtml</xsl:attribute> -->
      <xsl:element name="xsl:template" namespace="http://www.w3.org/1999/XSL/Transform">
	<xsl:attribute name="name">addDict</xsl:attribute>
	<xsl:apply-templates select="//stm:entry">
	  <!-- need translate below to prevent separating upper & lower case entries -->
	  <xsl:sort data-type="text" order="ascending" 
		    select="translate(@term,'abcdefghijklmnopqrstuvwxyz','ABCDEFGHIJKLMNOPQRSTUVWXYZ')"/>
	</xsl:apply-templates>
      </xsl:element>
    </xsl:element>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/dictcommon.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:cml="http://www.xml-cml.org/schema"
        xmlns="http://www.w3.org/1999/xhtml"
        exclude-result-prefixes="xsl cml"
        >

  <!-- For each entry in the dictionary -->
  <xsl:template match="cml:entry">
    <div class="dictAnchor">
      <a>
	<xsl:attribute name="name">
	  <xsl:value-of select="@id"/>
	</xsl:attribute>
      </a>
    </div>
    <div class="dictEntry">
      <xsl:choose>
	<xsl:when test="@term and @term!=''">
	  <xsl:value-of select="@term"/>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="@id"/>
	</xsl:otherwise>
    </xsl:choose>
    <xsl:text>:</xsl:text></div>
    <xsl:if test="cml:definition">
      <xsl:choose>
	<xsl:when test="//text()='definition to be supplied'">
	  <p><font color="blue"><xsl:value-of select="cml:definition"/></font></p>
	</xsl:when>
	<xsl:otherwise>
	  <div class="dictDefinition"><xsl:value-of select="cml:definition"/></div>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:if>
    <xsl:if test="cml:description">
      <xsl:copy-of select="cml:description/node()"/>
    </xsl:if>
    <hr/>
  </xsl:template>

  <!-- An empty entry -->
  
  <xsl:template name="empty-entry">
    <xsl:param name="id"/>
    <div class="dictAnchor">
      <a name="{$id}"/>
    </div>
    <div class="dictEntry">
      <xsl:value-of select="$id"/>
    <xsl:text>:</xsl:text></div>
    <p><font color="blue">definition to be supplied</font></p>
    <hr/>
  </xsl:template>
  
  <!-- for each description just copy everything -->
  <!-- REM do the same for MathML stuff          -->
<!--  <xsl:template match="stm:description/@*|node()">
    <xsl:copy>
      <xsl:apply-templates select="@*|node()"/>
    </xsl:copy>
  </xsl:template> -->


  
</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/dictionary.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:cml="http://www.xml-cml.org/schema"
        xmlns="http://www.w3.org/1999/xhtml"
        exclude-result-prefixes="xsl cml"
	>


  <xsl:template name="empty-entry-link">
    <xsl:param name="id"/>
    <span class="dictRef dotted">
      <xsl:attribute name="onmouseover">window.location.href='#<xsl:value-of select="$id"/>';</xsl:attribute>
      <xsl:value-of select="$id"/>
    </span>
  </xsl:template>
  

  <xsl:template name="get.dictionary.reference.html">
    <xsl:param name="dictRef"/>
    <xsl:param name="title"/>
    <xsl:choose>
      <xsl:when test="$dictRef">
	<xsl:variable name="dictURI"
		      select="namespace::*[name()=substring-before($dictRef,':')]"/>
	<xsl:variable name="dictEntry" select="substring-after(@dictRef, ':')"/>
	<xsl:choose>
	  <xsl:when test="document('dictionaries.xml')//cml:dictionary[@namespace=$dictURI]/cml:entry[@id=$dictEntry]">
	    <xsl:apply-templates select="document('dictionaries.xml')//cml:dictionary[@namespace=$dictURI]/cml:entry[@id=$dictEntry]" mode="htmlOutput">
	      <xsl:with-param name="title" select="$title"/>
	    </xsl:apply-templates>
	  </xsl:when>
	  <xsl:otherwise>
	    <xsl:call-template name="empty-entry-link">
	      <xsl:with-param name="id" select="$dictEntry"/>
	    </xsl:call-template>
	  </xsl:otherwise>
	</xsl:choose>
      </xsl:when>
      <xsl:when test="not($dictRef) and $title">
	<span class="dictRef">
	  <xsl:value-of select="$title"/>
	</span>
      </xsl:when>
    </xsl:choose>
  </xsl:template>
    
   <xsl:template match="cml:entry" mode="htmlOutput">
    <xsl:param name="title"/>
    <xsl:variable name="dictTitle">
      <xsl:choose>
	<xsl:when test="$title">
	  <xsl:value-of select="$title"/>
	</xsl:when>
	<xsl:when test="@term">
	  <xsl:value-of select="@term"/>             <!-- 2nd otherwise use @term -->
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="@id"/>            <!-- 3rd failing that use @dictRef -->
	</xsl:otherwise>
      </xsl:choose>
    </xsl:variable>  
    <span class="dictRef dotted">
      <xsl:attribute name="onmouseover">window.location.href='#<xsl:value-of select="@id"/>';</xsl:attribute>
      <xsl:value-of select="$dictTitle"/>
    </span>
  </xsl:template>

<!-- GRAPH -->
  <!-- GET DICTIONARY REFERENCE FOR USE WITHIN THE GRAPH OUTPUT -->	
  <xsl:template name="get.dictionary.reference.graph">
    <!-- if dictionary reference is given try to resolve it -->
    <xsl:param name="dictRef"/>
    <xsl:choose>
      <xsl:when test="$dictRef">
	<xsl:call-template name="resolve.dictionary.id.graph">
	  <xsl:with-param name="dictionary" 
	     select="document(concat(substring-before($dictRef, ':'), 'Dict.xml'))"/>
	  <xsl:with-param name="entry" select="substring-after($dictRef, ':')"/>
	</xsl:call-template>
      </xsl:when>
      <!-- else try to use the title attribute and flag a warning -->
      <xsl:when test="@title">
	<xsl:text>No dictionary reference given</xsl:text>
      </xsl:when>
      <!-- otherwise just write 'unknown' and flag a warning -->
      <xsl:otherwise>
	<xsl:text>No dictionary reference or title given</xsl:text>
      </xsl:otherwise>
    </xsl:choose>
  </xsl:template>
  
  
  <!-- RESOLVE DICTIONARY ID FOR THE GRAPH OUTPUT-->	
  <xsl:template name="resolve.dictionary.id.graph">
    <xsl:param name="dictionary"/>
    <xsl:param name="entry"/>
    <xsl:choose>
      
      <!-- If dictionary exists use it-->  
      <xsl:when test="$dictionary/dictionary">

        <!-- If entry found then use it -->
	<xsl:if test="$dictionary/dictionary/entry[@id =  $entry]">
	  <xsl:apply-templates select="$dictionary/dictionary/entry[@id =  $entry]" mode="graphOutput">
	    <xsl:with-param name="entry" select="$entry"/>
	  </xsl:apply-templates>
	</xsl:if>
	
	<!--  If entry NOT found then use entry name and flag a warning  -->
	<xsl:if test="not($dictionary/dictionary/entry[@id =  $entry])">
	  <xsl:text>Entry </xsl:text><xsl:value-of select="$entry"/>
	  <xsl:text> not found in the dictionary</xsl:text>
	</xsl:if>
      </xsl:when>
      
      <!-- If dictionary does NOT exist use entry name and flag a warning -->  
      <xsl:otherwise>
	<xsl:value-of select="$dictionary"/><xsl:text> dictionary not found.</xsl:text>
      </xsl:otherwise>
    </xsl:choose>
  </xsl:template>


  <!-- GET DICTIONARY ENTRY FOR GRAPH OUTPUT -->
  <xsl:template match="entry" mode="graphOutput">
    <xsl:param name="entry"/>

    <xsl:value-of select="definition"/>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/display.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>

<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
        xmlns:cml="http://www.xml-cml.org/schema"
        xmlns="http://www.w3.org/1999/xhtml"
        exclude-result-prefixes="xsl"
        >

<!-- JS/CSS includes -->
<xsl:import href="header.xsl"/>

<!-- CML -->
<xsl:import href="structure.xsl"/>
<xsl:import href="dictionary.xsl"/>
<xsl:import href="metadata.xsl"/>
<xsl:import href="parameter.xsl"/>
<xsl:import href="property.xsl"/>
<xsl:import href="bandList.xsl"/>
<xsl:import href="formula.xsl"/>
<xsl:import href="units.xsl"/>

<!-- CMLComp -->
<xsl:import href="module.xsl"/>
<xsl:import href="plottable.xsl"/>
<xsl:import href="lattice.xsl"/>

<!-- STMML -->
<xsl:import href="scalar.xsl"/>
<xsl:import href="array.xsl"/> 
<xsl:import href="matrix.xsl"/>
<xsl:import href="table.xsl"/>

<!-- Dictionary -->
<xsl:import href="dict2frag.xsl"/>
<xsl:import href="dictcommon.xsl"/>

<!-- Special templates -->
<xsl:import href="summary.xsl"/>
<xsl:import href="rdf.xsl"/>

<xsl:strip-space elements="*"/>

<xsl:key name="dictRef-keys" match="//cml:*[@dictRef]"
  use="concat(namespace::*[name()=substring-before(../@dictRef,':')], '#', substring-after(@dictRef, ':'))"/>

<xsl:template match="text()"/>
<xsl:template match="text()" mode="jmol"/>
<xsl:template match="text()" mode="structure"/>

<!-- Global Variable holding the program name -->
<xsl:param name="prog">
  <xsl:choose>
    <xsl:when test="/cml:cml/cml:metadataList/cml:metadata[@name='eMinerals:Program']">
      <xsl:value-of select="/cml:cml/cml:metadataList/cml:metadata[@name='eMinerals:Program']/@content"/>
    </xsl:when>
    <xsl:when test="/cml:cml/cml:metadataList/cml:metadata[@name='siesta:Program']">
      <xsl:value-of select="/cml:cml/cml:metadataList/cml:metadata[@name='siesta:Program']/@content"/>
    </xsl:when>
    <xsl:when test="/cml:cml/cml:metadataList/cml:metadata[@name='dl_poly:Program']">
      <xsl:value-of select="/cml:cml/cml:metadataList/cml:metadata[@name='dl_poly:Program']/@content"/>
    </xsl:when>
    <xsl:when test="contains(/cml:cml/cml:metadataList/cml:metadata[@name='dc:identifier']/@content,'DL_POLY')">
      <xsl:text>DL_POLY</xsl:text>
    </xsl:when>
    <xsl:when test="/cml:cml/cml:metadataList/cml:metadata[@name='dc:creator']">
      <xsl:value-of select="/cml:cml/cml:metadataList/cml:metadata[@name='dc:creator']/@content"/>
    </xsl:when>
    <xsl:otherwise>
      <xsl:text>Program</xsl:text>
    </xsl:otherwise>
  </xsl:choose>
</xsl:param>

<!-- Global variable - do we want jmol output or not? -->
  <xsl:param name="Jmol">
    <xsl:value-of select="boolean(//cml:molecule)"/>
  </xsl:param>

<!-- Global variable - how many steps do we want? -->
  <xsl:param name="stepinterval">
    <xsl:choose>
      <xsl:when test="count(cml:cml/cml:module[@role='step']) &gt; 100">
         10
      </xsl:when>
      <xsl:otherwise>
         1
      </xsl:otherwise>
    </xsl:choose>
  </xsl:param>


  <xsl:output method="xml" version="1.0" encoding="UTF-8" 
    omit-xml-declaration="no" standalone="yes"
    doctype-public="-//W3C//DTD XHTML 1.0 Strict//EN"
    doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"
    indent="no" media-type="application/xhtml+xml"/>


<!-- MAIN TEMPLATE -->
  <xsl:template match="/">
    <html>
      <xsl:call-template name="head"/>

      <body>
        <xsl:if test="$Jmol!='false'">
         <xsl:attribute name="onload">
           <xsl:text>jmolInitialize(" https://data.eminerals.org/ccViz/jmol/", true);</xsl:text>
         </xsl:attribute>
        </xsl:if>
 
        <div id="head"><div class="bigTitle">
           <xsl:value-of select="$prog"/>
           <xsl:text> Output</xsl:text>
        </div></div>

<!-- Generate body of document -->
        <div id="maindisplay">
          <div class="innerMain">

            <br/><div id="initialmetadata" class="divisionTitle clickable moduleDiv">
              <xsl:text>Initial Metadata</xsl:text>
            </div>
            <div class="sublevel">
              <xsl:apply-templates select="/cml:cml/cml:metadataList[position()=1]"/>
            </div><br/>

            <br/><div class="divisionTitle clickable moduleDiv">
              <xsl:text>Input Parameters</xsl:text>
            </div>
            <div class="sublevel">
              <xsl:apply-templates select="/cml:cml/cml:parameterList"/>
            <!--   <xsl:apply-templates select="/cml:cml/cml:parameterList[position()=1]"/> -->
            </div><br/>

	    <xsl:if test="/cml:cml/cml:module[@title='Initial System']">
              <div class="divisionTitle clickable moduleDiv">
                <xsl:text>Initial System</xsl:text>
              </div>
              <div class="sublevel">
                <xsl:apply-templates select="/cml:cml/cml:module[@title='Initial System']">
		  <xsl:with-param name="title" select="false"/>
		</xsl:apply-templates>
	      </div>
	    </xsl:if>

            <br/>
            <div class="divisionTitle clickable moduleDiv">
              <xsl:text>Main Body of Simulation</xsl:text>
            </div>
            <div class="sublevel">
              <xsl:apply-templates select="/cml:cml/cml:module[(@title!='Initial System' and @title!='Finalization') or not(@title)]"/>
            </div>
            <br/>

	    <xsl:if test="/cml:cml/cml:module[@title='Finalization']">
              <div class="divisionTitle clickable moduleDiv">
                <xsl:text>Final System</xsl:text>
              </div>
              <div class="sublevel">
                <xsl:apply-templates select="/cml:cml/cml:module[@title='Finalization']">
		  <xsl:with-param name="title" select="false"/>
		</xsl:apply-templates>
	      </div>
	    </xsl:if>

            <br/>
            <div class="divisionTitle clickable moduleDiv">
              <xsl:text>Summary Information</xsl:text>
            </div>
            <div class="sublevel">
              <xsl:call-template name="summary"/>
	    </div>
            <br/>
            <hr/>
          </div>
        </div>

<!-- Generate dictionary of document -->
        <div id="dictdisplay">
          <div class="innerDict">
            <xsl:call-template name="addDict"/>
          </div>
        </div>
<!-- -->

        <div id="foot">
          <i>Created using <a href="http://cmlcomp.org/ccViz/">ccViz</a>, by Toby White <a href="mailto://tow@uszla.me.uk">&lt;tow@uszla.me.uk&gt;</a>. See <a href="http://cmlcomp.org">CMLComp</a> for more information</i>
        </div>

      </body>
    </html>

  </xsl:template>

  <xsl:template name="top.level.section">
    <xsl:param name="uid"/>
    <xsl:param name="title"/>
    <xsl:param name="templates"/>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/formula.xsl << "EOF"
<xsl:stylesheet 
  xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
  version="1.0">

  <xsl:template match="formula">
    <P/>
    <H3>Formula</H3>
    <xsl:call-template name="format.form">
      <xsl:with-param name="formula" select="normalize-space(.)"/>
    </xsl:call-template>
  </xsl:template>
  

  <xsl:template name="format.form">
    <xsl:param name="formula"/>
    <xsl:if test="not($formula = '')">
      <xsl:variable name="substring" select="substring-before($formula,' ')"/>
      <xsl:variable name="remainder" select="substring-after($formula,' ')"/>
      <!-- Is variable a number or a string? -->
      <xsl:choose>
        <xsl:when test="string(number($substring)) = 'NaN'">      
          <xsl:value-of select="$substring"/>
        </xsl:when>
        <xsl:when test="string(number($substring)) != 'NaN' and $substring != 1">
          <SUB><xsl:value-of select="$substring"/></SUB>
        </xsl:when>
      </xsl:choose>
      <!-- on final iteration this will be processed instead -->
      <xsl:if test="substring-after($formula,' ') = ''">
        <xsl:choose>
        <xsl:when test="string(number($formula)) = 'NaN'">      
          <xsl:value-of select="$formula"/>
        </xsl:when>
        <xsl:when test="string(number($formula)) != 'NaN' and $formula != 1">
          <SUB><xsl:value-of select="$formula"/></SUB>
        </xsl:when>
      </xsl:choose>
      </xsl:if>
      <!-- Recurse -->
      <xsl:call-template name="format.form">
        <xsl:with-param name="formula" select="$remainder"/>
      </xsl:call-template>
    </xsl:if>
  </xsl:template>
  
  </xsl:stylesheet>
  
EOF
cat > $TMPXSLTDIR/graph_bits.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>
<xsl:stylesheet version="1.0"
	xmlns="http://www.uszla.me.uk/xsl/1.0/graph"
        xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
        xmlns:cml="http://www.xml-cml.org/schema"
	xmlns:g="http://www.uszla.me.uk/xsl/1.0/graph"
        xmlns:exsl="http://exslt.org/common"
        extension-element-prefixes="exsl"
        >

 <xsl:template name="drawGraphOf">
    <xsl:param name="subTree" select="/cml:cml"/>
    <xsl:param name="stepType"/>
    <xsl:param name="propertyName"/>
    <xsl:param name="title" select="$propertyName"/>
    <xsl:param name="xAxisTitle" select="'Step'"/>
    <xsl:param name="yAxisTitle" select="''"/>
    <xsl:variable name="pointList">
      <g:pointList>
        <xsl:for-each select="$subTree/cml:module[@dictRef=$stepType]">
          <xsl:variable name="x" select="@serial"/>
          <xsl:variable name="y" select="cml:propertyList/cml:property[@dictRef=$propertyName]/cml:scalar"/>
          <g:point x="{$x}" y="{$y}"/>
        </xsl:for-each>
      </g:pointList>
    </xsl:variable>
    <xsl:call-template name="drawGraph">
      <xsl:with-param name="title" select="$title"/>
      <xsl:with-param name="xAxisTitle" select="$xAxisTitle"/>
      <xsl:with-param name="yAxisTitle" select="$yAxisTitle"/>
      <xsl:with-param name="pointSet" select="exsl:node-set($pointList)"/>
    </xsl:call-template>
  </xsl:template>


  <xsl:template name="selectNestedGraphNodes">
    <xsl:param name="nodes"/>
    <xsl:param name="propertyName"/>
    <g:pointList>
      <!-- for each step, if the property exists, then add its value to the pointList -->
      <xsl:for-each select="$nodes">
        <xsl:if test="cml:propertyList/cml:property[@dictRef=$propertyName]">
          <xsl:variable name="x">
	    <xsl:choose>
	      <xsl:when test="@serial">
	        <xsl:value-of select="@serial"/>
	      </xsl:when>
	      <xsl:otherwise>
	        <xsl:value-of select="position()"/>
	      </xsl:otherwise>
	    </xsl:choose>
	  </xsl:variable>
          <xsl:variable name="y" select="cml:propertyList/cml:property[@dictRef=$propertyName]/cml:scalar"/>
          <g:point x="{$x}" y="{$y}"/>
	</xsl:if>
      </xsl:for-each>
    </g:pointList>
  </xsl:template> 

  <xsl:template name="selectRDFPoints">
    <!-- FIXME subject to change as we refine RDF XML format - this is bloody fragile -->
    <xsl:param name="nodes"/>
    <g:pointList>
      <xsl:for-each select="$nodes">
        <xsl:if test="@title='grid'">
          <xsl:variable name="pos" select="position()"/>
          <xsl:variable name="x" select="cml:scalar/text()"/>
          <xsl:variable name="y" select="../cml:property[position() = ($pos + 1)]/cml:scalar/text()"/>
          <g:point x="{$x}" y="{$y}"/>
	</xsl:if>
      </xsl:for-each>
    </g:pointList>
  </xsl:template>

  <xsl:template name="selectPointsFromNodes">
    <xsl:param name="nodes"/>
    <xsl:param name="propertyNames"/>
    <g:pointList>
      <!-- for each step, if the property exists, then add its value to the pointList -->
      <xsl:for-each select="$nodes">
        <xsl:variable name="x">
          <xsl:choose>
	    <xsl:when test="@serial">
	      <xsl:value-of select="@serial"/>
	    </xsl:when>
	    <xsl:otherwise>
	      <xsl:value-of select="position()"/>
	    </xsl:otherwise>
	  </xsl:choose>
	</xsl:variable>
        <xsl:variable name="here" select="."/>
        <xsl:for-each select="$propertyNames">
          <xsl:variable name="propertyName" select="."/>
          <g:group dictRef="{$propertyName}">
            <xsl:if test="$here/cml:propertyList/cml:property[@dictRef=$propertyName]">
              <xsl:variable name="y" select="$here/cml:propertyList/cml:property[@dictRef=$propertyName]/cml:scalar"/>
              <g:point x="{$x}" y="{$y}"/>
	    </xsl:if>
	  </g:group>
	</xsl:for-each>
      </xsl:for-each>
    </g:pointList>
  </xsl:template> 

  <xsl:template name="selectedPointsFromList">
    <xsl:param name="pointList"/>
    <xsl:param name="dictRef"/>
    <g:pointList>
      <xsl:for-each select="$pointList/g:pointList/g:group[@dictRef=$dictRef]">
        <xsl:copy-of select="g:point"/>
      </xsl:for-each>
    </g:pointList>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/graph_produce.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8"?>

<xsl:stylesheet version="1.0"
        xmlns:cml="http://www.xml-cml.org/schema"
        xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
        xmlns:g="http://www.uszla.me.uk/xsl/1.0/graph"
        >

<xsl:import href="toby_graph.xsl"/>
<xsl:import href="graphfuncs.xsl"/>

<xsl:output method="xml" encoding="utf-8" indent="yes"/>

<xsl:param name="graphTitle" select="default"/>
<xsl:param name="xAxisTitle" select="default"/>
<xsl:param name="yAxisTitle" select="default"/>

<!-- MAIN TEMPLATE -->
  <xsl:template match="/">
    <xsl:apply-templates select="*"/>
  </xsl:template>

  <xsl:template match="g:graphSet">

    <xsl:call-template name="drawGraph">
      <xsl:with-param name="graphTitle" select="$graphTitle"/>
      <xsl:with-param name="xAxisTitle" select="$xAxisTitle"/>
      <xsl:with-param name="yAxisTitle" select="$yAxisTitle"/>
      <xsl:with-param name="pointSet" select="."/>
    </xsl:call-template>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/graphfuncs.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8" ?>
<xsl:stylesheet
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:func="http://exslt.org/functions"
	xmlns:exsl="http://exslt.org/common"
        xmlns:tohw="http://www.uszla.me.uk/xsl/1.0/functions"
        xmlns:tohw_="http://www.uszla.me.uk/xsl/1.0/functions"
        xmlns:g="http://www.uszla.me.uk/xsl/1.0/graph"
        extension-element-prefixes="func exsl tohw"
	version="1.0">

<!--    <func:function name="tohw:min">
      <xsl:param name="values"/>
      <xsl:param name="current" select="$values[1]"/>
      <xsl:if test="count($values) = 0">
        <xsl:message terminate="yes">
tohw:min requires more than zero values
        </xsl:message>
      </xsl:if>
      <xsl:variable name="newcurrent">
	<xsl:choose>
	  <xsl:when test="$values[1] &lt; $current">
	    <xsl:value-of select="$values[1]"/>
	  </xsl:when>
	  <xsl:otherwise>
	    <xsl:value-of select="$current"/>
	  </xsl:otherwise>
	</xsl:choose>
      </xsl:variable>
      <func:result>
	<xsl:choose>
	  <xsl:when test="count($values) = 1">
	    <xsl:value-of select="$newcurrent"/>
	  </xsl:when>
	  <xsl:otherwise>
	    <xsl:value-of select="tohw:min($values[position()!=1], $newcurrent)"/>
	  </xsl:otherwise>
	</xsl:choose>
      </func:result>
    </func:function>

    <func:function name="tohw:max">
      <xsl:param name="values"/>
      <xsl:param name="current" select="$values[1]"/>
      <xsl:if test="count($values) = 0">
        <xsl:message terminate="yes">
tohw:max requires more than zero values
        </xsl:message>
      </xsl:if>
      <xsl:variable name="newcurrent">
	<xsl:choose>
	  <xsl:when test="$values[1] &gt; $current">
	    <xsl:value-of select="$values[1]"/>
	  </xsl:when>
	  <xsl:otherwise>
	    <xsl:value-of select="$current"/>
	  </xsl:otherwise>
	</xsl:choose>
      </xsl:variable>
      <func:result>
	<xsl:choose>
	  <xsl:when test="count($values) = 1">
	    <xsl:value-of select="$newcurrent"/>
	  </xsl:when>
	  <xsl:otherwise>
	    <xsl:value-of select="tohw:max($values[position()!=1], $newcurrent)"/>
	  </xsl:otherwise>
	</xsl:choose>
      </func:result>
    </func:function>
-->	

  <func:function name="tohw:intpow">
    <xsl:param name="x"/>
    <xsl:param name="y"/>
    <xsl:if test="$y != floor(number($y))">
      <xsl:message terminate="yes">
tohw:intpow requires an integer power
      </xsl:message>
    </xsl:if>
    <xsl:choose>
      <xsl:when test="$y = 0">
	<func:result select="1"/>
      </xsl:when>
      <xsl:when test="$y = 1">
	<func:result select="$x"/>
      </xsl:when>
      <xsl:when test="$y &lt; 0">
	<func:result select="1 div tohw:intpow($x,-1 * $y)"/>
      </xsl:when>
      <xsl:otherwise>
	<func:result select="$x * tohw:intpow($x, $y - 1)"/>
      </xsl:otherwise>
    </xsl:choose>
  </func:function>

  <func:function name="tohw:floorlog10">
    <xsl:param name="x"/>
    <xsl:variable name="stringLog">
      <xsl:choose>
	<xsl:when test="$x = 0.0">
          0	  
	</xsl:when>
	<xsl:when test="contains(string($x), 'e')">
	  <!-- non-conformant xpath implementation -->
	  <xsl:value-of select="substring-after(string($x),'e')"/>
	</xsl:when>
	<xsl:when test="contains(string($x),'E')">
	  <!-- non-conformant xpath implementation -->
	  <xsl:value-of select="substring-after(string($x),'E')"/>
	</xsl:when>
	<xsl:when test="$x &gt;= 1">
	  <xsl:choose>
	    <xsl:when test="contains($x, '.')">
	      <xsl:value-of select="string-length(substring-before(string($x),'.'))"/>
	    </xsl:when>
	    <xsl:otherwise>
	      <xsl:value-of select="string-length($x)"/>
	    </xsl:otherwise>
	  </xsl:choose>
	</xsl:when>
	<xsl:when test="$x &lt;= -1">
	  <xsl:choose>
	    <xsl:when test="contains($x, '.')">
	      <xsl:value-of select="string-length(substring-before(string($x),'.')) - 1"/>
	    </xsl:when>
	    <xsl:otherwise>
	      <xsl:value-of select="string-length($x) - 1"/>
	    </xsl:otherwise>
	  </xsl:choose>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="-1 * tohw:floorlog10(1 div $x)"/>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:variable>
    <xsl:choose>
      <xsl:when test="contains($stringLog,'+')">
	<func:result select="number(substring-after($stringLog,'+'))-1"/>
      </xsl:when>
      <xsl:otherwise>
	<func:result select="number($stringLog)-1"/>
      </xsl:otherwise>
    </xsl:choose>
  </func:function>

  <xsl:template name="tohw:addUp">
    <!-- Generate an (inclusive) list of 0*$size, 1*$size, ..., $endIter*$size -->
    <xsl:param name="size"/>
    <xsl:param name="iterator" select="0"/>
    <xsl:param name="endIter"/>
    <number value="{$iterator * $size}"/>
    <xsl:if test="$iterator &lt; $endIter">
      <xsl:call-template name="tohw:addUp">
	<xsl:with-param name="size" select="$size"/>
	<xsl:with-param name="iterator" select="$iterator+1"/>
	<xsl:with-param name="endIter" select="$endIter"/>
      </xsl:call-template>
    </xsl:if>
  </xsl:template>

  <func:function name="tohw:launderFP">
    <xsl:param name="x"/>
    <xsl:variable name="n">
      <xsl:choose>
	<xsl:when test="contains(string($x), 'e')">
	  <xsl:value-of select="number(substring-before(string($x),'e'))"/>
	</xsl:when>
	<xsl:when test="contains(string($x),'E')">
	  <xsl:value-of select="number(substring-before(string($x),'E'))"/>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="number($x)"/>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:variable>
    <xsl:variable name="p1">
      <xsl:choose>
	<xsl:when test="contains(string($x), 'e')">
	  <xsl:value-of select="substring-after(string($x),'e')"/>
	</xsl:when>
	<xsl:when test="contains(string($x),'E')">
	  <xsl:value-of select="substring-after(string($x),'E')"/>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="0"/>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:variable>
    <xsl:variable name="p">
      <xsl:choose>
	<xsl:when test="contains($p1,'+')">
	  <xsl:value-of select="number(substring-after($p1,'+'))"/>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:value-of select="number($p1)"/>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:variable>
    <func:result select="number($n)*tohw:intpow(10,$p)"/>
  </func:function>

  <xsl:template name="g:tickValues">
    <xsl:param name="minV"/>
    <xsl:param name="maxV"/>
    <xsl:param name="numTicks" select="4"/>
    <xsl:variable name="range" select="$maxV - $minV"/>
    <xsl:variable name="sectionSize" select="$range div ($numTicks + 1)"/>
    <xsl:variable name="ticks">
      <xsl:call-template name="tohw:addUp">
	<xsl:with-param name="size" select="$sectionSize"/>
	<xsl:with-param name="endIter" select="$numTicks+1"/>
      </xsl:call-template>
    </xsl:variable>
    <g:tickList>
      <xsl:for-each select="exsl:node-set($ticks)/number/@value">
	<g:tick value="{. + $minV}"/>
      </xsl:for-each>
    </g:tickList>
  </xsl:template>

  <xsl:template name="launderTree">
    <xsl:param name="tree"/>
    <xsl:for-each select="$tree/node()">
      <xsl:choose>
	<xsl:when test="local-name()='point' and namespace-uri()='http://www.uszla.me.uk/xsl/1.0/graph'">
	  <g:point x="{tohw:launderFP(@x)}" y="{tohw:launderFP(@y)}"/>
	</xsl:when>
	<xsl:when test="count(./child::node()) &gt; 0">
	  <xsl:element namespace="{namespace-uri()}" name="{local-name()}">
	    <xsl:call-template name="launderTree">
	      <xsl:with-param name="tree" select="."/>
	    </xsl:call-template>
	  </xsl:element>
	</xsl:when>
	<xsl:otherwise>
	  <xsl:copy-of select="."/>
	</xsl:otherwise>
      </xsl:choose>
    </xsl:for-each>
  </xsl:template>

</xsl:stylesheet>
EOF
cat > $TMPXSLTDIR/header.xsl << "EOF"
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet version="1.0"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
        xmlns="http://www.w3.org/1999/xhtml"
        exclude-result-prefixes="xsl"
        >

  <xsl:template name="head">
    <xsl:param name="Jmol"/>
    <head>  
      <title>
        <xsl:value-of select="$prog"/>
        <xsl:text> Output</xsl:text>
      </title>
      <style type="text/css">
        <xsl:call-template name="css-style"/>
      </style>
<xsl:text>
</xsl:text>
      <xsl:if test="$Jmol!='false'">
        <script type="text/javascript">
          <xsl:call-template name="jmoljs"/>
        </script>
      </xsl:if>
<xsl:text>
</xsl:text>
<xsl:comment><xsl:text>[if IE]</xsl:text>
      <script type="text/javascript">
        <xsl:call-template name="exCanvas"/>
      </script>
      <xsl:text>[endif]</xsl:text></xsl:comment>
<xsl:text>
</xsl:text>
      <script type="text/javascript">
        <xsl:call-template name="flot"/>
      </script>
<xsl:text>
</xsl:text>
      <script type="text/javascript">
        <xsl:call-template name="mainJavascript"/>
      </script>
    </head>
  </xsl:template>

  <xsl:template name="flot">
<xsl:text disable-output-escaping="yes">// &lt;![CDATA[</xsl:text>
<xsl:text disable-output-escaping="yes">
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yEnd=aY+(ms(aEndAngle)*aRadius)-Z2;if(xStart==xEnd&&!aClockwise){xStart+=0.125}this.currentPath_.push({type:arcType,x:aX,y:aY,radius:aRadius,xStart:xStart,yStart:yStart,xEnd:xEnd,yEnd:yEnd})};contextPrototype.rect=function(aX,aY,aWidth,aHeight){this.moveTo(aX,aY);this.lineTo(aX+aWidth,aY);this.lineTo(aX+aWidth,aY+aHeight);this.lineTo(aX,aY+aHeight);this.closePath()};contextPrototype.strokeRect=function(aX,aY,aWidth,aHeight){this.beginPath();this.moveTo(aX,aY);this.lineTo(aX+aWidth,aY);this.lineTo(aX+aWidth,aY+aHeight);this.lineTo(aX,aY+aHeight);this.closePath();this.stroke()};contextPrototype.fillRect=function(aX,aY,aWidth,aHeight){this.beginPath();this.moveTo(aX,aY);this.lineTo(aX+aWidth,aY);this.lineTo(aX+aWidth,aY+aHeight);this.lineTo(aX,aY+aHeight);this.closePath();this.fill()};contextPrototype.createLinearGradient=function(aX0,aY0,aX1,aY1){var gradient=new CanvasGradient_("gradient");return gradient};contextPrototype.createRadialGradient=function(aX0,aY0,aR0,aX1,aY1,aR1){var gradient=new CanvasGradient_("gradientradial");gradient.radius1_=aR0;gradient.radius2_=aR1;gradient.focus_.x=aX0;gradient.focus_.y=aY0;return gradient};contextPrototype.drawImage=function(image,var_args){var dx,dy,dw,dh,sx,sy,sw,sh;var oldRuntimeWidth=image.runtimeStyle.width;var oldRuntimeHeight=image.runtimeStyle.height;image.runtimeStyle.width='auto';image.runtimeStyle.height='auto';var w=image.width;var h=image.height;image.runtimeStyle.width=oldRuntimeWidth;image.runtimeStyle.height=oldRuntimeHeight;if(arguments.length==3){dx=arguments[1];dy=arguments[2];sx=sy=0;sw=dw=w;sh=dh=h}else if(arguments.length==5){dx=arguments[1];dy=arguments[2];dw=arguments[3];dh=arguments[4];sx=sy=0;sw=w;sh=h}else if(arguments.length==9){sx=arguments[1];sy=arguments[2];sw=arguments[3];sh=arguments[4];dx=arguments[5];dy=arguments[6];dw=arguments[7];dh=arguments[8]}else{throw"Invalid number of arguments";}var d=this.getCoords_(dx,dy);var w2=sw/2;var h2=sh/2;var vmlStr=[];var W=10;var H=10;vmlStr.push(' <g_vml_:group',' coordsize="',Z*W,',',Z*H,'"',' coordorigin="0,0"',' style="width:',W,';height:',H,';position:absolute;');if(this.m_[0][0]!=1||this.m_[0][1]){var filter=[];filter.push("M11='",this.m_[0][0],"',","M12='",this.m_[1][0],"',","M21='",this.m_[0][1],"',","M22='",this.m_[1][1],"',","Dx='",mr(d.x/Z),"',","Dy='",mr(d.y/Z),"'");var max=d;var c2=this.getCoords_(dx+dw,dy);var c3=this.getCoords_(dx,dy+dh);var c4=this.getCoords_(dx+dw,dy+dh);max.x=Math.max(max.x,c2.x,c3.x,c4.x);max.y=Math.max(max.y,c2.y,c3.y,c4.y);vmlStr.push("padding:0 ",mr(max.x/Z),"px ",mr(max.y/Z),"px 0;filter:progid:DXImageTransform.Microsoft.Matrix(",filter.join(""),", sizingmethod='clip');")}else{vmlStr.push("top:",mr(d.y/Z),"px;left:",mr(d.x/Z),"px;")}vmlStr.push(' ">','<g_vml_:image src="',image.src,'"',' style="width:',Z*dw,';',' height:',Z*dh,';"',' cropleft="',sx/w,'"',' croptop="',sy/h,'"',' cropright="',(w-sx-sw)/w,'"',' cropbottom="',(h-sy-sh)/h,'"',' />','</g_vml_:group>');this.element_.insertAdjacentHTML("BeforeEnd",vmlStr.join(""))};contextPrototype.stroke=function(aFill){var lineStr=[];var lineOpen=false;var a=processStyle(aFill?this.fillStyle:this.strokeStyle);var color=a[0];var opacity=a[1]*this.globalAlpha;var W=10;var H=10;lineStr.push('<g_vml_:shape',' fillcolor="',color,'"',' filled="',Boolean(aFill),'"',' style="position:absolute;width:',W,';height:',H,';"',' coordorigin="0 0" coordsize="',Z*W,' ',Z*H,'"',' stroked="',!aFill,'"',' strokeweight="',this.lineWidth,'"',' strokecolor="',color,'"',' path="');var newSeq=false;var min={x:null,y:null};var max={x:null,y:null};for(var i=0;i<this.currentPath_.length;i++){var p=this.currentPath_[i];if(p.type=="moveTo"){lineStr.push(" m ");var c=this.getCoords_(p.x,p.y);lineStr.push(mr(c.x),",",mr(c.y))}else if(p.type=="lineTo"){lineStr.push(" l ");var c=this.getCoords_(p.x,p.y);lineStr.push(mr(c.x),",",mr(c.y))}else if(p.type=="close"){lineStr.push(" x ")}else if(p.type=="bezierCurveTo"){lineStr.push(" c ");var c=this.getCoords_(p.x,p.y);var c1=this.getCoords_(p.cp1x,p.cp1y);var c2=this.getCoords_(p.cp2x,p.cp2y);lineStr.push(mr(c1.x),",",mr(c1.y),",",mr(c2.x),",",mr(c2.y),",",mr(c.x),",",mr(c.y))}else if(p.type=="at"||p.type=="wa"){lineStr.push(" ",p.type," ");var c=this.getCoords_(p.x,p.y);var cStart=this.getCoords_(p.xStart,p.yStart);var cEnd=this.getCoords_(p.xEnd,p.yEnd);lineStr.push(mr(c.x-this.arcScaleX_*p.radius),",",mr(c.y-this.arcScaleY_*p.radius)," ",mr(c.x+this.arcScaleX_*p.radius),",",mr(c.y+this.arcScaleY_*p.radius)," ",mr(cStart.x),",",mr(cStart.y)," ",mr(cEnd.x),",",mr(cEnd.y))}if(c){if(min.x==null||c.x<min.x){min.x=c.x}if(max.x==null||c.x>max.x){max.x=c.x}if(min.y==null||c.y<min.y){min.y=c.y}if(max.y==null||c.y>max.y){max.y=c.y}}}lineStr.push(' ">');if(typeof this.fillStyle=="object"){var focus={x:"50%",y:"50%"};var width=(max.x-min.x);var height=(max.y-min.y);var dimension=(width>height)?width:height;focus.x=mr((this.fillStyle.focus_.x/width)*100+50)+"%";focus.y=mr((this.fillStyle.focus_.y/height)*100+50)+"%";var colors=[];if(this.fillStyle.type_=="gradientradial"){var inside=(this.fillStyle.radius1_/dimension*100);var expansion=(this.fillStyle.radius2_/dimension*100)-inside}else{var inside=0;var expansion=100}var insidecolor={offset:null,color:null};var outsidecolor={offset:null,color:null};this.fillStyle.colors_.sort(function(cs1,cs2){return cs1.offset-cs2.offset});for(var i=0;i<this.fillStyle.colors_.length;i++){var fs=this.fillStyle.colors_[i];colors.push((fs.offset*expansion)+inside,"% ",fs.color,",");if(fs.offset>insidecolor.offset||insidecolor.offset==null){insidecolor.offset=fs.offset;insidecolor.color=fs.color}if(fs.offset<outsidecolor.offset||outsidecolor.offset==null){outsidecolor.offset=fs.offset;outsidecolor.color=fs.color}}colors.pop();lineStr.push('<g_vml_:fill',' color="',outsidecolor.color,'"',' color2="',insidecolor.color,'"',' type="',this.fillStyle.type_,'"',' focusposition="',focus.x,', ',focus.y,'"',' colors="',colors.join(""),'"',' opacity="',opacity,'" />')}else if(aFill){lineStr.push('<g_vml_:fill color="',color,'" opacity="',opacity,'" />')}else{lineStr.push('<g_vml_:stroke',' opacity="',opacity,'"',' joinstyle="',this.lineJoin,'"',' miterlimit="',this.miterLimit,'"',' endcap="',processLineCap(this.lineCap),'"',' weight="',this.lineWidth,'px"',' color="',color,'" />')}lineStr.push("</g_vml_:shape>");this.element_.insertAdjacentHTML("beforeEnd",lineStr.join(""))};contextPrototype.fill=function(){this.stroke(true)};contextPrototype.closePath=function(){this.currentPath_.push({type:"close"})};contextPrototype.getCoords_=function(aX,aY){return{x:Z*(aX*this.m_[0][0]+aY*this.m_[1][0]+this.m_[2][0])-Z2,y:Z*(aX*this.m_[0][1]+aY*this.m_[1][1]+this.m_[2][1])-Z2}};contextPrototype.save=function(){var o={};copyState(this,o);this.aStack_.push(o);this.mStack_.push(this.m_);this.m_=matrixMultiply(createMatrixIdentity(),this.m_)};contextPrototype.restore=function(){copyState(this.aStack_.pop(),this);this.m_=this.mStack_.pop()};contextPrototype.translate=function(aX,aY){var m1=[[1,0,0],[0,1,0],[aX,aY,1]];this.m_=matrixMultiply(m1,this.m_)};contextPrototype.rotate=function(aRot){var c=mc(aRot);var s=ms(aRot);var m1=[[c,s,0],[-s,c,0],[0,0,1]];this.m_=matrixMultiply(m1,this.m_)};contextPrototype.scale=function(aX,aY){this.arcScaleX_*=aX;this.arcScaleY_*=aY;var m1=[[aX,0,0],[0,aY,0],[0,0,1]];this.m_=matrixMultiply(m1,this.m_)};contextPrototype.clip=function(){};contextPrototype.arcTo=function(){};contextPrototype.createPattern=function(){return new CanvasPattern_};function CanvasGradient_(aType){this.type_=aType;this.radius1_=0;this.radius2_=0;this.colors_=[];this.focus_={x:0,y:0}}CanvasGradient_.prototype.addColorStop=function(aOffset,aColor){aColor=processStyle(aColor);this.colors_.push({offset:1-aOffset,color:aColor})};function CanvasPattern_(){}G_vmlCanvasManager=G_vmlCanvasManager_;CanvasRenderingContext2D=CanvasRenderingContext2D_;CanvasGradient=CanvasGradient_;CanvasPattern=CanvasPattern_})()}
// ]]]]></xsl:text>
  </xsl:template>

 <xsl:template name="jmoljs">
<xsl:text disable-output-escaping="yes">// &lt;![CDATA[
<![CDATA[
/* Jmol 11.4 script library Jmol.js 12:44 PM 12/10/2007 hansonr

 checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm

    based on:
 *
 * Copyright (C) 2004-2007  Miguel, Jmol Development, www.jmol.org
 *
 * Contact: hansonr@stolaf.edu
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 *  02111-1307  USA.
 */

// for documentation see www.jmol.org/jslibrary

try{if(typeof(_jmol)!="undefined")exit()

// place "?NOAPPLET" on your command line to check applet control action with a textarea

// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
// bob hanson -- fix for iframes not available for finding applet
// bob hanson -- added applet fake ?NOAPPLET URL flag
// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
//			used PRIOR to jmolApplet() or jmolAppletInline()
//               added 4th array element in jmolRadioGroup -- title
//               added <span> and id around link, checkbox, radio, menu
//               fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
//            -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
//	 	 renamed Jmol.js for Jmol 11 distribution
//            -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
// bh         -- jmolCommandInput()
// bh         -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
// bh         -- minor fixes suggested by Angel
// bh         -- adds jmolSetSyncId() and jmolGetSyncId()

// bh         -- workaround for Mac liveConnect bug not able to match method signature in loadInline:
//               ALWAYS USE jmolLoadInlineArray() or jmolLoadInlineString()


var defaultdir = "."
var defaultjar = "JmolApplet.jar"

var undefined; // for IE 5 ... wherein undefined is undefined

////////////////////////////////////////////////////////////////
// Basic Scripting infrastruture
////////////////////////////////////////////////////////////////

function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
  if (_jmol.initialized) {
    //alert("jmolInitialize() should only be called *ONCE* within a page");
    return;
  }
  if (! codebaseDirectory) {
    alert("codebaseDirectory is a required parameter to jmolInitialize");
    codebaseDirectory = ".";
  }

  if (codebaseDirectory.indexOf("http://") == 0 ||
      codebaseDirectory.indexOf("https://") == 0)
    alert("In general, an absolute URL is not recommended for codebaseDirectory.\n" +
	  "A directory- or docroot-relative reference is recommended.\n\n" +
	  "If you need to use an absolute URL (because, for example, the JAR and data\n" +
	  "files are on another server), then insert a space before\n" +
	  "\"http\" in your URL to avoid this warning message.");

  _jmolSetCodebase(codebaseDirectory);
  _jmolGetJarFilename(fileNameOrUseSignedApplet);
  _jmolOnloadResetForms();
  _jmol.initialized = true;
}

function jmolSetTranslation(TF) {
  _jmol.params.doTranslate = ''+TF;
}

function _jmolGetJarFilename(fileNameOrFlag) {
  _jmol.archivePath =
    (typeof(fileNameOrFlag) == "string"  ? fileNameOrFlag : (fileNameOrFlag ?  "JmolAppletSigned" : "JmolApplet") + "0.jar");
}

function jmolSetDocument(doc) {
  _jmol.currentDocument = doc;
}

function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
  _jmolInitCheck();
  _jmol.params.boxbgcolor = boxbgcolor;
  if (boxfgcolor)
    _jmol.params.boxfgcolor = boxfgcolor
  else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
    _jmol.params.boxfgcolor = "black";
  else
    _jmol.params.boxfgcolor = "white";
  if (progresscolor)
    _jmol.params.progresscolor = progresscolor;
  if (_jmol.debugAlert)
    alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
          " boxfgcolor=" + _jmol.params.boxfgcolor +
          " progresscolor=" + _jmol.params.progresscolor);
}

function jmolApplet(size, script, nameSuffix) {
  _jmolInitCheck();
  return _jmolApplet(size, null, script, nameSuffix);
}

////////////////////////////////////////////////////////////////
// Basic controls
////////////////////////////////////////////////////////////////

function jmolButton(script, label, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolButton" + _jmol.buttonCount;
  if (label == undefined || label == null)
    label = script.substring(0, 32);
  ++_jmol.buttonCount;
  var scriptIndex = _jmolAddScript(script);
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
          "' value='" + label +
          "' onClick='_jmolClick(" + scriptIndex + _jmol.targetText +
          ")' onMouseover='_jmolMouseOver(" + scriptIndex +
          ");return true' onMouseout='_jmolMouseOut()' " +
          _jmol.buttonCssText + "/></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
                      labelHtml, isChecked, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolCheckbox" + _jmol.checkboxCount;
  ++_jmol.checkboxCount;
  if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
      scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
    alert("jmolCheckbox requires two scripts");
    return;
  }
  if (labelHtml == undefined || labelHtml == null) {
    alert("jmolCheckbox requires a label");
    return;
  }
  var indexChecked = _jmolAddScript(scriptWhenChecked);
  var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
  var eospan = "</span>"
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
          "' onClick='_jmolCbClick(this," +
          indexChecked + "," + indexUnchecked + _jmol.targetText +
          ")' onMouseover='_jmolCbOver(this," + indexChecked + "," +
          indexUnchecked +
          ");return true' onMouseout='_jmolMouseOut()' " +
	  (isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>" 
  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
	t += eospan
	eospan = "";
  }
  t += labelHtml +eospan;
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolStartNewRadioGroup() {
  ++_jmol.radioGroupCount;
}

function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
  /*

    array: [radio1,radio2,radio3...]
    where radioN = ["script","label",isSelected,"id","title"]

  */

  _jmolInitCheck();
  var type = typeof arrayOfRadioButtons;
  if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
    alert("invalid arrayOfRadioButtons");
    return;
  }
  if (separatorHtml == undefined || separatorHtml == null)
    separatorHtml = "&nbsp; ";
  var len = arrayOfRadioButtons.length;
  jmolStartNewRadioGroup();
  if (!groupName)
    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
  var t = "<span id='"+(id ? id : groupName)+"'>";
  for (var i = 0; i < len; ++i) {
    if (i == len - 1)
      separatorHtml = "";
    var radio = arrayOfRadioButtons[i];
    type = typeof radio;
    if (type == "object") {
      t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);
    } else {
      t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
    }
  }
  t+="</span>"
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}


function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
  _jmolInitCheck();
  if (_jmol.radioGroupCount == 0)
    ++_jmol.radioGroupCount;
  var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolLink(script, label, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolLink" + _jmol.linkCount;
  if (label == undefined || label == null)
    label = script.substring(0, 32);
  ++_jmol.linkCount;
  var scriptIndex = _jmolAddScript(script);
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><a name='" + id + "' id='" + id + 
          "' href='javascript:_jmolClick(" + scriptIndex + _jmol.targetText + ");' onMouseover='_jmolMouseOver(" + scriptIndex +
          ");return true;' onMouseout='_jmolMouseOut()' " +
          _jmol.linkCssText + ">" + label + "</a></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolCommandInput(label, size, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolCmd" + _jmol.cmdCount;
  if (label == undefined || label == null)
    label = "Execute";
  if (size == undefined || isNaN(size))
    size = 60;
  ++_jmol.cmdCount;
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + 
          "' size='"+size+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
  if (_jmol.debugAlert)
    alert(t);
  return _jmolDocumentWrite(t);
}

function jmolMenu(arrayOfMenuItems, size, id, title) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolMenu" + _jmol.menuCount;
  ++_jmol.menuCount;
  var type = typeof arrayOfMenuItems;
  if (type != null && type == "object" && arrayOfMenuItems.length) {
    var len = arrayOfMenuItems.length;
    if (typeof size != "number" || size == 1)
      size = null;
    else if (size < 0)
      size = len;
    var sizeText = size ? " size='" + size + "' " : "";
    var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
            "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
            sizeText + _jmol.menuCssText + ">";
    for (var i = 0; i < len; ++i) {
      var menuItem = arrayOfMenuItems[i];
      type = typeof menuItem;
      var script, text;
      var isSelected = undefined;
      if (type == "object" && menuItem != null) {
        script = menuItem[0];
        text = menuItem[1];
        isSelected = menuItem[2];
      } else {
        script = text = menuItem;
      }
      if (text == undefined || text == null)
        text = script;		
	  if (script=="#optgroup") {
        t += "<optgroup label='" + text + "'>";	  
	  } else if (script=="#optgroupEnd") {
        t += "</optgroup>";	  
	  } else {		
        var scriptIndex = _jmolAddScript(script);
        var selectedText = isSelected ? "' selected>" : "'>";
        t += "<option value='" + scriptIndex + selectedText + text + "</option>";
	  }
    }
    t += "</select></span>";
    if (_jmol.debugAlert)
      alert(t);
    return _jmolDocumentWrite(t);
  }
}

function jmolHtml(html) {
  return _jmolDocumentWrite(html);
}

function jmolBr() {
  return _jmolDocumentWrite("<br />");
}

////////////////////////////////////////////////////////////////
// advanced scripting functions
////////////////////////////////////////////////////////////////

function jmolDebugAlert(enableAlerts) {
  _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
}

function jmolAppletInline(size, inlineModel, script, nameSuffix) {
  _jmolInitCheck();
  return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
                     script, nameSuffix);
}

function jmolSetTarget(targetSuffix) {
  _jmol.targetSuffix = targetSuffix;
  _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : "";
}

function jmolScript(script, targetSuffix) {
  if (script) {
    _jmolCheckBrowser();
    if (targetSuffix == "all") {
      with (_jmol) {
	for (var i = 0; i < appletSuffixes.length; ++i) {
	  var applet = _jmolGetApplet(appletSuffixes[i]);
          if (applet) applet.script(script);
        }
      }
    } else {
      var applet=_jmolGetApplet(targetSuffix);
      if (applet) applet.script(script);
    }
  }
}

//Java in MacOS X bug: cannot differentiate properly between signatures String and String[]
//so we have to do these explicitly

function jmolLoadInlineString(model, script, isAppend, targetSuffix) {
  if (!model)return
  if (!script)script ="";
  if (!isAppend)isAppend = false;
  if (!targetSuffix)targetSuffix = 0;
  var applet=_jmolGetApplet(targetSuffix);
  if (!applet)return;
  if (applet.loadInlineString) //Jmol 11.4
	applet.loadInlineString(model, script, isAppend);
  else //Jmol 11.2
	applet.loadInlineString(model, script);

}

//If the array contains strings that include newline characters, then the array is assumed to 
//be a set of models; if not, then the array is assumed to be a set of lines for one model

function jmolLoadInlineArray(model_or_models, script, isAppend, targetSuffix) {
  if (!model_or_models)return
  if (!script)script ="";
  if (!isAppend)isAppend = false;
  if (!targetSuffix)targetSuffix = 0;
  var applet=_jmolGetApplet(targetSuffix);
  if (!applet)return;
  if (applet.loadInlineArray) //Jmol 11.4
	applet.loadInlineArray(model_or_models, script, isAppend);
  else //Jmol 11.2
	applet.loadInline(model_or_models, script);
}


// modified to work under MAC OS

function jmolLoadInline(model, targetSuffix) {
  if (!model)return
  if (!targetSuffix)targetSuffix = 0;
  jmolLoadInlineString(model, "", false, targetSuffix);
}

// modified to work under MAC OS

function jmolLoadInlineScript(model, script, targetSuffix) {
  if (!model)return
  if (!script)script ="";
  if (!targetSuffix)targetSuffix = 0;
  if (typeof(model)=="object")
    jmolLoadInlineArray(model, script, false, targetSuffix);
  else
    jmolLoadInlineString(model, script, false, targetSuffix);
}

function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
  if (typeof action == "string") {
    action = action.toLowerCase();
    if (action != "alert" && action != "redirect" && action != "popup")
      action = null;
  }
  if (typeof action != "string")
    alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
          "action must be 'alert', 'redirect', or 'popup'");
  else {
    if (typeof urlOrMessage != "string")
      alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
            "urlOrMessage must be a string");
    else {
      _jmol.checkBrowserAction = action;
      _jmol.checkBrowserUrlOrMessage = urlOrMessage;
    }
  }
  if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
    _jmolCheckBrowser();
}

////////////////////////////////////////////////////////////////
// Cascading Style Sheet Class support
////////////////////////////////////////////////////////////////

function jmolSetAppletCssClass(appletCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.appletCssClass = appletCssClass;
    _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
  }
}

function jmolSetButtonCssClass(buttonCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.buttonCssClass = buttonCssClass;
    _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
  }
}

function jmolSetCheckboxCssClass(checkboxCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.checkboxCssClass = checkboxCssClass;
    _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
  }
}

function jmolSetRadioCssClass(radioCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.radioCssClass = radioCssClass;
    _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
  }
}

function jmolSetLinkCssClass(linkCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.linkCssClass = linkCssClass;
    _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
  }
}

function jmolSetMenuCssClass(menuCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.menuCssClass = menuCssClass;
    _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
  }
}

////////////////////////////////////////////////////////////////
// functions for INTERNAL USE ONLY which are subject to change
// use at your own risk ... you have been WARNED!
////////////////////////////////////////////////////////////////
var _jmol = {
  currentDocument: document,

  debugAlert: false,
  
  codebase: ".",
  modelbase: ".",
  
  appletCount: 0,
  appletSuffixes: [],
  
  buttonCount: 0,
  checkboxCount: 0,
  linkCount: 0,
  cmdCount: 0,
  menuCount: 0,
  radioCount: 0,
  radioGroupCount: 0,
  
  appletCssClass: null,
  appletCssText: "",
  buttonCssClass: null,
  buttonCssText: "",
  checkboxCssClass: null,
  checkboxCssText: "",
  radioCssClass: null,
  radioCssText: "",
  linkCssClass: null,
  linkCssText: "",
  menuCssClass: null,
  menuCssText: "",
  
  targetSuffix: 0,
  targetText: "",
  scripts: [""],
  params: {
	syncId: ("" + Math.random()).substring(3),
	progressbar: "true",
	progresscolor: "blue",
	boxbgcolor: "black",
	boxfgcolor: "white",
	boxmessage: "Downloading JmolApplet ..."
  },
  ua: navigator.userAgent.toLowerCase(),
  uaVersion: parseFloat(navigator.appVersion),
  
  os: "unknown",
  browser: "unknown",
  browserVersion: 0,
  hasGetElementById: !!document.getElementById,
  isJavaEnabled: navigator.javaEnabled(),
  isNetscape47Win: false,
  isIEWin: false,
  useIEObject: false,
  useHtml4Object: false,
  
  windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
  windowsCabUrl:
   "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab",

  isBrowserCompliant: false,
  isJavaCompliant: false,
  isFullyCompliant: false,

  initialized: false,
  initChecked: false,
  
  browserChecked: false,
  checkBrowserAction: "alert",
  checkBrowserUrlOrMessage: null,

  archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar

  previousOnloadHandler: null,
  ready: {}
}

with (_jmol) {
  function _jmolTestUA(candidate) {
    var ua = _jmol.ua;
    var index = ua.indexOf(candidate);
    if (index < 0)
      return false;
    _jmol.browser = candidate;
    _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
    return true;
  }
  
  function _jmolTestOS(candidate) {
    if (_jmol.ua.indexOf(candidate) < 0)
      return false;
    _jmol.os = candidate;
    return true;
  }
  
  _jmolTestUA("konqueror") ||
  _jmolTestUA("safari") ||
  _jmolTestUA("omniweb") ||
  _jmolTestUA("opera") ||
  _jmolTestUA("webtv") ||
  _jmolTestUA("icab") ||
  _jmolTestUA("msie") ||
  (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));
  
  _jmolTestOS("linux") ||
  _jmolTestOS("unix") ||
  _jmolTestOS("mac") ||
  _jmolTestOS("win");

  isNetscape47Win = (os == "win" && browser == "mozilla" &&
                     browserVersion >= 4.78 && browserVersion <= 4.8);

  if (os == "win") {
    isBrowserCompliant = hasGetElementById;
  } else if (os == "mac") { // mac is the problem child :-(
    if (browser == "mozilla" && browserVersion >= 5) {
      // miguel 2004 11 17
      // checking the plugins array does not work because
      // Netscape 7.2 OS X still has Java 1.3.1 listed even though
      // javaplugin.sf.net is installed to upgrade to 1.4.2
      eval("try {var v = java.lang.System.getProperty('java.version');" +
           " _jmol.isBrowserCompliant = v >= '1.4.2';" +
           " } catch (e) { }");
    } else if (browser == "opera" && browserVersion <= 7.54) {
      isBrowserCompliant = false;
    } else {
      isBrowserCompliant = hasGetElementById &&
        !((browser == "msie") ||
          (browser == "safari" && browserVersion < 125.12));
    }
  } else if (os == "linux" || os == "unix") {
    if (browser == "konqueror" && browserVersion <= 3.3)
      isBrowserCompliant = false;
    else
      isBrowserCompliant = hasGetElementById;
  } else { // other OS
    isBrowserCompliant = hasGetElementById;
  }

  // possibly more checks in the future for this
  isJavaCompliant = isJavaEnabled;

  isFullyCompliant = isBrowserCompliant && isJavaCompliant;

  // IE5.5 works just fine ... but let's push them to Sun Java
  isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);
  useIEObject = isIEWin;
  useHtml4Object =
   (os != "mac" && browser == "mozilla" && browserVersion >= 5) ||
   (os == "win" && browser == "opera" && browserVersion >= 8) ||
   (os == "mac" && browser == "safari" && browserVersion >= 412.2);

 doTranslate = true;
 haveSetTranslate = false;
}

function jmolSetCallback(callbackName,funcName) {
  _jmol.params[callbackName] = funcName
}

function jmolSetSyncId(n) {
  return _jmol.params["syncId"] = n
}

function jmolGetSyncId() {
  return _jmol.params["syncId"]
}

function jmolSetLogLevel(n) {
  _jmol.params.logLevel = ''+n;
}

	/*  AngelH, mar2007:
		By (re)setting these variables in the webpage before calling jmolApplet(), 
		a custom message can be provided (e.g. localized for user's language) when no Java is installed.
	*/
if (noJavaMsg==undefined) var noJavaMsg = 
        "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
        "Check the warning message from your browser and/or enable Java applets in<br />\n" +
        "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
if (noJavaMsg2==undefined) var noJavaMsg2 = 
        "You do not have the<br />\n" +
        "Java Runtime Environment<br />\n" +
        "installed for applet support.<br />\n" +
        "Visit <a href='http://www.java.com'>www.java.com</a>";
function _jmolApplet(size, inlineModel, script, nameSuffix) {
	/*  AngelH, mar2007
		Fixed percent / pixel business, to avoid browser errors:
		put "px" where needed, avoid where not.		
	*/
  with (_jmol) {
    if (! nameSuffix)
      nameSuffix = appletCount;
    appletSuffixes.push(nameSuffix);
    ++appletCount;
    if (! script)
      script = "select *";
    var sz = _jmolGetAppletSize(size);
    var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
    var tHeader, tFooter;

    if (useIEObject || useHtml4Object) {
      params.name = 'jmolApplet' + nameSuffix;
      params.archive = archivePath;
      params.mayscript = 'true';
      params.codebase = codebase;
    }
    if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
      winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
      tHeader = 
        "<object name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
        params.code = 'JmolApplet';
      tFooter = "</object>";
    } else if (useHtml4Object) { // use HTML4 object tag
      tHeader = 
        "<object name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
	" classid='java:JmolApplet'\n" +
        " type='application/x-java-applet'\n" +
        widthAndHeight + ">\n";
      tFooter = "</object>";
    } else { // use applet tag
      tHeader = 
        "<applet name='jmolApplet" + nameSuffix +
        "' id='jmolApplet" + nameSuffix +
        "' " + appletCssText +
        " code='JmolApplet'" +
        " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
		widthAndHeight +
        " mayscript='true'>\n";
      tFooter = "</applet>";
    }
    var visitJava;
    if (isIEWin || useHtml4Object) {
		var szX = "width:" + sz[0]
		if ( szX.indexOf("%")==-1 ) szX+="px" 
		var szY = "height:" + sz[1]
		if ( szY.indexOf("%")==-1 ) szY+="px" 
      visitJava =
        "<p style='background-color:yellow; color:black; " +
		szX + ";" + szY + ";" +
        // why doesn't this vertical-align work?
	"text-align:center;vertical-align:middle;'>\n" +
		noJavaMsg +
        "</p>";
    } else {
      visitJava =
        "<table bgcolor='yellow'><tr>" +
        "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
		noJavaMsg2 +
        "</font></td></tr></table>";
    }
    params.loadInline = (inlineModel ? inlineModel : "");
    params.script = (script ? _jmolSterilizeScript(script) : "");
    var t = tHeader + _jmolParams() + visitJava + tFooter;
    jmolSetTarget(nameSuffix);
    ready["jmolApplet" + nameSuffix] = false;
    if (_jmol.debugAlert)
      alert(t);
    return _jmolDocumentWrite(t);
  }
}

function _jmolParams() {
 var t = "";
 for (i in _jmol.params)
	if(_jmol.params[i]!="")
		 t+="  <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
 return t
}

function _jmolInitCheck() {
  if (_jmol.initChecked)
    return;
  _jmol.initChecked = true;
  if (_jmol.initialized)
    return;
  jmolInitialize(defaultdir, defaultjar)
}

function _jmolCheckBrowser() {
  with (_jmol) {
    if (browserChecked)
      return;
    browserChecked = true;
  
    if (isFullyCompliant)
      return true;

    if (checkBrowserAction == "redirect")
      location.href = checkBrowserUrlOrMessage;
    else if (checkBrowserAction == "popup")
      _jmolPopup(checkBrowserUrlOrMessage);
    else {
      var msg = checkBrowserUrlOrMessage;
      if (msg == null)
        msg = "Your web browser is not fully compatible with Jmol\n\n" +
              "browser: " + browser +
              "   version: " + browserVersion +
              "   os: " + os +
              "\n\n" + ua;
      alert(msg);
    }
  }
  return false;
}

function _jmolDocumentWrite(text) {
  if (_jmol.currentDocument)
    _jmol.currentDocument.write(text);
  return text;
}

function _jmolPopup(url) {
  var popup = window.open(url, "JmolPopup",
                          "left=150,top=150,height=400,width=600," +
                          "directories=yes,location=yes,menubar=yes," +
                          "toolbar=yes," +
                          "resizable=yes,scrollbars=yes,status=yes");
  if (popup.focus)
    poup.focus();
}

function _jmolReadyCallback(name) {
  if (_jmol.debugAlert)
    alert(name + " is ready");
  _jmol.ready["" + name] = true;
}

function _jmolSterilizeScript(script) {
  var inlineScript = script.replace(/'/g, "&#39;");
  if (_jmol.debugAlert)
    alert("script:\n" + inlineScript);
  return inlineScript;
}

function _jmolSterilizeInline(model) {
  var inlineModel =
    model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "&#39;");
  if (_jmol.debugAlert)
    alert("inline model:\n" + inlineModel);
  return inlineModel;
}

	/*  AngelH, mar2007:
		By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden.
	*/

	/* hansonr, jun2007:
		2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
	*/

if (allowedJmolSize==undefined) var allowedJmolSize = [25, 2048, 300]   // min, max, default (pixels)
function _jmolGetAppletSize(size) {
	/*  AngelH, mar2007
		Accepts single number or 2-value array, each one can be either:
	   percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
	   Size is now returned as string or number, no "px".
	*/
  var width, height;
  if ( (typeof size) == "object" && size != null ) {
    width = size[0]; height = size[1];
  } else {
    width = height = size;
  }
  // if percent, leave it as it is:
  if ( width.toString().charAt(width.toString().length-1) != "%" ) {
    width = parseFloat(width);	// convert to nr., or strip text, or make zero
	if ( width <= 1 && width > 0 ) { width = (width*100)+"%" }	// decimal: convert to percent and quit
	else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) }	// accept only that range (pixels)
	else { width = allowedJmolSize[2] }	// default size 300 pixels
  }
  if ( height.toString().charAt(height.toString().length-1) != "%" ) {
    height = parseFloat(height);
	if ( height <= 1 && height > 0 ) { height = (height*100)+"%" }
	else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) }
	else { height = allowedJmolSize[2] }
  }
  return [width, height];
}

function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
  ++_jmol.radioCount;
  if (groupName == undefined || groupName == null)
    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
  if (!script)
    return "";
  if (labelHtml == undefined || labelHtml == null)
    labelHtml = script.substring(0, 32);
  if (! separatorHtml)
    separatorHtml = "";
  var scriptIndex = _jmolAddScript(script);
  var eospan = "</span>"
  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" 
	+ groupName + "' id='"+id+"' type='radio' onClick='_jmolClick(" +
         scriptIndex + _jmol.targetText + ");return true;' onMouseover='_jmolMouseOver(" +
         scriptIndex + ");return true;' onMouseout='_jmolMouseOut()' " +
	 (isChecked ? "checked " : "") + _jmol.radioCssText + "/>"
  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
	t += eospan
	eospan = "";
  }
  t += labelHtml +eospan + separatorHtml;
  return t;
}

function _jmolFindApplet(target) {
  // first look for the target in the current window
  var applet = _jmolFindAppletInWindow(window, target);
  // THEN look for the target in child frames
  if (applet == undefined)
    applet = _jmolSearchFrames(window, target);
  // FINALLY look for the target in sibling frames
  if (applet == undefined)
    applet = _jmolSearchFrames(top, target); // look starting in top frame
  return applet;
}

function _jmolGetApplet(targetSuffix){
 var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
 var applet = _jmolFindApplet(target);
 if (applet) return applet
 if(!_jmol.alerted)alert("could not find applet " + target);
 _jmol.alerted = true;
 return null
}

function _jmolSearchFrames(win, target) {
  var applet;
  var frames = win.frames;
  if (frames && frames.length) { // look in all the frames below this window
    for (var i = 0; i < frames.length; ++i) {
      applet = _jmolSearchFrames(frames[i], target);
      if (applet)
        break;
    }
  } else { // look for the applet in this window
   applet = _jmolFindAppletInWindow(win, target)
  }
  return applet;
}

function _jmolFindAppletInWindow(win, target) {
    var doc = win.document;
    // getElementById fails on MacOSX Safari & Mozilla	
    if (_jmol.useHtml4Object || _jmol.useIEObject)
      return doc.getElementById(target);
    else if (doc.applets)
      return doc.applets[target];
    else
      return doc[target]; 
}

function _jmolAddScript(script) {
  if (! script)
    return 0;
  var index = _jmol.scripts.length;
  _jmol.scripts[index] = script;
  return index;
}

function _jmolClick(scriptIndex, targetSuffix) {
  jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
}

function _jmolMenuSelected(menuObject, targetSuffix) {
  var scriptIndex = menuObject.value;
  if (scriptIndex != undefined) {
    jmolScrip