<?xml version=“1.0” encoding=“ISO-8859-1”?> <xsl:stylesheet version=“1.0”

xmlns:xsl="http://www.w3.org/1999/XSL/Transform" 
xmlns:GAML="http://www.bioml.com/gaml/" >

<!– X! tandem default style sheet Copyright (C) 2003-2004 Ronald C. Beavis Version 2004.03.01 All Rights Reserved

This source code is distributed under the terms of the
Artistic License.

–> <xsl:template match=“/”>

 <html>
   <head>
     <title>thegpm site 000 <xsl:value-of select="/bioml/@label" /></title>
     <link rel="stylesheet" href="/tandem/tandem-style.css" />
<SCRIPT lanuage="JavaScript">

function changeState(id) {

var block = document.getElementById(id);
if(block.style.display == 'none')       {
        block.style.display = 'block';
}
else    {
        block.style.display = 'none';
}

}

</SCRIPT>
  </head>
  <body bgcolor="#FFFFFF">
      <TABLE bgcolor="#d0d0d0" CELLSPACING="2" CELLPADDING="2">
      <TR>
      <TD WIDTH="700" VALIGN="TOP" ALIGN="LEFT" class="top_note">X! tandem results</TD>
      </TR>
      <TR>
      <TD WIDTH="700" VALIGN="TOP" ALIGN="LEFT" class="top_note"><B><xsl:value-of select="/bioml/@label" /></B></TD>
      </TR>
      </TABLE>
      <BR></BR>
      <table border="1" bgcolor="#d0ffd0" cellpadding="2" cellspacing="2">
              <xsl:apply-templates select="/bioml/group" />
      </table>
   <xsl:if test="not(/bioml/group)">
      <TABLE CELLSPACING="2" CELLPADDING="2">
      <TR>
      <TD WIDTH="700" VALIGN="TOP" ALIGN="LEFT">No models were provided.</TD>
      </TR>
      </TABLE>
   </xsl:if>
  </body>
</html>

</xsl:template>

<xsl:template match=“group”>

<xsl:if test="not(contains(@label,'parameters'))">
        <tr><td>
        <DIV onClick="changeState('{generate-id()}');" class="e" title="click to see/hide sequences and evidence">
                                <SPAN CLASS="top_label">
                #<xsl:value-of select="@id" />, 
                e = <xsl:value-of select="@expect" />,
                M+H = <sup><xsl:value-of select="@z" /></sup><xsl:value-of select="@mh" />
                <sup><xsl:value-of select="./protein/peptide/domain/@delta" /></sup>,
                <SPAN class="aa_s"><xsl:value-of select="./protein/peptide/domain/@pre" /></SPAN>
                <SUP><xsl:value-of select="./protein/peptide/domain/@start" /></SUP>
                <SPAN class="aa_h"><xsl:value-of select="./protein/peptide/domain/@seq" /></SPAN>
                <SUP><xsl:value-of select="./protein/peptide/domain/@end" /></SUP>
                <SPAN class="aa_s"><xsl:value-of select="./protein/peptide/domain/@post" /></SPAN>,
                <xsl:for-each select="./protein[1]/peptide[1]/domain[1]/aa">
                        <SUP><xsl:value-of select="@at" /></SUP><xsl:value-of select="@type" />(<xsl:value-of select="@modified" />),
                </xsl:for-each>
                </SPAN><BR></BR>
                <SPAN CLASS="top_note"> 
                <span class="b"> log(E) = <xsl:value-of select="./protein/@expect" /></span>,
                <xsl:value-of select="@label" />
                </SPAN>
                </DIV>
                <DIV id="{generate-id()}" STYLE="display:none" class="k">
                <TABLE border="1" bgcolor="#ffd0ff" CELLPADDING="1" CELLSPACING="1">
                        <xsl:apply-templates select="protein" mode="sequence"/>
                </TABLE>
                        <xsl:apply-templates select="group" mode="support"/>
                </DIV>
        </td></tr>
</xsl:if>
<xsl:if test="contains(@label,'parameters')">
        <DIV onClick="changeState('{generate-id()}');" title="click to see/hide values" class="e">
        <SPAN CLASS="top_label">+ <xsl:value-of select="@label" />
        </SPAN>
        </DIV>
        <DIV id="{generate-id()}" class="k" STYLE="display:none">
        <BR></BR>
        <TABLE border="0" bgcolor="#ffd0d0" CELLPADDING="1" CELLSPACING="1">
        <SPAN CLASS="top_note"><xsl:apply-templates select="note" />
        </SPAN>
        </TABLE>
        <HR></HR>
        </DIV>
</xsl:if>

</xsl:template>

<xsl:template match=“protein” mode=“description”>

<BR></BR><SPAN CLASS="top_note"><B><xsl:value-of select="@id" /></B> : </SPAN><PRE><xsl:apply-templates select="note" /></PRE>

</xsl:template>

<xsl:template match=“protein” mode=“sequence”>

<tr><td>
<DIV onClick="changeState('{generate-id()}');" title="click to see/hide details">
<SPAN CLASS="top_label"><xsl:value-of select="@id" />: <xsl:value-of select="@label" />
<xsl:apply-templates select="file" /></SPAN>
</DIV>
<DIV id="{generate-id()}" class="k" STYLE="display:none">
<xsl:apply-templates select="peptide" />
</DIV>
</td></tr>

</xsl:template>

<xsl:template match=“file”>

<SPAN class="top_label">(<xsl:value-of select="@URL" />)</SPAN>

</xsl:template>

<xsl:template match=“aa”>

<SPAN class="top_note"><SUP><xsl:value-of select="@at" /></SUP><xsl:value-of select="@type" />(<xsl:value-of select="@modified" />),</SPAN>

</xsl:template>

<xsl:template match=“GAML:attribute”>

<SPAN class="small_label"><xsl:value-of select="@type" /> = <xsl:value-of select="text()" />, </SPAN>

</xsl:template>

<xsl:template match=“GAML:trace”>

        <SPAN class="small_label">
        <B>
                <xsl:value-of select="@type" />
        </B>
        </SPAN>
<TABLE BORDER="0" bgcolor="#ffffd0" CELLPADDING="1" CELLSPACING="1">
<xsl:if test="GAML:attribute">
        <TR>
        <TD WIDTH="500" VALIGN="TOP" ALIGN="LEFT">
        parameters: <xsl:apply-templates select="GAML:attribute" />
        </TD>
        </TR>
</xsl:if>
<TR>
<TD WIDTH="500" VALIGN="TOP" ALIGN="LEFT">
        x-values
</TD>
</TR>
<TR>
<TD WIDTH="500" VALIGN="TOP" ALIGN="LEFT">
        <xsl:value-of select="./GAML:Xdata/GAML:values/text()" />
</TD>
</TR>
<TR>
<TD WIDTH="500" VALIGN="TOP" ALIGN="LEFT">
        y-values
</TD>
</TR>
<TR>
<TD WIDTH="500" VALIGN="TOP" ALIGN="LEFT">
        <xsl:value-of select="./GAML:Ydata/GAML:values/text()" />
</TD>
</TR>
</TABLE>

</xsl:template>

<xsl:template match=“group” mode=“support”> <xsl:if test=“@type='support'”>

<DIV onClick="changeState('{generate-id()}');" class="e" title="click to see/hide evidence">
<SPAN CLASS="top_label">
                <xsl:value-of select="@label" />
</SPAN></DIV>
<DIV id="{generate-id()}" STYLE="display:none" class="k">
        <xsl:apply-templates select="GAML:trace" />
</DIV>
</xsl:if>

</xsl:template>

<xsl:template match=“peptide”>

        <xsl:apply-templates select="domain" />
<DIV onClick="changeState('{generate-id()}');" class="e" title="click to see/hide sequence">
                        <SPAN class="top_label">
                                log(e) = <xsl:value-of select="./../@expect" />,
                                <xsl:value-of select="./../@label" />
                        </SPAN>
</DIV>
<DIV id="{generate-id()}" STYLE="display:none">
        <TABLE BORDER="0" gbcolor="#d0d0ff">
                <TR>
                        <TD WIDTH="500" ALIGN="LEFT" VALIGN="TOP" CLASS="residues"><xsl:value-of select="text()" />
                        </TD>
                </TR>
        </TABLE>
</DIV>

</xsl:template>

<xsl:template match=“domain”>

<SPAN CLASS="top_note">
<B><xsl:value-of select="@id" /></B>: 
e = <xsl:value-of select="@expect" />,
<SUP><xsl:value-of select="@start" /></SUP><SPAN class="aa_h"><xsl:value-of select="@seq" /></SPAN><SUP><xsl:value-of select="@end" /></SUP>,
<xsl:apply-templates select="aa"/><BR></BR>
M+H = <xsl:value-of select="@mh" /> Da,
<SPAN CLASS="greek">d</SPAN> = <xsl:value-of select="@delta" />,
!score = <xsl:value-of select="@hyperscore" />,
y/b: scores = <xsl:value-of select="@y_score" />/<xsl:value-of select="@b_score" />,
ions = <xsl:value-of select="@y_ions" />/<xsl:value-of select="@b_ions" />
</SPAN>
<BR></BR>

</xsl:template>

<xsl:template match=“note”>

<xsl:if test="not(contains(@label,'description'))">
<TR>
        <TD WIDTH="350" ALIGN="RIGHT"><xsl:value-of select="@label" /> = </TD>
        <TD WIDTH="350" ALIGN="LEFT"><xsl:value-of select="text()" /></TD>
</TR>
</xsl:if>
<xsl:if test="contains(@label,'description')">
        <SPAN CLASS="top_note">
        <xsl:choose>
                <xsl:when test="contains(self::note,'ENSMUSP')">
                        <a target="_BLANK">
                        <xsl:attribute name="href">http://www.ensembl.org/Mus_musculus/protview?peptide=<xsl:value-of select="text()"/></xsl:attribute>
                        <xsl:attribute name="title">View Ensembl Protein Report</xsl:attribute>
                        <span class="ensembl"><xsl:value-of select="text()" /></span>
                        </a>
                </xsl:when>
                <xsl:when test="contains(self::note,'ENSRNOP')">
                        <a target="_BLANK">
                        <xsl:attribute name="href">http://www.ensembl.org/Rattus_norvegicus/protview?peptide=<xsl:value-of select="text()"/></xsl:attribute>
                        <xsl:attribute name="title">View Ensembl Protein Report</xsl:attribute>
                        <span class="ensembl"><xsl:value-of select="text()" /></span>
                        </a>
                </xsl:when>
                <xsl:when test="contains(self::note,'ENSP')">
                        <a target="_BLANK">
                        <xsl:attribute name="href">http://www.ensembl.org/Homo_sapiens/protview?peptide=<xsl:value-of select="text()"/></xsl:attribute>
                        <xsl:attribute name="title">View Ensembl Protein Report</xsl:attribute>
                        <span class="ensembl"><xsl:value-of select="text()" /></span>
                        </a>
                </xsl:when>
                <xsl:otherwise>
                        <xsl:value-of select="text()" />
                </xsl:otherwise>
        </xsl:choose>
        </SPAN>
</xsl:if>

</xsl:template>

</xsl:stylesheet>