pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/XSL/IdXML.xsl

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+<?xml version="1.0"	encoding="utf-8"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+<xsl:template match="IdXML">
+  <html> 
+  <body>  
+	  <xsl:apply-templates select="//IdentificationRun"/>
+  </body> 
+  </html>  
+</xsl:template>
+
+<xsl:template match="SearchParameters">
+    <tr>
+  	<td>Database</td>
+  	<td align="center">
+    		<xsl:value-of select="@db"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Database version</td>
+  	<td align="center">
+    		<xsl:value-of select="@db_version"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Taxonomy</td>
+  	<td align="center">
+    		<xsl:value-of select="@taxonomy"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Mass type</td>
+  	<td align="center">
+    		<xsl:value-of select="@mass_type"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Charges</td>
+  	<td align="center">
+    		<xsl:value-of select="@charges"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Enzyme</td>
+  	<td align="center">
+    		<xsl:value-of select="@enzyme"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Missed cleavages</td>
+  	<td align="center">
+    		<xsl:value-of select="@missed_cleavages"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Precursor peak tolerance</td>
+  	<td align="center">
+    		<xsl:value-of select="@precursor_peak_tolerance"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Peak mass tolerance</td>
+  	<td align="center">
+    		<xsl:value-of select="@peak_mass_tolerance"/> 
+  	</td>
+  	</tr>
+</xsl:template>
+
+<xsl:template match="IdentificationRun">
+	<table border="1" cellpadding="2" style="border-style:solid; border-collapse:collapse;" width="100%">
+    <tr><th>Search parameter</th>
+    <th>Value</th></tr>
+    <tr>
+  	<td>Date</td>
+  	<td align="center">
+    		<xsl:value-of select="@date"/> 
+  	</td>
+  	</tr>
+    <tr>
+  	<td>Search engine</td>
+  	<td align="center">
+    		<xsl:value-of select="@search_engine"/> 
+  	</td>
+		</tr>
+    <tr>
+  	<td>Search engine version</td>
+  	<td align="center">
+    		<xsl:value-of select="@search_engine_version"/> 
+  	</td>
+		</tr>
+	 	<xsl:variable name="search_parameters_reference">
+	 		<xsl:value-of select="@search_parameters_ref"/>
+  	</xsl:variable>
+	  <xsl:apply-templates select="parent::IdXML/SearchParameters[@id=$search_parameters_reference]"/>
+	</table>
+	<br/>
+	<table border="1" cellpadding="2" style="border-style:solid; border-collapse:collapse;" width="100%">
+    <tr><th>Protein</th>
+    	<th align="center">Score</th>
+    	<th align="center"> Corresponding identified peptides </th>	
+    </tr>
+	  <xsl:apply-templates select="ProteinIdentification/ProteinHit">
+  			<xsl:sort select="@score" data-type="number" order="descending"/>
+	  </xsl:apply-templates>
+	</table>
+	<br/>
+	<table border="1" cellpadding="2" width="100%" style="border-style:solid; border-collapse:collapse;">
+  	<tr><th><nobr>Unassigned peptides</nobr></th>
+   	<th>Score</th>
+   	<th><nobr>Charge</nobr></th>
+   	<th><nobr>RT</nobr></th>
+   	<th><nobr>MZ</nobr></th>
+   	<th><nobr>AA before</nobr></th>
+   	<th><nobr>AA after</nobr></th>
+	  <xsl:if test="PeptideIdentification/PeptideHit[not(@protein_refs)]/UserParam">
+			<th width="20%">Additional information</th>
+	  </xsl:if>
+ 		</tr>
+		<xsl:choose>
+		  <xsl:when test="PeptideIdentification/PeptideHit[not(@protein_refs)]/ancestor::PeptideIdentification[@higher_score_better='true']">
+			  <xsl:apply-templates select="PeptideIdentification/PeptideHit[not(@protein_refs)]">
+	  				<xsl:sort select="@score" data-type="number" order="descending"/>	
+			  </xsl:apply-templates>
+  		</xsl:when>
+		  <xsl:otherwise>
+			  <xsl:apply-templates select="PeptideIdentification/PeptideHit[not(@protein_refs)]">
+	  				<xsl:sort select="@score" data-type="number" order="ascending"/>	
+			  </xsl:apply-templates>
+			</xsl:otherwise>
+		</xsl:choose>
+	</table>
+	<br/><br/>
+</xsl:template>
+
+<xsl:template match="ProteinHit">
+  <tr>
+    <td>
+      <xsl:value-of select="@accession"/> 
+    </td>
+    <td align="center">
+      <xsl:value-of select="@score"/> 
+    </td>
+    <td>
+	  	<xsl:variable name="id_string">
+	  		<xsl:value-of select="@id"/><xsl:text> </xsl:text> 
+ 	  	</xsl:variable>
+	  	<xsl:variable name="id_string2">
+	  		<xsl:value-of select="@id"/>
+ 	  	</xsl:variable>
+    
+			<table border="1" cellpadding="2" width="100%" style="border-style:none; border-collapse:collapse;" >
+    	<tr><th width="20%">Sequence</th>
+	  	<th>Score</th>
+	  	<th><nobr>charge</nobr></th>
+	   	<th><nobr>RT</nobr></th>
+	   	<th><nobr>MZ</nobr></th>
+	   	<th><nobr>AA before</nobr></th>
+	   	<th><nobr>AA after</nobr></th>
+	 		<th width="20%"><nobr>Additional information</nobr></th>
+	  	</tr>
+			<xsl:choose>
+			  <xsl:when test="ancestor::IdentificationRun/PeptideIdentification/PeptideHit[contains(@protein_refs, $id_string) or (contains(@protein_refs, $id_string2) and substring-after(@protein_refs, $id_string2) = '')]/ancestor::PeptideIdentification[@higher_score_better='true']">
+		  		<xsl:apply-templates select="ancestor::IdentificationRun/PeptideIdentification/PeptideHit[contains(@protein_refs, $id_string) or (contains(@protein_refs, $id_string2) and substring-after(@protein_refs, $id_string2) = '')]">
+		  				<xsl:sort select="@score" data-type="number" order="descending"/>
+					</xsl:apply-templates>
+				</xsl:when>
+				<xsl:otherwise>
+		  		<xsl:apply-templates select="ancestor::IdentificationRun/PeptideIdentification/PeptideHit[contains(@protein_refs, $id_string) or (contains(@protein_refs, $id_string2) and substring-after(@protein_refs, $id_string2) = '')]">
+		  				<xsl:sort select="@score" data-type="number" order="ascending"/>
+					</xsl:apply-templates>
+				</xsl:otherwise>
+			</xsl:choose>
+			</table>
+    </td>
+  </tr>
+</xsl:template>
+<xsl:template match="PeptideHit">
+	<tr>
+  	<td>
+    		<xsl:value-of select="@sequence"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="@score"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="@charge"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="parent::PeptideIdentification/@RT"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="parent::PeptideIdentification/@MZ"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="@aa_before"/> 
+  	</td>
+  	<td align="center">
+    		<xsl:value-of select="@aa_after"/> 
+  	</td>
+  	<td><nobr>
+  		<xsl:if test="UserParam">
+ 				<xsl:for-each select="UserParam">
+  				<xsl:value-of select="@name"/><xsl:text>: </xsl:text><xsl:value-of select="@value"/><br/>
+	  		</xsl:for-each>
+  	</xsl:if>
+  	</nobr></td>
+	</tr>
+</xsl:template>
+</xsl:stylesheet>
+
+