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QueryDetails.html from Re-searcher at Krugle

Show QueryDetails.html syntax highlighted

<span jwcid="@Border">

<span jwcid="@If" condition="ognl:query.blastErrors != null">
	<table>
	<tr>
	<td>
		<div> <span jwcid="@Insert" value="message:stopped"/> </div>
		<div class="error-box" > 
			<pre>
				<span jwcid="@Insert" value="ognl:query.blastErrors"/>
			</pre> 
		</div> 
	</td>
	</tr>
	</table>
</span>	
<table style="margin-left: auto; margin-right: auto;">
	<tr>
	<td style="vertical-align: top;">		
	
		<!-- QUERY OPTIONS & SEARCH LOCATION -->
		<table style="margin-left: 0px; width: 100%">
		<tr>
		<td>
			<span jwcid="@Insert" value="message:queryInfo"/>
			<table class="form-box" style="margin-left: 0px;">
				<tr>
					<td class="title"> <span jwcid="@Insert" value="message:queryDesc"/> </td>
					<td> <span jwcid="@Insert" value="ognl:query.shortDetails"/> </td>
 				</tr>
				<tr>
					<td class="title"> <span jwcid="@Insert" value="message:lastSearchDate"/> </td>
					<td> <span jwcid="@Insert" value="ognl:@researcher.utils.Formatter@formatDate(query.lastSearchDate)"/> </td>
				</tr>
				<tr>
					<td class="title"> <span jwcid="@Insert" value="message:recentHitsDate"/> </td>
					<td> <span jwcid="@Insert" value="ognl:@researcher.utils.Formatter@formatDate(query.recentHitsDate)"/> </td>
				</tr>
				<tr>
					<td class="title"> <span jwcid="@Insert" value="message:hits"/> </td>
					<td> <span jwcid="@Insert" value="ognl:query.numberOfHits"/> </td>
				</tr>
				<tr>
					<td class="title"> <span jwcid="@Insert" value="message:newHits"/> </td>
					<td> <span jwcid="@Insert" value="ognl:query.numberOfNewHits"/> </td>
				</tr>								
				<tr>
					<td colspan="2"> <span jwcid="@DirectLink" listener="listener:onClickNewSequence"> <span jwcid="@Insert" value="message:newSequenceSameParam"/> </span> </td>
				</tr>
			</table>
	</td>
	</tr>
	<tr>
	<td> 
	
	
		<!-- PERIOD & EMAIL NOTIFICATION FORMS -->
		<table class="form-box" style="margin-left: 0px; width: 100%">
			<tr>
				<td class="newseq_window_title" >
					<span jwcid="@Insert" 
					      value="message:period"/>
				</td>
				<td>
					<span jwcid="period@Insert"
        				   value="ognl:query.period" />
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" value="message:notifyByMail"/>
				</td>
				<td>
					<span jwcid="notifyByMail@Insert" 
						   value="ognl:query.notifyByMail" />
				</td>				
			</tr>
			<tr>
				<td class="newseq_window_title" >
					<span jwcid="@Insert" 
					      value="message:maxNumberOfHits"/>
				</td>
				<td>
					<span jwcid="@Insert"
        				   value="ognl:query.maxNumberOfHits" />
				</td>			
			</tr>
		</table>
	
	</td>
	</tr>	

	<tr>
	<td>	
	
	
		<!-- SEQUENCE NAME & SEQUENCE FORMS -->
		<table class="form-box" style="margin-left: 0px; width: 100%;">
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" value="message:sequenceName"/>
			</td>
			<td>
				<span jwcid="@Insert" 
					   value="ognl:query.sequenceName"/>
			</td>
		</tr>				
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
                      value="message:sequence"/>	
			</td>
			<td>
		    	<span jwcid="@Insert" 
                      raw="true" 
                      value="ognl:@researcher.utils.Formatter@breakString(query.sequence, '<br/>', 45)"/>		    	
			</td>
		</tr>
		</table>
		
		
	</td>
	</tr>	

	<tr>
	<td>

		<!-- ALL OTHER OPTIONS FOR PRIMARY DATABASE -->
		<br/>
		<span jwcid="@Insert" value="message:primaryDatabaseSearch"/>
		<table class="form-box" style="margin-left: 0px; width: 100%;">
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:database"/>
			</td>
			<td>
				<span jwcid="@Insert" 
                      value="ognl:query.databaseName"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:compositionalAdjustments"/>
			</td>
			<td>		
				<select jwcid="@Insert" 
						value="ognl:query.compositionalAdjustments.psiblastName" />
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:filters"/>
			</td>
			<td>
				<span jwcid="@Insert" value="message:lowComplexity"/>
				<span jwcid="@Insert" 
					   value="ognl:query.lowComplexityFilter"/>
			    &nbsp;&nbsp;
   			    <span jwcid="@Insert" value="message:maskLookup"/>
				<span jwcid="@Insert" value="ognl:query.maskForLookupTableOnlyFilter"/> 
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:eValue"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.evalue"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:iterations"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.iterations"/>
			</td>
		</tr>		
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:eValueMultipass"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.evalueMultipass"/>
			</td>
		</tr>	
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:wordSize"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.wordSize"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:matrix"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.matrix"/>
			</td>
		</tr>
		
		<span jwcid="@If" condition="ognl:query.searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 
		<tr>
		<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:pssm"/>	
			</td>
			<td>
				<span jwcid="@Insert" 
                      value="ognl:@researcher.utils.Formatter@breakString(query.pssm, '<br/>', 45)"/>
			</td>
		</tr>
		</span>
		
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:costToOpenAGap"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.costToOpenAGap"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:costToExtendAGap"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.costToExtendAGap"/>
			</td>
		</tr>
		
		<span jwcid="@If" condition="ognl:query.searchLocation.equals(@researcher.blast.SearchLocation@LOCAL_SERVER)">		 
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:restartFile"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.inputAlignmentFileName"/>
			</td>						
		</tr>
		</span>
		
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:commandLineOptions"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.commandLineOptions"/>
			</td>
		</tr>	
		
		<span jwcid="@If" condition="ognl:query.searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:phiPattern"/>
			</td>
			<td>
				<span jwcid="phiPattern@Insert" 
				       value="ognl:query.phiPattern"/>
			</td>
		</tr>						
		</span>
	</table>

	</td>
	</tr>	

	<span jwcid="@If" condition="ognl:query.secondaryQuery != null">

	<tr>
	<td>	

		<!-- OPTIONS FOR SECONDARY SEARCH -->
		<br/>
		<span jwcid="@Insert" value="message:secondaryDatabaseSearch"/>
		<table class="form-box" style="margin-left: 0px; width: 100%;">
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:database"/>
			</td>
			<td>
				<span jwcid="@Insert" 
                      value="ognl:query.secondaryQuery.databaseName"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:compositionalAdjustments"/>
			</td>
			<td>		
				<select jwcid="@Insert" 
						value="ognl:query.secondaryQuery.compositionalAdjustments.psiblastName" />
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:filters"/>
			</td>
			<td>
				<span jwcid="@Insert" value="message:lowComplexity"/>
				<span jwcid="@Insert" 
					   value="ognl:query.secondaryQuery.lowComplexityFilter"/>
			    &nbsp;&nbsp;
   			    <span jwcid="@Insert" value="message:maskLookup"/>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.maskForLookupTableOnlyFilter"/> 
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:eValue"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.evalue"/>
			</td>
		</tr>			
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:wordSize"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.wordSize"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:matrix"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.matrix"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
					  value="message:costToOpenAGap"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.costToOpenAGap"/>
			</td>
		</tr>
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:costToExtendAGap"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.costToExtendAGap"/>
			</td>
		</tr>	
		<tr>
			<td class="newseq_window_title">
				<span jwcid="@Insert" 
				      value="message:commandLineOptions"/>
			</td>
			<td>
				<span jwcid="@Insert" value="ognl:query.secondaryQuery.commandLineOptions"/>
			</td>
		</tr>				
		</table>
		
	</td>
	</tr>

	
	</span>

	
</table>



</span>

See more files for this project here

Re-searcher

Re-searcher is the system for recurrent psiblast searches. It enables timely detection of new proteins on the protein sequence databases. Searches can be done on a local server or at NCBI. It has a user-friendly web interface.

Project homepage: http://sourceforge.net/projects/researcher
Programming language(s): Java,XML
License: other

  lib/
    activation.jar
    antlr-2.7.6rc1.jar
    asm-attrs.jar
    asm.jar
    bytecode-0.92.jar
    c3p0-0.9.1-pre6.jar
    cglib-2.1.3.jar
    commons-cli.jar
    commons-codec-1.3.jar
    commons-collections-2.1.1.jar
    commons-dbcp-1.1.jar
    commons-email-1.0.jar
    commons-fileupload-1.1.jar
    commons-httpclient-3.0.1.jar
    commons-io-1.1.jar
    commons-logging-1.0.4.jar
    commons-pool-1.1.jar
    derby.jar
    dom4j-1.6.1.jar
    ehcache-1.1.jar
    ejb3-persistence.jar
    ganymed-ssh2-build209.jar
    hibernate-annotations.jar
    hibernate3.jar
    hivemind-1.1.1.jar
    hivemind-lib-1.1.1.jar
    honeycomb.jar
    javassist-3.0.jar
    jericho-html-2.2.jar
    jta.jar
    log4j-1.2.11.jar
    mail.jar
    ognl-2.6.7.jar
    oro-2.0.8.jar
    servlet-api-2.5.jar
    tapestry-4.0.2.jar
    tapestry-annotations-4.0.2.jar
    tapestry-contrib-4.0.2.jar
    tapestry-portlet-4.0.2.jar
    xerces.jar
    xercesImpl.jar
    xml-apis.jar
  Alignments.jwc
  Alignments.properties
  Border.html
  Border.jwc
  Border.properties
  Configuration.html
  Configuration.page
  Configuration.properties
  FastaList.html
  FastaList.page
  HelpBox.html
  HelpBox.jwc
  HelpBox.script
  HitList.html
  HitList.page
  HitList.properties
  Home.html
  Home.page
  InsertNbsp.jwc
  Login.html
  Login.page
  Login.properties
  NewSequence.html
  NewSequence.page
  NewSequence.properties
  NewUser.html
  NewUser.page
  NewUser.properties
  QueryDetails.html
  QueryDetails.page
  QueryDetails.properties
  SequenceList.html
  SequenceList.page
  SequenceList.properties
  Subhits.html
  Subhits.page
  UserList.html
  UserList.page
  UserList.properties
  ViewSequence.html
  ViewSequence.page
  ViewSequence.properties
  researcher.application
  web.xml