NewSequence.html from Re-searcher at Krugle

Show NewSequence.html syntax highlighted

<span jwcid="@Border">
	
<form jwcid="form@Form"      
      delegate="ognl:beans.validation">

	<span jwcid="@If" condition="ognl:validation.hasErrors">
		<div class="error-box" > 
			<span jwcid="errors@Delegator"
			      delegate="ognl:validation.firstError"/> 
		</div> 
	</span>
	
	<span jwcid="@If" 
		  condition="ognl:infoMessage != null">
		<div class="info-box" > 
			<span jwcid="@Insert" value="ognl:infoMessage"/> 
		</div> 
	</span>		
	
	<table style="margin-left: auto; margin-right: auto;">
		<tr>
		<td style="vertical-align: top;">		
		
			<!-- SEARCH TYPE (NCBI/LOCAL SERVER) -->
			<table class="form-box" style="margin-left: 0px;">
			<tr>
				<td class="title">
					<span jwcid="@Insert" 
						  value="message:searchLocation"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
					      link="/Researcher/static_pages/help.html#searchLocationHelp" 
					      text="message:searchLocationHelp"/>
				</td>
			<td>		
				<select jwcid="@PropertySelection" 
						model="ognl:searchLocationItems" 
						value="ognl:searchLocation"
						onchange="javascript:this.form.events.refresh();"
						size="2" />
			</td>
			</table>
			
			
		</td>
		</tr>
		
		<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@LOCAL_SERVER) && !localSearchReady()">
					<div class="info-box" > 
						<span jwcid="@Insert" value="message:localNAWarning" />
					</div> 
		</span>
		<span jwcid="@Else">		
		
		<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"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#periodHelp" 
						      text="message:periodHelp"/>
					</td>
					<td>
						<input jwcid="period@TextField"
	        				   value="ognl:period"					       
	                           class="text-input" 
						       type="text"/>
					</td>
				</tr>
				<tr>
					<td class="newseq_window_title">
						<span jwcid="@FieldLabel" field="component:notifyByMail"/>	
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#notifyByMailHelp" 
						      text="message:notifyByMailHelp"/>											
					</td>
					<td>
						<input jwcid="notifyByMail@Checkbox" 
							   value="ognl:notifyByMail"
							   displayName="message:notifyByMail"/>
						<br/>
						<span jwcid="@If" condition="ognl:!mailConfigured()">
							<span jwcid="@Insert" raw="true" value="message:mailWarnining" />
						</span>
					</td>
				</tr>
				<tr>
					<td class="newseq_window_title" >
						<span jwcid="@Insert" 
						      value="message:maxNumberOfHits"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#maxNumberOfHitsHelp" 
						      text="message:maxNumberOfHitsHelp"/>
					</td>
					<td>
						<input jwcid="maxNumberOfHits@TextField"
	        				   value="ognl:maxNumberOfHits"					       
	                           class="text-input" 
						       type="text"/>
					</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"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
					      link="/Researcher/static_pages/help.html#sequenceNameHelp" 
					      text="message:sequenceNameHelp"/>
				</td>
				<td>
					<input jwcid="sequenceName" 
					       class="text-input" 
					       style="width: 20em;"/>
				</td>
			</tr>				
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:sequence"/>
			      	<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
			      	      link="/Researcher/static_pages/help.html#sequenceHelp" 
			      	      text="message:sequenceHelp"/>	
				</td>
				<td>
					<textarea jwcid="sequenceString@TextArea" 
							  value="ognl:sequenceString"
		                      class="text-input"
							  style="height: 10em; width: 20em;"/>
				</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"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#databaseHelp" 
						  text="message:databaseHelp"/>							  
						  
				</td>
				<td>
					<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 
						<input jwcid="ncbiDatabase@PropertySelection" 
							   model="ognl:ncbiDatabaseItems"
							   value="ognl:ncbiDatabase"
							   type="text" 
		                       class="text-input"
							   style="width: 20em;"/>
					</span>
					<span jwcid="@Else">
						<input jwcid="database@PropertySelection" 
							   model="ognl:databaseItems"
							   value="ognl:database"
							   type="text" 
		                       class="text-input"
							   style="width: 20em;"/>				
					</span>	   
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:compositionalAdjustments"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#compositionalAdjustmentsHelp" 
						      text="message:compositionalAdjustmentsHelp"
						      width="30em"/>							  
				</td>
				<td>		
					<select jwcid="@PropertySelection" 
							model="ognl:compositionalAdjustmentsItems" 
							value="ognl:compositionalAdjustments" />
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:filters"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#filtersHelp" 
						      text="message:filtersHelp"/>							  
				</td>
				<td>
					<span jwcid="@FieldLabel" field="component:lowComplexity"/>
					<input jwcid="lowComplexity@Checkbox" 
						   value="ognl:lowComplexity"
						   displayName="message:lowComplexity"/>
				    &nbsp;&nbsp;
	   			    <span jwcid="@FieldLabel" field="component:maskLookup"/>
					<input jwcid="maskLookup@Checkbox" 
						   value="ognl:maskLookup"
	   			       	   displayName="message:maskLookup"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:eValue"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#eValueHelp" 
						      text="message:eValueHelp"/>						      
				</td>
				<td>
					<input jwcid="@TextField"
						   value="ognl:eValue"
					       type="text"  
						   class="text-input" 				       
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:iterations"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#iterationsHelp" 
						      text="message:iterationsHelp"/>						      
				</td>
				<td>
					<input jwcid="numberOfIterations@TextField"
						   value="ognl:numberOfIterations"
			               class="text-input" 
					       type="text"
					       style="width: 20em;"/>
				</td>
			</tr>		
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:eValueMultipass"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#eValueMultipassHelp" 
						      text="message:eValueMultipassHelp"/>							  
				</td>
				<td>
					<input jwcid="eValueMultipass@TextField" 
						   value="ognl:eValueMultipass"
					 	   class="text-input" 
					       type="text" 
					       style="width: 20em;"/>
				</td>
			</tr>	
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:wordSize"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#wordSizeHelp" 
						      text="message:wordSizeHelp"/>					      
				</td>
				<td>
					<input jwcid="wordSize@TextField" 
						   value="ognl:wordSize"
					       type="text" 
					       class="select-box" 
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:matrix"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#matrixHelp" 
						      text="message:matrixHelp"/>					      
				</td>
				<td>
					<input jwcid="matrix@PropertySelection" 
						   model="ognl:matrixItems"
						   class="select-box"
						   value="ognl:matrix" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>
			
			<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 
			<tr>
			<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:pssm"/>	
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#pssmHelp" 
						  text="message:pssmHelp"/>					      
				</td>
				<td>
					<textarea jwcid="pssm@TextArea" 
							  value="ognl:pssm"
		                      class="text-input" 						  
							  style="height: 10em; width: 300px;margin-right:5px;margin-top:5px;"/>
				</td>
			</tr>
			</span>
			
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:costToOpenAGap"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#costsHelp" 
						  text="message:costToOpenAGapHelp"/>						  
				</td>
				<td>
					<input jwcid="costToOpenAGap@TextField" 
						   value="ognl:costToOpenAGap"
						   class="text-input" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:costToExtendAGap"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#costsHelp" 
						  text="message:costToExtendAGapHelp"/>						      
				</td>
				<td>
					<input jwcid="costToExtendAGap@TextField"
						   value="ognl:costToExtendAGap"
					       class="text-input" 
					       type="text" 				        
					       style="width: 20em;"/>
				</td>
			</tr>
			
			<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@LOCAL_SERVER)">		 
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:restartFile"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#restartFileHelp" 
						      text="message:restartFileHelp"/>						      
				</td>
				<td>
					<span jwcid="@If" condition="ognl:restartFileName == null">
						<input jwcid="restartFile@Upload"
							   file="ognl:restartFile"
	        				   class="text-input" 
						       type="text" 
						       />
					</span>
					<span jwcid="@Else">
						<span jwcid="@Insert" 
						      value="ognl:restartFileName"/>
						<span jwcid="@LinkSubmit" 
						      listener="listener:onRemoveRestartFile">
						      <span jwcid="@Insert" value="message:remove"/>
						</span>
					</span>
				</td>						
			</tr>
			</span>
			
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:commandLineOptions"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#commandLineOptionsHelp" 
						      text="message:commandLineOptionsHelp"/>						      
				</td>
				<td>
					<input jwcid="commandLineOptions@TextField" 
					       value="ognl:commandLineOptions"
					       class="text-input" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>	
			
			<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:phiPattern"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#phiPatternHelp" 
						  text="message:phiPatternHelp"/>					      
				</td>
				<td>
					<input jwcid="phiPattern@TextField" 
					       value="ognl:phiPattern"
					       class="text-input" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>						
			</span>
		</table>
		
		
		</td>
		</tr>
		<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"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#secondaryDatabaseHelp" 
						  text="message:secondaryDatabaseHelp"/>						  
				</td>
				<td>
					<span jwcid="@If" condition="ognl:searchLocation.equals(@researcher.blast.SearchLocation@NCBI)">		 		 
						<input jwcid="ncbiDatabase2@PropertySelection" 
							   model="ognl:ncbiSecondaryDatabaseItems"
							   value="ognl:ncbiDatabase2"
							   type="text" 
		                       class="text-input"
							   style="width: 20em;"/>
					</span>
					<span jwcid="@Else">
						<input jwcid="database2@PropertySelection" 
							   model="ognl:secondaryDatabaseItems"
							   value="ognl:database2"
							   type="text" 
		                       class="text-input"
							   style="width: 20em;"/>				
					</span>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:compositionalAdjustments"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#compositionalAdjustmentsHelp" 
						      text="message:compositionalAdjustmentsHelp"
						      width="30em"/>
				</td>
				<td>		
					<select jwcid="@PropertySelection" 
							model="ognl:compositionalAdjustmentsItems" 
							value="ognl:compositionalAdjustments2" />
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:filters"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#filtersHelp" 
						      text="message:filtersHelp"/>							  
				</td>
				<td>
					<span jwcid="@FieldLabel" field="component:lowComplexity2"/>
					<input jwcid="lowComplexity2@Checkbox" 
						   value="ognl:lowComplexity2"
						   displayName="message:lowComplexity"/>
				    &nbsp;&nbsp;
	   			    <span jwcid="@FieldLabel" field="component:maskLookup2"/>
					<input jwcid="maskLookup2@Checkbox" 
						   value="ognl:maskLookup2"
	   			       	   displayName="message:maskLookup"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:eValue"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#eValueHelp" 
						      text="message:eValueHelp"/>						      
				</td>
				<td>
					<input jwcid="@TextField"
						   value="ognl:eValue2"
					       type="text"  
						   class="text-input" 				       
					       style="width: 20em;"/>
				</td>
			</tr>			
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:wordSize"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#wordSizeHelp" 
						      text="message:wordSizeHelp"/>						      
				</td>
				<td>
					<input jwcid="@TextField" 
						   value="ognl:wordSize2"
					       type="text" 
					       class="select-box" 
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:matrix"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#matrixHelp" 
						      text="message:matrixHelp"/>						      
				</td>
				<td>
					<input jwcid="@PropertySelection" 
						   model="ognl:matrixItems"
						   class="select-box"
						   value="ognl:matrix2" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
						  value="message:costToOpenAGap"/>
						<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						      link="/Researcher/static_pages/help.html#costsHelp" 
						      text="message:costToOpenAGapHelp"/>							  
				</td>
				<td class="newseq_window_title">
					<input jwcid="@TextField" 
						   value="ognl:costToOpenAGap2"
						   class="text-input" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:costToExtendAGap"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#costsHelp" 
						  text="message:costToExtendAGapHelp"/>						      
				</td>
				<td>
					<input jwcid="@TextField"
						   value="ognl:costToExtendAGap2"
					       class="text-input" 
					       type="text" 				        
					       style="width: 20em;"/>
				</td>
			</tr>	
			<tr>
				<td class="newseq_window_title">
					<span jwcid="@Insert" 
					      value="message:commandLineOptions"/>
					<span jwcid="@HelpBox" style="background-color: #c4dbef;" 
						  link="/Researcher/static_pages/help.html#commandLineOptionsHelp" 
						  text="message:commandLineOptionsHelp"
						  top="-100"/>							      
				</td>
				<td>
					<input jwcid="@TextField" 
					       value="ognl:commandLineOptions2"
					       class="text-input" 
					       type="text" 				       
					       style="width: 20em;"/>
				</td>
			</tr>				
		</table>
			
		</td>
		</tr>
		<tr>
		<td style="text-align: right; padding-right: 0; vertical-align: middle;">
		
			<!-- RESET BUTTON -->

			<input type="reset" class="button" value="Reset Forms" style="margin:5px;"/>
			<span jwcid="@HelpBox"
			      link="/Researcher/static_pages/help.html#buttonsHelp" 
			      text="message:resetHelp" 
			      style="background-color: white;" 
			      left="-60" 
			      top="-160"/>
			&nbsp;&nbsp;&nbsp;
			<!-- SUBMIT BUTTONS -->
			<input jwcid="@Submit" class="button" action="listener:onAdd" value="message:add" style="margin:5px;"/>
			<span jwcid="@HelpBox" link="/Researcher/static_pages/help.html#buttonsHelp" text="message:addHelp" style="background-color: white;" left="-200" top="-100"/>
			&nbsp;&nbsp;&nbsp;
			<input jwcid="@Submit" class="button" action="listener:onOk" value="message:submit" style="margin:5px;"/>
			<span jwcid="@HelpBox" link="/Researcher/static_pages/help.html#buttonsHelp" text="message:submitHelp" style="background-color: white;" left="-300" top="-100"/>
	
		</td>	
		</tr>
		
	</span>		
	</table>	

</form>
</span>
See more files for this project here