| [497] | 1 | <%@ page import="net.sf.basedb.core.*"%> |
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| 2 | <%@ page import="net.sf.basedb.clients.web.*"%> |
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| 3 | <%@ page import="net.sf.basedb.util.*"%> |
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| 4 | <%@ page import="java.util.*"%> |
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| [512] | 5 | <%@ page import="java.lang.*"%> |
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| [497] | 6 | |
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| [532] | 7 | <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" /> |
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| [497] | 8 | <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name --> |
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| [511] | 9 | <jsp:setProperty name="inputDataBean" property="*" /> |
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| [497] | 10 | |
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| 11 | |
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| 12 | <html> |
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| [522] | 13 | |
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| [497] | 14 | <head> |
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| [522] | 15 | |
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| [511] | 16 | <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> |
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| [522] | 17 | <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> |
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| 18 | <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> |
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| 19 | |
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| 20 | <script language="JavaScript" type="text/javascript"> |
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| 21 | //submits form |
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| 22 | function submit() |
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| 23 | { |
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| 24 | document.protocols.submit(); |
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| 25 | } |
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| 26 | </script> |
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| 27 | |
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| [497] | 28 | </head> |
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| [522] | 29 | |
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| [497] | 30 | <body> |
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| 31 | |
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| [511] | 32 | |
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| [497] | 33 | <% |
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| 34 | final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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| 35 | final String ID = sc.getId(); |
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| [530] | 36 | final String requestId = request.getParameter("requestId"); |
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| [512] | 37 | |
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| 38 | |
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| 39 | //here we also need to deal with the multiple select inputs from the previous page |
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| 40 | //their selected values need to be extracted from the request and concatenated into a single String |
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| 41 | |
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| 42 | //first deal with quality control input |
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| 43 | String[] items = request.getParameterValues("qualityControl"); |
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| 44 | StringBuilder qualControl = new StringBuilder(); |
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| 45 | for(int i = 0; i< items.length; i++) |
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| 46 | { |
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| 47 | qualControl.append(items[i] ); |
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| 48 | //last one does not get a comma |
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| 49 | if(i!=items.length-1) |
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| 50 | { |
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| 51 | qualControl.append(","); |
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| 52 | } |
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| 53 | } |
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| 54 | //store this in the bean |
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| 55 | inputDataBean.setQualityControl(qualControl.toString()); |
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| 56 | |
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| 57 | //next deal with the experiment design type |
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| 58 | //this is slightly more complex as we are dealing with six separate list boxes and we need to combine all their inputs |
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| 59 | StringBuilder experimentalDesign = new StringBuilder(); |
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| 60 | |
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| 61 | String [] biologicalPropertyItems = request.getParameterValues("biologicalProperty"); |
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| 62 | if(biologicalPropertyItems !=null) |
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| 63 | { |
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| 64 | for(int i = 0; i< biologicalPropertyItems.length; i++) |
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| 65 | { |
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| 66 | experimentalDesign.append(biologicalPropertyItems[i] +","); |
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| 67 | } |
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| 68 | } |
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| 69 | |
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| 70 | String [] bioMolecularAnnotationItems = request.getParameterValues("bioMolecularAnnotation"); |
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| 71 | if(bioMolecularAnnotationItems !=null) |
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| 72 | { |
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| 73 | for(int i = 0; i<bioMolecularAnnotationItems.length; i++) |
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| 74 | { |
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| 75 | experimentalDesign.append(bioMolecularAnnotationItems[i] +","); |
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| 76 | } |
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| 77 | } |
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| 78 | |
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| 79 | String [] epidemiologicalDesignItems = request.getParameterValues("epidemiologicalDesign"); |
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| 80 | if(epidemiologicalDesignItems !=null) |
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| 81 | { |
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| 82 | for(int i = 0; i< epidemiologicalDesignItems.length; i++) |
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| 83 | { |
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| 84 | experimentalDesign.append(epidemiologicalDesignItems[i] +","); |
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| 85 | } |
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| 86 | } |
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| 87 | |
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| 88 | String [] methodologicalDesignItems = request.getParameterValues("methodologicalDesign"); |
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| 89 | if(methodologicalDesignItems !=null) |
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| 90 | { |
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| 91 | for(int i = 0; i< methodologicalDesignItems.length; i++) |
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| 92 | { |
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| 93 | experimentalDesign.append(methodologicalDesignItems[i] +","); |
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| 94 | } |
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| 95 | } |
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| 96 | |
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| 97 | String [] perturbationalDesignItems = request.getParameterValues("perturbationalDesign"); |
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| 98 | if(perturbationalDesignItems !=null) |
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| 99 | { |
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| 100 | for(int i = 0; i< perturbationalDesignItems.length; i++) |
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| 101 | { |
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| 102 | experimentalDesign.append(perturbationalDesignItems[i] +","); |
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| 103 | } |
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| 104 | } |
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| 105 | |
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| 106 | String [] technologicalDesignItems = request.getParameterValues("technologicalDesign"); |
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| 107 | if(technologicalDesignItems !=null) |
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| 108 | { |
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| 109 | for(int i = 0; i< technologicalDesignItems.length; i++) |
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| 110 | { |
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| 111 | experimentalDesign.append(technologicalDesignItems[i]+","); |
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| 112 | } |
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| 113 | } |
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| 114 | |
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| 115 | //store the combined String in the bean |
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| 116 | inputDataBean.setExperimentalDesign(experimentalDesign.toString()); |
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| 117 | |
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| [497] | 118 | %> |
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| 119 | |
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| [543] | 120 | <form name="protocols" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp?ID=<%=ID%>" method="post"> |
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| [511] | 121 | <input type="hidden" name="ID" value="<%=ID%>"> |
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| [530] | 122 | <input type="hidden"name="requestId" value="<%=requestId%>"> |
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| [497] | 123 | |
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| [532] | 124 | <h1>Tab2MAGE Import Wizard -- Your Protocols</h1> |
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| [511] | 125 | <p> |
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| 126 | <table cellpadding="10"> |
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| [497] | 127 | |
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| [511] | 128 | <tr> |
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| 129 | <td class="header"> |
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| 130 | <h3>Protocol name</h3> |
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| 131 | </td> |
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| 132 | <td class="header"> |
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| 133 | <h3>Protocol Text</h3> |
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| 134 | <p>The full text of the protocol. |
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| 135 | </td> |
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| 136 | <td class="header"> |
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| 137 | <h3>Parameters</h3> |
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| [522] | 138 | <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. |
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| 139 | Each parameter name must be unique within this form.<br /><br /> |
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| [511] | 140 | Leave blank if the protocol is unparameterized.</p> |
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| 141 | </td> |
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| 142 | </tr> |
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| [497] | 143 | |
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| [511] | 144 | <tr> |
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| 145 | <td class="boldText">Treatment</td> |
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| [547] | 146 | <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">treatment protocol text</textarea></td> |
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| [544] | 147 | <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">medium;CO2;antibiotics</textarea></td> |
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| [511] | 148 | </tr> |
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| 149 | |
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| 150 | <tr> |
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| 151 | <td class="boldText">Extraction</td> |
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| [547] | 152 | <td class="input"><textarea rows="8" cols="35" name="extractionProtocol">extraction protocol text</textarea></td> |
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| [544] | 153 | <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams"></textarea></td> |
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| [511] | 154 | </tr> |
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| 155 | |
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| 156 | <tr> |
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| 157 | <td class="boldText">Labeling</td> |
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| [544] | 158 | <td class="input"><textarea rows="8" cols="35" name="labelingProtocol">labeling protocol text </textarea></td> |
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| 159 | <td class="input_topaligned"><textarea rows="3" cols="35" name="labelingProtocolParams"></textarea></td> |
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| [511] | 160 | </tr> |
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| 161 | |
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| 162 | <tr> |
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| 163 | <td class="boldText">Hybridization</td> |
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| [544] | 164 | <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">hybs protocol text </textarea></td> |
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| 165 | <td class="input_topaligned"><textarea rows="3" cols="35" name="hybridizationProtocolParams">temperature(degree_C) ; duration(hr)</textarea></td> |
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| [511] | 166 | </tr> |
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| 167 | |
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| 168 | <tr> |
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| 169 | <td class="boldText">Scanning</td> |
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| [544] | 170 | <td class="input"><textarea rows="8" cols="35"name="scanningProtocol">scanning protocol text </textarea></td> |
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| 171 | <td class="input_topaligned"><textarea rows="3" cols="35" name="scanningProtocolParams"></textarea></td> |
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| [511] | 172 | </tr> |
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| 173 | |
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| 174 | </table> |
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| 175 | |
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| 176 | <p> |
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| [523] | 177 | <table align="center" class="noBorder" cellspacing="5" cellpadding="5"> |
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| 178 | <tr class="noBorder"> |
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| [524] | 179 | <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Next</td></tr></table></div></div></td> |
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| 180 | <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td> </tr> |
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| [521] | 181 | </table> |
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| [511] | 182 | |
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| [497] | 183 | </form> |
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| 184 | |
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| 185 | </body> |
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| 186 | </html> |
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| 187 | |
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