Ignore:
Timestamp:
Jan 23, 2008, 3:21:52 PM (13 years ago)
Author:
mbayer
Message:

have restructured the code completely that writes the hybs section

File:
1 edited

Legend:

Unmodified
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Removed
  • branches/uk_ac_ebi_Tab2MageImporter/html/hybridizations.html

    r522 r550  
    77<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" />
    88
     9<script type="text/javascript">
     10    function hideTwoChannelQuestions()
     11    {
     12      var dyeSwapRow = document.getElementById('dyeSwapRow');
     13      var refSampleRow = document.getElementById('refSampleRow');
     14      var poolingRow = document.getElementById('poolingRow');
     15
     16            //items are currently displayed, so hide them
     17          dyeSwapRow.style.display = "none";
     18          refSampleRow.style.display = "none";
     19          poolingRow.style.display = "none";
     20    }
     21   
     22    function showTwoChannelQuestions()
     23    {
     24      var dyeSwapRow = document.getElementById('dyeSwapRow');
     25      var refSampleRow = document.getElementById('refSampleRow');
     26      var poolingRow = document.getElementById('poolingRow');
     27
     28           //items are currently hidden, so display them
     29          dyeSwapRow.style.display = "table-row";
     30          refSampleRow.style.display = "table-row";
     31          poolingRow.style.display = "table-row";
     32    }
     33   
     34    function checkRefSampleLogic()
     35    {
     36        if(document.getElementById("dyeSwapYes").checked && document.getElementById("refSampleYes").checked)
     37        {
     38          alert('Reference Sample and Dye Swap cannot both be set to "yes"');
     39        }
     40    }
     41
     42   
     43    </script>
     44
    945</head>
     46
    1047<body>
    1148
    12 <h2>Tab2MAGE Importer -- Your Hybridizations</h2>
    13 Page 3 of 3
     49
     50
     51
     52
     53<form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp?ID=<%=ID%>" method="post">
     54<input type="hidden" name="ID" value="<%=ID%>">
     55<input type="hidden" name="cmd" value="SetParameters">
     56<input type="hidden"name="requestId" value="<%=requestId%>">
     57
     58<input type="hidden" name="file_id" value="">
     59<input type="hidden" name="zipFile" value="/home/michab/potato_small.zip"  id="zipFile">
     60
     61<h2>Tab2MAGE Import Wizard -- Your Hybridizations</h2>
     62
    1463<p>
    15 
    16 <form>
    17 
    1864<!--  table with the input form -->
    1965<table cellpadding="15">
    2066
    21   <!-- question 1 -->
    22   <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
     67  <!-- platform -->
     68  <tr >
    2369    <td class="boldText">Microarray platform:</td>
    24     <td class="input"><select name="parameter:platform">
    25     <option >Affymetrix</option>
    26     <option >Agilent</option>
    27     <option >AIDA</option>
    28     <option >BZScan</option>
    29     <option >ChipSkipper</option>
    30     <option >GenePix</option>
    31     <option >GeneTAC</option>
    32     <option >Illumina</option>
    33     <option >Imagene</option>
    34     <option >QuantArray Biotin</option>
    35     <option >QuantArray Cy</option>
    36     <option >Spotfinder</option>
    37     <option ><i>Custom</i></option>
     70    <td class="input">
     71    <select name="platform">
     72    <option onclick="hideTwoChannelQuestions();" selected="selected" >Affymetrix</option>
     73    <option onclick="showTwoChannelQuestions();">Agilent</option>
     74    <option onclick="showTwoChannelQuestions();">AIDA</option>
     75    <option onclick="showTwoChannelQuestions();">BZScan</option>
     76    <option onclick="showTwoChannelQuestions();">ChipSkipper</option>
     77    <option onclick="showTwoChannelQuestions();">GenePix</option>
     78    <option onclick="showTwoChannelQuestions();">GeneTAC</option>
     79    <option onclick="showTwoChannelQuestions();">Illumina</option>
     80    <option onclick="showTwoChannelQuestions();">Imagene</option>
     81    <option onclick="showTwoChannelQuestions();">QuantArray Biotin</option>
     82    <option onclick="showTwoChannelQuestions();">QuantArray Cy</option>
     83    <option onclick="showTwoChannelQuestions();">Spotfinder</option>
     84    <option onclick="showTwoChannelQuestions();"><i>Custom</i></option>
    3885    </select></td>
    3986    <td>The manufacturer of the microarray chip used.</td>
    4087  </tr>
    4188
    42   <!-- question 2 -->
     89  <!-- organism -->
    4390  <tr>
    4491    <td class="boldText">Experimental organism:</td>
    45     <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td>
     92    <td class="input"><input type="text" size="50" name="organism" value="Hordeum vulgare"/></td>
    4693    <td>The full scientific name of the experimental organism used.</td>
    4794  </tr>
    4895
    49   <!-- question 3 -->
     96  <!-- num array designs -->
    5097  <tr>
    5198    <td class="boldText">Number of different arrays designs used:</td>
    52     <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
    53     <td>If more than one array design was used in parallel, please specify the number here.</td>
    54   </tr>
    55 
    56   <!-- question 4 -->
    57   <tr>
    58     <td class="boldText">Dye-swap</td>
    59     <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
    60       name="parameter:dyeSwap" value="no" checked="checked"> <br>
    61      
    62     </td>
    63     <td>If you used a dye-swap design please indicate this here.</td>
    64   </tr>
    65 
    66   <!-- question 5 -->
    67   <tr>
    68     <td class="boldText">Reference sample</td>
    69     <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
    70       name="parameter:refSample" value="no" checked="checked"></td>
    71     <td>If you used a reference sample please indicate this here.</td>
    72   </tr>
    73 
    74   <!-- question 6 -->
     99    <td class="input"><input type="text" size="3" name="numDesigns" value="1"/></td>
     100    <td>If more than one array design was used in parallel, please specify the number here.
     101    We assume that all samples are applied once to each array design</td>
     102  </tr>
     103
     104
     105  <!-- num treatment grps -->
    75106  <tr>
    76107    <td class="boldText">Number of treatment groups:</td>
    77     <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
    78     <td>The number of permutations of factor values. <p>
     108    <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
     109    <td>The number of discrete combinations of factor values, i.e. the product of the number of factor levels(values) from all factors. <p>
    79110    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
    80111    </td>
    81112  </tr>
    82113
    83   <!-- question 7 -->
     114  <!-- exp factors -->
    84115  <tr>
    85116    <td class="boldText">Experimental factors:
    86117    </td>
    87     <td class="input"><textarea rows="7" cols="35" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
     118    <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td>
    88119    <td>Please list all experimental factors and value ranges using the following format (one per
    89120    line):<br>
    90121    <i>Factor 1(value1,value2,...valueN)<br></i>
    91122    <p>Example: <i><br>
    92     Compound(aspirin,ibuprofen,acetaminophen) <br>
     123    Compound(aspirin,ibuprofen) <br>
    93124    Dose(control,low,medium,high)</i></td>
    94125  </tr>
    95126
    96   <!-- question 8 -->
     127  <!-- num subjects -->
    97128  <tr>
    98129    <td class="boldText">Number of subjects per group:</td>
    99     <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
     130    <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td>
    100131    <td>This is the number of biological replicates in each treatment group.</td>
    101132  </tr>
    102133 
    103   <!-- question 9 -->
     134  <!-- subject labels -->
     135  <tr>
     136    <td class="boldText">Subject (replicate) labels:</td>
     137    <td class="input"><textarea rows="8" cols="32" name="subjectNames"></textarea></td>
     138    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
     139     in no particular order (copy and paste from Excel works).</td>
     140  </tr>
     141 
     142  <!-- tissues -->
    104143  <tr>
    105144    <td class="boldText">Target tissues:</td>
    106     <td class="input"><textarea rows="2" cols="35" name="parameter:tissues">stem</textarea></td>
    107     <td>List all target tissues (as a comma separated list).<br>
    108     Example: liver,heart,adipose tissue</td>
     145    <td class="input"><textarea rows="4" cols="32" name="tissues">stem</textarea></td>
     146    <td>List all target tissues one per line, in no particular order (copy and paste from Excel works).</td>
     147  </tr>
     148
     149
     150  <!-- dye swap -->
     151  <tr id="dyeSwapRow"  style="display:none">
     152    <td class="boldText">Dye-swap</td>
     153    <td class="input">
     154    <table class="noBorder" cellpadding="4">
     155      <tr>
     156        <td class="noBorder"><input type="radio" name="dyeSwap" id="dyeSwapYes" value="yes" onchange="checkRefSampleLogic();"/></td>
     157        <td class="noBorder">yes</td>
     158      </tr>
     159
     160      <tr>
     161        <td class="noBorder"><input type="radio" name="dyeSwap" id="dyeSwapNo" value="no" checked="checked"  onchange="checkRefSampleLogic();"/></td>
     162        <td class="noBorder">no</td>
     163      </tr>
     164    </table>     
     165    </td>
     166    <td>If you used a dye-swap design please indicate this here.</td>
     167  </tr>
     168
     169  <!-- ref sample -->
     170  <tr id="refSampleRow"  style="display:none">
     171    <td class="boldText">Reference sample</td>
     172    <td class="input"> 
     173    <table class="noBorder" cellpadding="4">
     174      <tr>
     175        <td class="noBorder"><input type="radio" name="refSample" id="refSampleYes" value="yes"  onchange="checkRefSampleLogic();"/></td>
     176        <td class="noBorder">yes</td>
     177      </tr>
     178
     179      <tr>
     180        <td class="noBorder"><input type="radio"name="refSample" id="refSampleNo" value="no"  checked="checked"  onchange="checkRefSampleLogic();"/></td>
     181        <td class="noBorder">no</td>
     182      </tr>
     183    </table>       
     184    </td>
     185    <td>If you used a reference sample please indicate this here.</td>
    109186  </tr>
    110187 
    111   <!-- question 10 -->
    112   <tr>
     188  <!-- pooling -->
     189  <tr id="poolingRow"  style="display:none">
    113190    <td class="boldText">Sample pooling:</td>
    114     <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
    115       name="parameter:pooling" value="no" checked="checked"></td>
     191    <td class="input">
     192    <table class="noBorder" cellpadding="4">
     193      <tr>
     194        <td class="noBorder"><input type="radio" name="pooling" value="yes"></td>
     195        <td class="noBorder">yes</td>
     196      </tr>
     197      <tr>
     198        <td class="noBorder"><input type="radio" name="pooling" value="no" checked="checked"></td>
     199        <td class="noBorder">no</td>
     200      </tr>
     201    </table>   
     202    </td>
    116203    <td>If the samples were pooled please indicate this here.</td>
    117204  </tr>
     
    123210
    124211    <td class="input">
    125     <table class="noBorder" border="0" cellspacing="0" cellpadding="0">
    126       <tr class="noBorder" valign="middle">
     212    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
     213      <tr class="noBorder" >
    127214     
    128         <td ><input type="text" name="path" size="40" value="">&nbsp;</td>
     215        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
    129216       
    130         <td>
    131         <div class="buttonclass"
    132           onmouseover="this.className='buttonclass_hover';"
    133           onmouseout="this.className='buttonclass';"
     217        <td  style="vertical-align: middle;border-style: none;">
     218        <div class="buttons"
     219          onmouseover="this.className='buttons_hover';"
     220          onmouseout="this.className='buttons';"
    134221          onclick="browseOnClick()">
    135         <div class="buttonclass_inner">
     222        <div class="buttons_inner">
    136223
    137224        <table class="noBorder" cellspacing="0" cellpadding="0">
    138225          <tr class="noBorder">
    139             <td>&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
    140             <td>Browse&hellip;</td>
     226            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
     227            <td style="border-style: none;">Browse&hellip;</td>
    141228          </tr>
    142229        </table>
     
    154241  </tr>
    155242
    156 
    157 
    158243</table>
    159244
    160245<p>
    161 <table class="noBorder" width="100%">
    162 <tr class="noBorder" ><td class="centered">
    163 <input type="submit"  value="Run Import"/>
    164 </td>
    165 </tr>
    166 </table>
    167 
    168 
     246
     247  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
     248  <tr class="noBorder">
     249    <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>
     250    <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>
     251  </table>
     252
     253
     254</form>
    169255
    170256</body>
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