Changeset 547


Ignore:
Timestamp:
Jan 21, 2008, 11:25:30 AM (13 years ago)
Author:
mbayer
Message:

number of issues fixed in UI

Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
1 added
11 edited

Legend:

Unmodified
Added
Removed
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/configureImporter.jsp

    r544 r547  
    147147<input type="hidden"name="parameter:legacyData" value="<%=inputDataBean.getLegacyData()%>" />
    148148<input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
     149<input type="hidden"name="parameter:spreadSheetMappings" value="<%= inputDataBean.getSpreadSheetMappings()%>"/>
     150
    149151<input type="hidden"name="parameter:fileList" value=""/>
    150152<input type="hidden"name="parameter:subjectList" value=""/>
    151153<input type="hidden"name="parameter:tissueList" value=""/>
     154<input type="hidden"name="parameter:combinationList" value=""/>
    152155
    153156
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

    r544 r547  
    1515  final String ID = sc.getId();
    1616  final String requestId = request.getParameter("requestId");
    17  
    18   System.out.println("mappings.jsp: inputDataBean = " + inputDataBean.toString());
    19   System.out.println("mappings.jsp: ID = " + ID);
     17
    2018%>
    2119
     
    7573      tissueList += frm.elements[i].value + '\t';
    7674    }
     75    if(id.match("combinationInput"))
     76    {
     77      combinationList += frm.elements[i].value + '\t';
     78    }
    7779  }
    7880  frm.fileList.value = fileList;
    7981  frm.subjectList.value = subjectList;
    8082  frm.tissueList.value = tissueList;
     83  frm.combinationList.value = combinationList;
    8184}
    8285
     
    98101<input type="hidden" id="subjectList" name="subjectList" value""/>
    99102<input type="hidden" id="tissueList" name="tissueList" value""/>
     103<input type="hidden" id="combinationList" name="combinationList" value""/>
    100104
    101105
    102106
    103107<%
    104 
    105108  //first extract the factor names and the possible values
    106109  String expFactors = inputDataBean.getExpFactors().trim();
     
    131134  System.out.println("zipFilePath = " + zipFilePath);
    132135  String zipFileDirStr = zipFilePath.substring(0, zipFilePath.lastIndexOf("/"));
    133   String zipFileName = zipFilePath.substring(zipFilePath.lastIndexOf("/")+1);
     136  String zipFileName = zipFilePath.substring(zipFilePath.lastIndexOf("/") + 1);
    134137
    135138  //get hold of the appropriate BASE objects for this
     
    147150    entry = zipStream.getNextEntry();
    148151  }
    149  
    150   String [] fileNamesArr = new String[fileNames.size()];
     152
     153  String[] fileNamesArr = new String[fileNames.size()];
    151154  fileNames.toArray(fileNamesArr);
    152155  Arrays.sort(fileNamesArr);
    153  
     156
    154157  dc.close();
    155  
     158
    156159  //next get the subjectNames and make up select boxes with these
    157160  //they too have to be mapped to filenames
    158   String [] subjectNames = inputDataBean.getSubjectNames().split("\n");
    159  
     161  String[] subjectNames = inputDataBean.getSubjectNames().split("\n");
     162
    160163  //we also need to parse out the tissues string to produce another column of select boxes
    161   String [] tissueNames = inputDataBean.getTissues().split("\n");
    162  
    163  
     164  String[] tissueNames = inputDataBean.getTissues().split("\n");
     165
    164166  //work out the number of hybridizations
    165167  int numReplicates = Integer.parseInt(inputDataBean.getNumReplicates());
    166   int numTreatmentGroups =Integer.parseInt(inputDataBean.getNumTreatmentGroups());
     168  int numTreatmentGroups = Integer.parseInt(inputDataBean.getNumTreatmentGroups());
    167169  int numTissues = inputDataBean.getTissues().split("\n").length;
    168   int numHybs = Tab2MageWriter.calcNumHybs( numReplicates, numTreatmentGroups, numTissues);
     170  int numHybs = Tab2MageWriter.calcNumHybs(numReplicates, numTreatmentGroups, numTissues);
    169171  System.out.println("numHybs = " + numHybs);
    170172  System.out.println("products.length = " + products.length);
     
    189191    <td class="header"><h3>Subject</h3></td>
    190192    <td class="header"><h3>Tissue</h3></td>
    191 
    192     <!-- factor names -->
    193     <%
    194       for (int i = 0; i < products[i].length; i++)
    195       {
    196     %>
    197     <td class="header"><h3><%=factorNames[i]%></h3></td>
    198     <%
    199     }
    200     %>
     193    <td class="header"><h3>Factor Value Combination</h3></td>
     194
    201195  </tr>
    202196
     
    255249    </select></td>
    256250
    257 <!-- now print the values of this factor value combination, each in a separate cell -->
    258     <%
    259         for (int j = 0; j < products[i].length; j++)
    260         {
    261     %>
    262     <td class="border"><%=products[i][j]%></td>
    263     <%
    264     }
    265     %>
    266 
     251<!-- need a single cell with a select box that lets the user select from a list of unique factor value combinations -->
     252
     253    <td>
     254    <select id="combinationInput<%=i %>">
     255      <%
     256          for (int k = 0; k < products.length; k++)
     257          {
     258            //make a String with all the factor values in this combination
     259            //separate values in each combi with a space
     260            String combi = "";
     261            for (int j = 0; j < products[k].length; j++)
     262            {
     263              combi += products[k][j] + " ";
     264            }
     265      %>
     266
     267      <option><%=combi%></option>
     268
     269      <%
     270      }
     271      %>
     272    </select>
     273    </td>
    267274
    268275  </tr>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r544 r547  
    144144  <tr>
    145145    <td class="boldText">Treatment</td>
    146     <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">All chemicals tested were supplied by Merck (Darmstadt, Germany) or Aldrich (Hannover, Germany). All were of highest purity grade.</textarea></td>
     146    <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">treatment protocol text</textarea></td>
    147147    <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">medium;CO2;antibiotics</textarea></td>
    148148  </tr>
     
    150150  <tr>
    151151    <td class="boldText">Extraction</td>
    152     <td class="input"><textarea rows="8" cols="35" name="extractionProtocol">RNA was isolated using a FastPrep instrument (Q-Biogene, Irvine USA) and Rneasy reagents (Qiagen, Hilden Germany). RNA quality was checked with a 2100 Bioanalyser (Agilent Technologies, Palo Alto USA) by assessing the 28S/18S rRNA ratio.</textarea></td>
     152    <td class="input"><textarea rows="8" cols="35" name="extractionProtocol">extraction protocol text</textarea></td>
    153153    <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams"></textarea></td>
    154154  </tr>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/spreadsheetdata.jsp

    r543 r547  
    2727function submit()
    2828{
    29   document.spreadSheetMappings.submit();
     29  document.spreadSheetMappingsForm.submit();
    3030}
    3131
     
    3737<h1>Tab2MAGE Import Wizard -- Enter Spreadsheet Data for Mappings</h1>
    3838
    39 <form id="spreadSheetMappings" name="spreadSheetMappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>">
     39<form name="spreadSheetMappingsForm" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>" method="post">
    4040
    41 <input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
     41<input type="hidden" name="ID" value="<%=ID%>">
    4242<input type="hidden"name="requestId" value="<%=requestId%>">
    4343
     
    5151<li>Columns must be in the order as below and the column headers must be exactly as follows (please replace 'myFactorName1' etc. with your actual factor names):<p>
    5252<b>
    53 File&nbsp;&nbsp;&nbsp;Sample&nbsp;&nbsp;&nbsp;FactorValue[myFactorName1]&nbsp;&nbsp;&nbsp;FactorValue[myFactorName2]&nbsp;&nbsp;&nbsp;etc....
     53File&nbsp;&nbsp;&nbsp;Subject&nbsp;&nbsp;&nbsp;Tissue&nbsp;&nbsp;&nbsp;FactorValue[myFactorName1]&nbsp;&nbsp;&nbsp;FactorValue[myFactorName2]&nbsp;&nbsp;&nbsp;etc....
    5454</b></p>
    5555</ul>
    5656</p>
    5757<hr/>
    58 <p align="center"><h3>Your Mappings:</h3></p>
    59 <p align="center"><textarea cols="90" rows="30">Paste your mappings here.....</textarea></p>
     58<p align="center"><h3>Paste your copied mappings here:</h3></p>
     59<p align="center">
     60<textarea name="spreadSheetMappings" cols="90" rows="25"></textarea>
     61</p>
    6062
    61 </form>
     63
    6264
    6365  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
     
    6668    <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>
    6769  </table>
     70 
     71  </form>
    6872
    6973
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/submit.jsp

    r544 r547  
    88
    99<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
     10<!-- 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 -->
     11<jsp:setProperty name="inputDataBean" property="*" />
    1012
    1113<html>
     
    3234<p>
    3335
    34 Please review the values you have entered and if you are happy with these, click 'Submit'.
     36Please review the values you have entered and click 'Submit'.
    3537<p>
    3638
    37 <table cellpadding="5">
     39<table cellpadding="5" align="center">
    3840
    3941  <tr>
    40   <td>Parameter>
     42  <td><h3 align="center">Parameter</h3>
    4143  </td>
    42   <td class="input">Value
     44  <td class="input"><h3 align="center">Value</h3>
    4345  </td>
    4446  </tr>
     
    4850  String ID = sc.getId();
    4951  String requestId = request.getParameter("requestId");
    50  
    5152
    52   String [] paramNames = Tab2MageImporter.getParamNames();
     53  String [] paramNames = new String []{"domain","accession","qualityControl","experimentalDesign",
     54    "experimentName","description","releaseDate","submissionDate","submitter","organization",
     55    "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
     56    "extractionProtocol","labelingProtocol","hybridizationProtocol","scanningProtocol",
     57    "treatmentProtocolParams","extractionProtocolParams","labelingProtocolParams",
     58    "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
     59    "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
     60    "tissues","pooling","path"};
     61   
     62    String [] friendlyNames = new String []{"Domain","Accession","Quality Control","Experimental Design",
     63    "Experiment Name","Description","Release Date","Submission Date","Submitter","Organization",
     64    "Publication Title","Authors","Journal","Volume","Issue","Pages","Year","Pubmed ID","Treatment SProtocol",
     65    "Extraction Protocol","Labeling Protocol","Hybridization Protocol","Scanning Protocol",
     66    "Treatment Protocol Parameters","Extraction Protocol Parameters","Labeling Protocol Parameters",
     67    "Hybridization Protocol Parameters","Scanning Protocol Parameters","Platform","Organism",
     68    "Number of Array Designs","Dye Swap","Reference Sample","Number of Treatment Groups","Experimental Factors","Number of Replicates per Group",
     69    "Tissues","Pooling","Zip File"};
    5370
    54   //print out all current parameter values in the bean
     71  //print out all relevant parameter values in the bean
    5572  Class cls = inputDataBean.getClass();
    5673  for (int i = 0; i < paramNames.length; i++)
     
    6077    String fieldName = field.getName();
    6178   
    62     if(!value.trim().equals("default"))
     79    //only print stuff that has a value -- default is empty String initialized in the bean
     80    if(!value.equals(""))
    6381    {
    6482%>   
    6583 
    6684  <tr>
    67   <td><%=fieldName %>
     85  <td><b><%=friendlyNames[i] %></b>
    6886  </td>
    6987  <td class="input"><%=value %>
     
    130148<input type="hidden"name="parameter:legacyData" value="<%=inputDataBean.getLegacyData()%>" />
    131149<input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
     150<input type="hidden"name="parameter:spreadSheetMappings" value="<%= inputDataBean.getSpreadSheetMappings()%>"/>
     151
    132152<input type="hidden"name="parameter:fileList" value=""/>
    133153<input type="hidden"name="parameter:subjectList" value=""/>
    134154<input type="hidden"name="parameter:tissueList" value=""/>
     155<input type="hidden"name="parameter:combinationList" value=""/>
    135156
    136157
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/DataBean.java

    r545 r547  
    5050  public String subjectList;
    5151  public String tissueList;
     52  public String combinationList;
    5253  public String useWizard;
    5354  public String legacyData;
    5455  public String mappingsMode;
     56  public String spreadSheetMappings;
    5557 
    5658  public DataBean()
     
    6264  //this is necessary because the plugin will not accept any null values and in some submissions not all vars will have values
    6365  private void initDefaults()
    64   {   
     66  {
     67    System.out.println("initing bean defaults");
    6568    try
    6669    {
     
    455458    this.path = path;
    456459  }
     460
     461  public String getSpreadSheetMappings()
     462  {
     463    return spreadSheetMappings;
     464  }
     465
     466  public void setSpreadSheetMappings(String spreadSheetMappings)
     467  {
     468    this.spreadSheetMappings = spreadSheetMappings;
     469  }
    457470 
    458471 
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

    r545 r547  
    9898    "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
    9999    "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
    100     "tissues","pooling","path", "subjectNames", "fileList", "subjectList", "tissueList","useWizard",
    101     "legacyData","mappingsMode"};
     100    "tissues","pooling","path", "subjectNames", "fileList", "subjectList", "tissueList","combinationList", "useWizard",
     101    "legacyData","mappingsMode","spreadSheetMappings"};
    102102
    103103
     
    121121
    122122    //create the parameter type - every parameter is a String
    123     StringParameterType stringPT = new StringParameterType(255, null, true);
     123    StringParameterType stringPT = new StringParameterType(null, null, true);
    124124
    125125    //a list to add the parameters to
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

    r544 r547  
    55import java.io.Writer;
    66import java.lang.reflect.Field;
     7import java.util.Arrays;
    78import java.util.HashMap;
    89import java.util.Iterator;
    910import java.util.LinkedList;
     11import java.util.List;
    1012import java.util.Map;
    1113
     
    2628  String[] paramNames;
    2729
    28   String[][] cartesianProduct;
    2930  String[] factorNames;
    3031  String [] fileNames;
    3132  String [] subjectNames;
    3233  String [] tissueNames;
     34  String [][] combinations;
    3335
    3436  public String experimentId;
     
    7577  public String subjectList;
    7678  public String tissueList;
     79  public String combinationList;
    7780  public String useWizard;
    7881  public String legacyData;
    7982  public String mappingsMode;
     83  public String spreadSheetMappings;
    8084
    8185
     
    118122      }
    119123
     124      //this extracts the individaul factor names from the String that comes from the web page
     125      extractFactorNames();
    120126      //now extract the factor values and store them suitably so we can access them
    121127      makeFactorValueCombinations();
     128
    122129    }
    123130    catch (Exception e)
     
    127134  }
    128135
     136
    129137  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    130138
    131139  public void makeFactorValueCombinations()
    132140  {
    133     //first extract the factor names and the possible values
     141    //if the mappings were manually selected by the user, do this
     142    if(mappingsMode.equals("manualSelect"))
     143    {
     144      //here we process the input from the mappings.jsp page where users select combinations of files, subjects, tissues and factor values   
     145      //we want the filenames in a separate array so we can match them to their appropriate combinations as selected
     146      //by the user in the UI
     147      //they then match the order of the subject names, tissues and factor value combinations
     148      fileNames = fileList.split("\t");
     149      //ditto for the other lists
     150      subjectNames = subjectList.split("\t");
     151      tissueNames = tissueList.split("\t");
     152
     153      //parse the list of factor value combinations and put it into a 2d array
     154      String [] allCombis = combinationList.split("\t");
     155      combinations = new String [allCombis.length][];
     156      for (int i = 0; i < allCombis.length; i++)
     157      {
     158        String [] combi = allCombis[i].split(" ");
     159        combinations[i] = combi;
     160      }
     161    }
     162   
     163    //if the mappings were copied and pasted from a spreadsheet we need to parse them into arrays to match the ones above
     164    else
     165    {
     166      String [] entriesWithHeader = spreadSheetMappings.split("\n");
     167     
     168      //need to remove the header row - this akward with arrays but we need to use arrays here
     169      String [] entries = new String [entriesWithHeader.length -1];
     170      for (int i = 0; i < entries.length; i++)
     171      {
     172        entries[i] = entriesWithHeader[i+1];
     173      }
     174   
     175      String [] headerNames = entries[0].split("\t");
     176      int numFactors = headerNames.length - 3;
     177     
     178      //init the arrays
     179      fileNames = new String [entries.length];
     180      subjectNames = new String [entries.length];
     181      tissueNames = new String [entries.length];
     182      combinations = new String [entries.length][];
     183     
     184      for (int i = 0; i < entries.length; i++)
     185      {
     186        String [] row = entries[i].split("\t");
     187        fileNames[i] = row [0];
     188        subjectNames[i] = row[1];
     189        tissueNames[i] = row[2];
     190        String [] combi = new String [numFactors];
     191        for (int j = 0; j < combi.length; j++)
     192        {
     193          combi[j] = row[j+3];
     194        }
     195        combinations[i] = combi;       
     196      }
     197    }
     198  }
     199
     200  // ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
     201 
     202  public void extractFactorNames()
     203  {
     204    //get the factor names
    134205    String[] rawFactors = expFactors.split("\n");
    135 
    136     String[][] factorValues = new String[rawFactors.length][];
    137206    factorNames = new String[rawFactors.length];
    138 
    139     for (int i = 0; i < rawFactors.length; i++)
     207    for (int i = 0; i < factorNames.length; i++)
    140208    {
    141209      //extract the factor name
    142210      String factorName = rawFactors[i].substring(0, rawFactors[i].indexOf("("));
    143211      factorNames[i] = factorName;
    144       //extract the possible values from between the parentheses
    145       String allValues = rawFactors[i].substring(rawFactors[i].indexOf("(") + 1,
    146               rawFactors[i].indexOf(")"));
    147       String[] values = allValues.split(",");
    148       factorValues[i] = values;
    149     }
    150 
    151     //here we get hold of the cartesian product of all the factor values
    152     cartesianProduct = CartesianProduct.getCartesianProduct(factorValues);
    153     for (int i = 0; i < cartesianProduct.length; i++)
    154     {
    155       System.out.print("factor value combination: ");
    156       for (int j = 0; j < factorValues.length; j++)
    157       {
    158         System.out.print(cartesianProduct[i][j] + "     ");
    159       }
    160       System.out.println();
    161     }
    162 
    163     //now we want the filenames in a separate array so we can add them to their appropriate combinations as selected
    164     //by the user in the UI
    165     //this requires us to parse out the file string (which had to be sent as a single parameter from the web page) and add the files to the
    166     //array in the order we find them in the string
    167     //they then match the order of the combinations in the cartesian product
    168     fileNames = fileList.split("\t");
    169     //ditto for the lists of subject names and tissues
    170     subjectNames = subjectList.split("\t");
    171     tissueNames = tissueList.split("\t");
     212      System.out.println("factorName = " + factorName);
     213    }
    172214  }
    173215
     
    316358            String subjectName = subjectNames[count-1];
    317359            System.out.println("subjectName = "+ subjectName);
    318            
     360
    319361            // file count first
    320362            t2mContent += fileNames[count-1] + "\t" +
    321            
     363
    322364            // accession no. i.e the array
    323365            // design
    324366            accession + "\t" +
    325            
     367
    326368            // bio source
    327369            subjectName + "\t" +
    328            
     370
    329371            // BioMaterialCharacteristics[Organism]
    330372            organism + "\t" +
    331            
     373
    332374            // BioMaterialCharacteristics[OrganismPart]
    333375            tissueNames[count-1] + "\t" +
    334            
     376
    335377            // BioMaterialCharacteristics[CellType]
    336378            "" + "\t" +
    337            
     379
    338380            // sample
    339381            subjectName + ".sample-" + k + "\t" +
    340            
     382
    341383            // Protocol[grow]
    342384            "P-DIET-1" + "\t" +
    343            
     385
    344386            // Extract
    345387            subjectName + ".sample-" + k + "-extract" + "\t" +
    346            
     388
    347389            // Protocol[extraction]
    348390            "P-EXTR-1" + "\t" +
    349            
     391
    350392            // LabeledExtract
    351393            subjectName + ".sample-" + k + "-extract-le" + "\t" +
    352            
     394
    353395            // Protocol[labeling]
    354396            "P-LABL-1" + "\t" ;
    355            
     397
    356398            // Dye
    357399            //depends on platform and repeat no.
     
    368410              t2mContent +="Cy5" + "\t";
    369411            }
    370            
     412
    371413            // Hybridization
    372414            t2mContent += "hybridization-" + count + "\t" +
    373            
     415
    374416            // Protocol[hybridization]
    375417            "P-HYBR-1" + "\t" +
    376            
     418
    377419            // Scan
    378420            "scan-" + count + "\t" +
    379            
     421
    380422            // Protocol[scanning]
    381423            "P-SCAN-1" + "\t";
     
    385427            //"trt_group" + i + "\t";
    386428            //System.out.println("cartesianProduct[0].length = " + cartesianProduct[0].length);
    387             for(int n=0; n< cartesianProduct[0].length; n++)
     429            for(int n=0; n< combinations[0].length; n++)
    388430            {
    389431              //System.out.println("n = "+ n);
    390               t2mContent +=cartesianProduct[i-1][n]+ "\t";
     432              t2mContent +=combinations[i-1][n]+ "\t";
    391433            }
    392434
    393435            // new line
    394436            t2mContent += "\n";
    395            
     437
    396438            //in two channel experiments increment the count only if this was the second printed block of data
    397439            if((singleChannel==false && r == 2) || singleChannel == true)
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriterTest.java

    r543 r547  
    5353      // hybs
    5454      writer.platform = "Affymetrix";
    55       writer.organism = "Danio rerio";
     55      writer.organism = "Solanum tuberosum";
    5656      writer.numDesigns = "1";
    5757      writer.dyeSwap = "no";
    5858      writer.refSample = "yes";
    59       writer.numTreatmentGroups = "15";
    60       writer.expFactors = "Time(0.25h,10h,11.7h,14d,16h,24h,30d,32h,48h,4d,5d,6h,8h,90d,9h)\n";
     59      writer.numTreatmentGroups = "4";
     60      writer.expFactors = "Strain(mutant,wildtype)\nTreatment(treated,control)";
    6161      writer.numReplicates = "2";
    6262      writer.tissues = "whole_organism";
    6363      writer.pooling = "no";
    6464      writer.path = "/home/michab/gen2.zip";
    65       writer.fileList ="Tue-10h-1.CEL\tTue-10h-2.CEL\tTue-11.7h-1.CEL\tTue-11.7h-2.CEL\tTue-14d-1.CEL\tTue-14d-2.CEL\tTue-16h-1.CEL\tTue-16h-2.CEL\tTue-1c-1.CEL\tTue-1c-2.CEL\tTue-24h-1.CEL\tTue-24h-2.CEL\tTue-30d-1.CEL\tTue-30d-2.CEL\tTue-32h-1.CEL\tTue-32h-2.CEL\tTue-48h-1.CEL\tTue-48h-2.CEL\tTue-4d-1.CEL\tTue-4d-2.CEL\tTue-5d-1.CEL\tTue-5d-2.CEL\tTue-6h-1.CEL\tTue-6h-2.CEL\tTue-8h-1.CEL\tTue-8h-2.CEL\tTue-90d-1.CEL\tTue-90d-2.CEL\tTue-9h-1.CEL\tTue-9h-2.CEL\t";
    66       writer.subjectList = "Danio rerio Tuebingen wildtype_10h-1\tDanio rerio Tuebingen wildtype_10h-2\tDanio rerio Tuebingen wildtype_11.7h-1\tDanio rerio Tuebingen wildtype_11.7h-2\tDanio rerio Tuebingen wildtype_14d-1\tDanio rerio Tuebingen wildtype_14d_2\tDanio rerio Tuebingen wildtype_16h-1\tDanio rerio Tuebingen wildtype_16h-2\tDanio rerio Tuebingen wildtype_1c-1\tDanio rerio Tuebingen wildtype_1c-2\tDanio rerio Tuebingen wildtype_24h-1\tDanio rerio Tuebingen wildtype_24h-2\tDanio rerio Tuebingen wildtype_30d-1\tDanio rerio Tuebingen wildtype_30d-2\tDanio rerio Tuebingen wildtype_32h-1\tDanio rerio Tuebingen wildtype_32h-2\tDanio rerio Tuebingen wildtype_48h-1\tDanio rerio Tuebingen wildtype_48h-2\tDanio rerio Tuebingen wildtype_4d-1\tDanio rerio Tuebingen wildtype_4d-2\tDanio rerio Tuebingen wildtype_5d-1\tDanio rerio Tuebingen wildtype_5d-2\tDanio rerio Tuebingen wildtype_6h-1\tDanio rerio Tuebingen wildtype_6h-2\tDanio rerio Tuebingen wildtype_8h-1\tDanio rerio Tuebingen wildtype_8h-2\tDanio rerio Tuebingen wildtype_90d-1\tDanio rerio Tuebingen wildtype_90d-2\tDanio rerio Tuebingen wildtype_9h-1\tDanio rerio Tuebingen wildtype_9h-2\t";
    67       writer.tissueList = "whole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\t";
     65      writer.fileList ="file1\tfile2\tfile3\tfile4\tfile5\tfile6\tfile7\tfile8";
     66      writer.subjectList = "subject1\tsubject2\tsubject3\tsubject4\tsubject5\tsubject6\tsubject7\tsubject8";
     67      writer.tissueList = "whole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism\twhole_organism";
     68      writer.combinationList = "mutant treated\twildtype treated\tmutant control\twildtype control\tmutant treated\twildtype treated\tmutant control\twildtype control";
     69      //writer.mappingsMode = "manualSelect";
     70      writer.mappingsMode = "copyPaste";
     71      writer.spreadSheetMappings = "File\tSample\tTissue\tFactorValue[Strain]\tFactorValue(Treatment)\nfile1\tsubject1\twhole_plant\tmutant\ttreated\nfile2\tsubject2\twhole_plant\twildtype\ttreated\nfile3\tsubject3\twhole_plant\tmutant\tcontrol\nfile4\tsubject4\twhole_plant\twildtype\tcontrol\nfile5\tsubject5\twhole_plant\tmutant\ttreated\nfile6\tsubject6\twhole_plant\twildtype\ttreated\nfile7\tsubject7\twhole_plant\tmutant\tcontrol\nfile8\tsubject8\twhole_plant\twildtype\tcontrol";
    6872     
     73      writer.extractFactorNames();
    6974      writer.makeFactorValueCombinations();
    7075     
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