Changeset 532


Ignore:
Timestamp:
Jan 15, 2008, 5:35:49 PM (13 years ago)
Author:
mbayer
Message:

-major expansion of system to allow for different use cases

  • now includes several new JSP pages which allow the user to make choices
Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
10 edited

Legend:

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

    r531 r532  
    44<%@ page import="java.util.*"%>
    55
    6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application"/>
     6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session"/>
    77<!-- 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 -->
    88<jsp:setProperty name="inputDataBean" property="*"/>
    99
    1010<%
    11 final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
    12 final String ID = sc.getId();
    13 final String requestId = request.getParameter("requestId");
    14 
    15 //we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
    16 ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
    17 int experimentID = cc.getId();
    18 DbControl dc = sc.newDbControl();
    19 Experiment experiment = Experiment.getById(dc,experimentID);
    20 String expName = experiment.getName();
    21 dc.close();
    22 
    23 //set the experiment id in the bean so we can get at it later in the plugin
    24 inputDataBean.setExperimentId(new Integer(experimentID).toString());
    25  %>
     11  final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
     12  final String ID = sc.getId();
     13  final String requestId = request.getParameter("requestId");
     14
     15  //we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
     16  ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
     17  int experimentID = cc.getId();
     18  DbControl dc = sc.newDbControl();
     19  Experiment experiment = Experiment.getById(dc, experimentID);
     20  String expName = experiment.getName();
     21  dc.close();
     22
     23  //set the experiment id in the bean so we can get at it later in the plugin
     24  inputDataBean.setExperimentId(new Integer(experimentID).toString());
     25%>
    2626
    2727<html>
     
    123123 
    124124
    125 <h1>Tab2MAGE Importer -- Your Experiment</h1>
    126 Page 1 of 4
     125<h1>Tab2MAGE Import Wizard -- Your Experiment</h1>
    127126<p>
    128127
     
    372371      <td class="boldText">Experiment Name:</td>
    373372      <td class="input"><textarea rows="4" cols="30"
    374         name="experimentName"><%=expName %></textarea></td>
     373        name="experimentName"><%=expName%></textarea></td>
    375374      <td class="helpText">The name you have chosen for the Experiment.</td>
    376375    </tr>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r531 r532  
    44<%@ page import="java.util.*"%>
    55
    6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
     6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
    77<!-- 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 -->
    88<jsp:setProperty name="inputDataBean" property="*" />
     
    8585
    8686
    87 <form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.jsp" method="post">
    88 <input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
     87<form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp" method="post">
     88<input type="hidden" name="ID" value="<%=ID%>">
     89<input type="hidden" name="cmd" value="SetParameters">
    8990<input type="hidden"name="requestId" value="<%=requestId%>">
    9091
     
    9293<input type="hidden" name="zipFile" value=""  id="zipFile">
    9394
    94 <h1>Tab2MAGE Importer -- Your Hybridizations</h1>
    95 Page 3 of 4
     95<h1>Tab2MAGE Import Wizard -- Your Hybridizations</h1>
     96
    9697<p>
    9798<!--  table with the input form -->
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

    r531 r532  
    77<%@ page import="uk.ac.ebi.nugo.plugins.*"%>
    88
    9 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
     9<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
    1010<!-- 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 -->
    1111<jsp:setProperty name="inputDataBean" property="*" />
     
    8686
    8787
    88 <form name="mappings" action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
     88<form name="mappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp" method="post">
    8989
    9090<input type="hidden" name="ID" value="<%=ID%>">
    9191<input type="hidden" name="cmd" value="SetParameters">
    9292<input type="hidden" name="requestId" value="<%=requestId%>">
    93 <input type="hidden" id="fileList" name="parameter:fileList" value""/>
    94 <input type="hidden" id="subjectList" name="parameter:subjectList" value""/>
    95 <input type="hidden" id="tissueList" name="parameter:tissueList" value""/>
    96 
    97 <!-- these are the parameters from the previous input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->
    98 
    99 <!-- inputs from experiment.jsp page -->
    100 <input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>">
    101 <input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>">
    102 <input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>">
    103 <input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>">
    104 <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">
    105 <input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>">
    106 <input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>">
    107 <input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>">
    108 <input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>">
    109 <input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>">
    110 <input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>">
    111 <input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>">
    112 <input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>">
    113 <input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>">
    114 <input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>">
    115 <input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>">
    116 <input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>">
    117 <input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>">
    118 <input type="hidden" name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>">
    119 <!-- inputs from protocols.jsp page -->
    120 <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">
    121 <input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>">
    122 <input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>">
    123 <input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>">
    124 <input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>">
    125 <input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>">
    126 <input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>">
    127 <input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>">
    128 <input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>">
    129 <input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>">
    130 <!-- inputs from hybridizations.jsp page -->
    131 <input type="hidden" name="parameter:platform" value="<%=inputDataBean.getPlatform()%>">
    132 <input type="hidden" name="parameter:organism" value="<%=inputDataBean.getOrganism()%>">
    133 <input type="hidden" name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>">
    134 <input type="hidden" name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>">
    135 <input type="hidden" name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>">
    136 <input type="hidden" name="parameter:numTreatmentGroups" value="<%=inputDataBean.getNumTreatmentGroups()%>">
    137 <input type="hidden" name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>">
    138 <input type="hidden" name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>">
    139 <input type="hidden" name="parameter:tissues" value="<%=inputDataBean.getTissues()%>">
    140 <input type="hidden" name="parameter:pooling" value="<%=inputDataBean.getPooling()%>">
    141 <input type="hidden" name="parameter:zipFile" value="<%=request.getParameter("path") %>" id="zipFile">
    142 <input type="hidden" name="parameter:subjectNames" value="<%=inputDataBean.getSubjectNames()%>">
     93
     94<input type="hidden" id="fileList" name="fileList" value""/>
     95<input type="hidden" id="subjectList" name="subjectList" value""/>
     96<input type="hidden" id="tissueList" name="tissueList" value""/>
     97
    14398
    14499
    145100<%
    146   System.out.println("all parameter values for mappings.jsp:");
    147   for (java.util.Enumeration e = request.getParameterNames(); e.hasMoreElements();)
    148   {
    149     String name = (String) e.nextElement();
    150     String value = request.getParameter(name);
    151     System.out.println("parameter " + name + " = " + value);
    152   }
    153101
    154102  //first extract the factor names and the possible values
     
    177125
    178126  //first parse the filepath from the input page 
    179   String zipFilePath = (String) request.getParameter("path");
     127  String zipFilePath = inputDataBean.getPath();
     128  System.out.println("zipFilePath = " + zipFilePath);
    180129  String zipFileDirStr = zipFilePath.substring(0, zipFilePath.lastIndexOf("/"));
    181130  String zipFileName = zipFilePath.substring(zipFilePath.lastIndexOf("/")+1);
     
    204153  //next get the subjectNames and make up select boxes with these
    205154  //they too have to be mapped to filenames
    206   String [] subjectNames = request.getParameter("subjectNames").split("\n");
     155  String [] subjectNames = inputDataBean.getSubjectNames().split("\n");
    207156 
    208157  //we also need to parse out the tissues string to produce another column of select boxes
    209   String [] tissueNames = request.getParameter("tissues").split("\n");
     158  String [] tissueNames = inputDataBean.getTissues().split("\n");
    210159%>
    211160
    212 <h1>Tab2MAGE Importer -- File Mappings</h1>
    213 Page 4 of 4
     161<h1>Tab2MAGE Import Wizard -- File Mappings</h1>
    214162<p>
    215163
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r531 r532  
    55<%@ page import="java.lang.*"%>
    66
    7 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
     7<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
    88<!-- 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 -->
    99<jsp:setProperty name="inputDataBean" property="*" />
     
    122122<input type="hidden"name="requestId" value="<%=requestId%>">
    123123
    124 <h1>Tab2MAGE Importer -- Your Protocols</h1>
    125 Page 2 of 4
     124<h1>Tab2MAGE Import Wizard -- Your Protocols</h1>
    126125<p>
    127126<table cellpadding="10">
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/DataBean.java

    r531 r532  
    44{
    55
    6   String domain;
    7   String accession;
    8   String qualityControl;
    9   String experimentalDesign;
    10   String experimentName;
    11   String description;
    12   String releaseDate;
    13   String submissionDate;
    14   String submitter;
    15   String organization;
    16   String publicationTitle;
    17   String authors;
    18   String journal;
    19   String volume;
    20   String issue;
    21   String pages;
    22   String year;
    23   String pubmedId;
    24   String treatmentProtocol;
    25   String extractionProtocol;
    26   String labelingProtocol;
    27   String hybridizationProtocol;
    28   String scanningProtocol;
    29   String treatmentProtocolParams;
    30   String extractionProtocolParams;
    31   String labelingProtocolParams;
    32   String hybridizationProtocolParams;
    33   String scanningProtocolParams;
    34   String platform;
    35   String organism;
    36   String numDesigns;
    37   String dyeSwap;
    38   String refSample;
    39   String numTreatmentGroups;
    40   String expFactors;
    41   String numReplicates;
    42   String tissues;
    43   String pooling;
    44   String zipFile;
    45   String experimentId;
    46   String subjectNames;
     6  public String domain;
     7  public String accession;
     8  public String qualityControl;
     9  public String experimentalDesign;
     10  public String experimentName;
     11  public String description;
     12  public String releaseDate;
     13  public String submissionDate;
     14  public String submitter;
     15  public String organization;
     16  public String publicationTitle;
     17  public String authors;
     18  public String journal;
     19  public String volume;
     20  public String issue;
     21  public String pages;
     22  public String year;
     23  public String pubmedId;
     24  public String treatmentProtocol;
     25  public String extractionProtocol;
     26  public String labelingProtocol;
     27  public String hybridizationProtocol;
     28  public String scanningProtocol;
     29  public String treatmentProtocolParams;
     30  public String extractionProtocolParams;
     31  public String labelingProtocolParams;
     32  public String hybridizationProtocolParams;
     33  public String scanningProtocolParams;
     34  public String platform;
     35  public String organism;
     36  public String numDesigns;
     37  public String dyeSwap;
     38  public String refSample;
     39  public String numTreatmentGroups;
     40  public String expFactors;
     41  public String numReplicates;
     42  public String tissues;
     43  public String pooling;
     44  public String path;
     45  public String experimentId;
     46  public String subjectNames;
     47  public String fileList;
     48  public String subjectList;
     49  public String tissueList;
     50  public String useWizard;
     51  public String legacyData;
     52  public String mappingsMode;
    4753 
    4854 
     
    343349    this.year = year;
    344350  }
    345   public String getZipFile()
    346   {
    347     return zipFile;
    348   }
    349   public void setZipFile(String zipFile)
    350   {
    351     this.zipFile = zipFile;
    352   }
    353351  public String getExperimentId()
    354352  {
     
    374372  {
    375373    this.subjectNames = subjectNames;
     374  }
     375  public String getUseWizard()
     376  {
     377    return useWizard;
     378  }
     379  public void setUseWizard(String useWizard)
     380  {
     381    this.useWizard = useWizard;
     382  }
     383  public String getLegacyData()
     384  {
     385    return legacyData;
     386  }
     387  public void setLegacyData(String legacyData)
     388  {
     389    this.legacyData = legacyData;
     390  }
     391  public String getMappingsMode()
     392  {
     393    return mappingsMode;
     394  }
     395  public void setMappingsMode(String mappingsMode)
     396  {
     397    this.mappingsMode = mappingsMode;
     398  }
     399  public String getFileList()
     400  {
     401    return fileList;
     402  }
     403  public void setFileList(String fileList)
     404  {
     405    this.fileList = fileList;
     406  }
     407  public String getSubjectList()
     408  {
     409    return subjectList;
     410  }
     411  public void setSubjectList(String subjectList)
     412  {
     413    this.subjectList = subjectList;
     414  }
     415  public String getTissueList()
     416  {
     417    return tissueList;
     418  }
     419  public void setTissueList(String tissueList)
     420  {
     421    this.tissueList = tissueList;
     422  }
     423  public String getPath()
     424  {
     425    return path;
     426  }
     427  public void setPath(String path)
     428  {
     429    this.path = path;
    376430  }
    377431 
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

    r531 r532  
    106106 
    107107  //add all the parameter names to a String array for processing
    108   String [] paramNames = new String []{"experimentId","domain","accession","qualityControl","experimentalDesign",
     108  static String [] paramNames = new String []{"experimentId","domain","accession","qualityControl","experimentalDesign",
    109109          "experimentName","description","releaseDate","submissionDate","submitter","organization",
    110110          "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
     
    113113          "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
    114114          "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
    115           "tissues","pooling","zipFile", "fileList", "subjectList", "tissueList"};
     115          "tissues","pooling","path", "subjectNames", "fileList", "subjectList", "tissueList","useWizard",
     116          "legacyData","mappingsMode"};
    116117 
    117118
     
    166167        {
    167168          response.setError(errors.size() + " invalid parameters were found in the request",errors);
    168           return;
    169169        }
    170170
     
    258258      //the request information object provides the parameter list and the name of the custom input page to navigate to for
    259259      //the configuration of the plugin run
    260       requestInformation = new RequestInformation(Request.COMMAND_CONFIGURE_JOB, null, null, params, "experiment.jsp");
     260      requestInformation = new RequestInformation(Request.COMMAND_CONFIGURE_JOB, null, null, params, "userchoice1.jsp");
    261261    }
    262262    catch (Throwable e)
     
    571571
    572572
     573  public static String[] getParamNames()
     574  {
     575    return paramNames;
     576  }
     577
     578
     579
    573580//  ---------------------------------------------------------------------------------------------------------------------------------------------- 
    574581
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

    r531 r532  
    303303        for (int k = 1; k <= numTissues; k++)
    304304        {
    305           for(int r = 0; r< numPrintRepeats; r++)
    306           {
     305          for(int r = 1; r<= numPrintRepeats; r++)
     306          {         
    307307            String subjectName = subjectNames[count-1];
     308            System.out.println("subjectName = "+ subjectName);
    308309           
    309310            // file count first
     
    350351              t2mContent +="biotin" + "\t";
    351352            }
    352             if(!singleChannel && numPrintRepeats==0)
     353            if(!singleChannel && r==1)
    353354            {
    354355              t2mContent +="Cy3" + "\t";
    355356            }
    356             if(!singleChannel && numPrintRepeats==1)
     357            if(!singleChannel && r==2)
    357358            {
    358359              t2mContent +="Cy5" + "\t";
     
    374375            // FactorValue[Treatment Type]
    375376            //"trt_group" + i + "\t";
    376             System.out.println("cartesianProduct[0].length = " + cartesianProduct[0].length);
     377            //System.out.println("cartesianProduct[0].length = " + cartesianProduct[0].length);
    377378            for(int n=0; n< cartesianProduct[0].length; n++)
    378379            {
    379               System.out.println("n = "+ n);
     380              //System.out.println("n = "+ n);
    380381              t2mContent +=cartesianProduct[i-1][n]+ "\t";
    381382            }
     
    383384            // new line
    384385            t2mContent += "\n";
    385             count++;
     386           
     387            //in two channel experiments increment the count only if this was the second printed block of data
     388            if((singleChannel==false && r == 2) || singleChannel == true)
     389            {
     390              System.out.println("incrementing count");
     391              count++;
     392            }           
    386393          }
    387394        }
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriterTest.java

    r531 r532  
    2121      writer.experimentId = "2";
    2222      writer.domain = "scri.ac.uk";
    23       writer.accession = "Affymetrix1";
     23      writer.accession = "E-SCRI-001";
    2424      writer.qualityControl = "biological replicate,spike quality control";
    2525      writer.experimentalDesign = "cell_component_comparison_design,RNA_stability_design,family_history_design,";
     
    5252
    5353      // hybs
    54       writer.platform = "Genepix";
    55       writer.organism = "Solanum tuberosum";
     54      writer.platform = "Affymetrix";
     55      writer.organism = "Danio rerio";
    5656      writer.numDesigns = "1";
    5757      writer.dyeSwap = "no";
    5858      writer.refSample = "yes";
    59       writer.numTreatmentGroups = "4";
    60       writer.expFactors = "Strain(mutant,wildtype)\nTreatment(treated,control)";
     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";
    6161      writer.numReplicates = "2";
    62       writer.tissues = "stem";
     62      writer.tissues = "whole_organism";
    6363      writer.pooling = "no";
    64       writer.zipFile = "/home/michab/potato_small.zip";
    65       writer.fileList = "file1.CEL\tfile2.CEL\tfile3.CEL\tfile4.CEL\tfile5.CEL\tfile6.CEL\tfile7.CEL\tfile8.CEL";
    66       writer.subjectList = "plant1\tplant2\tplant3\tplant4\tplant5\tplant6\tplant7\tplant8";
    67       writer.tissueList = "stem\tleaf\troot\tstem\tleaf\troot\tstem\tleaf";
     64      writer.zipFile = "/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";
    6868     
    69       writer.makeFactorValueCombinations();
    70      
     69      writer.makeFactorValueCombinations();
    7170     
    7271      String t2mContent = writer.generateFileContents();
Note: See TracChangeset for help on using the changeset viewer.