Changeset 863


Ignore:
Timestamp:
Dec 2, 2008, 11:24:18 PM (13 years ago)
Author:
Jari Häkkinen
Message:

Addresses #50. Working on the Java wrapper.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.thep.wenni/trunk/base/base2/WeNNI.java

    r858 r863  
    2626import net.sf.basedb.plugins.AbstractRunBinaryPlugin;
    2727
    28 import net.sf.basedb.core.DbControl;
    29 import net.sf.basedb.core.Experiment;
     28import net.sf.basedb.core.DbControl; // Jari, remove this?
     29import net.sf.basedb.core.Experiment; // Jari, remove this?
     30import net.sf.basedb.core.Item;
     31import net.sf.basedb.core.Permission;
    3032import net.sf.basedb.core.ProgressReporter;
    31 import net.sf.basedb.core.RawBioAssay;
     33import net.sf.basedb.core.RawBioAssay; // Jari, remove this?
    3234
    3335import net.sf.basedb.core.plugin.AboutImpl;
     36import net.sf.basedb.core.plugin.Permissions;
    3437import net.sf.basedb.core.plugin.Plugin;
    3538
    3639import java.io.IOException;
    3740
     41import java.util.EnumSet;
    3842import java.util.List;
    3943
     
    5761
    5862  public WeNNI() {
    59     // set about information
     63
    6064    about = new AboutImpl
    61       ( "WeNNI plug-in", "An Unreliable expression value of a gene is " +
     65      ( "WeNNI", "An Unreliable expression value of a gene is " +
    6266        "imputed as the average expression in the most similar genes.\n" +
    6367        "\nThe method is published in \"Improving missing value imputation " +
     
    6973        null, null,
    7074        "http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI" );
     75
     76    defaultChildName = "WeNNI imputed bioassayset";
     77
     78    // Permisssions to request
     79    permissions.add(new Permissions(Item.EXPERIMENT, null,
     80                                    EnumSet.of(Permission.USE)));
     81    permissions.add(new Permissions(Item.JOB, null,
     82                                    EnumSet.of(Permission.READ)));
     83
    7184    // set the type of the plug-in
    7285    plugin_maintype=Plugin.MainType.ANALYZE;
    7386  }
    7487
     88  /**
     89     List of background correction methods.
     90
     91     Note, changing the string in the list will affect the behaviour
     92     of the plug-in and most certaintly unexpected results will be
     93     generated. As an example, changing 'Illumina BeadStudio median'
     94     will break the median method.
     95
     96  private static final
     97  PluginParameter<String> methodParameter = new PluginParameter<String>
     98    ( "method",
     99      "Correction method",
     100      "These methods are implemented:\n\n" +
     101      "Illumina BeadStudio inspired mean 'negative control'\n" +
     102      "Illumina BeadStudio inspired median 'negative control'",
     103      new StringParameterType(255, "Illumina BeadStudio median", true, 1, 0, 0,
     104                              Arrays.asList(
     105                                new String[] { "Illumina BeadStudio mean" ,
     106                                               "Illumina BeadStudio median" }
     107                                )
     108        )
     109      );
     110  */
    75111
    76112  protected void runBinary(List<RawBioAssay> sources,
     
    78114    throws InterruptedException, IOException
    79115  {
     116    String[] cmd = { getBinaryPath(this.getClass(),"nni") , "--help" };
     117    execute(cmd,progress);
    80118  }
    81119
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