Changeset 858


Ignore:
Timestamp:
Dec 2, 2008, 4:33:59 PM (13 years ago)
Author:
Jari Häkkinen
Message:

Addresses #50. Working with BASE-plugin communication issues and building a proper WeNNI.java

Location:
plugins/base1/se.lu.thep.wenni/trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.thep.wenni/trunk/INSTALL

    r856 r858  
    190190    $ make install-plugin
    191191    }}}
     192    If you prefer to install the plug-in manually you must place
     193    `nni`, `WeNNI.jar`, and `PluginUtilities-0.1pre.jar` in the same
     194    installation directory.
     195    [[br]] [[br]]
    192196    Note! `make install` will install in location `${exec_prefix}/bin`
    193     which maybe something else than the BASE plugin directory.
     197    which may be something else than your BASE plugin directory.
    194198
    195199 6. Make BASE2 aware of the plugin, see BASE2 documentation
    196     http://base.thep.lu.se/chrome/site/doc/html/index.html
     200    http://base.thep.lu.se/chrome/site/doc/html/index.html and use
     201    the below information with appropriate change of Path
     202    {{{
     203    Class: se.lu.thep.wenni.WeNNI
     204    Path : /path/to/base/pluginsse/lu/thep/wenni-0.7/WeNNI.jar
     205    }}}
     206    Path should be the absolute path to the WeNNI.jar file.
    197207
    198208
  • plugins/base1/se.lu.thep.wenni/trunk/base/base2/Makefile.am

    r856 r858  
    2525SUBDIR = se/lu/thep/wenni
    2626BUILDDIR = $(TOPBUILDDIR)/$(SUBDIR)
     27MANIFEST_FILE = "$(TOPBUILDDIR)/META-INF/MANIFEST.MF"
    2728
    2829JAVA = WeNNI.java
     
    5354  $(INSTALL) "$(PLUGINutilities)/$(PLUGINutilities).jar" "$(PLUGINDIR)"
    5455
    55 $(JAR): $(BUILDDIR) $(PLUGINutilities) $(DOWNLOADDEP) $(CLASS)
     56$(JAR): $(BUILDDIR) $(PLUGINutilities) $(DOWNLOADDEP) $(CLASS) manifest
    5657  @echo Creating $(JAR)
    57   @(cd $(TOPBUILDDIR) ; \
    58     jar cf ../$(JAR) $(SUBDIR)/*.class)
     58  @(cd $(TOPBUILDDIR) ; jar cf ../$(JAR) .)
     59
     60manifest: $(TOPBUILDDIR)
     61  @$(MKDIR_P) $(TOPBUILDDIR)/META-INF
     62  @echo "Manifest-Version: 1.0" > "$(MANIFEST_FILE)"
     63  @echo "Class-Path: $(PLUGINutilities).jar" >> $(MANIFEST_FILE)
    5964
    6065$(BUILDDIR)/$(JAVA): $(srcdir)/$(JAVA) Makefile
     
    6570
    6671$(BUILDDIR):
     72  @$(MKDIR_P) $@
     73
     74$(TOPBUILDDIR):
    6775  @$(MKDIR_P) $@
    6876
  • plugins/base1/se.lu.thep.wenni/trunk/base/base2/WeNNI.java

    r844 r858  
    33
    44  Copyright (C) 2007 Peter Johansson
     5  Copyright (C) 2008 Jari Häkkinen
    56 
    6   This file is part of BASEPlugIns - Non-core plug-ins for BASE,
    7   BioArray Software Environment.
    8   BASEPlugIns is available at http://baseplugins.thep.lu.se/
    9   BASE is available at http://base.thep.lu.se/
     7  This file is part of WeNNI,
     8  http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI
    109
    11   BASEPlugIns is free software; you can redistribute it and/or modify
    12   it under the terms of the GNU General Public License as published by
     10  WeNNI is free software; you can redistribute it and/or modify it
     11  under the terms of the GNU General Public License as published by
    1312  the Free Software Foundation; either version 3 of the License, or
    1413  (at your option) any later version.
    1514
    16   BASEPlugIns is distributed in the hope that it will be useful, but
    17   WITHOUT ANY WARRANTY; without even the implied warranty of
    18   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    19   General Public License for more details.
     15  WeNNI is distributed in the hope that it will be useful, but WITHOUT
     16  ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
     17  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
     18  License for more details.
    2019
    2120  You should have received a copy of the GNU General Public License
     
    3231import net.sf.basedb.core.RawBioAssay;
    3332
    34 import net.sf.basedb.core.plugin.About;
    3533import net.sf.basedb.core.plugin.AboutImpl;
     34import net.sf.basedb.core.plugin.Plugin;
    3635
    3736import java.io.IOException;
     
    4039
    4140/**
    42    This plugin provides means to calculate the fold changes for a root bioassayset
    43    using PLIER. It needs the following parameters:
     41   WeNNI plug-in. An Unreliable expression value of a gene is imputed
     42   as the average expression in the most similar genes.
    4443
    45    <pre>
    46    String              : name; The name of the new bioassayset.
    47    Experiment          : experiment; The experiment we are working on.
    48    List&gt;RawBioAssay&lt;   : rawBioAssays; The raw bioassays to create bioassays for
    49                          (must be part of the experiment).
    50    </pre>
     44   The method is published in "Improving missing value imputation of
     45   microarray data by using spot quality weights", P. Johansson and
     46   J. Häkkinen. BMC Bioinformatics 7, 306 (2006)
    5147
    52    @author Peter Johansson
     48   @author Jari Häkkinen, Peter Johansson
    5349   @version MAKESUBSTOFVERSIONNUMBER
     50   @since BASE 2.9
    5451   @base.modified $Date$
    5552*/
     
    5956{
    6057
    61   public WeNNI() {}
    62 
    63   public About getAbout() { return about; }
     58  public WeNNI() {
     59    // set about information
     60    about = new AboutImpl
     61      ( "WeNNI plug-in", "An Unreliable expression value of a gene is " +
     62        "imputed as the average expression in the most similar genes.\n" +
     63        "\nThe method is published in \"Improving missing value imputation " +
     64        "of microarray data by using spot quality weights\", P. Johansson " +
     65        "and J. Häkkinen. BMC Bioinformatics 7, 306 (2006)",
     66        "Version: MAKESUBSTOFVERSIONNUMBER $Revision$ " +
     67        "$Date$",
     68        "2008 Jari Häkkinen, Peter Johansson",
     69        null, null,
     70        "http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI" );
     71    // set the type of the plug-in
     72    plugin_maintype=Plugin.MainType.ANALYZE;
     73  }
    6474
    6575
     
    7787  }
    7888
    79 
    80 
    81 
    82 
    83   private static final About about = new AboutImpl
    84     ("WeNNI plug-in", "An Unreliable expression value of a gene is " +
    85      "imputed as the average expression in the most similar genes.",
    86      "Version: MAKESUBSTOFVERSIONNUMBER $Revision$ " +
    87      "$Date$",
    88      "2007 Peter Johansson, " +
    89      "Department of Theoretical Physics, Lund University",
    90      null, null,
    91      "http://baseplugins.thep.lu.se/wiki/WeNNI" );
    9289}
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