Changeset 858

Timestamp:

Dec 2, 2008, 4:33:59 PM (15 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:

• INSTALL (modified) (1 diff)
• base/base2/Makefile.am (modified) (3 diffs)
• base/base2/WeNNI.java (modified) (5 diffs)

plugins/base1/se.lu.thep.wenni/trunk/INSTALL

@@ -190 +190 @@
     $ make install-plugin
     }}}
+    If you prefer to install the plug-in manually you must place
+    `nni`, `WeNNI.jar`, and `PluginUtilities-0.1pre.jar` in the same
+    installation directory.
+    [[br]] [[br]]
     Note! `make install` will install in location `${exec_prefix}/bin`
-    which maybe something else than the BASE plugin directory.
+    which may be something else than your BASE plugin directory.
 
  6. Make BASE2 aware of the plugin, see BASE2 documentation
-    http://base.thep.lu.se/chrome/site/doc/html/index.html
+    http://base.thep.lu.se/chrome/site/doc/html/index.html and use
+    the below information with appropriate change of Path
+    {{{
+    Class: se.lu.thep.wenni.WeNNI
+    Path : /path/to/base/pluginsse/lu/thep/wenni-0.7/WeNNI.jar
+    }}}
+    Path should be the absolute path to the WeNNI.jar file.
 
 

plugins/base1/se.lu.thep.wenni/trunk/base/base2/Makefile.am

@@ -25 +25 @@
 SUBDIR = se/lu/thep/wenni
 BUILDDIR = $(TOPBUILDDIR)/$(SUBDIR)
+MANIFEST_FILE = "$(TOPBUILDDIR)/META-INF/MANIFEST.MF"
 
 JAVA = WeNNI.java 
@@ -53 +54 @@
   $(INSTALL) "$(PLUGINutilities)/$(PLUGINutilities).jar" "$(PLUGINDIR)"
 
-$(JAR): $(BUILDDIR) $(PLUGINutilities) $(DOWNLOADDEP) $(CLASS)
+$(JAR): $(BUILDDIR) $(PLUGINutilities) $(DOWNLOADDEP) $(CLASS) manifest
   @echo Creating $(JAR)
-  @(cd $(TOPBUILDDIR) ; \
-    jar cf ../$(JAR) $(SUBDIR)/*.class)
+  @(cd $(TOPBUILDDIR) ; jar cf ../$(JAR) .)
+
+manifest: $(TOPBUILDDIR)
+  @$(MKDIR_P) $(TOPBUILDDIR)/META-INF
+  @echo "Manifest-Version: 1.0" > "$(MANIFEST_FILE)"
+  @echo "Class-Path: $(PLUGINutilities).jar" >> $(MANIFEST_FILE)
 
 $(BUILDDIR)/$(JAVA): $(srcdir)/$(JAVA) Makefile
@@ -65 +70 @@
 
 $(BUILDDIR):
+  @$(MKDIR_P) $@
+
+$(TOPBUILDDIR):
   @$(MKDIR_P) $@
 

plugins/base1/se.lu.thep.wenni/trunk/base/base2/WeNNI.java

@@ -3 +3 @@
 
   Copyright (C) 2007 Peter Johansson
+  Copyright (C) 2008 Jari Häkkinen
   
-  This file is part of BASEPlugIns - Non-core plug-ins for BASE,
-  BioArray Software Environment.
-  BASEPlugIns is available at http://baseplugins.thep.lu.se/
-  BASE is available at http://base.thep.lu.se/
+  This file is part of WeNNI,
+  http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI
 
-  BASEPlugIns is free software; you can redistribute it and/or modify
-  it under the terms of the GNU General Public License as published by
+  WeNNI is free software; you can redistribute it and/or modify it
+  under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 3 of the License, or
   (at your option) any later version.
 
-  BASEPlugIns is distributed in the hope that it will be useful, but
-  WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  General Public License for more details.
+  WeNNI is distributed in the hope that it will be useful, but WITHOUT
+  ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
+  License for more details.
 
   You should have received a copy of the GNU General Public License
@@ -32 +31 @@
 import net.sf.basedb.core.RawBioAssay;
 
-import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
+import net.sf.basedb.core.plugin.Plugin;
 
 import java.io.IOException;
@@ -40 +39 @@
 
 /**
-   This plugin provides means to calculate the fold changes for a root bioassayset 
-   using PLIER. It needs the following parameters:
+   WeNNI plug-in. An Unreliable expression value of a gene is imputed
+   as the average expression in the most similar genes.
 
-   <pre>
-   String              : name; The name of the new bioassayset.
-   Experiment          : experiment; The experiment we are working on.
-   List&gt;RawBioAssay&lt;   : rawBioAssays; The raw bioassays to create bioassays for
-                         (must be part of the experiment).
-   </pre>
+   The method is published in "Improving missing value imputation of
+   microarray data by using spot quality weights", P. Johansson and
+   J. Häkkinen. BMC Bioinformatics 7, 306 (2006)
 
-   @author Peter Johansson
+   @author Jari Häkkinen, Peter Johansson
    @version MAKESUBSTOFVERSIONNUMBER
+   @since BASE 2.9
    @base.modified $Date$
 */
@@ -59 +56 @@
 {
 
-  public WeNNI() {}
-
-  public About getAbout() { return about; }
+  public WeNNI() {
+    // set about information
+    about = new AboutImpl
+      ( "WeNNI plug-in", "An Unreliable expression value of a gene is " +
+        "imputed as the average expression in the most similar genes.\n" +
+        "\nThe method is published in \"Improving missing value imputation " +
+        "of microarray data by using spot quality weights\", P. Johansson " +
+        "and J. Häkkinen. BMC Bioinformatics 7, 306 (2006)",
+        "Version: MAKESUBSTOFVERSIONNUMBER $Revision$ " +
+        "$Date$",
+        "2008 Jari Häkkinen, Peter Johansson",
+        null, null,
+        "http://baseplugins.thep.lu.se/wiki/se.lu.thep.WeNNI" );
+    // set the type of the plug-in
+    plugin_maintype=Plugin.MainType.ANALYZE;
+  }
 
 
@@ -77 +87 @@
   }
 
-
-
-
-
-  private static final About about = new AboutImpl
-    ("WeNNI plug-in", "An Unreliable expression value of a gene is " +
-     "imputed as the average expression in the most similar genes.",
-     "Version: MAKESUBSTOFVERSIONNUMBER $Revision$ " +
-     "$Date$",
-     "2007 Peter Johansson, " +
-     "Department of Theoretical Physics, Lund University",
-     null, null,
-     "http://baseplugins.thep.lu.se/wiki/WeNNI" );
 }