Changeset 2176

Timestamp:

Dec 12, 2013, 11:39:47 AM (9 years ago)

Author:

Jari Häkkinen

Message:

Changes from release procedure and other minor things.

Location:

plugins/base2/net.sf.basedb.normalizers/trunk

Files:

• INSTALL (modified) (2 diffs)
• META-INF/extensions.xml (modified) (4 diffs)
• build.xml (modified) (1 diff)
• src/net/sf/basedb/normalizers/Normalizations.java (modified) (1 diff)

plugins/base2/net.sf.basedb.normalizers/trunk/INSTALL

@@ -5 +5 @@
 Copyright (C) 2008, 2009 Jari Häkkinen, Martin Svensson
 Copyright (C) 2010 Jari Häkkinen
+Copyright (C) 2011 Nicklas Nordborg
+Copyright (C) 2013 Jari Häkkinen
 
 This file is part of the Normalizers plug-in package for BASE
@@ -32 +34 @@
 == Requirements ==
 
- 1. BASE 3.0 or later.
+ 1. BASE 3.2.4 or later.
 
 == Installation/Upgrade ==

plugins/base2/net.sf.basedb.normalizers/trunk/META-INF/extensions.xml

@@ -1 +1 @@
 <?xml version="1.0" encoding="UTF-8" ?>
+<!--
+    $Id$
+
+    Copyright (C) 2011 Nicklas Nordborg
+    Copyright (C) 2013 Jari Häkkinen, Olle Månsson
+
+    This file is part of the Normalizers plug-in package for BASE
+    (net.sf.based.normalizers). The package is available at
+    http://baseplugins.thep.lu.se/ BASE main site is
+    http://base.thep.lu.se/
+
+    This 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.
+
+    The software 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
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
+
 <extensions xmlns="http://base.thep.lu.se/extensions.xsd">
   <about>
@@ -10 +35 @@
       used.
     </description>
-    <version>1.1-beta</version>
+    <version>1.1-beta2</version>
     <min-base-version>3.2.4</min-base-version>
     <copyright>BASE development team</copyright>
@@ -50 +75 @@
         rows will contain mixed probes (also known as reporters or genes) 
         decided by their rank. For each row in the matrix, the expression 
-        values are replaced with the row average value. Finally, each assay 
+        values are replaced with the row average value (geometric or 
+        arithmetic selectable by user). Finally, each assay is 
         is reordered into its original order to retain a standard 
         expression matrix where each row represents one probe. Assays are 
@@ -58 +84 @@
         bioassay set before running this plug-in. The bioassay set must not 
         contain any missing values.
-        
-        Data stored in logarithmic format will be untransformed before averaging,
-        and then transformed back to logarithmic format before results are stored.
         
         This plug-in supports 1-channel and 2-channel data.

plugins/base2/net.sf.basedb.normalizers/trunk/build.xml

@@ -56 +56 @@
   <!-- variables used -->  
   <property name="name" value="normalization-plugins" />  
-  <property name="version" value="1.1-beta" description="Version number of the package" />
+  <property name="version" value="1.1-beta2"  description="Version number of the package" />
   <property name="src" value="src" />
   <property name="build" value="build" description="Location of build class files"/>  

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/normalizers/Normalizations.java

@@ -36 +36 @@
     The current version of this package.
   */
-  public static final String VERSION = "1.1-beta";
+  public static final String VERSION = "1.1-beta2";
   
 }