renamed

diff --git a/forester/java/src/org/forester/application/shin.java b/forester/java/src/org/forester/application/sdix.java
similarity index 97%
rename from forester/java/src/org/forester/application/shin.java
rename to forester/java/src/org/forester/application/sdix.java
index 5e03b47..a14d459 100644 (file)
--- a/forester/java/src/org/forester/application/shin.java
+++ b/forester/java/src/org/forester/application/sdix.java
@@ -36,16 +36,15 @@ import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sdi.Shin;
+import org.forester.sdi.SDIx;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.ForesterUtil;
 
-public class shin {
+public class sdix {
 
     final static private String HELP_OPTION_1   = "help";
     final static private String HELP_OPTION_2   = "h";
-    final static private String DEFAULT_OUTFILE = "out";
-    final static private String PRG_NAME        = "shin";
+    final static private String PRG_NAME        = "sdix";
     final static private String PRG_VERSION     = "0.001 alpha";
     final static private String PRG_DATE        = "2009.10.14";
 
@@ -140,7 +139,7 @@ public class shin {
         }
         ForesterUtil.programMessage( PRG_NAME, "going to analyze " + gene_tree_files.size() + " gene trees from ["
                 + gene_trees_dir + "]" );
-        final Shin shin = new Shin();
+        final SDIx shin = new SDIx();
         try {
             shin.method1( gene_tree_files, species_trees, out_dir );
         }

diff --git a/forester/java/src/org/forester/application/perfume.java b/forester/java/src/org/forester/application/simple_node_processor.java
similarity index 98%
rename from forester/java/src/org/forester/application/perfume.java
rename to forester/java/src/org/forester/application/simple_node_processor.java
index a24f0a6..399f9f2 100644 (file)
--- a/forester/java/src/org/forester/application/perfume.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -36,7 +36,7 @@ import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.CommandLineArguments;
 
-public class perfume {
+public class simple_node_processor {
 
     private final static String BASE = "b_";
 

diff --git a/forester/java/src/org/forester/sdi/Shin.java b/forester/java/src/org/forester/sdi/SDIx.java
similarity index 99%
rename from forester/java/src/org/forester/sdi/Shin.java
rename to forester/java/src/org/forester/sdi/SDIx.java
index 436e8d5..d7786c0 100644 (file)
--- a/forester/java/src/org/forester/sdi/Shin.java
+++ b/forester/java/src/org/forester/sdi/SDIx.java
@@ -43,9 +43,9 @@ import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 
-public class Shin {
+public class SDIx {
 
-    public Shin() {
+    public SDIx() {
     }
 
     private void analyze( final Phylogeny gene_tree,