rio, refactoring

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index ad0c33a..7d7632c 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -39,8 +39,8 @@ 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.RIO;
-import org.forester.sdi.RIOException;
+import org.forester.rio.RIO;
+import org.forester.rio.RIOException;
 import org.forester.sdi.SDIException;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.EasyWriter;

diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/rio/RIO.java
similarity index 99%
rename from forester/java/src/org/forester/sdi/RIO.java
rename to forester/java/src/org/forester/rio/RIO.java
index 25adc9d..c2cea38 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -25,7 +25,7 @@
 // Contact: phylosoft @ gmail . com
 // WWW: www.phylosoft.org/forester
 
-package org.forester.sdi;
+package org.forester.rio;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -47,6 +47,8 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sdi.SDIException;
+import org.forester.sdi.SDIR;
 import org.forester.util.ForesterUtil;
 
 public final class RIO {

diff --git a/forester/java/src/org/forester/sdi/RIOException.java b/forester/java/src/org/forester/rio/RIOException.java
similarity index 91%
rename from forester/java/src/org/forester/sdi/RIOException.java
rename to forester/java/src/org/forester/rio/RIOException.java
index b9b7eb6..44114c2 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIOException.java
+++ b/forester/java/src/org/forester/rio/RIOException.java
@@ -1,5 +1,5 @@
 
-package org.forester.sdi;
+package org.forester.rio;
 
 public class RIOException extends Exception {
 

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index b1bb3c6..19d01c1 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -87,8 +87,8 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.protein.Protein;
+import org.forester.rio.RIO;
 import org.forester.sdi.GSDI;
-import org.forester.sdi.RIO;
 import org.forester.sdi.SDI;
 import org.forester.sdi.SDIR;
 import org.forester.sdi.SDIse;