From 5c494e04b1cb40db2f1ac11c9dd9f459c9fab7f5 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Mon, 10 Dec 2012 01:39:33 +0000 Subject: [PATCH] rio, refactoring --- forester/java/src/org/forester/application/rio.java | 4 ++-- forester/java/src/org/forester/{sdi => rio}/RIO.java | 4 +++- forester/java/src/org/forester/{sdi => rio}/RIOException.java | 2 +- forester/java/src/org/forester/test/Test.java | 2 +- 4 files changed, 7 insertions(+), 5 deletions(-) rename forester/java/src/org/forester/{sdi => rio}/RIO.java (99%) rename forester/java/src/org/forester/{sdi => rio}/RIOException.java (91%) diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index ad0c33a..7d7632c 100644 --- 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 --- 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 --- 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 --- 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; -- 1.7.10.2