From be90bb1fc9228c4b2939b5603da38a5638f9fae0 Mon Sep 17 00:00:00 2001 From: Alex Aiezza Date: Thu, 5 May 2016 13:49:45 -0400 Subject: [PATCH] ByteBufferOutputStream and HexPrinter are only used by in the edu.rit.flick.genetics package Since they are only used there, they should sub-package it instead of being at such a high level in the project. --- src/edu/rit/flick/genetics/FastFileDeflator.java | 2 +- src/edu/rit/flick/genetics/FastFileInflator.java | 2 +- src/edu/rit/flick/genetics/FastaFileDeflator.java | 2 +- src/edu/rit/flick/genetics/FastaFileInflator.java | 2 +- src/edu/rit/flick/genetics/FastqFileDeflator.java | 4 ++-- .../rit/{ => flick/genetics}/util/ByteBufferOutputStream.java | 2 +- src/edu/rit/{ => flick/genetics}/util/HexPrinter.java | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) rename src/edu/rit/{ => flick/genetics}/util/ByteBufferOutputStream.java (96%) rename src/edu/rit/{ => flick/genetics}/util/HexPrinter.java (93%) diff --git a/src/edu/rit/flick/genetics/FastFileDeflator.java b/src/edu/rit/flick/genetics/FastFileDeflator.java index e68c2a8..8115857 100644 --- a/src/edu/rit/flick/genetics/FastFileDeflator.java +++ b/src/edu/rit/flick/genetics/FastFileDeflator.java @@ -30,7 +30,7 @@ import edu.rit.flick.FileDeflator; import edu.rit.flick.config.Configuration; -import edu.rit.util.ByteBufferOutputStream; +import edu.rit.flick.genetics.util.ByteBufferOutputStream; import it.unimi.dsi.io.ByteBufferInputStream; import net.lingala.zip4j.core.ZipFile; import net.lingala.zip4j.exception.ZipException; diff --git a/src/edu/rit/flick/genetics/FastFileInflator.java b/src/edu/rit/flick/genetics/FastFileInflator.java index 5d5a9d7..bd33ec0 100644 --- a/src/edu/rit/flick/genetics/FastFileInflator.java +++ b/src/edu/rit/flick/genetics/FastFileInflator.java @@ -29,7 +29,7 @@ import edu.rit.flick.FileInflator; import edu.rit.flick.config.Configuration; -import edu.rit.util.ByteBufferOutputStream; +import edu.rit.flick.genetics.util.ByteBufferOutputStream; import it.unimi.dsi.io.ByteBufferInputStream; import it.unimi.dsi.lang.MutableString; import net.lingala.zip4j.core.ZipFile; diff --git a/src/edu/rit/flick/genetics/FastaFileDeflator.java b/src/edu/rit/flick/genetics/FastaFileDeflator.java index 7b5eebc..2ea7f3e 100644 --- a/src/edu/rit/flick/genetics/FastaFileDeflator.java +++ b/src/edu/rit/flick/genetics/FastaFileDeflator.java @@ -17,7 +17,7 @@ import java.util.Collections; import java.util.List; -import edu.rit.util.ByteBufferOutputStream; +import edu.rit.flick.genetics.util.ByteBufferOutputStream; /** * @author Alex Aiezza diff --git a/src/edu/rit/flick/genetics/FastaFileInflator.java b/src/edu/rit/flick/genetics/FastaFileInflator.java index 37db442..44b5fe7 100644 --- a/src/edu/rit/flick/genetics/FastaFileInflator.java +++ b/src/edu/rit/flick/genetics/FastaFileInflator.java @@ -15,7 +15,7 @@ import java.util.Scanner; import java.util.StringTokenizer; -import edu.rit.util.HexPrinter; +import edu.rit.flick.genetics.util.HexPrinter; /** * @author Alex Aiezza diff --git a/src/edu/rit/flick/genetics/FastqFileDeflator.java b/src/edu/rit/flick/genetics/FastqFileDeflator.java index a6872df..5825450 100644 --- a/src/edu/rit/flick/genetics/FastqFileDeflator.java +++ b/src/edu/rit/flick/genetics/FastqFileDeflator.java @@ -18,8 +18,8 @@ import java.util.Collections; import java.util.List; -import edu.rit.util.ByteBufferOutputStream; -import edu.rit.util.HexPrinter; +import edu.rit.flick.genetics.util.ByteBufferOutputStream; +import edu.rit.flick.genetics.util.HexPrinter; /** * @author Alex Aiezza diff --git a/src/edu/rit/util/ByteBufferOutputStream.java b/src/edu/rit/flick/genetics/util/ByteBufferOutputStream.java similarity index 96% rename from src/edu/rit/util/ByteBufferOutputStream.java rename to src/edu/rit/flick/genetics/util/ByteBufferOutputStream.java index f657d42..2de08c2 100644 --- a/src/edu/rit/util/ByteBufferOutputStream.java +++ b/src/edu/rit/flick/genetics/util/ByteBufferOutputStream.java @@ -4,7 +4,7 @@ * See the LICENSE for the specific language governing permissions and * limitations under the License provided with this project. */ -package edu.rit.util; +package edu.rit.flick.genetics.util; import java.io.File; import java.io.IOException; diff --git a/src/edu/rit/util/HexPrinter.java b/src/edu/rit/flick/genetics/util/HexPrinter.java similarity index 93% rename from src/edu/rit/util/HexPrinter.java rename to src/edu/rit/flick/genetics/util/HexPrinter.java index 275900c..b692748 100644 --- a/src/edu/rit/util/HexPrinter.java +++ b/src/edu/rit/flick/genetics/util/HexPrinter.java @@ -4,7 +4,7 @@ * See the LICENSE for the specific language governing permissions and * limitations under the License provided with this project. */ -package edu.rit.util; +package edu.rit.flick.genetics.util; import static java.lang.Integer.toHexString;