IOUtils moved to bg-commons

chris-zen · chris-zen · commit 7e5a397bb0e7 · 2010-07-08T08:53:14.000Z
git-svn-id: https://bg.upf.edu/svn/gitools/trunk@912 1b512f91-3386-4a98-81e7-b8836ddf8916
diff --git a/bg-commons/src/main/java/edu/upf/bg/fileutils/IOUtils.java b/bg-commons/src/main/java/edu/upf/bg/fileutils/IOUtils.java
@@ -1,5 +1,6 @@
-package org.gitools.utils;
+package edu.upf.bg.fileutils;
 
+import java.io.BufferedOutputStream;
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
 import java.io.File;
@@ -16,7 +17,6 @@
 import java.io.Reader;
 import java.io.Writer;
 import java.nio.ByteBuffer;
-import java.nio.channels.Channel;
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.ReadableByteChannel;
@@ -26,40 +26,58 @@
 
 public class IOUtils {
 
-	public static Reader openReader(File path) throws FileNotFoundException, IOException {
+	public static Reader openReader(File path) throws IOException {
 		if (path == null)
 			return null;
-		
+
 		if (path.getName().endsWith(".gz"))
 			return
 				new InputStreamReader(
 					new GZIPInputStream(
 							new FileInputStream(path)));
 		else
-			return 
+			return
 				new BufferedReader(
 					new FileReader(path));
 	}
-	
-	public static Writer openWriter(File path) throws FileNotFoundException, IOException {
+
+	public static Writer openWriter(File path) throws IOException {
 		return openWriter(path, false);
 	}
-	
-	public static Writer openWriter(File path, boolean append) throws FileNotFoundException, IOException {
+
+	public static Writer openWriter(File path, boolean append) throws IOException {
 		if (path == null)
 			return null;
-		
+
 		if (path.getName().endsWith(".gz"))
 			return
 				new OutputStreamWriter(
 					new GZIPOutputStream(
 							new FileOutputStream(path, append)));
 		else
-			return 
+			return
 				new BufferedWriter(
 					new FileWriter(path, append));
 	}
 
+	public static OutputStream openOutputStream(File path) throws IOException {
+		return openOutputStream(path, false);
+	}
+
+	public static OutputStream openOutputStream(File path, boolean append) throws IOException {
+		if (path == null)
+			return null;
+
+		if (path.getName().endsWith(".gz"))
+			return
+				new GZIPOutputStream(
+						new FileOutputStream(path, append));
+		else
+			return
+				new BufferedOutputStream(
+					new FileOutputStream(path, append));
+	}
+
 	public static void copyFile(File sourceFile, File destFile) throws IOException {
 		if (!destFile.exists()) {
 			destFile.createNewFile();
diff --git a/deploy.sh b/deploy.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+mvn package install assembly:assembly -DskipTests=true
+
diff --git a/gitools-core/pom.xml b/gitools-core/pom.xml
@@ -45,9 +45,9 @@
 		</dependency>
 
 		<dependency>
-          <groupId>weka</groupId>
-          <artifactId>weka</artifactId>
-          <version>3.6.2</version>
+			<groupId>weka</groupId>
+			<artifactId>weka</artifactId>
+			<version>3.6.2</version>
 		</dependency>
 	</dependencies>
 
diff --git a/gitools-core/src/main/java/org/gitools/exporter/TextMatrixViewExporter.java b/gitools-core/src/main/java/org/gitools/exporter/TextMatrixViewExporter.java
@@ -7,7 +7,7 @@
 
 import org.gitools.matrix.model.IMatrixView;
 import org.gitools.matrix.model.element.IElementAttribute;
-import org.gitools.utils.IOUtils;
+import edu.upf.bg.fileutils.IOUtils;
 
 public class TextMatrixViewExporter {
 
diff --git a/gitools-core/src/main/java/org/gitools/persistence/PersistenceUtils.java b/gitools-core/src/main/java/org/gitools/persistence/PersistenceUtils.java
@@ -1,78 +1,33 @@
 package org.gitools.persistence;
 
-import java.io.BufferedOutputStream;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
+import edu.upf.bg.fileutils.IOUtils;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 import java.io.Reader;
 import java.io.Writer;
 import java.util.regex.Pattern;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
 
 public class PersistenceUtils {
 
 	public static Reader openReader(File path) throws IOException {
-		if (path == null)
-			return null;
-		
-		if (path == null)
-			return null;
-		
-		if (path.getName().endsWith(".gz"))
-			return
-				new InputStreamReader(
-					new GZIPInputStream(
-							new FileInputStream(path)));
-		else
-			return 
-				new BufferedReader(
-					new FileReader(path));
+		return IOUtils.openReader(path);
 	}
 	
 	public static Writer openWriter(File path) throws IOException {
-		return openWriter(path, false);
+		return IOUtils.openWriter(path);
 	}
 	
 	public static Writer openWriter(File path, boolean append) throws IOException {
-		if (path == null)
-			return null;
-		
-		if (path.getName().endsWith(".gz"))
-			return
-				new OutputStreamWriter(
-					new GZIPOutputStream(
-							new FileOutputStream(path, append)));
-		else
-			return 
-				new BufferedWriter(
-					new FileWriter(path, append));
+		return IOUtils.openWriter(path, append);
 	}
 
 	public static OutputStream openOutputStream(File path) throws IOException {
-		return openOutputStream(path, false);
+		return IOUtils.openOutputStream(path);
 	}
 
 	public static OutputStream openOutputStream(File path, boolean append) throws IOException {
-		if (path == null)
-			return null;
-
-		if (path.getName().endsWith(".gz"))
-			return
-				new GZIPOutputStream(
-						new FileOutputStream(path, append));
-		else
-			return
-				new BufferedOutputStream(
-					new FileOutputStream(path, append));
+		return IOUtils.openOutputStream(path, append);
 	}
 
 	// Copied from http://stackoverflow.com/questions/204784/how-to-construct-a-relative-path-in-java-from-two-absolute-paths-or-urls

-Original file line number
+Diff line change
@@ @@ -0,0 +1,4 @@ @@
 +#!/bin/bash
++
 +mvn package install assembly:assembly -DskipTests=true
++