Refactor to avoid deprecated API of commons-cli.

CHANGELOG

@@ -1,13 +1,14 @@
-MelodyShape 1.4, XX-Aug-2016
+MelodyShape 1.4, 08-Aug-2016
 ============================
 * Changed to MIT License.
++ Use Maven to build.
 
 MelodyShape 1.3, 25-Oct-2015
 ============================
 + Added support for the MIREX 2015 submissions.
-* Fixed #5: enclose erroneous arguments in single quotes.
-* Fixed #4: show the name of files that fail to load.
-* Fixed #2: alignment score in LocalAligner.
+- Fixed #5: enclose erroneous arguments in single quotes.
+- Fixed #4: show the name of files that fail to load.
+- Fixed #2: alignment score in LocalAligner.
 
 MelodyShape 1.2, 21-Oct-2014
 ============================

README.md

@@ -7,8 +7,8 @@ All these algorithms have obtained the best results in the [MIREX](http://music-
 
 MelodyShape can be run both as a graphical user interface and as a command line tool:
 
-	$ java -jar melodyshape-1.3.jar
-	usage: melodyshape-1.3 -q <file/dir> -c <dir> -a <name> [-k <cutoff>] [-l] [-t <num>] [-v] [-vv] [-gui] [-h]
+	$ java -jar melodyshape-1.4.jar
+	usage: melodyshape-1.4 -q <file/dir> -c <dir> -a <name> [-k <cutoff>] [-l] [-t <num>] [-v] [-vv] [-gui] [-h]
 	-q <file/dir>  path to the query melody or melodies.
 	-c <dir>       path to the collection of documents.
 	-a <name>      algorithm to run:
@@ -26,7 +26,7 @@ MelodyShape can be run both as a graphical user interface and as a command line
 	-gui           run with graphical user interface.
 	-h             show this help message.
 
-	MelodyShape 1.3  Copyright (C) 2013-2016  Julian Urbano <[email protected]>
+	MelodyShape 1.4  Copyright (C) 2013-2016  Julian Urbano <[email protected]>
 	This program is distributed under the terms of the MIT License.
 
 A detailed user manual in PDF is available from the [releases page](https://github.com/julian-urbano/MelodyShape/releases).
@@ -37,7 +37,9 @@ Dependencies
 * The MelodyShape library uses the [Math library](http://commons.apache.org/proper/commons-math/) from Apache Commons.
 * The command line tool uses the [CLI library](http://commons.apache.org/proper/commons-cli/) from Apache Commons.
 
+Dependencies and building can be managed directly with Maven.
+
 Current Version
 ---------------
 
-The current version is [MelodyShape 1.3](https://github.com/julian-urbano/MelodyShape/releases/tag/v1.3), and it is compiled for Java 7. It can be redistributed and/or modified under the terms of the MIT License. Javadoc documentation and a user manual are available as well.
+The current version is [MelodyShape 1.4](https://github.com/julian-urbano/MelodyShape/releases/tag/v1.4), and it is compiled for Java 7. It can be redistributed and/or modified under the terms of the MIT License. Javadoc documentation and a user manual are available as well.

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>jurbano</groupId>
     <artifactId>melodyshape</artifactId>
-    <version>1.3</version>
+    <version>1.4</version>
     <name>MelodyShape</name>
     <description>A Library and Tool for Symbolic Melodic Similarity based on Shape Similarity</description>
     <url>https://github.com/julian-urbano/MelodyShape</url>

src/jurbano/melodyshape/MelodyShape.java

@@ -41,7 +41,7 @@ public class MelodyShape
 	/**
 	 * The release version number.
 	 */
-	public static String VERSION = "1.3";
+	public static String VERSION = "1.4";
 	/**
 	 * The copyright notice, including date and version.
 	 */
@@ -91,7 +91,7 @@ public static ArrayList<Melody> readQueries(File path) {
 
 	/**
 	 * Returns a melody collection found in a path.
-	 * 
+	 *
 	 * @param path
 	 *            the path to the directory containing all melodies.
 	 * @return the melody collection.

src/jurbano/melodyshape/ranking/UntieResultRanker.java

@@ -3,12 +3,12 @@
 
 package jurbano.melodyshape.ranking;
 
-import java.util.Arrays;
-import java.util.Comparator;
-
 import jurbano.melodyshape.comparison.MelodyComparer;
 import jurbano.melodyshape.model.Melody;
 
+import java.util.Arrays;
+import java.util.Comparator;
+
 /**
  * A ranking function that sorts by decreasing similarity score, then by
  * decreasing similarity according to a second {@link MelodyComparer}, then by

src/jurbano/melodyshape/ui/ConsoleUIObserver.java

@@ -3,29 +3,17 @@
 
 package jurbano.melodyshape.ui;
 
-import java.io.File;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Locale;
-
-import org.apache.commons.cli.BasicParser;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-
 import jurbano.melodyshape.MelodyShape;
 import jurbano.melodyshape.comparison.MelodyComparer;
 import jurbano.melodyshape.model.Melody;
 import jurbano.melodyshape.model.MelodyCollection;
 import jurbano.melodyshape.ranking.Result;
 import jurbano.melodyshape.ranking.ResultRanker;
+import org.apache.commons.cli.*;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.*;
 
 /**
  * Runs an algorithm with options specified through the command line.
@@ -68,29 +56,25 @@ public ConsoleUIObserver(String[] args) {
 
 		this.options = new Options();
 		// required arguments
-		this.options.addOption(OptionBuilder.isRequired().hasArg().withArgName("file/dir")
-				.withDescription("path to the query melody or melodies.").create("q"));
-		this.options.addOption(OptionBuilder.isRequired().hasArg().withArgName("dir")
-				.withDescription("path to the collection of documents.").create("c"));
-		this.options.addOption(OptionBuilder.isRequired().hasArg().withArgName("name")
-				.withDescription(
-						"algorithm to run:" + "\n- 2010-domain, 2010-pitchderiv, 2010-shape"
+		this.options.addOption(Option.builder("q").required().hasArg().argName("file/dir")
+				.desc("path to the query melody or melodies.").build());
+		this.options.addOption(Option.builder("c").required().hasArg().argName("dir")
+				.desc("path to the collection of documents.").build());
+		this.options.addOption(Option.builder("a").required().hasArg().argName("name")
+				.desc("algorithm to run:" + "\n- 2010-domain, 2010-pitchderiv, 2010-shape"
 								+ "\n- 2011-shape, 2011-pitch, 2011-time"
 								+ "\n- 2012-shapeh, 2012-shapel, 2012-shapeg, 2012-time, 2012-shapetime"
 								+ "\n- 2013-shapeh, 2013-time, 2013-shapetime"
 								+ "\n- 2014-shapeh, 2014-time, 2014-shapetime"
-								+ "\n- 2015-shapeh, 2015-time, 2015-shapetime").create("a"));
+								+ "\n- 2015-shapeh, 2015-time, 2015-shapetime").build());
 		// optional arguments
-		this.options.addOption(OptionBuilder
-				.withDescription("show results in a single line (omits similarity scores).").create("l"));
-		this.options.addOption(OptionBuilder.hasArg().withArgName("num")
-				.withDescription("run a fixed number of threads.").create("t"));
-		this.options.addOption(OptionBuilder.hasArg().withArgName("cutoff")
-				.withDescription("number of documents to retrieve.").create("k"));
-		this.options.addOption(OptionBuilder.withDescription("verbose, to stderr.").create("v"));
-		this.options.addOption(OptionBuilder.withDescription("verbose a lot, to stderr.").create("vv"));
-		this.options.addOption(OptionBuilder.withDescription("show this help message.").create("h"));
-		this.options.addOption(OptionBuilder.withDescription("run with graphical user interface.").create("gui"));
+		this.options.addOption(Option.builder("l").desc("show results in a single line (omits similarity scores).").build());
+		this.options.addOption(Option.builder("t").hasArg().argName("num").desc("run a fixed number of threads.").build());
+		this.options.addOption(Option.builder("k").hasArg().argName("cutoff").desc("number of documents to retrieve.").build());
+		this.options.addOption(Option.builder("v").desc("verbose, to stderr.").build());
+		this.options.addOption(Option.builder("vv").desc("verbose a lot, to stderr.").build());
+		this.options.addOption(Option.builder("h").desc("show this help message.").build());
+		this.options.addOption(Option.builder("gui").desc("run with graphical user interface.").build());
 	}
 
 	/**
@@ -168,7 +152,7 @@ public void start() {
 	}
 
 	protected boolean parseArguments() {
-		CommandLineParser parser = new BasicParser();
+		CommandLineParser parser = new DefaultParser();
 
 		// help? Cannot wait to parse args because it will throw exception
 		// before