Commits

Lars Yencken committed 931459f

Adds the initial Scala GPAligner project.

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Files changed (26)

+\.orig$
+\.orig\..*$
+\.chg\..*$
+\.rej$
+\.conflict\~$
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- You may freely edit this file. See commented blocks below for -->
+<!-- some examples of how to customize the build. -->
+<!-- (If you delete it and reopen the project it will be recreated.) -->
+<project name="GPAligner" default="default" basedir=".">
+    <description>Builds, tests, and runs the project GPAligner.</description>
+    <import file="nbproject/build-impl.xml"/>
+    <!--
+
+    There exist several targets which are by default empty and which can be 
+    used for execution of your tasks. These targets are usually executed 
+    before and after some main targets. They are: 
+
+      -pre-init:                 called before initialization of project properties
+      -post-init:                called after initialization of project properties
+      -pre-compile:              called before javac compilation
+      -post-compile:             called after javac compilation
+      -pre-compile-single:       called before javac compilation of single file
+      -post-compile-single:      called after javac compilation of single file
+      -pre-compile-test:         called before javac compilation of JUnit tests
+      -post-compile-test:        called after javac compilation of JUnit tests
+      -pre-compile-test-single:  called before javac compilation of single JUnit test
+      -post-compile-test-single: called after javac compilation of single JUunit test
+      -pre-jar:                  called before JAR building
+      -post-jar:                 called after JAR building
+      -post-clean:               called after cleaning build products
+
+    (Targets beginning with '-' are not intended to be called on their own.)
+
+    Example of inserting an obfuscator after compilation could look like this:
+
+        <target name="-post-compile">
+            <obfuscate>
+                <fileset dir="${build.classes.dir}"/>
+            </obfuscate>
+        </target>
+
+    For list of available properties check the imported 
+    nbproject/build-impl.xml file. 
+
+
+    Another way to customize the build is by overriding existing main targets.
+    The targets of interest are: 
+
+      -init-macrodef-javac:     defines macro for javac compilation
+      -init-macrodef-junit:     defines macro for junit execution
+      -init-macrodef-debug:     defines macro for class debugging
+      -init-macrodef-java:      defines macro for class execution
+      -do-jar-with-manifest:    JAR building (if you are using a manifest)
+      -do-jar-without-manifest: JAR building (if you are not using a manifest)
+      run:                      execution of project 
+      -javadoc-build:           Javadoc generation
+      test-report:              JUnit report generation
+
+    An example of overriding the target for project execution could look like this:
+
+        <target name="run" depends="GPAligner-impl.jar">
+            <exec dir="bin" executable="launcher.exe">
+                <arg file="${dist.jar}"/>
+            </exec>
+        </target>
+
+    Notice that the overridden target depends on the jar target and not only on 
+    the compile target as the regular run target does. Again, for a list of available 
+    properties which you can use, check the target you are overriding in the
+    nbproject/build-impl.xml file. 
+
+    -->
+</project>

lib/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar

Binary file added.

lib/junit/junit-3.8.2-api.zip

Binary file added.

lib/junit/junit-3.8.2.jar

Binary file added.

lib/junit_4/junit-4.5-api.zip

Binary file added.

lib/junit_4/junit-4.5-src.jar

Binary file added.

lib/junit_4/junit-4.5.jar

Binary file added.

lib/nblibraries.properties

+libs.junit.classpath=\
+    ${base}/junit/junit-3.8.2.jar
+libs.junit.javadoc=\
+    ${base}/junit/junit-3.8.2-api.zip
+libs.junit_4.classpath=\
+    ${base}/junit_4/junit-4.5.jar
+libs.junit_4.javadoc=\
+    ${base}/junit_4/junit-4.5-api.zip
+libs.junit_4.src=\
+    ${base}/junit_4/junit-4.5-src.jar
+libs.CopyLibs.classpath=\
+    ${base}/CopyLibs/org-netbeans-modules-java-j2seproject-copylibstask.jar

lib/scala-library.jar

Binary file added.
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+

nbproject/build-impl.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+*** GENERATED FROM project.xml - DO NOT EDIT  ***
+***         EDIT ../build.xml INSTEAD         ***
+
+For the purpose of easier reading the script
+is divided into following sections:
+
+  - initialization
+  - compilation
+  - jar
+  - execution
+  - debugging
+  - javadoc
+  - junit compilation
+  - junit execution
+  - junit debugging
+  - applet
+  - cleanup
+
+        
+        -->
+<project xmlns:jaxrpc="http://www.netbeans.org/ns/scala-project/jax-rpc" xmlns:scalaProject1="http://www.netbeans.org/ns/scala-project/1" basedir=".." default="default" name="GPAligner-impl">
+    <target depends="test,jar,javadoc" description="Build and test whole project." name="default"/>
+    <!--
+                ======================
+                INITIALIZATION SECTION 
+                ======================
+            -->
+    <target name="-pre-init">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="-pre-init" name="-init-private">
+        <property file="nbproject/private/config.properties"/>
+        <property file="nbproject/private/configs/${config}.properties"/>
+        <property file="nbproject/private/private.properties"/>
+        <property environment="env"/>
+        <condition property="scala.home" value="${env.SCALA_HOME}">
+            <isset property="env.SCALA_HOME"/>
+        </condition>
+        <fail unless="scala.home">
+You must set SCALA_HOME or environment property and append "-J-Dscala.home=scalahomepath"
+property to the end of "netbeans_default_options" in NetBeansInstallationPath/etc/netbeans.conf to point to
+Scala installation directory.
+                </fail>
+        <property name="scala.compiler" value="${scala.home}/lib/scala-compiler.jar"/>
+        <property name="scala.library" value="${scala.home}/lib/scala-library.jar"/>
+        <property name="scala.lib" value="${scala.home}/lib"/>
+        <taskdef resource="scala/tools/ant/antlib.xml">
+            <classpath>
+                <pathelement location="${scala.compiler}"/>
+                <pathelement location="${scala.library}"/>
+            </classpath>
+        </taskdef>
+        <chmod dir="${scala.home}/bin" includes="**/*" perm="u+rx"/>
+    </target>
+    <target depends="-pre-init,-init-private" name="-init-libraries">
+        <property location="./lib/nblibraries.properties" name="libraries.1.path"/>
+        <dirname file="${libraries.1.path}" property="libraries.1.dir.nativedirsep"/>
+        <pathconvert dirsep="/" property="libraries.1.dir">
+            <path path="${libraries.1.dir.nativedirsep}"/>
+        </pathconvert>
+        <basename file="${libraries.1.path}" property="libraries.1.basename" suffix=".properties"/>
+        <touch file="${libraries.1.dir}/${libraries.1.basename}-private.properties"/>
+        <loadproperties srcfile="${libraries.1.dir}/${libraries.1.basename}-private.properties">
+            <filterchain>
+                <replacestring from="$${base}" to="${libraries.1.dir}"/>
+            </filterchain>
+        </loadproperties>
+        <loadproperties srcfile="${libraries.1.path}">
+            <filterchain>
+                <replacestring from="$${base}" to="${libraries.1.dir}"/>
+            </filterchain>
+        </loadproperties>
+    </target>
+    <target depends="-pre-init,-init-private,-init-libraries" name="-init-user">
+        <property file="${user.properties.file}"/>
+        <!-- The two properties below are usually overridden -->
+        <!-- by the active platform. Just a fallback. -->
+        <property name="default.javac.source" value="1.4"/>
+        <property name="default.javac.target" value="1.4"/>
+    </target>
+    <target depends="-pre-init,-init-private,-init-libraries,-init-user" name="-init-project">
+        <property file="nbproject/configs/${config}.properties"/>
+        <property file="nbproject/project.properties"/>
+    </target>
+    <target depends="-pre-init,-init-private,-init-libraries,-init-user,-init-project,-init-macrodef-property" name="-do-init">
+        <available file="${manifest.file}" property="manifest.available"/>
+        <condition property="manifest.available+main.class">
+            <and>
+                <isset property="manifest.available"/>
+                <isset property="main.class"/>
+                <not>
+                    <equals arg1="${main.class}" arg2="" trim="true"/>
+                </not>
+            </and>
+        </condition>
+        <condition property="manifest.available+main.class+mkdist.available">
+            <and>
+                <istrue value="${manifest.available+main.class}"/>
+                <isset property="libs.CopyLibs.classpath"/>
+            </and>
+        </condition>
+        <condition property="have.tests">
+            <or>
+                <available file="${test.src.dir}"/>
+            </or>
+        </condition>
+        <condition property="have.sources">
+            <or>
+                <available file="${src.dir}"/>
+            </or>
+        </condition>
+        <condition property="netbeans.home+have.tests">
+            <and>
+                <isset property="netbeans.home"/>
+                <isset property="have.tests"/>
+            </and>
+        </condition>
+        <condition property="no.javadoc.preview">
+            <and>
+                <isset property="javadoc.preview"/>
+                <isfalse value="${javadoc.preview}"/>
+            </and>
+        </condition>
+        <property name="run.jvmargs" value=""/>
+        <property name="javac.compilerargs" value=""/>
+        <property name="work.dir" value="${basedir}"/>
+        <condition property="no.deps">
+            <and>
+                <istrue value="${no.dependencies}"/>
+            </and>
+        </condition>
+        <property name="javac.debug" value="true"/>
+        <property name="javadoc.preview" value="true"/>
+        <property name="application.args" value=""/>
+        <property name="source.encoding" value="${file.encoding}"/>
+        <condition property="javadoc.encoding.used" value="${javadoc.encoding}">
+            <and>
+                <isset property="javadoc.encoding"/>
+                <not>
+                    <equals arg1="${javadoc.encoding}" arg2=""/>
+                </not>
+            </and>
+        </condition>
+        <property name="javadoc.encoding.used" value="${source.encoding}"/>
+        <property name="includes" value="**"/>
+        <property name="excludes" value=""/>
+        <property name="do.depend" value="false"/>
+        <condition property="do.depend.true">
+            <istrue value="${do.depend}"/>
+        </condition>
+        <condition else="" property="javac.compilerargs.jaxws" value="-Djava.endorsed.dirs='${jaxws.endorsed.dir}'">
+            <and>
+                <isset property="jaxws.endorsed.dir"/>
+                <available file="nbproject/jaxws-build.xml"/>
+            </and>
+        </condition>
+    </target>
+    <target name="-post-init">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="-pre-init,-init-private,-init-libraries,-init-user,-init-project,-do-init" name="-init-check">
+        <fail unless="src.dir">Must set src.dir</fail>
+        <fail unless="test.src.dir">Must set test.src.dir</fail>
+        <fail unless="build.dir">Must set build.dir</fail>
+        <fail unless="dist.dir">Must set dist.dir</fail>
+        <fail unless="build.classes.dir">Must set build.classes.dir</fail>
+        <fail unless="dist.javadoc.dir">Must set dist.javadoc.dir</fail>
+        <fail unless="build.test.classes.dir">Must set build.test.classes.dir</fail>
+        <fail unless="build.test.results.dir">Must set build.test.results.dir</fail>
+        <fail unless="build.classes.excludes">Must set build.classes.excludes</fail>
+        <fail unless="dist.jar">Must set dist.jar</fail>
+    </target>
+    <target name="-init-macrodef-property">
+        <macrodef name="property" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute name="name"/>
+            <attribute name="value"/>
+            <sequential>
+                <property name="@{name}" value="${@{value}}"/>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-macrodef-javac">
+        <macrodef name="javac" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${src.dir}" name="srcdir"/>
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <attribute default="${javac.classpath}" name="classpath"/>
+            <attribute default="${includes}" name="includes"/>
+            <attribute default="${excludes}" name="excludes"/>
+            <attribute default="${javac.debug}" name="debug"/>
+            <attribute default="" name="sourcepath"/>
+            <element name="customize" optional="true"/>
+            <sequential>
+                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}">
+                    <classpath>
+                        <path path="@{classpath}"/>
+                        <fileset dir="${scala.lib}">
+                            <include name="**/*.jar"/>
+                        </fileset>
+                    </classpath>
+                    <compilerarg line="${javac.compilerargs} ${javac.compilerargs.jaxws}"/>
+                    <customize/>
+                </javac>
+            </sequential>
+        </macrodef>
+        <macrodef name="depend" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${src.dir}" name="srcdir"/>
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <attribute default="${javac.classpath}" name="classpath"/>
+            <sequential>
+                <depend cache="${build.dir}/depcache" destdir="@{destdir}" excludes="${excludes}" includes="${includes}" srcdir="@{srcdir}">
+                    <classpath>
+                        <path path="@{classpath}"/>
+                    </classpath>
+                </depend>
+            </sequential>
+        </macrodef>
+        <macrodef name="force-recompile" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <sequential>
+                <fail unless="javac.includes">Must set javac.includes</fail>
+                <pathconvert pathsep="," property="javac.includes.binary">
+                    <path>
+                        <filelist dir="@{destdir}" files="${javac.includes}"/>
+                    </path>
+                    <globmapper from="*.java" to="*.class"/>
+                </pathconvert>
+                <delete>
+                    <files includes="${javac.includes.binary}"/>
+                </delete>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-macrodef-scalac">
+        <macrodef name="scalac" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${src.dir}" name="srcdir"/>
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <attribute default="${javac.classpath}" name="classpath"/>
+            <attribute default="${includes}" name="includes"/>
+            <attribute default="${excludes}" name="excludes"/>
+            <attribute default="${javac.compilerargs}" name="addparams"/>
+            <attribute default="" name="sourcepath"/>
+            <element name="customize" optional="true"/>
+            <sequential>
+                <fsc addparams="@{addparams}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" includes="@{includes}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="jvm-${javac.target}">
+                    <classpath>
+                        <path path="@{classpath}"/>
+                        <fileset dir="${scala.lib}">
+                            <include name="**/*.jar"/>
+                        </fileset>
+                    </classpath>
+                    <customize/>
+                </fsc>
+            </sequential>
+        </macrodef>
+        <macrodef name="depend" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${src.dir}" name="srcdir"/>
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <attribute default="${javac.classpath}" name="classpath"/>
+            <sequential>
+                <depend cache="${build.dir}/depcache" destdir="@{destdir}" excludes="${excludes}" includes="${includes}" srcdir="@{srcdir}">
+                    <classpath>
+                        <path path="@{classpath}"/>
+                    </classpath>
+                </depend>
+            </sequential>
+        </macrodef>
+        <macrodef name="force-recompile" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${build.classes.dir}" name="destdir"/>
+            <sequential>
+                <fail unless="javac.includes">Must set javac.includes</fail>
+                <pathconvert pathsep="," property="javac.includes.binary">
+                    <path>
+                        <filelist dir="@{destdir}" files="${javac.includes}"/>
+                    </path>
+                    <globmapper from="*.scala" to="*.class"/>
+                </pathconvert>
+                <delete>
+                    <files includes="${javac.includes.binary}"/>
+                </delete>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-macrodef-junit">
+        <macrodef name="junit" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${includes}" name="includes"/>
+            <attribute default="${excludes}" name="excludes"/>
+            <attribute default="**" name="testincludes"/>
+            <sequential>
+                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" showoutput="true">
+                    <batchtest todir="${build.test.results.dir}">
+                        <fileset dir="${build.test.classes.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
+                            <filename name="@{testincludes}"/>
+                        </fileset>
+                    </batchtest>
+                    <classpath>
+                        <path path="${run.test.classpath}"/>
+                        <fileset dir="${scala.lib}">
+                            <include name="**/*.jar"/>
+                        </fileset>
+                    </classpath>
+                    <syspropertyset>
+                        <propertyref prefix="test-sys-prop."/>
+                        <mapper from="test-sys-prop.*" to="*" type="glob"/>
+                    </syspropertyset>
+                    <formatter type="brief" usefile="false"/>
+                    <formatter type="xml"/>
+                    <jvmarg line="${run.jvmargs}"/>
+                </junit>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-macrodef-nbjpda">
+        <macrodef name="nbjpdastart" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${main.class}" name="name"/>
+            <attribute default="${debug.classpath}" name="classpath"/>
+            <attribute default="" name="stopclassname"/>
+            <sequential>
+                <nbjpdastart addressproperty="jpda.address" name="@{name}" stopclassname="@{stopclassname}" transport="dt_socket">
+                    <classpath>
+                        <path path="@{classpath}"/>
+                    </classpath>
+                </nbjpdastart>
+            </sequential>
+        </macrodef>
+        <macrodef name="nbjpdareload" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${build.classes.dir}" name="dir"/>
+            <sequential>
+                <nbjpdareload>
+                    <fileset dir="@{dir}" includes="${fix.includes}*.class"/>
+                </nbjpdareload>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-debug-args">
+        <property name="version-output" value="java version &quot;${ant.java.version}"/>
+        <condition property="have-jdk-older-than-1.4">
+            <or>
+                <contains string="${version-output}" substring="java version &quot;1.0"/>
+                <contains string="${version-output}" substring="java version &quot;1.1"/>
+                <contains string="${version-output}" substring="java version &quot;1.2"/>
+                <contains string="${version-output}" substring="java version &quot;1.3"/>
+            </or>
+        </condition>
+        <condition else="-Xdebug" property="debug-args-line" value="-Xdebug -Xnoagent -Djava.compiler=none">
+            <istrue value="${have-jdk-older-than-1.4}"/>
+        </condition>
+    </target>
+    <target depends="-init-debug-args" name="-init-macrodef-debug">
+        <macrodef name="debug" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${main.class}" name="classname"/>
+            <attribute default="${debug.classpath}" name="classpath"/>
+            <element name="customize" optional="true"/>
+            <sequential>
+                <java classname="@{classname}" dir="${work.dir}" fork="true">
+                    <jvmarg line="${debug-args-line}"/>
+                    <jvmarg value="-Xrunjdwp:transport=dt_socket,address=${jpda.address}"/>
+                    <jvmarg line="${run.jvmargs}"/>
+                    <classpath>
+                        <path path="@{classpath}"/>
+                        <fileset dir="${scala.lib}">
+                            <include name="**/*.jar"/>
+                        </fileset>
+                    </classpath>
+                    <syspropertyset>
+                        <propertyref prefix="run-sys-prop."/>
+                        <mapper from="run-sys-prop.*" to="*" type="glob"/>
+                    </syspropertyset>
+                    <customize/>
+                </java>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-macrodef-java">
+        <macrodef name="java" uri="http://www.netbeans.org/ns/scala-project/1">
+            <attribute default="${main.class}" name="classname"/>
+            <element name="customize" optional="true"/>
+            <sequential>
+                <java classname="@{classname}" dir="${work.dir}" fork="true">
+                    <jvmarg line="${run.jvmargs}"/>
+                    <classpath>
+                        <path path="${run.classpath}"/>
+                        <fileset dir="${scala.lib}">
+                            <include name="**/*.jar"/>
+                        </fileset>
+                    </classpath>
+                    <syspropertyset>
+                        <propertyref prefix="run-sys-prop."/>
+                        <mapper from="run-sys-prop.*" to="*" type="glob"/>
+                    </syspropertyset>
+                    <customize/>
+                </java>
+            </sequential>
+        </macrodef>
+    </target>
+    <target name="-init-presetdef-jar">
+        <presetdef name="jar" uri="http://www.netbeans.org/ns/scala-project/1">
+            <jar compress="${jar.compress}" jarfile="${dist.jar}">
+                <scalaProject1:fileset dir="${build.classes.dir}"/>
+            </jar>
+        </presetdef>
+    </target>
+    <target depends="-pre-init,-init-private ,-init-libraries,-init-user,-init-project,-do-init,-post-init,-init-check,-init-macrodef-property,-init-macrodef-javac,-init-macrodef-scalac,-init-macrodef-junit,-init-macrodef-nbjpda,-init-macrodef-debug,-init-macrodef-java,-init-presetdef-jar" name="init"/>
+    <!--
+                ===================
+                COMPILATION SECTION
+                ===================
+            -->
+    <target depends="init" name="deps-jar" unless="no.deps"/>
+    <target depends="init,deps-jar" name="-pre-pre-compile">
+        <mkdir dir="${build.classes.dir}"/>
+    </target>
+    <target name="-pre-compile">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target if="do.depend.true" name="-compile-depend">
+        <scalaProject1:depend/>
+    </target>
+    <target depends="init,deps-jar,-pre-pre-compile,-pre-compile,-compile-depend" if="have.sources" name="-do-compile">
+        <scalaProject1:scalac/>
+        <scalaProject1:javac/>
+        <copy todir="${build.classes.dir}">
+            <fileset dir="${src.dir}" excludes="${build.classes.excludes},${excludes}&#10;                        " includes="${includes}"/>
+        </copy>
+    </target>
+    <target name="-post-compile">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,deps-jar,-pre-pre-compile,-pre-compile,-do-compile,-post-compile" description="Compile project." name="compile"/>
+    <target name="-pre-compile-single">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,deps-jar,-pre-pre-compile" name="-do-compile-single">
+        <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
+        <scalaProject1:force-recompile/>
+        <scalaProject1:scalac excludes="" includes="${javac.includes}" sourcepath="${src.dir}"/>
+    </target>
+    <target name="-post-compile-single">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,deps-jar,-pre-pre-compile,-pre-compile-single,-do-compile-single,-post-compile-single" name="compile-single"/>
+    <!--
+                ====================
+                JAR BUILDING SECTION
+                ====================
+            -->
+    <target depends="init" name="-pre-pre-jar">
+        <dirname file="${dist.jar}" property="dist.jar.dir"/>
+        <mkdir dir="${dist.jar.dir}"/>
+    </target>
+    <target name="-pre-jar">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,compile,-pre-pre-jar,-pre-jar" name="-do-jar-without-manifest" unless="manifest.available">
+        <scalaProject1:jar/>
+    </target>
+    <target depends="init,compile,-pre-pre-jar,-pre-jar" if="manifest.available" name="-do-jar-with-manifest" unless="manifest.available+main.class">
+        <scalaProject1:jar manifest="${manifest.file}"/>
+    </target>
+    <target depends="init,compile,-pre-pre-jar,-pre-jar" if="manifest.available+main.class" name="-do-jar-with-mainclass" unless="manifest.available+main.class+mkdist.available">
+        <scalaProject1:jar manifest="${manifest.file}">
+            <scalaProject1:manifest>
+                <scalaProject1:attribute name="Main-Class" value="${main.class}"/>
+            </scalaProject1:manifest>
+        </scalaProject1:jar>
+        <echo>To run this application from the command line without Ant, try:</echo>
+        <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
+        <property location="${dist.jar}" name="dist.jar.resolved"/>
+        <pathconvert property="run.classpath.with.dist.jar">
+            <path path="${run.classpath}"/>
+            <map from="${build.classes.dir.resolved}" to="${dist.jar.resolved}"/>
+        </pathconvert>
+        <echo>java -cp "${run.classpath.with.dist.jar}" ${main.class}
+                </echo>
+    </target>
+    <target depends="init,compile,-pre-pre-jar,-pre-jar" if="manifest.available+main.class+mkdist.available" name="-do-jar-with-libraries">
+        <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
+        <pathconvert property="run.classpath.without.build.classes.dir">
+            <path path="${run.classpath}"/>
+            <map from="${build.classes.dir.resolved}" to=""/>
+        </pathconvert>
+        <pathconvert pathsep=" " property="jar.classpath">
+            <path path="${run.classpath.without.build.classes.dir}"/>
+            <chainedmapper>
+                <flattenmapper/>
+                <globmapper from="*" to="lib/*"/>
+            </chainedmapper>
+        </pathconvert>
+        <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
+        <copylibs compress="${jar.compress}" jarfile="${dist.jar}" manifest="${manifest.file}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
+            <fileset dir="${build.classes.dir}"/>
+            <manifest>
+                <attribute name="Main-Class" value="${main.class}"/>
+                <attribute name="Class-Path" value="${jar.classpath}"/>
+            </manifest>
+        </copylibs>
+        <echo>To run this application from the command line without Ant, try:</echo>
+        <property location="${dist.jar}" name="dist.jar.resolved"/>
+        <echo>java -jar "${dist.jar.resolved}"
+                </echo>
+    </target>
+    <target name="-post-jar">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,compile,-pre-jar,-do-jar-with-manifest,-do-jar-without-manifest,-do-jar-with-mainclass,-do-jar-with-libraries,-post-jar" description="Build JAR." name="jar"/>
+    <!--
+                =================
+                EXECUTION SECTION
+                =================
+            -->
+    <target depends="init,compile" description="Run a main class." name="run">
+        <scalaProject1:java>
+            <customize>
+                <arg line="${application.args}"/>
+            </customize>
+        </scalaProject1:java>
+    </target>
+    <target name="-do-not-recompile">
+        <property name="javac.includes.binary" value=""/>
+    </target>
+    <target depends="init,-do-not-recompile,compile-single" name="run-single">
+        <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
+        <scalaProject1:java classname="${run.class}"/>
+    </target>
+    <!--
+                =================
+                DEBUGGING SECTION
+                =================
+            -->
+    <target depends="init" if="netbeans.home" name="-debug-start-debugger">
+        <scalaProject1:nbjpdastart name="${debug.class}"/>
+    </target>
+    <target depends="init,compile" name="-debug-start-debuggee">
+        <scalaProject1:debug>
+            <customize>
+                <arg line="${application.args}"/>
+            </customize>
+        </scalaProject1:debug>
+    </target>
+    <target depends="init,compile,-debug-start-debugger,-debug-start-debuggee" description="Debug project in IDE." if="netbeans.home" name="debug"/>
+    <target depends="init" if="netbeans.home" name="-debug-start-debugger-stepinto">
+        <scalaProject1:nbjpdastart stopclassname="${main.class}"/>
+    </target>
+    <target depends="init,compile,-debug-start-debugger-stepinto,-debug-start-debuggee" if="netbeans.home" name="debug-stepinto"/>
+    <target depends="init,compile-single" if="netbeans.home" name="-debug-start-debuggee-single">
+        <fail unless="debug.class">Must select one file in the IDE or set debug.class</fail>
+        <scalaProject1:debug classname="${debug.class}"/>
+    </target>
+    <target depends="init,-do-not-recompile,compile-single,-debug-start-debugger,-debug-start-debuggee-single" if="netbeans.home" name="debug-single"/>
+    <target depends="init" name="-pre-debug-fix">
+        <fail unless="fix.includes">Must set fix.includes</fail>
+        <property name="javac.includes" value="${fix.includes}.java"/>
+    </target>
+    <target depends="init,-pre-debug-fix,compile-single" if="netbeans.home" name="-do-debug-fix">
+        <scalaProject1:nbjpdareload/>
+    </target>
+    <target depends="init,-pre-debug-fix,-do-debug-fix" if="netbeans.home" name="debug-fix"/>
+    <!--
+                ===============
+                JAVADOC SECTION
+                ===============
+            -->
+    <target depends="init" name="-javadoc-build">
+        <mkdir dir="${dist.javadoc.dir}"/>
+        <javadoc additionalparam="${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
+            <classpath>
+                <path path="${javac.classpath}"/>
+            </classpath>
+            <fileset dir="${src.dir}" excludes="${excludes}" includes="${includes}">
+                <filename name="**/*.java"/>
+            </fileset>
+        </javadoc>
+    </target>
+    <target depends="init,-javadoc-build" if="netbeans.home" name="-javadoc-browse" unless="no.javadoc.preview">
+        <nbbrowse file="${dist.javadoc.dir}/index.html"/>
+    </target>
+    <target depends="init,-javadoc-build,-javadoc-browse" description="Build Javadoc." name="javadoc"/>
+    <!--
+                =========================
+                JUNIT COMPILATION SECTION
+                =========================
+            -->
+    <target depends="init,compile" if="have.tests" name="-pre-pre-compile-test">
+        <mkdir dir="${build.test.classes.dir}"/>
+    </target>
+    <target name="-pre-compile-test">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target if="do.depend.true" name="-compile-test-depend">
+        <scalaProject1:depend classpath="${javac.test.classpath}" destdir="${build.test.classes.dir}" srcdir="${test.src.dir}"/>
+    </target>
+    <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test,-compile-test-depend" if="have.tests" name="-do-compile-test">
+        <scalaProject1:scalac classpath="${javac.test.classpath}" destdir="${build.test.classes.dir}" srcdir="${test.src.dir}"/>
+        <copy todir="${build.test.classes.dir}">
+            <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}&#10;                        " includes="${includes}"/>
+        </copy>
+    </target>
+    <target name="-post-compile-test">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test,-do-compile-test,-post-compile-test" name="compile-test"/>
+    <target name="-pre-compile-test-single">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test-single" if="have.tests" name="-do-compile-test-single">
+        <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
+        <scalaProject1:force-recompile destdir="${build.test.classes.dir}"/>
+        <scalaProject1:scalac classpath="${javac.test.classpath}" debug="true" destdir="${build.test.classes.dir}" excludes="" includes="${javac.includes}" sourcepath="${test.src.dir}" srcdir="${test.src.dir}"/>
+        <copy todir="${build.test.classes.dir}">
+            <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}&#10;                        " includes="${includes}"/>
+        </copy>
+    </target>
+    <target name="-post-compile-test-single">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test-single,-do-compile-test-single,-post-compile-test-single" name="compile-test-single"/>
+    <!--
+                =======================
+                JUNIT EXECUTION SECTION
+                =======================
+            -->
+    <target depends="init" if="have.tests" name="-pre-test-run">
+        <mkdir dir="${build.test.results.dir}"/>
+    </target>
+    <target depends="init,compile-test,-pre-test-run" if="have.tests" name="-do-test-run">
+        <scalaProject1:junit testincludes="**/*Test.class"/>
+    </target>
+    <target depends="init,compile-test,-pre-test-run,-do-test-run" if="have.tests" name="-post-test-run">
+        <fail if="tests.failed">Some tests failed; see details above.</fail>
+    </target>
+    <target depends="init" if="have.tests" name="test-report"/>
+    <target depends="init" if="netbeans.home+have.tests" name="-test-browse"/>
+    <target depends="init,compile-test,-pre-test-run,-do-test-run,test-report,-post-test-run,-test-browse" description="Run unit tests." name="test"/>
+    <target depends="init" if="have.tests" name="-pre-test-run-single">
+        <mkdir dir="${build.test.results.dir}"/>
+    </target>
+    <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-do-test-run-single">
+        <fail unless="test.includes">Must select some files in the IDE or set test.includes</fail>
+        <scalaProject1:junit excludes="" includes="${test.includes}"/>
+    </target>
+    <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single" if="have.tests" name="-post-test-run-single">
+        <fail if="tests.failed">Some tests failed; see details above.</fail>
+    </target>
+    <target depends="init,-do-not-recompile,compile-test-single,-pre-test-run-single,-do-test-run-single,-post-test-run-single" description="Run single unit test." name="test-single"/>
+    <!--
+                =======================
+                JUNIT DEBUGGING SECTION
+                =======================
+            -->
+    <target depends="init,compile-test" if="have.tests" name="-debug-start-debuggee-test">
+        <fail unless="test.class">Must select one file in the IDE or set test.class</fail>
+        <property location="${build.test.results.dir}/TEST-${test.class}.xml" name="test.report.file"/>
+        <delete file="${test.report.file}"/>
+        <mkdir dir="${build.test.results.dir}"/>
+        <scalaProject1:debug classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner" classpath="${ant.home}/lib/ant.jar:${ant.home}/lib/ant-junit.jar:${debug.test.classpath}">
+            <customize>
+                <syspropertyset>
+                    <propertyref prefix="test-sys-prop."/>
+                    <mapper from="test-sys-prop.*" to="*" type="glob"/>
+                </syspropertyset>
+                <arg value="${test.class}"/>
+                <arg value="showoutput=true"/>
+                <arg value="formatter=org.apache.tools.ant.taskdefs.optional.junit.BriefJUnitResultFormatter"/>
+                <arg value="formatter=org.apache.tools.ant.taskdefs.optional.junit.XMLJUnitResultFormatter,${test.report.file}"/>
+            </customize>
+        </scalaProject1:debug>
+    </target>
+    <target depends="init,compile-test" if="netbeans.home+have.tests" name="-debug-start-debugger-test">
+        <scalaProject1:nbjpdastart classpath="${debug.test.classpath}" name="${test.class}"/>
+    </target>
+    <target depends="init,-do-not-recompile,compile-test-single,-debug-start-debugger-test,-debug-start-debuggee-test" name="debug-test"/>
+    <target depends="init,-pre-debug-fix,compile-test-single" if="netbeans.home" name="-do-debug-fix-test">
+        <scalaProject1:nbjpdareload dir="${build.test.classes.dir}"/>
+    </target>
+    <target depends="init,-pre-debug-fix,-do-debug-fix-test" if="netbeans.home" name="debug-fix-test"/>
+    <!--
+                =========================
+                APPLET EXECUTION SECTION
+                =========================
+            -->
+    <target depends="init,compile-single" name="run-applet">
+        <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
+        <scalaProject1:java classname="sun.applet.AppletViewer">
+            <customize>
+                <arg value="${applet.url}"/>
+            </customize>
+        </scalaProject1:java>
+    </target>
+    <!--
+                =========================
+                APPLET DEBUGGING  SECTION
+                =========================
+            -->
+    <target depends="init,compile-single" if="netbeans.home" name="-debug-start-debuggee-applet">
+        <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
+        <scalaProject1:debug classname="sun.applet.AppletViewer">
+            <customize>
+                <arg value="${applet.url}"/>
+            </customize>
+        </scalaProject1:debug>
+    </target>
+    <target depends="init,compile-single,-debug-start-debugger,-debug-start-debuggee-applet" if="netbeans.home" name="debug-applet"/>
+    <!--
+                ===============
+                CLEANUP SECTION
+                ===============
+            -->
+    <target depends="init" name="deps-clean" unless="no.deps"/>
+    <target depends="init" name="-do-clean">
+        <delete dir="${build.dir}"/>
+        <delete dir="${dist.dir}"/>
+    </target>
+    <target name="-post-clean">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="init,deps-clean,-do-clean,-post-clean" description="Clean build products." name="clean"/>
+</project>

nbproject/genfiles.properties

+build.xml.data.CRC32=f5ee89e7
+build.xml.script.CRC32=eaba27af
+build.xml.stylesheet.CRC32=ca9d572e@1.3.0
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=f5ee89e7
+nbproject/build-impl.xml.script.CRC32=b25d7e58
+nbproject/build-impl.xml.stylesheet.CRC32=bc42a706@1.3.0

nbproject/project.properties

+application.title=GPAligner
+application.vendor=lars
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form,**/*.scala
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+debug.classpath=\
+    ${run.classpath}
+debug.test.classpath=\
+    ${run.test.classpath}
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/GPAligner.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
+file.reference.scala-library.jar=lib/scala-library.jar
+includes=**
+jar.compress=false
+java.platform.active=java_default_platform
+javac.classpath=
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.source=1.5
+javac.target=1.5
+javac.test.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}:\
+    ${libs.junit.classpath}:\
+    ${libs.junit_4.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=gpaligner.Main
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+platform.active=default_platform
+run.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}:\
+    ${file.reference.scala-library.jar}
+# Space-separated list of JVM arguments used when running the project
+# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
+# or test-sys-prop.name=value to set system properties for unit tests):
+run.jvmargs=
+run.test.classpath=\
+    ${javac.test.classpath}:\
+    ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test

nbproject/project.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.scala.project</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/scala-project/1">
+            <name>GPAligner</name>
+            <minimum-ant-version>1.6.5</minimum-ant-version>
+            <source-roots>
+                <root id="src.dir"/>
+            </source-roots>
+            <test-roots>
+                <root id="test.src.dir"/>
+            </test-roots>
+        </data>
+        <libraries xmlns="http://www.netbeans.org/ns/ant-project-libraries/1">
+            <definitions>./lib/nblibraries.properties</definitions>
+        </libraries>
+    </configuration>
+</project>

src/gpaligner/AlignedOutput.scala

+/*
+ * AlignedOutput.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import scala.io.Source
+
+import java.io.{FileWriter,BufferedWriter}
+
+class AlignedOutput(filename : String) {
+    private val ostream = new BufferedWriter(new FileWriter(filename))
+
+    def consume(ap : AlignedPair) : Unit = {
+        ostream.write("%s %s:".format(ap.gpPair.graphemes, ap.gpPair.phonemes))
+        ostream.write((for { s <- ap.alignment.segments } yield s._1).mkString("|"))
+        ostream.write(' ')
+        ostream.write((for { s <- ap.alignment.segments } yield s._2).mkString("|"))
+        ostream.newLine
+    }
+
+    def close() : Unit = ostream.close
+}

src/gpaligner/AlignmentGenerator.scala

+/*
+ * AlignmentGenerator.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import scala.collection.mutable.ListBuffer
+
+trait AlignmentGenerator {
+    def generate(entry : GPPair) : List[Alignment] = {
+        for {
+            graphemeSeg <- graphemeSegmentations(entry.graphemes)
+            phonemeSeg <- phonemeSegmentations(graphemeSeg, entry.phonemes)
+        } yield new Alignment(graphemeSeg zip phonemeSeg)
+    }
+
+    def graphemeSegmentations(graphemes : String) : List[List[String]]
+
+    def phonemeSegmentations(graphemes : List[String], phonemes : String) : List[List[String]]
+}
+
+object LinguisticGenerator extends AlignmentGenerator {
+    def graphemeSegmentations(graphemes : String) : List[List[String]] = {
+        require(graphemes.length > 0)
+        for {
+            segLists <- Combinatorics.segmentCombinations(graphemes.toCharArray.toList)
+            segStrings = segLists.map(s => s.mkString)
+        } yield segStrings
+    }
+
+    def phonemeSegmentations(graphemes : List[String], phonemes : String) : List[List[String]] = {
+        val nSegs = graphemes.length
+        for {
+            segs <- Combinatorics.segmentCombinations(phonemes.toCharArray.toList)
+            if segs.length == nSegs
+        } yield segs.map(s => s.mkString)
+    }
+}
+
+object JapaneseGenerator extends AlignmentGenerator {
+    def graphemeSegmentations(graphemeString : String) : List[List[String]] = {
+        for {
+            graphemes <- LinguisticGenerator.graphemeSegmentations(graphemeString)
+            if (true /: graphemes.map(isValidGrapheme))(_ && _)
+        } yield graphemes
+    }
+
+    def phonemeSegmentations(graphemes : List[String], phonemeString : String) : List[List[String]] = {
+        for {
+            phonemes <- LinguisticGenerator.phonemeSegmentations(graphemes, phonemeString)
+            segments = graphemes zip phonemes
+            if segments.length > 0 && (true /: segments.map(isValidSegment))(_ && _)
+        } yield phonemes
+    }
+
+    def isValidGrapheme(grapheme : String) : Boolean = {
+        Japanese.countScripts(grapheme) == 1
+    }
+
+    def isValidSegment(segment : Tuple2[String, String]) : Boolean = {
+        val (grapheme, phoneme) = segment
+        Japanese.scriptType(grapheme) match {
+            case ScriptType.Hiragana => grapheme == phoneme
+            case ScriptType.Katakana => grapheme == phoneme
+            case _ => !phoneme.startsWith(Japanese.nKana.toString)
+        }
+    }
+}
+
+object Combinatorics { 
+    def segmentCombinations[A](xs : List[A]) : List[List[List[A]]] = {
+        require(xs.length > 0)
+        val nCombinations = 1 << (xs.length - 1)
+        for {
+            i <- List.range(0, nCombinations)
+        } yield segmentCombinationN(xs, i)
+    }
+
+    private def segmentCombinationN[A](xss : List[A], n : Int) : List[List[A]] = xss match {
+        case List() => throw new RuntimeException("list should not be empty")
+        case List(x) => List(List(x))
+        case x :: xs => {
+            if (n % 2 == 0) {
+                val result = segmentCombinationN(xs, n / 2)
+                (x :: result.head) :: result.tail
+            } else {
+                List(x) :: segmentCombinationN(xs, n / 2)
+            }
+        }
+    }
+}

src/gpaligner/FreqDist.scala

+/*
+ * FreqDist.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import scala.collection.mutable.HashMap
+import scala.Math.log
+
+class FreqDist[A] {
+    private val map = new HashMap[A, Int]()
+    private var total : Int = 0
+    
+    def inc(key : A) : Unit = {
+        val count : Int = map.getOrElse(key, 0)
+        map.put(key, count + 1)
+        total += 1
+    }
+
+    def inc(key : A, n : Int) : Unit = {
+        require(n >= 1)
+        val count : Int = map.getOrElse(key, 0)
+        map.put(key, count + n)
+        total += n
+    }
+
+    def dec(key : A) : Unit = {
+        val maybeCount = map.get(key)
+        require(maybeCount.isDefined)
+        val count = maybeCount.get
+        require(count >= 1)
+        if (count == 1) {
+            map.removeKey(key)
+        } else {
+            map.put(key, count - 1)
+        }
+        total -= 1
+    }
+
+    def dec(key : A, n : Int) : Unit = {
+        val maybeCount = map.get(key)
+        require(maybeCount.isDefined)
+        val count = maybeCount.get
+        require(count >= n)
+        if (count == n) {
+            map.removeKey(key)
+        } else {
+            map.put(key, count - n)
+        }
+        total -= n
+    }
+
+    def logProb(key : A) : Option[Double] = map.get(key) match {
+        case Some(count : Int) => Some(log(count.toDouble / total))
+        case None => None
+    }
+
+    def prob(key : A) : Double = map.get(key) match {
+        case Some(count : Int) => count.toDouble / total
+        case None => 0.0
+    }
+
+    def getCount(key : A) : Int = map.get(key) match {
+        case Some(count : Int) => count
+        case None => 0
+    }
+
+    def getTotal() = total
+}

src/gpaligner/GPAligner.scala

+/*
+ * GPAligner.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+class GPAligner(inputFile : String, outputFile : String) {
+    type Segment = Pair[String, String]
+    type GPContext = Tuple3[Option[Segment], Segment, Option[Segment]]
+    type ScoredAlignment = Pair[Double, Alignment]
+    
+    val input = new GPInput(inputFile)
+    val output = new AlignedOutput(outputFile)
+    val solvedModel = new AlignmentModel
+    val unsolvedModel = new AlignmentModel
+
+    val alpha = 0.2
+    val solvedWeight = 0.8
+    val unsolvedWeight = 0.2
+
+    def align() : Unit = {
+        var clouds = buildClouds
+        while (clouds.length > 0) {
+            if (clouds.length % 10 == 0) {
+                println("%d remaining".format(clouds.length))
+            }
+            clouds = rescore(clouds)
+            clouds = clouds.sort(_.bestScore > _.bestScore)
+            val bestCloud = clouds.head
+            val (alignedPair, remainder) = bestCloud.resolve
+            solvedModel.inc(alignedPair.alignment)
+            unsolvedModel.dec(remainder)
+            output.consume(alignedPair)
+            clouds = clouds.tail
+        }
+        output.close
+    }
+
+    private def buildClouds() : List[AlignmentCloud] = {
+        var cs = List[AlignmentCloud]()
+        var nOverconstrained = 0
+        var nResolved = 0
+        for (gpPair <- input.read()) {
+            val cloud = buildCloud(gpPair)
+            if (cloud.isOverconstrained) {
+                nOverconstrained += 1
+            } else if (cloud.isResolved) {
+                nResolved += 1
+                val (alignedPair, remainder) = cloud.resolve
+                solvedModel.inc(alignedPair.alignment)
+                unsolvedModel.dec(remainder)
+                output.consume(alignedPair)
+            } else if (cloud.isAmbiguous) {
+                unsolvedModel.inc(cloud.alignments)
+                cs = cloud :: cs
+            } else {
+                throw new RuntimeException("unexpected cloud status")
+            }
+        }
+        println("%d overconstrained/%d resolved/%d ambiguous".format(nOverconstrained, nResolved, cs.length))
+        cs
+    }
+
+    private def buildCloud(gpPair : GPPair) : AlignmentCloud = {
+        val alignments = JapaneseGenerator.generate(gpPair)
+        val scoredAlignments = for {a <- alignments} yield Pair(-1.0, a)
+        AlignmentCloud(gpPair, scoredAlignments)
+    }
+
+    private def rescore(cs : List[AlignmentCloud]) : List[AlignmentCloud] = cs.map(rescore(_))
+
+    private def rescore(c : AlignmentCloud) : AlignmentCloud = {
+        new AlignmentCloud(c.gpPair, c.scoredAlignments.map(rescore(_)))
+    }
+
+    private def rescore(sa : ScoredAlignment) : ScoredAlignment = {
+        Pair(rescore(sa._2), sa._2)
+    }
+
+    private def rescore(a : Alignment) : Double = {
+        mean(for { gpc <- AlignmentModel.withContext(a.segments) } yield rescore(gpc))
+    }
+
+    private def rescore(gpc : GPContext) : Double = {
+        val tf = (wtf(gpc._2) - unsolvedWeight + alpha) / wtf(gpc._2._1)
+        val idf = Math.log(wtf(gpc._2) / (wtf(gpc) - unsolvedWeight + alpha))
+        tf * idf
+    }
+
+    private def wtf(grapheme : String) = 0.0
+    private def wtf(gp : Segment) = 0.0
+    private def wtf(gpc : GPContext) = 0.0
+
+    def mean(xs : List[Double]) : Double = (0.0 /: xs)(_ + _) / xs.length
+}
+
+object AlignmentModel {
+    def withContext[A](seq : List[A]) : List[Tuple3[Option[A], A, Option[A]]] = seq match {
+        case List() => List()
+        case List(x) => List(Tuple3(None, x, None))
+        case x :: y :: xs => Tuple3(None, x, Some(y)) :: withContext(x, y :: xs)
+    }
+
+    private def withContext[A](head : A, seq : List[A]) : List[Tuple3[Option[A], A, Option[A]]] = seq match {
+        case List(x) => List(Tuple3(Some(head), x, None))
+        case x :: y :: xs => Tuple3(Some(head), x, Some(y)) :: withContext(x, y :: xs)
+    }
+}
+
+class AlignmentModel {
+    type Segment = Pair[String, String]
+    type GPContext = Tuple3[Option[Segment], Segment, Option[Segment]]
+    
+    val gDist = new FreqDist[String]()
+    val gpDist = new FreqDist[Segment]()
+    val gpcDist = new FreqDist[GPContext]()
+
+    def inc(alignment : Alignment) : Unit = {
+        for (gpc <- AlignmentModel.withContext(alignment.segments)) {
+            gpcDist.inc(gpc)
+            gpDist.inc(gpc._2)
+            gDist.inc(gpc._2._1)
+        }
+    }
+
+    def inc(alignments : List[Alignment]) : Unit = { alignments.map(a => inc(a)) }
+
+    def dec(alignment : Alignment) : Unit = {
+        for (gpc <- AlignmentModel.withContext(alignment.segments)) {
+            gpcDist.dec(gpc)
+            gpDist.dec(gpc._2)
+            gDist.dec(gpc._2._1)
+        }
+    }
+
+    def dec(alignments : List[Alignment]) : Unit = { alignments.map(a => dec(a)) }
+}

src/gpaligner/GPInput.scala

+/*
+ * GPInput.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import scala.io.Source
+
+import java.io.IOException
+
+class GPInput(filename : String) {
+    def read() : List[GPPair] = {
+        var result = List[GPPair]()
+        var i = 1
+        for (line <- Source.fromFile(filename).getLines) {
+            val a : Array[String] = line.stripLineEnd.split(' ')
+            if (a.length != 2) {
+                throw new IOException("file %s has bad format on line %d".format(filename, i))
+            }
+            result = GPPair(a(0), a(1)) :: result
+            i += 1
+        }
+        result
+    }
+}

src/gpaligner/GPPair.scala

+/*
+ * GPPair.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import scala.Math
+
+case class GPPair(graphemes : String, phonemes : String)
+
+case class Alignment(segments : List[Tuple2[String, String]])
+
+case class AlignmentCloud(gpPair : GPPair, scoredAlignments : List[Pair[Double, Alignment]]) {
+    type ScoredPair = Pair[Double, Alignment]
+    val bestScore : Double = max(for { (s, _) <- scoredAlignments } yield s)
+    val size : Int = scoredAlignments.length
+
+    def isOverconstrained = scoredAlignments.length == 0
+    def isResolved = scoredAlignments.length == 1
+    def isAmbiguous = scoredAlignments.length > 1
+
+    def alignments() : List[Alignment] = for { (_, a) <- scoredAlignments } yield a
+
+    def resolve() : Pair[AlignedPair, List[Alignment]] = {
+        require(scoredAlignments.length > 0)
+        val (x :: xs) = scoredAlignments
+        val (alignment, remainingAlignments) = best(x, List(), xs)
+        Pair(AlignedPair(gpPair, alignment), remainingAlignments)
+    }
+
+    def max(a : List[Double]) = (Double.MinValue /: a)(Math.max(_, _))
+
+    private def best(bestSoFar : ScoredPair, remainder : List[Alignment], rest : List[ScoredPair]) : Pair[Alignment, List[Alignment]] = rest match {
+        case List() => Pair(bestSoFar._2, remainder)
+        case x :: xs => {
+            if (x._1 > bestSoFar._1) {
+                best(x, bestSoFar._2 :: remainder, xs)
+            } else {
+                best(bestSoFar, x._2 :: remainder, xs)
+            }
+        }
+    }
+}
+
+case class AlignedPair(gpPair : GPPair, alignment : Alignment)

src/gpaligner/Japanese.scala

+/*
+ * Japanese.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import java.lang.Character.UnicodeBlock
+
+object ScriptType extends Enumeration {
+    val Kanji = Value
+    val Hiragana = Value
+    val Katakana = Value
+    val Roman = Value
+    val DoubleWidthRoman = Value
+    val Other = Value
+}
+
+object Japanese {
+    val nKana = '\u3093'
+
+    def scriptType(c : Char) : ScriptType.Value = UnicodeBlock.of(c) match {
+        case UnicodeBlock.HIRAGANA => ScriptType.Hiragana
+        case UnicodeBlock.KATAKANA => ScriptType.Katakana
+        case UnicodeBlock.CJK_UNIFIED_IDEOGRAPHS => ScriptType.Kanji
+        case UnicodeBlock.BASIC_LATIN => ScriptType.Roman
+        case _ => ScriptType.Other
+    }
+
+    def scriptType(s : String) : ScriptType.Value = {
+        require(s.length > 0)
+        scriptType(s.charAt(0))
+    }
+
+    def scriptTypes(s : String) : Set[ScriptType.Value] = {
+        var set = Set[ScriptType.Value]()
+        for (c <- s) {
+            set += scriptType(c)
+        }
+        set
+    }
+
+    def countScripts(s : String) : Int = scriptTypes(s).size
+}

src/gpaligner/Main.scala

+/*
+ * Main.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+object Main {
+
+    /**
+     * @param args the command line arguments
+     */
+    def main(args: Array[String]) : Unit = {
+        //        if (args.size != 2) {
+        //            usage()
+        //        } else {
+        val inputFile = "/home/lars/Documents/phd/data/aligned/evaluation.input" //args(0)
+        val outputFile = "/home/lars/output.aligned"//args(1)
+        val aligner = new GPAligner(inputFile, outputFile)
+        aligner.align
+        //        }
+    }
+
+    def usage() : Unit = {
+        println("Usage: gpaligner inputFile outputFile")
+    }
+}

test/gpaligner/CombinatoricsTest.scala

+/*
+ * CombinatoricsTest.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import org.junit.After
+import org.junit.Before
+import org.junit.Test
+import org.junit.Assert._
+
+class CombinatoricsTest {
+
+    @Before
+    def setUp: Unit = {
+    }
+
+    @After
+    def tearDown: Unit = {
+    }
+
+    @Test
+    def segments = {
+        val x = Combinatorics.segmentCombinations(List(1, 2, 3))
+        assert(x.length == 4)
+        assert(x == List(
+                List(List(1, 2, 3)),
+                List(List(1), List(2, 3)),
+                List(List(1, 2), List(3)),
+                List(List(1), List(2), List(3))
+            )
+        )
+    }
+
+    @Test
+    def graphemeSegments = {
+        val x = LinguisticGenerator.graphemeSegmentations("dog")
+        assert(x.length == 4)
+        assert(x == List(
+                List("dog"),
+                List("d", "og"),
+                List("do", "g"),
+                List("d", "o", "g")
+            ))
+    }
+
+    @Test
+    def alignments = {
+        val x = LinguisticGenerator.generate(new GPPair("too", "TU"))
+        assert(x.length == 3)
+        assert(x == List(
+                Alignment(List(("too", "TU"))),
+                Alignment(List(("t", "T"), ("oo", "U"))),
+                Alignment(List(("to", "T"), ("o", "U"))),
+            ))
+    }
+
+}

test/gpaligner/FreqDistTest.scala

+/*
+ * FreqDistTest.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import org.junit.After
+import org.junit.Before
+import org.junit.Test
+import org.junit.Assert._
+import scala.Math
+
+class FreqDistTest {
+    val eps = 1e-6
+    @Before
+    def setUp: Unit = {
+    }
+
+    @After
+    def tearDown: Unit = {
+    }
+
+    def assertAlmostEqual(actual : Double, expected : Double) : Unit = {
+        assert(Math.abs(actual - expected) < eps)
+    }
+
+    @Test
+    def basicOps = {
+        val dist = new FreqDist[String]
+        assert(dist.getTotal == 0)
+        dist.inc("dog")
+        assert(dist.getTotal == 1)
+        assertAlmostEqual(dist.prob("dog"), 1.0)
+        assertAlmostEqual(dist.logProb("dog").get, 0.0)
+
+        dist.inc("cat")
+        assert(dist.getTotal == 2)
+        assertAlmostEqual(dist.prob("dog"), 0.5)
+        assertAlmostEqual(dist.prob("cat"), 0.5)
+        assertAlmostEqual(dist.logProb("dog").get, Math.log(0.5))
+
+        dist.inc("cat", 2)
+        assert(dist.getTotal == 4)
+        assertAlmostEqual(dist.prob("cat"), 0.75)
+        assert(dist.getCount("cat") == 3)
+        assertAlmostEqual(dist.prob("dog"), 0.25)
+
+        dist.dec("dog")
+        assertAlmostEqual(dist.prob("dog"), 0.0)
+        assertAlmostEqual(dist.prob("cat"), 1.0)
+        assert(dist.getTotal == 3)
+
+        dist.inc("dog")
+        assert(dist.getTotal == 4)
+        assertAlmostEqual(dist.prob("cat"), 0.75)
+        assert(dist.getCount("cat") == 3)
+        assertAlmostEqual(dist.prob("dog"), 0.25)
+    }
+}

test/gpaligner/JapaneseTest.scala

+/*
+ * JapaneseTest.scala
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package gpaligner
+
+import org.junit.After
+import org.junit.Before
+import org.junit.Test
+import org.junit.Assert._
+
+class JapaneseTest {
+
+    @Before
+    def setUp: Unit = {
+    }
+
+    @After
+    def tearDown: Unit = {
+    }
+
+    @Test
+    def countScripts = {
+        assert(Japanese.countScripts("引き時") == 2)
+    }
+
+}