Commit 3f21436b authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.6.0+dfsg

parent 5d49e7d8

build.xml

+242 −5
Original line number Diff line number Diff line 
<!-- Build BEAST 2. It is also used by Hudson BEAST_2 project. JUnit test is available for this build. -->

<project basedir="." default="build_jar_all_BEAST" name="BUILD_BEAST_2">

<project basedir="." default="build_jar_all_BEAST" name="BUILD_BEAST_2" 

	xmlns:fx="javafx:com.sun.javafx.tools.ant">

    <description>

        Build BEAST 2.

        Also used by Hudson BEAST_2 project.
@@ -89,6 +90,7 @@ 
        <delete file="${build}/beast/app/treeannotator/TreeAnnotatorLauncher.class" />

        <delete file="${build}/beast/app/util/Utils6.class" />

        <delete file="${build}/beast/app/BEASTVersion.class" />

        <delete file="${build}/beast/util/BEASTClassLoader.class" />

        <delete>

	      <fileset dir="${build}/beast/core/util/" includes="Log*.class" />

    	  <fileset dir="${build}/beast/app/beastapp/" includes="BeastLauncher*.class" />
@@ -113,6 +115,7 @@ 
            <include name="beast/util/Package*.java" />

            <include name="beast/app/util/Arguments.java" />

            <include name="beast/core/util/Log.java" />

	    <include name="beast/util/BEASTClassLoader.java" />

        </javac>

        <copy todir="${build}">

            <fileset dir="${src}" includes="**/*.properties" />
@@ -145,6 +148,27 @@ 
            <zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />

            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>

        </jar>

        

        

        <jar jarfile="${dist}/beauti.jar">

            <manifest>

                <attribute name="Built-By" value="${user.name}" />

                <attribute name="Main-Class" value="beast.app.beauti.Beauti" />

            </manifest>

            <fileset dir="${build}">

                <include name="beast/**/*.class" />

                <include name="beast/**/*.properties" />

                <include name="beast/**/*.png" />

                <include name="beagle/**/*.class" />

                <include name="org/**/*.class" />

            </fileset>

            <zipgroupfileset dir="${lib}" includes="jam.jar" />

            <zipgroupfileset dir="${lib}" includes="beagle.jar" />

            <zipgroupfileset dir="${lib}" includes="colt.jar" />

            <zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />

            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>

        </jar>

        

        <jar jarfile="${dist}/launcher.jar">

            <fileset dir="${build}">

                <include name="beast/**/*Launcher*.class" />
@@ -155,10 +179,13 @@ 
                <include name="beast/**/Version.class" />

		    	<include name="beast/app/util/Arguments*.class" />

                <include name="beast/util/Package*.class" />

		<include name="beast/util/BEASTClassLoader.class" />

                <include name="beast/app/draw/icons/beauti.png"/>

                <include name="beast/core/util/Log*.class" />

           </fileset>

        </jar>

        



        <jar jarfile="${dist}/beast.src.jar">

            <fileset dir="${src}">

                <include name="beast/**/*.java" />
@@ -256,10 +283,10 @@ 




    <!-- Release -->

    <property name="version" value="2.5.2" />

    <property name="version_number" value="2.5.2" />

    <property name="version" value="2.5.3" />

    <property name="version_number" value="2.5.3" />

    <property name="release_dir" value="release" />

    <property name="copyright" value="Beast 2 development team 2011-2018" />

    <property name="copyright" value="Beast 2 development team 2011-2019" />



    <property name="BEAST_name" value="BEAST" />

    <property name="beast_name" value="beast" />
@@ -1053,6 +1080,8 @@ 
    </target>





	<property environment="env"/>

	

    <!-- Create the app bundle -->

    <target name="macjre">

        <delete dir="${Mac_package_dir}" />
@@ -1300,6 +1329,214 @@ 






	<target name="init-fx-tasks">

		<echo message="java.home = ${java.home} "/>

		<path id="fxant">

			<filelist>

				<file name="${java.home}/../lib/ant-javafx.jar"/>

				<file name="${java.home}/../lib/jfxrt.jar"/> <!-- jdk9, jdk10 -->

				<file name="${java.home}/../jre/lib/ext/jfxrt.jar"/> <!-- jdk8 -->

			</filelist>

		</path>

	

		<taskdef resource="com/sun/javafx/tools/ant/antlib.xml"      

			uri="javafx:com.sun.javafx.tools.ant"

			classpathref="fxant"/>



	</target>



    <!-- Create the app bundle -->

    <target name="macjre3" depends="init-fx-tasks">

    



        <delete dir="${Mac_package_dir}" />

        <!--<delete file="${Mac_dir}/pack.temp.dmg"/>-->

        <delete file="${Mac_dir}/BEAST v${version}.dmg"/>

        <!-- Create the release directory -->

        <mkdir dir="${Mac_package_dir}" />



        <copy todir="${Mac_package_dir}/bin">

            <fileset dir="${Linux_dir}/jrebin" />

        </copy>

        <chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**" />



        <copy todir="${Mac_package_dir}/examples/">

            <fileset dir="examples/">

                <include name="*.xml" />

                <include name="nexus/**" />

                <exclude name="benchmark/**" />

            </fileset>

        </copy>



<!--    <copy file="${dist}/beauti.jar" todir="${Mac_package_dir}/lib" /> -->

        <copy file="${dist}/launcher.jar" todir="${Mac_package_dir}/lib" />

        <copy file="${dist}/beast.jar" todir="${Mac_package_dir}/lib" />

        <copy file="${dist}/beast.src.jar" todir="${Mac_package_dir}/lib" />

        <!-- <copy file="${dist}/beast-beagle.jar" todir="${Mac_package_dir}/lib"/>

        <copy todir="${Mac_package_dir}/lib">

            <fileset dir="${Mac_dir}/lib" />

        </copy> -->



        <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Mac_package_dir}" />

        <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}" />

        <copy file="${common_dir}/LICENSE.txt" todir="${Mac_package_dir}" />

        

        

		<!--

		<fx:signjar destdir="/tmp" alias="${AppleSigner}" verbose="true" storePass="" keyPass="">

			<fx:fileset dir='${dist}' includes='*.jar'/>

		</fx:signjar>

		-->

		

		<fx:resources id="appRes">

			<fx:fileset dir="${dist}" includes="launcher.jar"/>

			<fx:fileset dir="${dist}" includes="beast.jar"/>

			<!--

			<fx:fileset dir="${dist}" includes="beast.src.jar"/>

  	        <fx:fileset dir="${common_dir}" includes="VERSION HISTORY.txt"/>

    	    <fx:fileset dir="${common_dir}" includes="README.txt"/>

        	<fx:fileset dir="${common_dir}" includes="LICENSE.txt"/>

            <fx:fileset dir="./examples/" includes="*.xml" />

            <fx:fileset dir="./examples/nexus" includes="**" />

            <fx:fileset dir="./templates" includes="**" />

            -->

		</fx:resources> 

		

		<fx:application id="fxApplication"

			name="${BEAST_name}"

			mainClass="beast.app.beastapp.BeastMain"

			toolkit="fx"

		    version="${version}"

		>

            <fx:argument>-window</fx:argument>

            <fx:argument>-working</fx:argument>

            <fx:argument>-options</fx:argument>

		</fx:application>

	

		<mkdir dir="${Mac_package_dir}/build/classes/META-INF" />

		

				<fx:deploy

			embedJNLP="true"

			extension="false"

			width="1200" height="800" 

			includeDT="false"

			offlineAllowed="true"

			outdir="${Mac_package_dir}"

			outfile="${BEAUti_name}" 

			nativeBundles="image"

			updatemode="background" >

	

	    	<fx:info title="${BEAUti_name}" vendor="${appVendor}"

            	copyright="${BEAUti_name}, ${copyright}" description="${BEAUti_name}">

        		<fx:icon href="${common_dir}/icons/beauti.icns"/>   

    		</fx:info>

			<fx:application id="BEAUtiApplication"

				name="${BEAUti_name}"

				mainClass="beast.app.beauti.Beauti"

				toolkit="fx"

			    version="${version}"

			>

            	<fx:argument>-capture</fx:argument>

			</fx:application>

			<fx:resources id="appResBEAUti">

				<fx:fileset dir="${dist}" includes="beauti.jar"/>

			</fx:resources> 

			<fx:platform>

            	<fx:jvmarg value="-Xmx4g"/>

	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>

    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>

        	    <fx:jvmarg value="-Duser.language=en"/>            

            	<fx:jvmarg value="-Dbeast.load.jars=true"/>

			</fx:platform>







<!--

			<fx:secondaryLauncher name="BEAUti"

			    mainClass="beast.app.beauti.Beauti"

			    version="${version}"

			    title="BEAUti"

			    description="BEAUti"

			    copyright="${copyright}"

			    menu="true"

     			shortcut="false"

     		>

     			<fx:argument>-capture</fx:argument>

            	<fx:jvmarg value="-Xmx4g"/>

	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>

    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>

        	    <fx:jvmarg value="-Duser.language=en"/>            

            	<fx:jvmarg value="-Dbeast.load.jars=true"/>

			</fx:secondaryLauncher>

-->			

		</fx:deploy>

		

		<!-- Need to use ${basedir} because somehow the ant task is calculating the directory differently -->

		<fx:deploy

			embedJNLP="true"

			extension="false"

			width="1200" height="800" 

			includeDT="false"

			offlineAllowed="true"

			outdir="${Mac_package_dir}"

			outfile="${BEAST_name}" 

			nativeBundles="image"

			updatemode="background" >

	

	    	<fx:info title="${BEAST_name}" vendor="${appVendor}"

            	copyright="${BEAST_name}, ${copyright}" description="${BEAST_name}">

        		<fx:icon href="${common_dir}/icons/beast.icns"/>   

    		</fx:info>

			<fx:application refId="fxApplication"/>

			<fx:resources id="appResBEAUST">

				<fx:fileset dir="${dist}" includes="beast.jar"/>

			</fx:resources> 

			<fx:platform>

            	<fx:jvmarg value="-Xmx4g"/>

	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>

    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>

        	    <fx:jvmarg value="-Duser.language=en"/>            

            	<fx:jvmarg value="-Dbeast.load.jars=true"/>

			</fx:platform>







<!--

			<fx:secondaryLauncher name="BEAUti"

			    mainClass="beast.app.beauti.Beauti"

			    version="${version}"

			    title="BEAUti"

			    description="BEAUti"

			    copyright="${copyright}"

			    menu="true"

     			shortcut="false"

     		>

     			<fx:argument>-capture</fx:argument>

            	<fx:jvmarg value="-Xmx4g"/>

	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>

    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>

        	    <fx:jvmarg value="-Duser.language=en"/>            

            	<fx:jvmarg value="-Dbeast.load.jars=true"/>

			</fx:secondaryLauncher>

-->			

		</fx:deploy>







        <echo message="Signing..." />



        <exec executable="codesign">

            <arg value="-s"/>

            <arg value="${AppleSigner}"/>

            <arg value="-v"/>

            <arg value="${Mac_dir}/${BEAST_name}/BEAST-${version}.dmg"/>

        </exec>



        <echo message="Mac with JRE version release is finished." />

    </target>









    <target name="doc" description="Create Developer Docs for Beast 2" depends='javadoc'>

        <copy file="doc/tutorial.slides.part1.pdf" tofile="release/common/doc/develop/" />

examples/testHKY.json

+21 −30
Original line number Diff line number Diff line 
{version: "2.3",

{version: "2.5",

namespace: "beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood",



// this is a comment, which is non-standard JSON
@@ -10,40 +10,32 @@ map: [ 
],



beast: [

	{id: "alignment.org",

	{id: "alignment",

	 spec: "Alignment",

	 bonobo    :"AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA",

	 chimp     :"AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA",

	 gorilla   :"AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA",

	 human     :"AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA",

	 orangutan :"AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA",

	 siamang   :"AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA"

	 sequence: [

		 {spec: "Sequence", totalcount: 4, taxon: "human", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA\n " },

		 {spec: "Sequence", totalcount: 4, taxon: "chimp", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA\n " },

		 {spec: "Sequence", totalcount: 4, taxon: "bonobo", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA\n " },

		 {spec: "Sequence", totalcount: 4, taxon: "gorilla", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA\n " },

		 {spec: "Sequence", totalcount: 4, taxon: "orangutan", value: "\n AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA\n " },

		 {spec: "Sequence", totalcount: 4, taxon: "siamang", value: "\n AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA\n " }

	  ]

	},



	{id: "mcmc",

	 spec: "MCMC", chainLength: 10000000,

	 state: { storeEvery: 100000,

		 stateNode: [

			 {id: "hky.kappa", lower: 0.0, value: [ 1.0 ] },

			 {id: "tree", spec: "beast.evolution.tree.Tree" }

		  ]

		},

	 spec: "MCMC", chainLength: "5000000", preBurnin: 50000,

	 init: [

		{id: "coalescentSimulator",

		 spec: "beast.evolution.tree.RandomTree", initial: "@tree",

		 taxa: {id: "alignment",

			 spec: "FilteredAlignment", filter: "::", data: "@alignment.org",

				 constantSiteWeights: { lower: 0, upper: 0, dimension: 4, value: [ 100, 200, 300, 400 ] }

			},

		 populationModel: {spec: "ConstantPopulation",

				 popSize: { value: [ 1.0 ] }

			}

		 spec: "beast.evolution.tree.RandomTree", taxa: "@alignment",

			 populationModel: {spec: "ConstantPopulation", popSize: "1.0" },

			 initial: {id: "tree", spec: "beast.evolution.tree.Tree" }

		}

	  ],

	 distribution: {id: "posterior",

		 spec: "util.CompoundDistribution",

		 distribution: [

			{spec: "beast.math.distributions.Prior", x: "@hky.kappa",

			{spec: "beast.math.distributions.Prior",

				 x: {id: "hky.kappa", spec: "parameter.RealParameter", lower: 0.0, value: [ 1.0 ] },

				 distr: {spec: "beast.math.distributions.OneOnX" }

			},

			{id: "treeLikelihood",
@@ -52,7 +44,7 @@ beast: [ 
				 spec: "SiteModel", gammaCategoryCount: 1,

				 substModel: {id: "hky",

					 spec: "HKY", kappa: "@hky.kappa",

						 frequencies: {id: "freqs", data: "@alignment" }

						 frequencies: {id: "freqs", spec: "Frequencies", data: "@alignment" }

					}

				}

			}
@@ -61,27 +53,26 @@ beast: [ 
	 operator: [

		 {id: "kappaScaler", spec: "ScaleOperator", parameter: "@hky.kappa", scaleFactor: 0.5, weight: 1.0 },

		 {id: "treeScaler", spec: "ScaleOperator", tree: "@tree", scaleFactor: 0.5, weight: 1.0 },

		 {id: "subtreeSlide1", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },

		 {id: "subtreeSlide", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },

		 {id: "uniform", spec: "Uniform", tree: "@tree", weight: 10.0 },

		 {id: "subtreeSlide2", spec: "SubtreeSlide", optimise: false, tree: "@tree", weight: 5.0 },

		 {id: "narrow", spec: "Exchange", tree: "@tree", weight: 1.0 },

		 {id: "wide", spec: "Exchange", isNarrow: false, tree: "@tree", weight: 1.0 },

		 {id: "wilsonBalding", spec: "WilsonBalding", tree: "@tree", weight: 1.0 }

	  ],

	 logger: [

		{ fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",

		{spec: "Logger", fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",

		 log: [

			 {idref: "treeLikelihood" },

			 {idref: "hky.kappa" },

			 {spec: "beast.evolution.tree.TreeHeightLogger", tree: "@tree" }

		  ]

		},

		{ fileName: "test.$(seed).trees", logEvery: 10000,

		{spec: "Logger", fileName: "test.$(seed).trees", logEvery: 10000,

		 log: [

			 {idref: "tree" }

		  ]

		},

		{ logEvery: 10000, model: "@treeLikelihood",

		{spec: "Logger", logEvery: 10000, model: "@treeLikelihood",

		 log: [

			 {idref: "treeLikelihood" },

			 {spec: "util.ESS", arg: "@treeLikelihood" },

examples/testUCLNclock.json

+12 −8

File changed.

Preview size limit exceeded, changes collapsed.

release/Windows/AppLauncher_launch4j.xml

+1 −1
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ 
  </jre>    

  <versionInfo>

    <fileDescription>AppLauncher</fileDescription>

    <copyright>Beast 2 development team 2002-2018</copyright>

    <copyright>Beast 2 development team 2002-2019</copyright>

    <productName>AppLauncher</productName>

    <internalName>AppLauncher</internalName>

    <originalFilename>AppLauncher.exe</originalFilename>

release/Windows/AppLauncher_launch4j_jre.xml

+1 −1
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ 
  </jre>    

  <versionInfo>

    <fileDescription>AppLauncher</fileDescription>

    <copyright>Beast 2 development team 2002-2018</copyright>

    <copyright>Beast 2 development team 2002-2019</copyright>

    <productName>AppLauncher</productName>

    <internalName>AppLauncher</internalName>

    <originalFilename>AppLauncher.exe</originalFilename>