Tagged version for the new release.

beast-dev · Feb 15, 2013 · c6ba467 · c6ba467
1 parent 4861565
commit c6ba467
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Showing 425 changed files with 8,375 additions and 38,334 deletions.
diff --git a/.classpath b/.classpath
@@ -10,11 +10,11 @@
 	<classpathentry kind="lib" path="lib/jebl.jar"/>
 	<classpathentry kind="lib" path="lib/JRI.jar"/>
 	<classpathentry kind="lib" path="lib/junit-4.4.jar"/>
+	<classpathentry kind="lib" path="lib/libjri.jnilib"/>
 	<classpathentry kind="lib" path="lib/mpj.jar"/>
 	<classpathentry kind="lib" path="lib/mtj.jar"/>
 	<classpathentry kind="lib" path="lib/options.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
-
diff --git a/build.xml b/build.xml
@@ -5,8 +5,6 @@
         $Id: build_BEAST_MCMC.xml,v 1.5 2009/04/15 Walter Xie Exp $
     </description>
 
-    <property name="JDK_VERSION" value="1.6"/>
-
     <!-- set global properties for this build -->
     <property name="src" location="src"/>
     <property name="build" location="build"/>
@@ -49,7 +47,7 @@
         <mkdir dir="${build}"/>
 
         <!-- Compile the java code from ${src} into ${build} /bin -->
-        <javac source="${JDK_VERSION}" target="${JDK_VERSION}" srcdir="${src}" destdir="${build}" classpathref="classpath"
+        <javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}" classpathref="classpath"
                fork="true"
                memoryinitialsize="256m"
                memorymaximumsize="1024m">
@@ -266,8 +264,8 @@
     </target>
 
 
-    <property name="version" value="1.8.0pre"/>
-    <property name="version_number" value="1.8.0"/>
+    <property name="version" value="1.7.5"/>
+    <property name="version_number" value="1.7.5"/>
     <property name="release_dir" value="release"/>
     <property name="BEAST_name" value="BEAST"/>
     <property name="BEASTMC3_name" value="BEASTMC3"/>
@@ -484,7 +482,7 @@
                     vmoptions="-Xmx1024M"
                     arguments="-window -working -options"
                     version="${version}"
-                    infostring="${BEAST_name} v${version}, Copyright 2002-2012, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    infostring="${BEAST_name} v${version}, Copyright 2002-2013, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
                     bundleid="dr.app.beast">
             <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
             <javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib"/>
@@ -505,7 +503,7 @@
                     vmoptions="-Xmx1024M"
                     arguments="-window -working -options"
                     version="${version}"
-                    infostring="${BEASTMC3_name} v${version}, Copyright 2002-2012, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    infostring="${BEASTMC3_name} v${version}, Copyright 2002-2013, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
                     bundleid="dr.app.beast">
             <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
             <javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib"/>
@@ -526,7 +524,7 @@
                     vmoptions="-Xmx1024M"
                     arguments=""
                     version="${version}"
-                    infostring="${BEAUti_name} v${version}, Copyright 2002-2012, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    infostring="${BEAUti_name} v${version}, Copyright 2002-2013, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
                     bundleid="dr.app.beauti">
             <documenttype name="BEAUti document"
                           extensions="beauti bti"
@@ -553,7 +551,7 @@
                     vmoptions="-Xmx1024M"
                     arguments=""
                     version="${version}"
-                    infostring="${LogCombiner_name} v${version}, Copyright 2002-2012, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    infostring="${LogCombiner_name} v${version}, Copyright 2002-2013, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
                     bundleid="dr.app.tools.logcombiner">
             <jarfileset dir="${Mac_package_dir}/lib">
                 <include name="**/beast.jar"/>
@@ -587,7 +585,7 @@
                     vmoptions="-Xmx1024M"
                     arguments=""
                     version="${version}"
-                    infostring="${TreeStat_name} v${version}, Copyright 2002-2012, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
+                    infostring="${TreeStat_name} v${version}, Copyright 2002-2013, Alexei Drummond, Andrew Rambaut, Marc Suchard and Walter Xie"
                     bundleid="dr.app.treestat">
             <jarfileset dir="${Mac_package_dir}/lib">
                 <include name="**/beast.jar"/>

diff --git a/build_bss.xml b/build_bss.xml
diff --git a/build_eclipse.xml b/build_eclipse.xml
@@ -14,7 +14,7 @@
         <pathelement location="bin"/>
         <pathelement location="lib/beagle.jar"/>
         <pathelement location="lib/colt.jar"/>
-        <pathelement location="lib/commons-math-2.2.jar"/>
+        <pathelement location="lib/commons-math-2.0.jar"/>
         <pathelement location="lib/figtreepanel.jar"/>
         <pathelement location="lib/itext-1.4.5.jar"/>
         <pathelement location="lib/jam.jar"/>

diff --git a/build_tracer.xml b/build_tracer.xml
@@ -56,7 +56,7 @@
     <target name="compile-basic" depends="init">
         <!-- Compile the java code from ${src} into ${build} -->
         <javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}"
-               classpath="${lib}/colt.jar:${lib}/commons-math-2.2.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
+               classpath="${lib}/colt.jar:${lib}/commons-math-2.0.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
             <include name="dr/app/tracer/**"/>
             <include name="dr/app/util/**"/>
             <include name="dr/app/gui/**"/>
@@ -145,7 +145,7 @@
 
     <!-- Need to either install Launch4j under {BEAST workspace}/${release}
                  or install it in the default directory and change the location of launch4j.dir -->
-    <target name="windows" depends="dist" description="release Windows version of Tracer">
+    <target name="windows_Release" depends="dist" description="release Windows version of Tracer">
 
         <delete dir="${Windows_package_dir}" />
         <!-- Create the release directory -->
@@ -176,7 +176,7 @@
         <echo message="Windows version release is finished." />
     </target>
 
-    <target name="linux" description="release Linux/Unix version of Tracer">
+    <target name="linux_unix_Release" description="release Linux/Unix version of Tracer">
         <delete dir="${Linux_package_dir}" />
         <!-- Create the release directory -->
         <mkdir dir="${Linux_package_dir}" />
@@ -199,7 +199,7 @@
         <echo message="Linux/Unix version release is finished." />
     </target>
 
-    <target name="mac"
+    <target name="mac_Release"
                                    description="release Mac version of Tracer">
         <delete dir="${Mac_package_dir}" />
         <!-- Create the release directory -->

diff --git a/examples/release/continuousTraits/RacRABV.nex b/examples/release/continuousTraits/RacRABV.nex
diff --git a/examples/release/continuousTraits/RacRABVLocations.txt b/examples/release/continuousTraits/RacRABVLocations.txt
@@ -0,0 +1,48 @@
+Traits	Lat	Long
+hOH10_97.2	41.053	80.706
+hWVa01_93.2	40.505	80.575
+NY01_03.4	41.057	73.794
+NY03_03.4	42.934	76.565
+NY04_03.4	42.617	75.037
+NY12_03.4	42.996	78.170
+NY516_92.5	42.137	75.888
+NY771_92.5	41.125	74.015
+PA.R89_89.6	40.803	75.031
+PA11_04.7	40.033	78.480
+PA13_04.7	40.871	79.930
+PA23_04.6	39.924	78.091
+PA28_04.5	40.588	77.634
+PA30_04.2	39.998	79.029
+PA39_04.7	40.326	79.562
+PA62_03.2	40.183	80.139
+rDE01_87.7	39.696	75.612
+rMA01_92.7	42.330	71.840
+rMD03_82.7	39.615	77.774
+rMD06_82.2	39.622	78.803
+rNC01_92.1	35.916	77.640
+rNH01_92.0	42.896	71.583
+rNH02_92.3	43.896	71.895
+rNH03_92.9	42.963	71.078
+rNJ02_94.3	39.088	74.799
+rNJ08_03.4	41.100	74.665
+rNJ10_03.5	39.955	74.776
+rPA04_04.5	41.537	75.961
+rTN02_03.4	36.310	82.188
+rVA01_84.1	38.213	77.598
+rVA04_85.3	37.714	77.444
+rVA05_89.0	36.886	76.260
+rVA06_92.4	37.174	80.395
+rVA07_92.4	37.250	80.000
+rVA08_94.0	37.797	75.635
+rVA14_94.8	38.024	78.535
+rVT01_94.5	43.029	73.108
+rWV01_87.6	39.090	79.180
+WV19_02.6	39.304	77.842
+WV23_02.7	39.433	78.936
+WV26_03.8	39.129	80.008
+WVa02_02.6	37.901	80.508
+WVa03_02.6	37.565	80.574
+WVa04_02.6	37.347	81.155
+WVa08_02.6	38.677	79.349
+WVa14_02.7	39.050	78.886
+WVa22_02.7	39.635	79.995