[med-svn] [librdp-taxonomy-tree-java] 09/14: New upstream version 1.2.0
Andreas Tille
tille at debian.org
Thu Nov 30 15:37:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository librdp-taxonomy-tree-java.
commit a929c263b0689b0228ae7bf3eb1ac110eb4ab4f0
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 30 16:24:46 2017 +0100
New upstream version 1.2.0
---
.gitignore | 8 +
LICENSE | 619 +++++++++
README | 1 +
build.xml | 151 +++
debian/changelog | 17 -
debian/compat | 1 -
debian/control | 22 -
debian/copyright | 16 -
debian/jlibs | 1 -
debian/rules | 18 -
debian/source/format | 1 -
debian/watch | 3 -
ivy.xml | 6 +
manifest.mf | 3 +
nbproject/build-impl.xml | 1421 ++++++++++++++++++++
nbproject/genfiles.properties | 8 +
nbproject/project.properties | 75 ++
nbproject/project.xml | 25 +
src/edu/msu/cme/rdp/taxatree/ConcretRoot.java | 74 +
src/edu/msu/cme/rdp/taxatree/Node.java | 34 +
src/edu/msu/cme/rdp/taxatree/Taxon.java | 77 ++
src/edu/msu/cme/rdp/taxatree/TaxonHolder.java | 188 +++
src/edu/msu/cme/rdp/taxatree/VisitInfo.java | 66 +
.../cme/rdp/taxatree/interfaces/TreeVisitor.java | 35 +
.../cme/rdp/taxatree/utils/NewickPrintVisitor.java | 101 ++
.../cme/rdp/taxatree/utils/NewickTreeBuilder.java | 205 +++
.../msu/cme/rdp/taxatree/utils/PrintVisitor.java | 72 +
.../rdp/taxatree/utils/NewickPrintVisitorTest.java | 47 +
.../rdp/taxatree/utils/NewickTreeBuilderTest.java | 58 +
.../cme/rdp/taxatree/utils/PrintVisitorTest.java | 51 +
30 files changed, 3325 insertions(+), 79 deletions(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..d07fff2
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+.svn
+build
+dist
+*~
+#*#
+*tmp*
+lib/
+private/
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..bc08fe2
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,619 @@
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+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
diff --git a/README b/README
new file mode 100644
index 0000000..2608f60
--- /dev/null
+++ b/README
@@ -0,0 +1 @@
+The TaxonomyTree project is a library used by other RDP tools
diff --git a/build.xml b/build.xml
new file mode 100644
index 0000000..fb26f18
--- /dev/null
+++ b/build.xml
@@ -0,0 +1,151 @@
+<?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.) -->
+<!-- By default, only the Clean and Build commands use this build script. -->
+<!-- Commands such as Run, Debug, and Test only use this build script if -->
+<!-- the Compile on Save feature is turned off for the project. -->
+<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
+<!-- in the project's Project Properties dialog box.-->
+<project name="RDPTaxonomyTree" default="default" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant" xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3">
+ <description>Builds, tests, and runs the project RDPTaxonomyTree.</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="${build.classes.dir}"/>
+ </obfuscate>
+ </target>
+
+ For list of available properties check the imported
+ nbproject/build-impl.xml file.
+
+
+ Another way to customize the build is by overriding existing main targets.
+ The targets of interest are:
+
+ -init-macrodef-javac: defines macro for javac compilation
+ -init-macrodef-junit: defines macro for junit execution
+ -init-macrodef-debug: defines macro for class debugging
+ -init-macrodef-java: defines macro for class execution
+ -do-jar-with-manifest: JAR building (if you are using a manifest)
+ -do-jar-without-manifest: JAR building (if you are not using a manifest)
+ run: execution of project
+ -javadoc-build: Javadoc generation
+ test-report: JUnit report generation
+
+ An example of overriding the target for project execution could look like this:
+
+ <target name="run" depends="RDPTaxonomyTree-impl.jar">
+ <exec dir="bin" executable="launcher.exe">
+ <arg file="${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.
+
+ -->
+ <property name="ivy.install.version" value="2.1.0-rc2" />
+ <condition property="ivy.home" value="${env.IVY_HOME}">
+ <isset property="env.IVY_HOME" />
+ </condition>
+ <property name="ivy.home" value="${user.home}/.ant" />
+ <property name="ivy.jar.dir" value="${ivy.home}/lib" />
+ <property name="ivy.jar.file" value="${ivy.jar.dir}/ivy.jar" />
+
+ <target name="download-ivy" unless="offline">
+
+ <mkdir dir="${ivy.jar.dir}"/>
+ <!-- download Ivy from web site so that it can be used even without any special installation -->
+ <get src="http://repo2.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/ivy-${ivy.install.version}.jar"
+ dest="${ivy.jar.file}" usetimestamp="true"/>
+ </target>
+
+ <target name="init-ivy" depends="download-ivy">
+ <!-- try to load ivy here from ivy home, in case the user has not already dropped
+ it into ant's lib dir (note that the latter copy will always take precedence).
+ We will not fail as long as local lib dir exists (it may be empty) and
+ ivy is in at least one of ant's lib dir or the local lib dir. -->
+ <path id="ivy.lib.path">
+ <fileset dir="${ivy.jar.dir}" includes="*.jar"/>
+
+ </path>
+ <taskdef resource="org/apache/ivy/ant/antlib.xml"
+ uri="antlib:org.apache.ivy.ant" classpathref="ivy.lib.path"/>
+ </target>
+
+ <target name="resolve" description="--> retrieve dependencies with ivy" depends="init-ivy">
+ <ivy:retrieve />
+ </target>
+
+ <target name="-pre-compile" depends="resolve" />
+
+ <target depends="resolve,init,compile,-pre-jar,-post-jar" description="Build JAR." name="jar">
+ <property location="${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="${run.classpath.without.build.classes.dir}"/>
+ <chainedmapper>
+ <flattenmapper/>
+ <globmapper from="*" to="lib/*"/>
+ </chainedmapper>
+ </pathconvert>
+ <copy todir="${dist.dir}/lib" flatten="true">
+ <path>
+ <pathelement path="${run.classpath.without.build.classes.dir}"/>
+ </path>
+ </copy>
+ <j2seproject1:jar manifest="${manifest.file}">
+ <j2seproject1:manifest>
+ <j2seproject1:attribute name="Main-Class" value="${main.class}"/>
+ <j2seproject1:attribute name="Class-Path" value="${jar.classpath}"/>
+ <!-- if you deal with versions -->
+ <!-- j2seproject1:attribute name="Build-Version" value="${version}" / -->
+ </j2seproject1:manifest>
+ </j2seproject1:jar>
+ <echo>To run this application from the command line without Ant, try:</echo>
+ <property location="${dist.jar}" name="dist.jar.resolved"/>
+ <echo>java -jar "${dist.jar.resolved}"</echo>
+ </target>
+
+ <target name="junit" depends="compile-test">
+ <junit printsummary="yes" haltonfailure="yes" showoutput="yes">
+ <classpath path="${javac.test.classpath}:${build.classes.dir}:${build.test.classes.dir}"/>
+
+ <formatter type="xml"/>
+
+ <batchtest fork="yes">
+ <fileset dir="${test.src.dir}" includes="**/*Test.java"/>
+ </batchtest>
+ </junit>
+</target>
+</project>
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index af59960..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,17 +0,0 @@
-librdp-taxonomy-tree-java (1.2.0-1) unstable; urgency=medium
-
- * Initial upload to Debian (Closes: #779567)
-
- -- Andreas Tille <tille at debian.org> Sun, 01 Mar 2015 18:10:55 +0100
-
-librdp-taxonomy-tree-java (0.1.20140606-0biolinux1) trusty; urgency=medium
-
- * New upstream for rdp-classifier 2.9
-
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 06 Oct 2014 18:20:47 +0100
-
-librdp-taxonomy-tree-java (0.1.20130830-0biolinux1) trusty; urgency=low
-
- * Initial package to help rdp-classifier
-
- -- Tim Booth <tbooth at ceh.ac.uk> Wed, 30 Apr 2014 17:40:04 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 2b7bc12..0000000
--- a/debian/control
+++ /dev/null
@@ -1,22 +0,0 @@
-Source: librdp-taxonomy-tree-java
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
-Section: java
-Priority: optional
-Build-Depends: debhelper (>= 9),
- default-jdk,
- javahelper
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/librdp-taxonomy-tree-java/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/librdp-taxonomy-tree-java/trunk/
-Homepage: https://github.com/rdpstaff/TaxonomyTree
-
-Package: librdp-taxonomy-tree-java
-Architecture: all
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${java:Depends}
-Description: taxonomy tree library from Ribosomal Database Project (RDP)
- The TaxonomyTree project is a library used by other Ribosomal Database
- Project (RDP) tools.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index b9b9b67..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,16 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: TaxonomyTree
-Upstream-Contact: https://github.com/wangqion
-Source: https://github.com/rdpstaff/TaxonomyTree/releases
-
-Files: *
-Copyright: Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
-License: GPL-3
-
-Files: debian/*
-Copyright: © Tim Booth <tbooth at ceh.ac.uk>
-License: GPL-3
-
-License: GPL-3
- On Debian systems, you can read the full text of the GNU General Public
- License in ‘/usr/share/common-licenses/GPL-3’.
diff --git a/debian/jlibs b/debian/jlibs
deleted file mode 100644
index d392f0e..0000000
--- a/debian/jlibs
+++ /dev/null
@@ -1 +0,0 @@
-*.jar
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 7abf8f0..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/make -f
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-
-%:
- dh $@ --with javahelper
-
-override_dh_auto_clean:
- true
-
-override_dh_clean:
- dh_clean
- rm -f debian/*.log *.jar
-
-override_dh_auto_build:
- jh_build rdp-taxonomy-tree.jar src
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 4c8f96d..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-
-https://github.com/rdpstaff/TaxonomyTree/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
diff --git a/ivy.xml b/ivy.xml
new file mode 100644
index 0000000..fcc2977
--- /dev/null
+++ b/ivy.xml
@@ -0,0 +1,6 @@
+<ivy-module version="2.0">
+ <info organisation="edu.cme.rdp" module="RDPTaxonomyTree"/>
+ <dependencies>
+ <dependency org="junit" name="junit" rev="4.8.2"/>
+ </dependencies>
+</ivy-module>
\ No newline at end of file
diff --git a/manifest.mf b/manifest.mf
new file mode 100644
index 0000000..328e8e5
--- /dev/null
+++ b/manifest.mf
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
diff --git a/nbproject/build-impl.xml b/nbproject/build-impl.xml
new file mode 100644
index 0000000..ecb81ea
--- /dev/null
+++ b/nbproject/build-impl.xml
@@ -0,0 +1,1421 @@
+<?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
+ - test compilation
+ - test execution
+ - test debugging
+ - applet
+ - cleanup
+
+ -->
+<project xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" basedir=".." default="default" name="TaxonomyTree-impl">
+ <fail message="Please build using Ant 1.8.0 or higher.">
+ <condition>
+ <not>
+ <antversion atleast="1.8.0"/>
+ </not>
+ </condition>
+ </fail>
+ <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"/>
+ </target>
+ <target depends="-pre-init,-init-private" name="-init-user">
+ <property file="${user.properties.file}"/>
+ <!-- The two properties below are usually overridden -->
+ <!-- by the active platform. Just a fallback. -->
+ <property name="default.javac.source" value="1.4"/>
+ <property name="default.javac.target" value="1.4"/>
+ </target>
+ <target depends="-pre-init,-init-private,-init-user" name="-init-project">
+ <property file="nbproject/configs/${config}.properties"/>
+ <property file="nbproject/project.properties"/>
+ </target>
+ <target depends="-pre-init,-init-private,-init-user,-init-project,-init-macrodef-property" name="-do-init">
+ <property name="platform.java" value="${java.home}/bin/java"/>
+ <available file="${manifest.file}" property="manifest.available"/>
+ <condition property="splashscreen.available">
+ <and>
+ <not>
+ <equals arg1="${application.splash}" arg2="" trim="true"/>
+ </not>
+ <available file="${application.splash}"/>
+ </and>
+ </condition>
+ <condition property="main.class.available">
+ <and>
+ <isset property="main.class"/>
+ <not>
+ <equals arg1="${main.class}" arg2="" trim="true"/>
+ </not>
+ </and>
+ </condition>
+ <condition property="profile.available">
+ <and>
+ <isset property="javac.profile"/>
+ <length length="0" string="${javac.profile}" when="greater"/>
+ <matches pattern="1\.[89](\..*)?" string="${javac.source}"/>
+ </and>
+ </condition>
+ <condition property="do.archive">
+ <not>
+ <istrue value="${jar.archive.disabled}"/>
+ </not>
+ </condition>
+ <condition property="do.mkdist">
+ <and>
+ <isset property="do.archive"/>
+ <isset property="libs.CopyLibs.classpath"/>
+ <not>
+ <istrue value="${mkdist.disabled}"/>
+ </not>
+ </and>
+ </condition>
+ <condition property="do.archive+manifest.available">
+ <and>
+ <isset property="manifest.available"/>
+ <istrue value="${do.archive}"/>
+ </and>
+ </condition>
+ <condition property="do.archive+main.class.available">
+ <and>
+ <isset property="main.class.available"/>
+ <istrue value="${do.archive}"/>
+ </and>
+ </condition>
+ <condition property="do.archive+splashscreen.available">
+ <and>
+ <isset property="splashscreen.available"/>
+ <istrue value="${do.archive}"/>
+ </and>
+ </condition>
+ <condition property="do.archive+profile.available">
+ <and>
+ <isset property="profile.available"/>
+ <istrue value="${do.archive}"/>
+ </and>
+ </condition>
+ <condition property="have.tests">
+ <or>
+ <available file="${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="run.jvmargs.ide" 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="${file.encoding}"/>
+ <property name="runtime.encoding" value="${source.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>
+ <path id="endorsed.classpath.path" path="${endorsed.classpath}"/>
+ <condition else="" property="endorsed.classpath.cmd.line.arg" value="-Xbootclasspath/p:'${toString:endorsed.classpath.path}'">
+ <and>
+ <isset property="endorsed.classpath"/>
+ <not>
+ <equals arg1="${endorsed.classpath}" arg2="" trim="true"/>
+ </not>
+ </and>
+ </condition>
+ <condition else="" property="javac.profile.cmd.line.arg" value="-profile ${javac.profile}">
+ <isset property="profile.available"/>
+ </condition>
+ <condition else="false" property="jdkBug6558476">
+ <and>
+ <matches pattern="1\.[56]" string="${java.specification.version}"/>
+ <not>
+ <os family="unix"/>
+ </not>
+ </and>
+ </condition>
+ <property name="javac.fork" value="${jdkBug6558476}"/>
+ <property name="jar.index" value="false"/>
+ <property name="jar.index.metainf" value="${jar.index}"/>
+ <property name="copylibs.rebase" value="true"/>
+ <available file="${meta.inf.dir}/persistence.xml" property="has.persistence.xml"/>
+ <condition property="junit.available">
+ <or>
+ <available classname="org.junit.Test" classpath="${run.test.classpath}"/>
+ <available classname="junit.framework.Test" classpath="${run.test.classpath}"/>
+ </or>
+ </condition>
+ <condition property="testng.available">
+ <available classname="org.testng.annotations.Test" classpath="${run.test.classpath}"/>
+ </condition>
+ <condition property="junit+testng.available">
+ <and>
+ <istrue value="${junit.available}"/>
+ <istrue value="${testng.available}"/>
+ </and>
+ </condition>
+ <condition else="testng" property="testng.mode" value="mixed">
+ <istrue value="${junit+testng.available}"/>
+ </condition>
+ <condition else="" property="testng.debug.mode" value="-mixed">
+ <istrue value="${junit+testng.available}"/>
+ </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-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/j2se-project/1">
+ <attribute name="name"/>
+ <attribute name="value"/>
+ <sequential>
+ <property name="@{name}" value="${@{value}}"/>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-ap-cmdline-properties" if="ap.supported.internal" name="-init-macrodef-javac-with-processors">
+ <macrodef name="javac" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${src.dir}" name="srcdir"/>
+ <attribute default="${build.classes.dir}" name="destdir"/>
+ <attribute default="${javac.classpath}" name="classpath"/>
+ <attribute default="${javac.processorpath}" name="processorpath"/>
+ <attribute default="${build.generated.sources.dir}/ap-source-output" name="apgeneratedsrcdir"/>
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="${javac.debug}" name="debug"/>
+ <attribute default="${empty.dir}" name="sourcepath"/>
+ <attribute default="${empty.dir}" name="gensrcdir"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property location="${build.dir}/empty" name="empty.dir"/>
+ <mkdir dir="${empty.dir}"/>
+ <mkdir dir="@{apgeneratedsrcdir}"/>
+ <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
+ <src>
+ <dirset dir="@{gensrcdir}" erroronmissingdir="false">
+ <include name="*"/>
+ </dirset>
+ </src>
+ <classpath>
+ <path path="@{classpath}"/>
+ </classpath>
+ <compilerarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <compilerarg line="${javac.profile.cmd.line.arg}"/>
+ <compilerarg line="${javac.compilerargs}"/>
+ <compilerarg value="-processorpath"/>
+ <compilerarg path="@{processorpath}:${empty.dir}"/>
+ <compilerarg line="${ap.processors.internal}"/>
+ <compilerarg line="${annotation.processing.processor.options}"/>
+ <compilerarg value="-s"/>
+ <compilerarg path="@{apgeneratedsrcdir}"/>
+ <compilerarg line="${ap.proc.none.internal}"/>
+ <customize/>
+ </javac>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-ap-cmdline-properties" name="-init-macrodef-javac-without-processors" unless="ap.supported.internal">
+ <macrodef name="javac" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${src.dir}" name="srcdir"/>
+ <attribute default="${build.classes.dir}" name="destdir"/>
+ <attribute default="${javac.classpath}" name="classpath"/>
+ <attribute default="${javac.processorpath}" name="processorpath"/>
+ <attribute default="${build.generated.sources.dir}/ap-source-output" name="apgeneratedsrcdir"/>
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="${javac.debug}" name="debug"/>
+ <attribute default="${empty.dir}" name="sourcepath"/>
+ <attribute default="${empty.dir}" name="gensrcdir"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property location="${build.dir}/empty" name="empty.dir"/>
+ <mkdir dir="${empty.dir}"/>
+ <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
+ <src>
+ <dirset dir="@{gensrcdir}" erroronmissingdir="false">
+ <include name="*"/>
+ </dirset>
+ </src>
+ <classpath>
+ <path path="@{classpath}"/>
+ </classpath>
+ <compilerarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <compilerarg line="${javac.profile.cmd.line.arg}"/>
+ <compilerarg line="${javac.compilerargs}"/>
+ <customize/>
+ </javac>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-javac-with-processors,-init-macrodef-javac-without-processors" name="-init-macrodef-javac">
+ <macrodef name="depend" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${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="${includes}" srcdir="@{srcdir}">
+ <classpath>
+ <path path="@{classpath}"/>
+ </classpath>
+ </depend>
+ </sequential>
+ </macrodef>
+ <macrodef name="force-recompile" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${build.classes.dir}" name="destdir"/>
+ <sequential>
+ <fail unless="javac.includes">Must set javac.includes</fail>
+ <pathconvert pathsep="${line.separator}" property="javac.includes.binary">
+ <path>
+ <filelist dir="@{destdir}" files="${javac.includes}"/>
+ </path>
+ <globmapper from="*.java" to="*.class"/>
+ </pathconvert>
+ <tempfile deleteonexit="true" property="javac.includesfile.binary"/>
+ <echo file="${javac.includesfile.binary}" message="${javac.includes.binary}"/>
+ <delete>
+ <files includesfile="${javac.includesfile.binary}"/>
+ </delete>
+ <delete>
+ <fileset file="${javac.includesfile.binary}"/>
+ </delete>
+ </sequential>
+ </macrodef>
+ </target>
+ <target if="${junit.available}" name="-init-macrodef-junit-init">
+ <condition else="false" property="nb.junit.batch" value="true">
+ <and>
+ <istrue value="${junit.available}"/>
+ <not>
+ <isset property="test.method"/>
+ </not>
+ </and>
+ </condition>
+ <condition else="false" property="nb.junit.single" value="true">
+ <and>
+ <istrue value="${junit.available}"/>
+ <isset property="test.method"/>
+ </and>
+ </condition>
+ </target>
+ <target name="-init-test-properties">
+ <property name="test.binaryincludes" value="<nothing>"/>
+ <property name="test.binarytestincludes" value=""/>
+ <property name="test.binaryexcludes" value=""/>
+ </target>
+ <target if="${nb.junit.single}" name="-init-macrodef-junit-single" unless="${nb.junit.batch}">
+ <macrodef name="junit" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property name="junit.forkmode" value="perTest"/>
+ <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
+ <test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <formatter type="brief" usefile="false"/>
+ <formatter type="xml"/>
+ <jvmarg value="-ea"/>
+ <customize/>
+ </junit>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-test-properties" if="${nb.junit.batch}" name="-init-macrodef-junit-batch" unless="${nb.junit.single}">
+ <macrodef name="junit" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property name="junit.forkmode" value="perTest"/>
+ <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
+ <batchtest todir="${build.test.results.dir}">
+ <fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
+ <filename name="@{testincludes}"/>
+ </fileset>
+ <fileset dir="${build.test.classes.dir}" excludes="@{excludes},${excludes},${test.binaryexcludes}" includes="${test.binaryincludes}">
+ <filename name="${test.binarytestincludes}"/>
+ </fileset>
+ </batchtest>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <formatter type="brief" usefile="false"/>
+ <formatter type="xml"/>
+ <jvmarg value="-ea"/>
+ <customize/>
+ </junit>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-junit-init,-init-macrodef-junit-single, -init-macrodef-junit-batch" if="${junit.available}" name="-init-macrodef-junit"/>
+ <target if="${testng.available}" name="-init-macrodef-testng">
+ <macrodef name="testng" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <condition else="" property="testng.methods.arg" value="@{testincludes}.@{testmethods}">
+ <isset property="test.method"/>
+ </condition>
+ <union id="test.set">
+ <fileset dir="${test.src.dir}" excludes="@{excludes},**/*.xml,${excludes}" includes="@{includes}">
+ <filename name="@{testincludes}"/>
+ </fileset>
+ </union>
+ <taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
+ <testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="TaxonomyTree" testname="TestNG tests" workingDir="${work.dir}">
+ <xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
+ <propertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </propertyset>
+ <customize/>
+ </testng>
+ </sequential>
+ </macrodef>
+ </target>
+ <target name="-init-macrodef-test-impl">
+ <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element implicit="true" name="customize" optional="true"/>
+ <sequential>
+ <echo>No tests executed.</echo>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-junit" if="${junit.available}" name="-init-macrodef-junit-impl">
+ <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element implicit="true" name="customize" optional="true"/>
+ <sequential>
+ <j2seproject3:junit excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
+ <customize/>
+ </j2seproject3:junit>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-testng" if="${testng.available}" name="-init-macrodef-testng-impl">
+ <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element implicit="true" name="customize" optional="true"/>
+ <sequential>
+ <j2seproject3:testng excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
+ <customize/>
+ </j2seproject3:testng>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-test-impl,-init-macrodef-junit-impl,-init-macrodef-testng-impl" name="-init-macrodef-test">
+ <macrodef name="test" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <sequential>
+ <j2seproject3:test-impl excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
+ <customize>
+ <classpath>
+ <path path="${run.test.classpath}"/>
+ </classpath>
+ <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <jvmarg line="${run.jvmargs}"/>
+ <jvmarg line="${run.jvmargs.ide}"/>
+ </customize>
+ </j2seproject3:test-impl>
+ </sequential>
+ </macrodef>
+ </target>
+ <target if="${junit.available}" name="-init-macrodef-junit-debug" unless="${nb.junit.batch}">
+ <macrodef name="junit-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property name="junit.forkmode" value="perTest"/>
+ <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
+ <test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <formatter type="brief" usefile="false"/>
+ <formatter type="xml"/>
+ <jvmarg value="-ea"/>
+ <jvmarg line="${debug-args-line}"/>
+ <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+ <customize/>
+ </junit>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-test-properties" if="${nb.junit.batch}" name="-init-macrodef-junit-debug-batch">
+ <macrodef name="junit-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property name="junit.forkmode" value="perTest"/>
+ <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
+ <batchtest todir="${build.test.results.dir}">
+ <fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
+ <filename name="@{testincludes}"/>
+ </fileset>
+ <fileset dir="${build.test.classes.dir}" excludes="@{excludes},${excludes},${test.binaryexcludes}" includes="${test.binaryincludes}">
+ <filename name="${test.binarytestincludes}"/>
+ </fileset>
+ </batchtest>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <formatter type="brief" usefile="false"/>
+ <formatter type="xml"/>
+ <jvmarg value="-ea"/>
+ <jvmarg line="${debug-args-line}"/>
+ <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+ <customize/>
+ </junit>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-junit-debug,-init-macrodef-junit-debug-batch" if="${junit.available}" name="-init-macrodef-junit-debug-impl">
+ <macrodef name="test-debug-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <element implicit="true" name="customize" optional="true"/>
+ <sequential>
+ <j2seproject3:junit-debug excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
+ <customize/>
+ </j2seproject3:junit-debug>
+ </sequential>
+ </macrodef>
+ </target>
+ <target if="${testng.available}" name="-init-macrodef-testng-debug">
+ <macrodef name="testng-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${main.class}" name="testClass"/>
+ <attribute default="" name="testMethod"/>
+ <element name="customize2" optional="true"/>
+ <sequential>
+ <condition else="-testclass @{testClass}" property="test.class.or.method" value="-methods @{testClass}.@{testMethod}">
+ <isset property="test.method"/>
+ </condition>
+ <condition else="-suitename TaxonomyTree -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
+ <matches pattern=".*\.xml" string="@{testClass}"/>
+ </condition>
+ <delete dir="${build.test.results.dir}" quiet="true"/>
+ <mkdir dir="${build.test.results.dir}"/>
+ <j2seproject3:debug classname="org.testng.TestNG" classpath="${debug.test.classpath}">
+ <customize>
+ <customize2/>
+ <jvmarg value="-ea"/>
+ <arg line="${testng.debug.mode}"/>
+ <arg line="-d ${build.test.results.dir}"/>
+ <arg line="-listener org.testng.reporters.VerboseReporter"/>
+ <arg line="${testng.cmd.args}"/>
+ </customize>
+ </j2seproject3:debug>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-testng-debug" if="${testng.available}" name="-init-macrodef-testng-debug-impl">
+ <macrodef name="testng-debug-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${main.class}" name="testClass"/>
+ <attribute default="" name="testMethod"/>
+ <element implicit="true" name="customize2" optional="true"/>
+ <sequential>
+ <j2seproject3:testng-debug testClass="@{testClass}" testMethod="@{testMethod}">
+ <customize2/>
+ </j2seproject3:testng-debug>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-junit-debug-impl" if="${junit.available}" name="-init-macrodef-test-debug-junit">
+ <macrodef name="test-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <attribute default="${main.class}" name="testClass"/>
+ <attribute default="" name="testMethod"/>
+ <sequential>
+ <j2seproject3:test-debug-impl excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
+ <customize>
+ <classpath>
+ <path path="${run.test.classpath}"/>
+ </classpath>
+ <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <jvmarg line="${run.jvmargs}"/>
+ <jvmarg line="${run.jvmargs.ide}"/>
+ </customize>
+ </j2seproject3:test-debug-impl>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-testng-debug-impl" if="${testng.available}" name="-init-macrodef-test-debug-testng">
+ <macrodef name="test-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${includes}" name="includes"/>
+ <attribute default="${excludes}" name="excludes"/>
+ <attribute default="**" name="testincludes"/>
+ <attribute default="" name="testmethods"/>
+ <attribute default="${main.class}" name="testClass"/>
+ <attribute default="" name="testMethod"/>
+ <sequential>
+ <j2seproject3:testng-debug-impl testClass="@{testClass}" testMethod="@{testMethod}">
+ <customize2>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ </customize2>
+ </j2seproject3:testng-debug-impl>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-init-macrodef-test-debug-junit,-init-macrodef-test-debug-testng" name="-init-macrodef-test-debug"/>
+ <!--
+ pre NB7.2 profiling section; consider it deprecated
+ -->
+ <target depends="-profile-pre-init, init, -profile-post-init, -profile-init-macrodef-profile, -profile-init-check" if="profiler.info.jvmargs.agent" name="profile-init"/>
+ <target if="profiler.info.jvmargs.agent" name="-profile-pre-init">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target if="profiler.info.jvmargs.agent" name="-profile-post-init">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target if="profiler.info.jvmargs.agent" name="-profile-init-macrodef-profile">
+ <macrodef name="resolve">
+ <attribute name="name"/>
+ <attribute name="value"/>
+ <sequential>
+ <property name="@{name}" value="${env.@{value}}"/>
+ </sequential>
+ </macrodef>
+ <macrodef name="profile">
+ <attribute default="${main.class}" name="classname"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property environment="env"/>
+ <resolve name="profiler.current.path" value="${profiler.info.pathvar}"/>
+ <java classname="@{classname}" dir="${profiler.info.dir}" fork="true" jvm="${profiler.info.jvm}">
+ <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <jvmarg value="${profiler.info.jvmargs.agent}"/>
+ <jvmarg line="${profiler.info.jvmargs}"/>
+ <env key="${profiler.info.pathvar}" path="${profiler.info.agentpath}:${profiler.current.path}"/>
+ <arg line="${application.args}"/>
+ <classpath>
+ <path path="${run.classpath}"/>
+ </classpath>
+ <syspropertyset>
+ <propertyref prefix="run-sys-prop."/>
+ <mapper from="run-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <customize/>
+ </java>
+ </sequential>
+ </macrodef>
+ </target>
+ <target depends="-profile-pre-init, init, -profile-post-init, -profile-init-macrodef-profile" if="profiler.info.jvmargs.agent" name="-profile-init-check">
+ <fail unless="profiler.info.jvm">Must set JVM to use for profiling in profiler.info.jvm</fail>
+ <fail unless="profiler.info.jvmargs.agent">Must set profiler agent JVM arguments in profiler.info.jvmargs.agent</fail>
+ </target>
+ <!--
+ end of pre NB7.2 profiling section
+ -->
+ <target depends="-init-debug-args" name="-init-macrodef-nbjpda">
+ <macrodef name="nbjpdastart" uri="http://www.netbeans.org/ns/j2se-project/1">
+ <attribute default="${main.class}" name="name"/>
+ <attribute default="${debug.classpath}" name="classpath"/>
+ <attribute default="" name="stopclassname"/>
+ <sequential>
+ <nbjpdastart addressproperty="jpda.address" name="@{name}" stopclassname="@{stopclassname}" transport="${debug-transport}">
+ <classpath>
+ <path path="@{classpath}"/>
+ </classpath>
+ </nbjpdastart>
+ </sequential>
+ </macrodef>
+ <macrodef name="nbjpdareload" uri="http://www.netbeans.org/ns/j2se-project/1">
+ <attribute default="${build.classes.dir}" name="dir"/>
+ <sequential>
+ <nbjpdareload>
+ <fileset dir="@{dir}" includes="${fix.classes}">
+ <include name="${fix.includes}*.class"/>
+ </fileset>
+ </nbjpdareload>
+ </sequential>
+ </macrodef>
+ </target>
+ <target name="-init-debug-args">
+ <property name="version-output" value="java version "${ant.java.version}"/>
+ <condition property="have-jdk-older-than-1.4">
+ <or>
+ <contains string="${version-output}" substring="java version "1.0"/>
+ <contains string="${version-output}" substring="java version "1.1"/>
+ <contains string="${version-output}" substring="java version "1.2"/>
+ <contains string="${version-output}" substring="java version "1.3"/>
+ </or>
+ </condition>
+ <condition else="-Xdebug" property="debug-args-line" value="-Xdebug -Xnoagent -Djava.compiler=none">
+ <istrue value="${have-jdk-older-than-1.4}"/>
+ </condition>
+ <condition else="dt_socket" property="debug-transport-by-os" value="dt_shmem">
+ <os family="windows"/>
+ </condition>
+ <condition else="${debug-transport-by-os}" property="debug-transport" value="${debug.transport}">
+ <isset property="debug.transport"/>
+ </condition>
+ </target>
+ <target depends="-init-debug-args" name="-init-macrodef-debug">
+ <macrodef name="debug" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${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="${endorsed.classpath.cmd.line.arg}"/>
+ <jvmarg line="${debug-args-line}"/>
+ <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
+ <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
+ <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
+ <jvmarg line="${run.jvmargs}"/>
+ <jvmarg line="${run.jvmargs.ide}"/>
+ <classpath>
+ <path path="@{classpath}"/>
+ </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/j2se-project/1">
+ <attribute default="${main.class}" name="classname"/>
+ <attribute default="${run.classpath}" name="classpath"/>
+ <attribute default="jvm" name="jvm"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <java classname="@{classname}" dir="${work.dir}" fork="true">
+ <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
+ <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
+ <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
+ <jvmarg line="${run.jvmargs}"/>
+ <jvmarg line="${run.jvmargs.ide}"/>
+ <classpath>
+ <path path="@{classpath}"/>
+ </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-copylibs">
+ <macrodef name="copylibs" uri="http://www.netbeans.org/ns/j2se-project/3">
+ <attribute default="${manifest.file}" name="manifest"/>
+ <element name="customize" optional="true"/>
+ <sequential>
+ <property location="${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="${run.classpath.without.build.classes.dir}"/>
+ <chainedmapper>
+ <flattenmapper/>
+ <filtermapper>
+ <replacestring from=" " to="%20"/>
+ </filtermapper>
+ <globmapper from="*" to="lib/*"/>
+ </chainedmapper>
+ </pathconvert>
+ <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
+ <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
+ <fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
+ <manifest>
+ <attribute name="Class-Path" value="${jar.classpath}"/>
+ <customize/>
+ </manifest>
+ </copylibs>
+ </sequential>
+ </macrodef>
+ </target>
+ <target name="-init-presetdef-jar">
+ <presetdef name="jar" uri="http://www.netbeans.org/ns/j2se-project/1">
+ <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}">
+ <j2seproject1:fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
+ </jar>
+ </presetdef>
+ </target>
+ <target name="-init-ap-cmdline-properties">
+ <property name="annotation.processing.enabled" value="true"/>
+ <property name="annotation.processing.processors.list" value=""/>
+ <property name="annotation.processing.processor.options" value=""/>
+ <property name="annotation.processing.run.all.processors" value="true"/>
+ <property name="javac.processorpath" value="${javac.classpath}"/>
+ <property name="javac.test.processorpath" value="${javac.test.classpath}"/>
+ <condition property="ap.supported.internal" value="true">
+ <not>
+ <matches pattern="1\.[0-5](\..*)?" string="${javac.source}"/>
+ </not>
+ </condition>
+ </target>
+ <target depends="-init-ap-cmdline-properties" if="ap.supported.internal" name="-init-ap-cmdline-supported">
+ <condition else="" property="ap.processors.internal" value="-processor ${annotation.processing.processors.list}">
+ <isfalse value="${annotation.processing.run.all.processors}"/>
+ </condition>
+ <condition else="" property="ap.proc.none.internal" value="-proc:none">
+ <isfalse value="${annotation.processing.enabled}"/>
+ </condition>
+ </target>
+ <target depends="-init-ap-cmdline-properties,-init-ap-cmdline-supported" name="-init-ap-cmdline">
+ <property name="ap.cmd.line.internal" value=""/>
+ </target>
+ <target depends="-pre-init,-init-private,-init-user,-init-project,-do-init,-post-init,-init-check,-init-macrodef-property,-init-macrodef-javac,-init-macrodef-test,-init-macrodef-test-debug,-init-macrodef-nbjpda,-init-macrodef-debug,-init-macrodef-java,-init-presetdef-jar,-init-ap-cmdline" name="init"/>
+ <!--
+ ===================
+ COMPILATION SECTION
+ ===================
+ -->
+ <target name="-deps-jar-init" unless="built-jar.properties">
+ <property location="${build.dir}/built-jar.properties" name="built-jar.properties"/>
+ <delete file="${built-jar.properties}" quiet="true"/>
+ </target>
+ <target if="already.built.jar.${basedir}" name="-warn-already-built-jar">
+ <echo level="warn" message="Cycle detected: TaxonomyTree was already built"/>
+ </target>
+ <target depends="init,-deps-jar-init" name="deps-jar" unless="no.deps">
+ <mkdir dir="${build.dir}"/>
+ <touch file="${built-jar.properties}" verbose="false"/>
+ <property file="${built-jar.properties}" prefix="already.built.jar."/>
+ <antcall target="-warn-already-built-jar"/>
+ <propertyfile file="${built-jar.properties}">
+ <entry key="${basedir}" value=""/>
+ </propertyfile>
+ <antcall target="-maybe-call-dep">
+ <param name="call.built.properties" value="${built-jar.properties}"/>
+ <param location="${project.ReadSeq}" name="call.subproject"/>
+ <param location="${project.ReadSeq}/build.xml" name="call.script"/>
+ <param name="call.target" value="jar"/>
+ <param name="transfer.built-jar.properties" value="${built-jar.properties}"/>
+ </antcall>
+ </target>
+ <target depends="init,-check-automatic-build,-clean-after-automatic-build" name="-verify-automatic-build"/>
+ <target depends="init" name="-check-automatic-build">
+ <available file="${build.classes.dir}/.netbeans_automatic_build" property="netbeans.automatic.build"/>
+ </target>
+ <target depends="init" if="netbeans.automatic.build" name="-clean-after-automatic-build">
+ <antcall target="clean"/>
+ </target>
+ <target depends="init,deps-jar" name="-pre-pre-compile">
+ <mkdir dir="${build.classes.dir}"/>
+ </target>
+ <target name="-pre-compile">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target if="do.depend.true" name="-compile-depend">
+ <pathconvert property="build.generated.subdirs">
+ <dirset dir="${build.generated.sources.dir}" erroronmissingdir="false">
+ <include name="*"/>
+ </dirset>
+ </pathconvert>
+ <j2seproject3:depend srcdir="${src.dir}:${build.generated.subdirs}"/>
+ </target>
+ <target depends="init,deps-jar,-pre-pre-compile,-pre-compile, -copy-persistence-xml,-compile-depend" if="have.sources" name="-do-compile">
+ <j2seproject3:javac gensrcdir="${build.generated.sources.dir}"/>
+ <copy todir="${build.classes.dir}">
+ <fileset dir="${src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
+ </copy>
+ </target>
+ <target if="has.persistence.xml" name="-copy-persistence-xml">
+ <mkdir dir="${build.classes.dir}/META-INF"/>
+ <copy todir="${build.classes.dir}/META-INF">
+ <fileset dir="${meta.inf.dir}" includes="persistence.xml orm.xml"/>
+ </copy>
+ </target>
+ <target name="-post-compile">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target depends="init,deps-jar,-verify-automatic-build,-pre-pre-compile,-pre-compile,-do-compile,-post-compile" description="Compile project." name="compile"/>
+ <target name="-pre-compile-single">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target depends="init,deps-jar,-pre-pre-compile" name="-do-compile-single">
+ <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
+ <j2seproject3:force-recompile/>
+ <j2seproject3:javac excludes="" gensrcdir="${build.generated.sources.dir}" 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,-verify-automatic-build,-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" if="do.archive" name="-do-jar-create-manifest" unless="manifest.available">
+ <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
+ <touch file="${tmp.manifest.file}" verbose="false"/>
+ </target>
+ <target depends="init" if="do.archive+manifest.available" name="-do-jar-copy-manifest">
+ <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
+ <copy file="${manifest.file}" tofile="${tmp.manifest.file}"/>
+ </target>
+ <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+main.class.available" name="-do-jar-set-mainclass">
+ <manifest file="${tmp.manifest.file}" mode="update">
+ <attribute name="Main-Class" value="${main.class}"/>
+ </manifest>
+ </target>
+ <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+profile.available" name="-do-jar-set-profile">
+ <manifest file="${tmp.manifest.file}" mode="update">
+ <attribute name="Profile" value="${javac.profile}"/>
+ </manifest>
+ </target>
+ <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+splashscreen.available" name="-do-jar-set-splashscreen">
+ <basename file="${application.splash}" property="splashscreen.basename"/>
+ <mkdir dir="${build.classes.dir}/META-INF"/>
+ <copy failonerror="false" file="${application.splash}" todir="${build.classes.dir}/META-INF"/>
+ <manifest file="${tmp.manifest.file}" mode="update">
+ <attribute name="SplashScreen-Image" value="META-INF/${splashscreen.basename}"/>
+ </manifest>
+ </target>
+ <target depends="init,-init-macrodef-copylibs,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen" if="do.mkdist" name="-do-jar-copylibs">
+ <j2seproject3:copylibs manifest="${tmp.manifest.file}"/>
+ <echo level="info">To run this application from the command line without Ant, try:</echo>
+ <property location="${dist.jar}" name="dist.jar.resolved"/>
+ <echo level="info">java -jar "${dist.jar.resolved}"</echo>
+ </target>
+ <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen" if="do.archive" name="-do-jar-jar" unless="do.mkdist">
+ <j2seproject1:jar manifest="${tmp.manifest.file}"/>
+ <property location="${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>
+ <condition else="" property="jar.usage.message" value="To run this application from the command line without Ant, try:${line.separator}${platform.java} -cp ${run.classpath.with.dist.jar} ${main.class}">
+ <isset property="main.class.available"/>
+ </condition>
+ <condition else="debug" property="jar.usage.level" value="info">
+ <isset property="main.class.available"/>
+ </condition>
+ <echo level="${jar.usage.level}" message="${jar.usage.message}"/>
+ </target>
+ <target depends="-do-jar-copylibs" if="do.archive" name="-do-jar-delete-manifest">
+ <delete>
+ <fileset file="${tmp.manifest.file}"/>
+ </delete>
+ </target>
+ <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-do-jar-jar,-do-jar-delete-manifest" name="-do-jar-without-libraries"/>
+ <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-do-jar-copylibs,-do-jar-delete-manifest" name="-do-jar-with-libraries"/>
+ <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-without-libraries,-do-jar-with-libraries,-post-jar" name="-do-jar"/>
+ <target depends="init,compile,-pre-jar,-do-jar,-post-jar" description="Build JAR." name="jar"/>
+ <!--
+ =================
+ EXECUTION SECTION
+ =================
+ -->
+ <target depends="init,compile" description="Run a main class." name="run">
+ <j2seproject1:java>
+ <customize>
+ <arg line="${application.args}"/>
+ </customize>
+ </j2seproject1:java>
+ </target>
+ <target name="-do-not-recompile">
+ <property name="javac.includes.binary" value=""/>
+ </target>
+ <target depends="init,compile-single" name="run-single">
+ <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
+ <j2seproject1:java classname="${run.class}"/>
+ </target>
+ <target depends="init,compile-test-single" name="run-test-with-main">
+ <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
+ <j2seproject1:java classname="${run.class}" classpath="${run.test.classpath}"/>
+ </target>
+ <!--
+ =================
+ DEBUGGING SECTION
+ =================
+ -->
+ <target depends="init" if="netbeans.home" name="-debug-start-debugger">
+ <j2seproject1:nbjpdastart name="${debug.class}"/>
+ </target>
+ <target depends="init" if="netbeans.home" name="-debug-start-debugger-main-test">
+ <j2seproject1:nbjpdastart classpath="${debug.test.classpath}" name="${debug.class}"/>
+ </target>
+ <target depends="init,compile" name="-debug-start-debuggee">
+ <j2seproject3:debug>
+ <customize>
+ <arg line="${application.args}"/>
+ </customize>
+ </j2seproject3: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">
+ <j2seproject1:nbjpdastart stopclassname="${main.class}"/>
+ </target>
+ <target depends="init,compile,-debug-start-debugger-stepinto,-debug-start-debuggee" if="netbeans.home" name="debug-stepinto"/>
+ <target depends="init,compile-single" if="netbeans.home" name="-debug-start-debuggee-single">
+ <fail unless="debug.class">Must select one file in the IDE or set debug.class</fail>
+ <j2seproject3:debug classname="${debug.class}"/>
+ </target>
+ <target depends="init,compile-single,-debug-start-debugger,-debug-start-debuggee-single" if="netbeans.home" name="debug-single"/>
+ <target depends="init,compile-test-single" if="netbeans.home" name="-debug-start-debuggee-main-test">
+ <fail unless="debug.class">Must select one file in the IDE or set debug.class</fail>
+ <j2seproject3:debug classname="${debug.class}" classpath="${debug.test.classpath}"/>
+ </target>
+ <target depends="init,compile-test-single,-debug-start-debugger-main-test,-debug-start-debuggee-main-test" if="netbeans.home" name="debug-test-with-main"/>
+ <target depends="init" name="-pre-debug-fix">
+ <fail unless="fix.includes">Must set fix.includes</fail>
+ <property name="javac.includes" value="${fix.includes}.java"/>
+ </target>
+ <target depends="init,-pre-debug-fix,compile-single" if="netbeans.home" name="-do-debug-fix">
+ <j2seproject1:nbjpdareload/>
+ </target>
+ <target depends="init,-pre-debug-fix,-do-debug-fix" if="netbeans.home" name="debug-fix"/>
+ <!--
+ =================
+ PROFILING SECTION
+ =================
+ -->
+ <!--
+ pre NB7.2 profiler integration
+ -->
+ <target depends="profile-init,compile" description="Profile a project in the IDE." if="profiler.info.jvmargs.agent" name="-profile-pre72">
+ <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
+ <nbprofiledirect>
+ <classpath>
+ <path path="${run.classpath}"/>
+ </classpath>
+ </nbprofiledirect>
+ <profile/>
+ </target>
+ <target depends="profile-init,compile-single" description="Profile a selected class in the IDE." if="profiler.info.jvmargs.agent" name="-profile-single-pre72">
+ <fail unless="profile.class">Must select one file in the IDE or set profile.class</fail>
+ <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
+ <nbprofiledirect>
+ <classpath>
+ <path path="${run.classpath}"/>
+ </classpath>
+ </nbprofiledirect>
+ <profile classname="${profile.class}"/>
+ </target>
+ <target depends="profile-init,compile-single" if="profiler.info.jvmargs.agent" name="-profile-applet-pre72">
+ <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
+ <nbprofiledirect>
+ <classpath>
+ <path path="${run.classpath}"/>
+ </classpath>
+ </nbprofiledirect>
+ <profile classname="sun.applet.AppletViewer">
+ <customize>
+ <arg value="${applet.url}"/>
+ </customize>
+ </profile>
+ </target>
+ <target depends="profile-init,compile-test-single" if="profiler.info.jvmargs.agent" name="-profile-test-single-pre72">
+ <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
+ <nbprofiledirect>
+ <classpath>
+ <path path="${run.test.classpath}"/>
+ </classpath>
+ </nbprofiledirect>
+ <junit dir="${profiler.info.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" jvm="${profiler.info.jvm}" showoutput="true">
+ <env key="${profiler.info.pathvar}" path="${profiler.info.agentpath}:${profiler.current.path}"/>
+ <jvmarg value="${profiler.info.jvmargs.agent}"/>
+ <jvmarg line="${profiler.info.jvmargs}"/>
+ <test name="${profile.class}"/>
+ <classpath>
+ <path path="${run.test.classpath}"/>
+ </classpath>
+ <syspropertyset>
+ <propertyref prefix="test-sys-prop."/>
+ <mapper from="test-sys-prop.*" to="*" type="glob"/>
+ </syspropertyset>
+ <formatter type="brief" usefile="false"/>
+ <formatter type="xml"/>
+ </junit>
+ </target>
+ <!--
+ end of pre NB72 profiling section
+ -->
+ <target if="netbeans.home" name="-profile-check">
+ <condition property="profiler.configured">
+ <or>
+ <contains casesensitive="true" string="${run.jvmargs.ide}" substring="-agentpath:"/>
+ <contains casesensitive="true" string="${run.jvmargs.ide}" substring="-javaagent:"/>
+ </or>
+ </condition>
+ </target>
+ <target depends="-profile-check,-profile-pre72" description="Profile a project in the IDE." if="profiler.configured" name="profile" unless="profiler.info.jvmargs.agent">
+ <startprofiler/>
+ <antcall target="run"/>
+ </target>
+ <target depends="-profile-check,-profile-single-pre72" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-single" unless="profiler.info.jvmargs.agent">
+ <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
+ <startprofiler/>
+ <antcall target="run-single"/>
+ </target>
+ <target depends="-profile-test-single-pre72" description="Profile a selected test in the IDE." name="profile-test-single"/>
+ <target depends="-profile-check" description="Profile a selected test in the IDE." if="profiler.configured" name="profile-test" unless="profiler.info.jvmargs">
+ <fail unless="test.includes">Must select some files in the IDE or set test.includes</fail>
+ <startprofiler/>
+ <antcall target="test-single"/>
+ </target>
+ <target depends="-profile-check" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-test-with-main">
+ <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
+ <startprofiler/>
+ <antcal target="run-test-with-main"/>
+ </target>
+ <target depends="-profile-check,-profile-applet-pre72" if="profiler.configured" name="profile-applet" unless="profiler.info.jvmargs.agent">
+ <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
+ <startprofiler/>
+ <antcall target="run-applet"/>
+ </target>
+ <!--
+ ===============
+ JAVADOC SECTION
+ ===============
+ -->
+ <target depends="init" if="have.sources" name="-javadoc-build">
+ <mkdir dir="${dist.javadoc.dir}"/>
+ <condition else="" property="javadoc.endorsed.classpath.cmd.line.arg" value="-J${endorsed.classpath.cmd.line.arg}">
+ <and>
+ <isset property="endorsed.classpath.cmd.line.arg"/>
+ <not>
+ <equals arg1="${endorsed.classpath.cmd.line.arg}" arg2=""/>
+ </not>
+ </and>
+ </condition>
+ <javadoc additionalparam="${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="*.java,${excludes}" includes="${includes}">
+ <filename name="**/*.java"/>
+ </fileset>
+ <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
+ <include name="**/*.java"/>
+ <exclude name="*.java"/>
+ </fileset>
+ <arg line="${javadoc.endorsed.classpath.cmd.line.arg}"/>
+ </javadoc>
+ <copy todir="${dist.javadoc.dir}">
+ <fileset dir="${src.dir}" excludes="${excludes}" includes="${includes}">
+ <filename name="**/doc-files/**"/>
+ </fileset>
+ <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
+ <include name="**/doc-files/**"/>
+ </fileset>
+ </copy>
+ </target>
+ <target depends="init,-javadoc-build" if="netbeans.home" name="-javadoc-browse" unless="no.javadoc.preview">
+ <nbbrowse file="${dist.javadoc.dir}/index.html"/>
+ </target>
+ <target depends="init,-javadoc-build,-javadoc-browse" description="Build Javadoc." name="javadoc"/>
+ <!--
+ =========================
+ TEST COMPILATION SECTION
+ =========================
+ -->
+ <target depends="init,compile" if="have.tests" name="-pre-pre-compile-test">
+ <mkdir dir="${build.test.classes.dir}"/>
+ </target>
+ <target name="-pre-compile-test">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target if="do.depend.true" name="-compile-test-depend">
+ <j2seproject3:depend classpath="${javac.test.classpath}" destdir="${build.test.classes.dir}" srcdir="${test.src.dir}"/>
+ </target>
+ <target depends="init,deps-jar,compile,-pre-pre-compile-test,-pre-compile-test,-compile-test-depend" if="have.tests" name="-do-compile-test">
+ <j2seproject3:javac apgeneratedsrcdir="${build.test.classes.dir}" classpath="${javac.test.classpath}" debug="true" destdir="${build.test.classes.dir}" processorpath="${javac.test.processorpath}" srcdir="${test.src.dir}"/>
+ <copy todir="${build.test.classes.dir}">
+ <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${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,deps-jar,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>
+ <j2seproject3:force-recompile destdir="${build.test.classes.dir}"/>
+ <j2seproject3:javac apgeneratedsrcdir="${build.test.classes.dir}" classpath="${javac.test.classpath}" debug="true" destdir="${build.test.classes.dir}" excludes="" includes="${javac.includes}" processorpath="${javac.test.processorpath}" sourcepath="${test.src.dir}" srcdir="${test.src.dir}"/>
+ <copy todir="${build.test.classes.dir}">
+ <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
+ </copy>
+ </target>
+ <target name="-post-compile-test-single">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test-single,-do-compile-test-single,-post-compile-test-single" name="compile-test-single"/>
+ <!--
+ =======================
+ TEST EXECUTION SECTION
+ =======================
+ -->
+ <target depends="init" if="have.tests" name="-pre-test-run">
+ <mkdir dir="${build.test.results.dir}"/>
+ </target>
+ <target depends="init,compile-test,-pre-test-run" if="have.tests" name="-do-test-run">
+ <j2seproject3:test testincludes="**/*Test.java"/>
+ </target>
+ <target depends="init,compile-test,-pre-test-run,-do-test-run" if="have.tests" name="-post-test-run">
+ <fail if="tests.failed" unless="ignore.failing.tests">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="${build.test.results.dir}"/>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-do-test-run-single">
+ <fail unless="test.includes">Must select some files in the IDE or set test.includes</fail>
+ <j2seproject3:test excludes="" includes="${test.includes}" testincludes="${test.includes}"/>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single" if="have.tests" name="-post-test-run-single">
+ <fail if="tests.failed" unless="ignore.failing.tests">Some tests failed; see details above.</fail>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single,-post-test-run-single" description="Run single unit test." name="test-single"/>
+ <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-do-test-run-single-method">
+ <fail unless="test.class">Must select some files in the IDE or set test.class</fail>
+ <fail unless="test.method">Must select some method in the IDE or set test.method</fail>
+ <j2seproject3:test excludes="" includes="${javac.includes}" testincludes="${test.class}" testmethods="${test.method}"/>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single-method" if="have.tests" name="-post-test-run-single-method">
+ <fail if="tests.failed" unless="ignore.failing.tests">Some tests failed; see details above.</fail>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single-method,-post-test-run-single-method" description="Run single unit test." name="test-single-method"/>
+ <!--
+ =======================
+ TEST DEBUGGING SECTION
+ =======================
+ -->
+ <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-debug-start-debuggee-test">
+ <fail unless="test.class">Must select one file in the IDE or set test.class</fail>
+ <j2seproject3:test-debug excludes="" includes="${javac.includes}" testClass="${test.class}" testincludes="${javac.includes}"/>
+ </target>
+ <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-debug-start-debuggee-test-method">
+ <fail unless="test.class">Must select one file in the IDE or set test.class</fail>
+ <fail unless="test.method">Must select some method in the IDE or set test.method</fail>
+ <j2seproject3:test-debug excludes="" includes="${javac.includes}" testClass="${test.class}" testMethod="${test.method}" testincludes="${test.class}" testmethods="${test.method}"/>
+ </target>
+ <target depends="init,compile-test" if="netbeans.home+have.tests" name="-debug-start-debugger-test">
+ <j2seproject1:nbjpdastart classpath="${debug.test.classpath}" name="${test.class}"/>
+ </target>
+ <target depends="init,compile-test-single,-debug-start-debugger-test,-debug-start-debuggee-test" name="debug-test"/>
+ <target depends="init,compile-test-single,-debug-start-debugger-test,-debug-start-debuggee-test-method" name="debug-test-method"/>
+ <target depends="init,-pre-debug-fix,compile-test-single" if="netbeans.home" name="-do-debug-fix-test">
+ <j2seproject1:nbjpdareload dir="${build.test.classes.dir}"/>
+ </target>
+ <target depends="init,-pre-debug-fix,-do-debug-fix-test" if="netbeans.home" name="debug-fix-test"/>
+ <!--
+ =========================
+ APPLET EXECUTION SECTION
+ =========================
+ -->
+ <target depends="init,compile-single" name="run-applet">
+ <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
+ <j2seproject1:java classname="sun.applet.AppletViewer">
+ <customize>
+ <arg value="${applet.url}"/>
+ </customize>
+ </j2seproject1: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>
+ <j2seproject3:debug classname="sun.applet.AppletViewer">
+ <customize>
+ <arg value="${applet.url}"/>
+ </customize>
+ </j2seproject3:debug>
+ </target>
+ <target depends="init,compile-single,-debug-start-debugger,-debug-start-debuggee-applet" if="netbeans.home" name="debug-applet"/>
+ <!--
+ ===============
+ CLEANUP SECTION
+ ===============
+ -->
+ <target name="-deps-clean-init" unless="built-clean.properties">
+ <property location="${build.dir}/built-clean.properties" name="built-clean.properties"/>
+ <delete file="${built-clean.properties}" quiet="true"/>
+ </target>
+ <target if="already.built.clean.${basedir}" name="-warn-already-built-clean">
+ <echo level="warn" message="Cycle detected: TaxonomyTree was already built"/>
+ </target>
+ <target depends="init,-deps-clean-init" name="deps-clean" unless="no.deps">
+ <mkdir dir="${build.dir}"/>
+ <touch file="${built-clean.properties}" verbose="false"/>
+ <property file="${built-clean.properties}" prefix="already.built.clean."/>
+ <antcall target="-warn-already-built-clean"/>
+ <propertyfile file="${built-clean.properties}">
+ <entry key="${basedir}" value=""/>
+ </propertyfile>
+ <antcall target="-maybe-call-dep">
+ <param name="call.built.properties" value="${built-clean.properties}"/>
+ <param location="${project.ReadSeq}" name="call.subproject"/>
+ <param location="${project.ReadSeq}/build.xml" name="call.script"/>
+ <param name="call.target" value="clean"/>
+ <param name="transfer.built-clean.properties" value="${built-clean.properties}"/>
+ </antcall>
+ </target>
+ <target depends="init" name="-do-clean">
+ <delete dir="${build.dir}"/>
+ <delete dir="${dist.dir}" followsymlinks="false" includeemptydirs="true"/>
+ </target>
+ <target name="-post-clean">
+ <!-- Empty placeholder for easier customization. -->
+ <!-- You can override this target in the ../build.xml file. -->
+ </target>
+ <target depends="init,deps-clean,-do-clean,-post-clean" description="Clean build products." name="clean"/>
+ <target name="-check-call-dep">
+ <property file="${call.built.properties}" prefix="already.built."/>
+ <condition property="should.call.dep">
+ <and>
+ <not>
+ <isset property="already.built.${call.subproject}"/>
+ </not>
+ <available file="${call.script}"/>
+ </and>
+ </condition>
+ </target>
+ <target depends="-check-call-dep" if="should.call.dep" name="-maybe-call-dep">
+ <ant antfile="${call.script}" inheritall="false" target="${call.target}">
+ <propertyset>
+ <propertyref prefix="transfer."/>
+ <mapper from="transfer.*" to="*" type="glob"/>
+ </propertyset>
+ </ant>
+ </target>
+</project>
diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties
new file mode 100644
index 0000000..1679c49
--- /dev/null
+++ b/nbproject/genfiles.properties
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=3f3ed509
+build.xml.script.CRC32=1e159869
+build.xml.stylesheet.CRC32=28e38971 at 1.50.1.46
+# 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=01159767
+nbproject/build-impl.xml.script.CRC32=c48bdce2
+nbproject/build-impl.xml.stylesheet.CRC32=5a01deb7 at 1.68.1.46
diff --git a/nbproject/project.properties b/nbproject/project.properties
new file mode 100644
index 0000000..7eb98be
--- /dev/null
+++ b/nbproject/project.properties
@@ -0,0 +1,75 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+application.title=TaxonomyTree
+application.vendor=fishjord
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+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}/TaxonomyTree.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+endorsed.classpath=
+excludes=
+file.reference.junit-4.8.2.jar=lib/junit-4.8.2.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+ ${reference.ReadSeq.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.5
+javac.target=1.5
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}:\
+ ${file.reference.junit-4.8.2.jar}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${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=
+jaxbwiz.endorsed.dirs="${netbeans.home}/../ide12/modules/ext/jaxb/api"
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+project.ReadSeq=../ReadSeq
+reference.ReadSeq.jar=${project.ReadSeq}/dist/ReadSeq.jar
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# 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
diff --git a/nbproject/project.xml b/nbproject/project.xml
new file mode 100644
index 0000000..6b13fb3
--- /dev/null
+++ b/nbproject/project.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+ <type>org.netbeans.modules.java.j2seproject</type>
+ <configuration>
+ <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
+ <name>TaxonomyTree</name>
+ <source-roots>
+ <root id="src.dir"/>
+ </source-roots>
+ <test-roots>
+ <root id="test.src.dir"/>
+ </test-roots>
+ </data>
+ <references xmlns="http://www.netbeans.org/ns/ant-project-references/1">
+ <reference>
+ <foreign-project>ReadSeq</foreign-project>
+ <artifact-type>jar</artifact-type>
+ <script>build.xml</script>
+ <target>jar</target>
+ <clean-target>clean</clean-target>
+ <id>jar</id>
+ </reference>
+ </references>
+ </configuration>
+</project>
diff --git a/src/edu/msu/cme/rdp/taxatree/ConcretRoot.java b/src/edu/msu/cme/rdp/taxatree/ConcretRoot.java
new file mode 100644
index 0000000..51d13ac
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/ConcretRoot.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree;
+
+import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ *
+ * @author fishjord
+ */
+public class ConcretRoot<E extends Node> {
+ protected TaxonHolder<E> root;
+ protected Map<Integer, TaxonHolder<E>> taxonMap = new HashMap();
+
+ public ConcretRoot(E rootTaxon) {
+ this.root = new TaxonHolder<E>(rootTaxon);
+ taxonMap.put(rootTaxon.getTaxid(), root);
+ }
+
+ public int getRootTaxid() {
+ return root.getTaxon().getTaxid();
+ }
+
+ public TaxonHolder<E> getRootTaxonHodler(){
+ return root;
+ }
+
+ public TaxonHolder<E> getChild(int txid) {
+ return taxonMap.get(txid);
+ }
+
+ public E getChildTaxon(int txid) {
+ TaxonHolder<E> holder = taxonMap.get(txid);
+ if(holder == null)
+ return null;
+ return holder.getTaxon();
+ }
+
+ public void addChild(E child, int parentId) {
+ if(taxonMap.containsKey(parentId)) {
+ TaxonHolder<E> parentHolder = taxonMap.get(parentId);
+ TaxonHolder<E> childHolder = new TaxonHolder<E>(child, parentHolder);
+
+ parentHolder.addChild(childHolder);
+ taxonMap.put(child.getTaxid(), childHolder);
+ } else
+ throw new IllegalArgumentException("Failed to find parent with taxid=" + parentId + " in tree");
+ }
+
+ public void topDownVisit(TreeVisitor<E> visitor) {
+ root.topDownVisit(visitor);
+ }
+
+ public void biDirectionDepthFirst(TreeVisitor visitor) {
+ root.biDirectionDepthFirst(visitor);
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/Node.java b/src/edu/msu/cme/rdp/taxatree/Node.java
new file mode 100644
index 0000000..9bcbd92
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/Node.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree;
+
+/**
+ *
+ * @author fishjord
+ */
+public abstract class Node {
+ protected int taxid;
+
+ public Node(int taxid) {
+ this.taxid = taxid;
+ }
+
+ public int getTaxid() {
+ return taxid;
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/Taxon.java b/src/edu/msu/cme/rdp/taxatree/Taxon.java
new file mode 100644
index 0000000..487f0cb
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/Taxon.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree;
+
+/**
+ * Main tree node that can be extended
+ *
+ * @author fishjord
+ */
+public class Taxon extends Node {
+
+ public static int getUnclassifiedId(int id) {
+ return (-id) - 1;
+ }
+
+ public static Taxon ROOT_TAXON = new Taxon(0, "Root", "no rank");
+
+ private String name;
+ private String rank;
+ private boolean unclassified = false;
+
+ public Taxon(int taxid, String name, String rank) {
+ this(taxid, name, rank, false);
+ }
+
+ public Taxon(Taxon copy) {
+ this(copy.getTaxid(), copy.getName(), copy.getRank(), copy.isUnclassified());
+ }
+
+ public Taxon(int taxid, String name, String rank, boolean unclassified) {
+ super(taxid);
+ this.name = name;
+ this.rank = rank;
+ this.unclassified = unclassified;
+ }
+
+ @Override
+ public int getTaxid() {
+ if(unclassified)
+ return getUnclassifiedId(taxid);
+ else
+ return taxid;
+ }
+
+ public String getName() {
+ if(unclassified)
+ return "unclassified_" + name;
+ else
+ return name;
+ }
+
+ public String getRank() {
+ if(unclassified)
+ return "";
+ else
+ return rank;
+ }
+
+ public boolean isUnclassified() {
+ return unclassified;
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/TaxonHolder.java b/src/edu/msu/cme/rdp/taxatree/TaxonHolder.java
new file mode 100644
index 0000000..aa2a574
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/TaxonHolder.java
@@ -0,0 +1,188 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree;
+
+import edu.msu.cme.rdp.taxatree.VisitInfo.VisitType;
+import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ *
+ * This class handles the main work of the actual tree structure
+ * It maintains a reference to a taxon representing the actual data of the node
+ * and a list of holders that are the children
+ *
+ * @author fishjord
+ */
+public class TaxonHolder<E extends Node> {
+ final private E taxon;
+ private TaxonHolder<E> parent;
+ private List<TaxonHolder<E>> children = new ArrayList();
+
+ public TaxonHolder(E taxon) {
+ this.taxon = taxon;
+ }
+
+ TaxonHolder(E taxon, TaxonHolder<E> parent) {
+ this.taxon = taxon;
+ this.parent = parent;
+ }
+
+ public E getTaxon() {
+ return taxon;
+ }
+
+ public void addChild(E child, int parentId) {
+ TaxonHolder<E> parentHolder = getChild(parentId);
+
+ if(parentHolder != null) {
+ TaxonHolder<E> childHolder = new TaxonHolder<E>(child, parentHolder);
+ parentHolder.addChild(childHolder);
+ }
+ }
+
+ public Collection<E> getChildren() {
+ List<E> ret = new ArrayList();
+ for(TaxonHolder<E> child : children)
+ ret.add(child.getTaxon());
+
+ return ret;
+ }
+
+ public List<TaxonHolder<E>> getChildHolders() {
+ return Collections.unmodifiableList(children);
+ }
+
+ /**
+ * Convenience method that returns the enclosed taxon
+ * instead of the taxonholder for the given id
+ *
+ * @param idToFind
+ * @return the taxon if found, null otherwise
+ */
+ public E getChildTaxon(int idToFind) {
+ TaxonHolder<E> result = getChild(idToFind);
+
+ if(result == null)
+ return null;
+
+ return result.getTaxon();
+ }
+
+ /*
+ * returns only the immediate child taxon with matching name
+ */
+ public TaxonHolder<E> getImediateChildTaxon(String name){
+ for ( TaxonHolder<E> child: children){
+ if ( ((Taxon)child.getTaxon()).getName().equals(name)){
+ return child;
+ }
+ }
+ return null;
+ }
+ /**
+ * Find a taxon with the given id in the sub tree
+ * rooted at this node
+ *
+ * @param idToFind
+ * @return the holder that contains the taxon with the specified id
+ * null otherwise
+ */
+ public TaxonHolder<E> getChild(int idToFind) {
+ return findSubNode(idToFind);
+ }
+
+ void setParent(TaxonHolder<E> parent) {
+ this.parent = parent;
+ }
+
+ public TaxonHolder<E> getParent() {
+ return parent;
+ }
+
+ void addChild(TaxonHolder<E> childHolder) {
+ children.add(childHolder);
+ }
+
+ private TaxonHolder<E> findSubNode(int taxid) {
+ if(taxid == taxon.getTaxid())
+ return this;
+
+ TaxonHolder<E> ret = null;
+
+ for(TaxonHolder<E> child : children) {
+ if((ret = child.findSubNode(taxid)) != null)
+ return ret;
+ }
+
+ return null;
+ }
+
+ /**
+ *
+ * Operations
+ *
+ */
+
+ /**
+ * Visits all the nodes in the tree in top down depth first order
+ * @param visitor
+ */
+ public void topDownVisit(TreeVisitor<E> visitor) {
+ topDownVisit(this, visitor, 0);
+ }
+
+ private static boolean topDownVisit(TaxonHolder t, TreeVisitor v, int depth) {
+ if(!v.visitNode(new VisitInfo(t, VisitType.down)))
+ return false;
+
+ for(TaxonHolder child : (Collection<TaxonHolder>)t.getChildHolders())
+ if(!topDownVisit(child, v, depth + 1))
+ return false;
+
+ return true;
+ }
+
+
+ /**
+ * Visits all the nodes in the tree once on the way down
+ * and then again on the way back up (on the way up the depth is
+ * negative of the way down)
+ * @param visitor
+ */
+ public void biDirectionDepthFirst(TreeVisitor visitor) {
+ biDirectionDepthFirst(this, visitor, 0);
+ }
+
+ private static boolean biDirectionDepthFirst(TaxonHolder t, TreeVisitor v, int depth) {
+ if(!v.visitNode(new VisitInfo(t, VisitType.down)))
+ return false;
+
+ for(TaxonHolder child : (Collection<TaxonHolder>)t.getChildHolders())
+ if(!biDirectionDepthFirst(child, v, depth + 1))
+ return false;
+
+ if(!v.visitNode(new VisitInfo(t, VisitType.up)))
+ return false;
+
+ return true;
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/VisitInfo.java b/src/edu/msu/cme/rdp/taxatree/VisitInfo.java
new file mode 100644
index 0000000..50da593
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/VisitInfo.java
@@ -0,0 +1,66 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree;
+
+/**
+ *
+ * @author fishjord
+ */
+public class VisitInfo<E extends Node> {
+
+ public enum VisitType { down, up };
+
+ private TaxonHolder<E> holder;
+ private VisitType visitType;
+
+ public VisitInfo(TaxonHolder<E> holder, VisitType type) {
+ this.holder = holder;
+ this.visitType = type;
+ }
+
+ public int getDepth() {
+ int depth = 0;
+
+ TaxonHolder<E> parent = holder.getParent();
+ while(parent != null) {
+ depth++;
+ parent = parent.getParent();
+ }
+
+ return depth;
+ }
+
+ public E getTaxon() {
+ return holder.getTaxon();
+ }
+
+ public boolean isLastChild() {
+ if(holder.getParent() == null)
+ return true;
+
+ return holder.getParent().getChildHolders().indexOf(holder) == holder.getParent().getChildHolders().size() - 1;
+ }
+
+ public boolean hasChildren() {
+ return holder.getChildHolders().size() != 0;
+ }
+
+ public VisitType getVisitType() {
+ return visitType;
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/interfaces/TreeVisitor.java b/src/edu/msu/cme/rdp/taxatree/interfaces/TreeVisitor.java
new file mode 100644
index 0000000..b2d1721
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/interfaces/TreeVisitor.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree.interfaces;
+
+import edu.msu.cme.rdp.taxatree.Node;
+import edu.msu.cme.rdp.taxatree.VisitInfo;
+
+/**
+ *
+ * @author fishjord
+ */
+public interface TreeVisitor<E extends Node> {
+
+ /**
+ * Visits a node
+ * @param taxon
+ * @return true - tells the TreeBuilder to keep traversing the tree, false - causes the TreeBuilder to return
+ */
+ public boolean visitNode(VisitInfo<E> visitInfo);
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitor.java b/src/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitor.java
new file mode 100644
index 0000000..8e9226d
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitor.java
@@ -0,0 +1,101 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.Taxon;
+import edu.msu.cme.rdp.taxatree.VisitInfo;
+import edu.msu.cme.rdp.taxatree.VisitInfo.VisitType;
+import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
+import java.io.PrintStream;
+import java.io.PrintWriter;
+import java.util.Arrays;
+
+/**
+ *
+ * @author fishjord
+ */
+public class NewickPrintVisitor<E extends Taxon> implements TreeVisitor<E> {
+
+ public static interface NewickDistanceFactory {
+ public float getDistance(int taxid);
+ }
+
+ private PrintStream writer;
+ private NewickDistanceFactory distFactory;
+ private boolean printInnerNodeLabels;
+
+ public NewickPrintVisitor(PrintStream writer) {
+ this(writer, true, new NewickDistanceFactory() {
+ public float getDistance(int taxid) {
+ return 1;
+ }
+
+ });
+ }
+
+ public NewickPrintVisitor(PrintStream writer, boolean innerNodeLabels) {
+ this(writer, innerNodeLabels, new NewickDistanceFactory() {
+ public float getDistance(int taxid) {
+ return 1;
+ }
+
+ });
+ }
+
+ public NewickPrintVisitor(PrintStream writer, boolean innerNodeLabels, NewickDistanceFactory factory) {
+ this.writer = writer;
+ this.distFactory = factory;
+ this.printInnerNodeLabels = innerNodeLabels;
+ }
+
+ public boolean visitNode(VisitInfo<E> visitInfo) {
+// char [] indentChars = new char[visitInfo.getDepth() * 4];
+// Arrays.fill(indentChars, ' ');
+ String indent = "";//new String(indentChars);
+
+ if(visitInfo.getVisitType() == VisitType.down) {
+ if(visitInfo.hasChildren())
+ writer.print(indent + "(");
+ } else if(visitInfo.getVisitType() == VisitType.up) {
+ String paren = "";
+ if(visitInfo.hasChildren())
+ paren = ")";
+
+ String label = "";
+ if(printInnerNodeLabels || !visitInfo.hasChildren()) {
+ label = visitInfo.getTaxon().getName();
+ if(label.contains(" "))
+ label = "\"" + label + "\"";
+ }
+
+ if(visitInfo.getDepth() > 0)
+ writer.print(indent + paren + label + ":" + distFactory.getDistance(visitInfo.getTaxon().getTaxid()));
+ else
+ writer.print(indent + paren + label + ";");
+
+ if(!visitInfo.isLastChild())
+ writer.print(",");
+// else
+// writer.print();
+ }
+
+
+ return true;
+ }
+
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilder.java b/src/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilder.java
new file mode 100644
index 0000000..1cb1a73
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilder.java
@@ -0,0 +1,205 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.ConcretRoot;
+import edu.msu.cme.rdp.taxatree.Taxon;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PushbackReader;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Stack;
+
+/**
+ *
+ * @author fishjord
+ */
+public class NewickTreeBuilder<E extends Taxon> {
+
+ public static interface NewickTaxonFactory<E extends Taxon> {
+ public E buildTaxon(int taxid, String name, float distance);
+ }
+
+ private static class IdGen {
+ private static int id = 1;
+
+ public static int nextId() {
+ return id++;
+ }
+ }
+
+ private static class TaxaNameGen {
+ private static int id = 1;
+
+ public static String nextLabel() {
+ return "Unknown_Taxon_" + (id++);
+ }
+ }
+
+ private static class NewickTaxon<E extends Taxon> {
+ E t;
+ int parent;
+ }
+
+ private PushbackReader reader;
+ private NewickTaxonFactory<E> taxonFactory;
+ private ConcretRoot<E> root;
+ private int lineno = 1, col = 1;
+
+ private Map<String, Integer> nameToIdMap = new HashMap();
+
+ public NewickTreeBuilder(E rootTaxon, InputStream is, NewickTaxonFactory<E> taxonFactory) throws IOException {
+ root = new ConcretRoot<E>(rootTaxon);
+ reader = new PushbackReader(new InputStreamReader(is));
+ this.taxonFactory = taxonFactory;
+ parseNewick();
+ }
+
+ public NewickTreeBuilder(ConcretRoot<E> root, InputStream is, NewickTaxonFactory<E> taxonFactory) throws IOException {
+ this.root = root;
+ reader = new PushbackReader(new InputStreamReader(is));
+ this.taxonFactory = taxonFactory;
+ parseNewick();
+ }
+
+ public ConcretRoot<E> getRoot() {
+ return root;
+ }
+
+ public Integer getTaxidByName(String name) {
+ return nameToIdMap.get(name);
+ }
+
+ private char read() throws IOException {
+ int ret = ' ';
+
+ do {
+ ret = reader.read();
+ if(ret == '\n') {
+ lineno++;
+ col = 1;
+ } else {
+ col++;
+ }
+
+ } while(ret > 0 && Character.isWhitespace(ret));
+
+ if(ret == -1)
+ throw new IOException("Unexpected end of file");
+
+ return (char)ret;
+ }
+
+ private void parseNewick() throws IOException {
+ Stack<NewickTaxon<E>> taxaStack = new Stack();
+
+ parseTaxon(root.getRootTaxid(), taxaStack);
+ char next = read();
+ if(next != ';')
+ doError("Unexpected " + next + ", expected ;");
+
+ while(!taxaStack.empty()) {
+ NewickTaxon<E> taxon = taxaStack.pop();
+ root.addChild(taxon.t, taxon.parent);
+
+ nameToIdMap.put(taxon.t.getName(), taxon.t.getTaxid());
+ }
+ }
+
+ private void parseTaxon(int parentId, Stack<NewickTaxon<E>> taxa) throws IOException {
+ int taxid = IdGen.nextId();
+ char next = read();
+ if(next == '(') {
+
+ while(true) {
+ parseTaxon(taxid, taxa);
+
+ next = read();
+ if(next == ')')
+ break;
+ else if(next == ',')
+ continue;
+ else
+ doError("Unexpected " + next + ", expected ) or ,");
+ }
+ } else
+ reader.unread(next);
+
+ NewickTaxon taxon = new NewickTaxon();
+ taxon.t = parseTaxonObject(taxid);
+ taxon.parent = parentId;
+ taxa.push(taxon);
+ }
+
+ private Taxon parseTaxonObject(int taxid) throws IOException {
+ StringBuffer buf = new StringBuffer();
+ float dist = 0;
+
+ boolean singleQuote = false, doubleQuote = false;
+ while(true) {
+ char next = read();
+ if(!singleQuote && !doubleQuote && next == ':') {
+ dist = parseDistance();
+ break;
+ } else if(!singleQuote && !doubleQuote && (next == ',' || next == ';')) {
+ reader.unread(next);
+ break;
+ } else if(next == '\'' && !doubleQuote)
+ singleQuote = !singleQuote;
+ else if(next == '"' && !singleQuote)
+ doubleQuote = !doubleQuote;
+
+ buf.append(next);
+ }
+
+ String name = buf.toString();
+ if(name.length() == 0)
+ name = TaxaNameGen.nextLabel();
+
+ return taxonFactory.buildTaxon(taxid, name, dist);
+ }
+
+ private float parseDistance() throws IOException {
+ StringBuffer ret = new StringBuffer();
+ char next = read();
+
+ while(Character.isDigit(next) || next == '.' || next == '-') {
+ ret.append(next);
+ next = read();
+ }
+
+ reader.unread(next);
+
+ float dist = 0.0f;
+ try {
+ dist = Float.parseFloat(ret.toString());
+ if(dist < 0)
+ dist = 0.0f;
+ } catch(NumberFormatException e) {
+ doError("Invalid distance value \"" + ret.toString() + "\"");
+ }
+
+ return dist;
+ }
+
+ private void doError(String message) throws IOException {
+ throw new IOException("Error line=" + lineno + " col=" + col + ": " + message);
+ }
+}
diff --git a/src/edu/msu/cme/rdp/taxatree/utils/PrintVisitor.java b/src/edu/msu/cme/rdp/taxatree/utils/PrintVisitor.java
new file mode 100644
index 0000000..c1dc7be
--- /dev/null
+++ b/src/edu/msu/cme/rdp/taxatree/utils/PrintVisitor.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.Taxon;
+import edu.msu.cme.rdp.taxatree.VisitInfo;
+import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
+import java.io.PrintStream;
+import java.util.Arrays;
+
+/**
+ *
+ * @author fishjord
+ */
+public class PrintVisitor<E extends Taxon> implements TreeVisitor<E> {
+
+ private char indentCharacter;
+ private int indent;
+ private PrintStream out;
+
+ public PrintVisitor() {
+ this(4, ' ', System.out);
+ }
+
+ public PrintVisitor(int indent) {
+ this(indent, ' ', System.out);
+ }
+
+ public PrintVisitor(int indent, char indentCharacter) {
+ this(indent, indentCharacter, System.out);
+ }
+
+ public PrintVisitor(int indent, PrintStream out) {
+ this(indent, ' ', out);
+ }
+
+ public PrintVisitor(PrintStream out) {
+ this(4, ' ', out);
+ }
+
+ public PrintVisitor(int indent, char indentCharacter, PrintStream out) {
+ this.indent = indent;
+ this.indentCharacter = indentCharacter;
+ this.out = out;
+ }
+
+ public boolean visitNode(VisitInfo<E> visitInfo) {
+ char [] indentChars = new char[visitInfo.getDepth() * indent];
+ Arrays.fill(indentChars, indentCharacter);
+ String indentString = new String(indentChars);
+
+ out.println(indentString + visitInfo.getTaxon().getName() + " rank=" + visitInfo.getTaxon().getRank() + " taxid=" + visitInfo.getTaxon().getTaxid());
+ return true;
+ }
+
+
+}
diff --git a/test/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitorTest.java b/test/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitorTest.java
new file mode 100644
index 0000000..aa45a60
--- /dev/null
+++ b/test/edu/msu/cme/rdp/taxatree/utils/NewickPrintVisitorTest.java
@@ -0,0 +1,47 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.Taxon;
+import edu.msu.cme.rdp.taxatree.TaxonHolder;
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ *
+ * @author Jordan Fish <fishjord at msu.edu>
+ */
+public class NewickPrintVisitorTest {
+
+ public NewickPrintVisitorTest() {
+ }
+
+ @Test
+ public void testNewickVisitor() {
+ Taxon root = new Taxon(0, "root", "root_rank");
+ Taxon phylum1 = new Taxon(1, "Proteobacteria", "phylum");
+ Taxon phylum2 = new Taxon(2, "Acidobacteria", "phylum");
+ Taxon class1 = new Taxon(3, "Alphaproteobacteria", "class");
+ Taxon class2 = new Taxon(4, "Betaproteobacteria", "class");
+
+ TaxonHolder rootHolder = new TaxonHolder(root);
+ rootHolder.addChild(phylum1, 0);
+ rootHolder.addChild(phylum2, 0);
+ rootHolder.addChild(class1, 1);
+ rootHolder.addChild(class2, 1);
+
+ ByteArrayOutputStream outstream = new ByteArrayOutputStream();
+ NewickPrintVisitor visitor = new NewickPrintVisitor(new PrintStream(outstream));
+
+ System.out.println("test biDirectionDepthFirst()");
+ rootHolder.biDirectionDepthFirst(visitor);
+
+ String[] lines = outstream.toString().split("\n");
+ assertEquals(lines[0], "((Alphaproteobacteria:1.0,Betaproteobacteria:1.0)Proteobacteria:1.0,Acidobacteria:1.0)root;");
+
+ }
+}
\ No newline at end of file
diff --git a/test/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilderTest.java b/test/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilderTest.java
new file mode 100644
index 0000000..1602305
--- /dev/null
+++ b/test/edu/msu/cme/rdp/taxatree/utils/NewickTreeBuilderTest.java
@@ -0,0 +1,58 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.ConcretRoot;
+import edu.msu.cme.rdp.taxatree.Taxon;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ *
+ * @author Jordan Fish <fishjord at msu.edu>
+ */
+public class NewickTreeBuilderTest {
+
+ public static class TestTaxon extends Taxon{
+ private float bl;
+ public TestTaxon(int taxid, String name, String rank, float bl) {
+ super(taxid, name, rank, false);
+ this.bl = bl;
+ }
+
+ public float getBl() {
+ return bl;
+ }
+ }
+
+ public NewickTreeBuilderTest() {
+ }
+
+ @Test
+ public void testNewickBuilder() throws IOException {
+ TestTaxon root = new TestTaxon(0, "root", "root_rank", 0);
+ String newick = "((Alphaproteobacteria:0.01,Betaproteobacteria:1.0)Proteobacteria:1.0,Acidobacteria:1.0)root;" ;
+ InputStream is = new ByteArrayInputStream(newick.getBytes("UTF-8"));
+ NewickTreeBuilder builder = new NewickTreeBuilder(root, is, new NewickTreeBuilder.NewickTaxonFactory<TestTaxon>() {
+
+ public TestTaxon buildTaxon(int taxid, String name, float distance) {
+ return new TestTaxon(taxid, name, "", distance);
+ }
+ });
+
+ ConcretRoot<TestTaxon> rootTaxon = builder.getRoot();
+ assertEquals(root.getTaxid(), rootTaxon.getRootTaxid());
+ assertEquals(2, (int)builder.getTaxidByName("Proteobacteria"));
+ assertEquals(4, (int)builder.getTaxidByName("Betaproteobacteria"));
+ assertEquals(5, (int)builder.getTaxidByName("Acidobacteria"));
+
+ // test branch length
+ TestTaxon alphaTaxon = rootTaxon.getChildTaxon(3);
+ assertEquals(0.01f, alphaTaxon.getBl(), 0.01);
+ }
+}
\ No newline at end of file
diff --git a/test/edu/msu/cme/rdp/taxatree/utils/PrintVisitorTest.java b/test/edu/msu/cme/rdp/taxatree/utils/PrintVisitorTest.java
new file mode 100644
index 0000000..74c1189
--- /dev/null
+++ b/test/edu/msu/cme/rdp/taxatree/utils/PrintVisitorTest.java
@@ -0,0 +1,51 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package edu.msu.cme.rdp.taxatree.utils;
+
+import edu.msu.cme.rdp.taxatree.Taxon;
+import edu.msu.cme.rdp.taxatree.TaxonHolder;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.io.StringReader;
+import static org.junit.Assert.assertEquals;
+import org.junit.Test;
+
+/**
+ *
+ * @author Jordan Fish <fishjord at msu.edu>
+ */
+public class PrintVisitorTest {
+
+ public PrintVisitorTest() {
+ }
+
+ @Test
+ public void testPrintVisitor() throws IOException {
+ Taxon root = new Taxon(0, "root", "root_rank");
+ Taxon phylum1 = new Taxon(1, "Proteobacteria", "phylum");
+ Taxon phylum2 = new Taxon(2, "Acidobacteria", "phylum");
+ Taxon class1 = new Taxon(3, "Alphaproteobacteria", "class");
+ Taxon class2 = new Taxon(4, "Betaproteobacteria", "class");
+
+ TaxonHolder rootHolder = new TaxonHolder(root);
+ rootHolder.addChild(phylum1, 0);
+ rootHolder.addChild(phylum2, 0);
+ rootHolder.addChild(class1, 1);
+ rootHolder.addChild(class2, 1);
+
+ ByteArrayOutputStream outstream = new ByteArrayOutputStream();
+ PrintVisitor visitor = new PrintVisitor(new PrintStream(outstream));
+
+ System.out.println("test topDownVisit()");
+ rootHolder.topDownVisit(visitor);
+
+ String[] lines = outstream.toString().split("\n");
+ assertEquals(lines[0], "root rank=root_rank taxid=0");
+ assertEquals(lines[3], " Betaproteobacteria rank=class taxid=4");
+ assertEquals(lines[4], " Acidobacteria rank=phylum taxid=2");
+
+ }
+}
\ No newline at end of file
--
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