treeCmp

TreeCmp: comparison of trees in polynomial time. See the manual for usage.

Compilation from the command line

Normally, compilation is done via an IDE like NetBeans or Eclipse. However, to compile via the command line, follow these steps:

Recursively clone the repository

git clone --recursive https://github.com/TreeCmp/TreeCmp.git

cd into the cloned repository and make output diriectories

cd TreeCmp && mkdir -p out/class

Export CLASSPATH to the jar's in the lib directory

export CLASSPATH=lib/commons-cli-1.4.jar:\
lib/commons-collections4-4.3.jar:\
lib/commons-compress-1.18.jar:\
lib/commons-io-2.6.jar:\
lib/poi-4.1.0.jar:\
lib/poi-ooxml-4.1.0.jar:\
lib/poi-ooxml-schemas-4.1.0.jar:\
lib/xmlbeans-3.1.0.jar:$CLASSPATH

Compile

javac -d out/class src/treecmp/*.java src/treecmp/*/*.java src/pal/*/*.java src/treecmp/metric/weighted/*.java src/distanceAlg1/*.java src/polyAlg/*.java

The resulting compiled files can be run directly, for example by issuing the command java -cp out/class:lib/commons-cli-1.4.jar treecmp.Main (you will need to replace the colon with a semicolon on windows systems). However, it is usually easier to create a stand-alone .jar executable as below.

Creating a jar executable from the command line

The jar executable (e.g. TreeCmp.jar) should be created in the bin directory, as it expects to find the config/config.xml file one level above the directory in which the executable resides. Once the class files have been compiled in the out/class directory as above, this jar file can be created in the correct place using the MANIFEST.MF file in src/META-INF:

jar cvfm bin/TreeCmp.jar src/META-INF/MANIFEST.MF -C out/class/ .

As defined in the manifest, extra libraries are expected to be placed in lib directory in the same place as the jar file. An easy way to do this is to move or copy the lib folder (containing commons-cli-1.4.jar) into the bin directory. For example, on unix-like systems you could do cp -a lib bin/, on windows xcopy lib bin\.

Once the commons-cli-1.4.jar library has been copied to the correct place, the TreeCmp.jar file can be run as described in the manual (e.g. java -jar bin/TreeCmp.jar -w 2 -d ms -i examples/beast/testBSP.newick -o testBSP.newick_w_2.out -I