Some tips on Java convention

Compile the java program under the condition of command line.
1. go to the project directory, e.g.: cd MNPhyloTreeBuilder. (this is the project directory)
2. type \>javac -classpath [lib] [the main class of the project]
Before the compile, the jar files should be copied into the lib directory. And if the jar files used as lib are more than one, they should be listed one by one. For example：
\>javac -classpath lib/poi.jar;lib/junit.jar src/mytest/PoiExcelReader.java

Since this compiling approach is a little complex, you can use IDE to do the compilation(say, JBuilder), but to run the java program, especially having errors on memory, you'd better use java command.

The following is the basic package structure for the project named phylotree:

org.tingting.bn.mn.phylotree.domain - domain objects
org.tingting.bn.mn.phylotree.core - core functions
org.tingting.bn.mn.phylotree.util - utility classes used by this phylotree project
org.tingting.bn.mn.phylotree.swing - swing interface