FAQs

FAQs & Code examples

Here we collected some questions that were asked quite often ...

Q: How to create an AlphabetContainer instance for DNA sequences?
A: AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );

Q: Why shall I use the AlphabetContainer and not just a simple Alphabet instance in the models, ...?
A: Because for some data you will not have the same alphabet at each position of the sequence, e.g. for phenotypic data, ...

Q: How can I create a simple sequence?
A: Try to use the create method of Sequence, e.q. Sequence.create( new AlphabetContainer( new DNAAlphabet() ), "ACGTACGT" );

Q: How can I load my own data?
A: JAN ...

Q: How can store and load my model, classifier, ...?
A: All classes that implement Storable should have a method toXML() that returns a StringBuffer containing the instance as XML. Furthermore, such classes should have a proper constructor with a single argument StringBuffer. This can be used to create a new instance form a StringBuffer that contains an instance as XML. In addition, The class FileManger allows to read and write StringBuffer to the hard drive.

Q: Why does Jstacs use XML to save instances?
A: Because it is human readable.

Q: The class UserTime does not work? Why?
A: The class UserTime uses native code. Therefore there are at least two possibilities
1) you have forgotten to set the Java library path: -Djava.library.path=... or
2) you have to compile the native code on your system.