FAQs: Difference between revisions

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== Handling data ==
== Handling data ==
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'''Q: How to create an AlphabetContainer instance for DNA sequences?'''<br />
'''Q: How to create an [http://www.jstacs.de/api/de/jstacs/data/AlphabetContainer.html | AlphabetContainer] instance for DNA sequences?'''<br />
'''A:''' AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
'''A:''' AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
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'''Q: Why shall I use the AlphabetContainer and not just a simple Alphabet instance in the models, ...?'''<br />
'''Q: Why shall I use the AlphabetContainer and not just a simple Alphabet instance?'''<br />
'''A:''' Because for some data you will not have the same alphabet at each position of the sequence, e.g. for phenotypic data, ...
'''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?'''''<br>
'''''Q: How can I create a simple sequence?'''''<br>

Revision as of 11:10, 7 September 2008

Handling data

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?
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:

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:
A1: You have forgotten to set the Java library path: -Djava.library.path=...
A2: You have to compile the native code on your system.