[Biojava-dev] BioJava 3 code usage examples

[Hongyu Zhang]

Hi Richard,

Thanks for your great work! I noticed from your examples that you decided to continue to use the Symbol object-based model to represent sequences even though in the Biojava3 design page ( http://biojava.org/wiki/BioJava3_Design ) it said
"Sequences are perfectly happy as Strings unless you want to do complex
things like store base quality information, and only at that point
should you want to convert them into more complex object models."

 
The original Biojava tutorial ( http://biojava.org/wiki/BioJava:Tutorial:Symbols_and_SymbolLists#Doesn.27t_this_all_waste_memory.3F ) discussed the memoery space difference between Symbol object-based sequence representation and String-based sequence representation, but it didn't address speed issue. One of the advantages of Java String library is that it was optimized using native machine codes, so  I think an Sybmol object-based sequence representation would be slower than String-based sequence representation for certain operations such as substring search.

Let me know if I missed something. Thanks!

Best,

Hongyu Zhang, Ph.D.
Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750