search

CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
236 stars 83 forks source link

Investigate NCL - BEAST interface #161

Open rbouckaert opened 10 years ago

rbouckaert commented 10 years ago

NCL http://ncl.sourceforge.net/ is the standard implementation for Nexus parsing. Can we integrate this with BEAST? What are the issues?

tgvaughan commented 10 years ago

Good idea, but you don't think its being written in C++ will be a problem? I guess you could go the JNI route...

Would it make sense to instead use JEBL's parser?

rbouckaert commented 10 years ago

Yes, we are looking at JNI -- and what issues are involved in that.

JEBL is not as complete as I would like, hence the investigation of NCL.

On Sun, 2014-07-13 at 22:42 -0700, Tim Vaughan wrote:

Good idea, but you don't think its being written in C++ will be a problem? I guess you could go the JNI route...

Would it make sense to instead use JEBL's parser?

— Reply to this email directly or view it on GitHub.

walterxie commented 10 years ago

http://www.ibm.com/developerworks/java/tutorials/j-jni/j-jni.html

http://www.javaworld.com/javaworld/javatips/jw-javatip17.html

http://www.javamex.com/tutorials/jni/getting_started.shtml

JNIEasy ? http://java.dzone.com/news/how-bring-your-venerable-cc-co

walterxie commented 10 years ago

BioJava NexusParser failed to parse TITLE in TAXA to show its limitation.

walterxie commented 10 years ago

another choice http://www.antlr.org

walterxie commented 10 years ago

The estimated work for NCL:

1) jvm.lib, and jvm.dll or jvm.so files respectively for 3 OS, they need to update every time if OS is upgrading, which may be annoyed;

2) write Java code which will declares the native method and convert NCL object to BEAST object.

3) not sure if the change of C++ head file is required.

walterxie commented 10 years ago

The estimated work for ANTLR 4:

1) learning curve of grammar;

2) no experience how it works for bioinformatics data.