Simplealign

[yinjun111]

Hi, Chris,

This is my implementation of Bio::SimpleAlign. I have a detailed report describing the improvement to the code, and explaining the failed tests using t/Align/SimpleAlign.t. If you need any help, please just let me know.

Cheers,
Jun

[hyphaltip]

Oops - comments from me not a student in my class...

So this currently fails in the travis build -- can someone comment about what it will take to fix it.
Where is the detailed report on what was added Jun - is it in the code or in a mail to the mailing list?

[yinjun111]

I have send the update log to Chris Fields, who was my mentor during my coding project in Google summer of code. I think I can put the update log in the BioPerl wiki, so everybody can see it. If you pull the new SimpleAlign code, you will expect some failed tests from t/Align/SimpleAlign.t, you will see the explanation in the report.

[yinjun111]

See the wiki page for details of the updates:
http://www.bioperl.org/wiki/SimpleAlign_Updates#Abstract

[jhannah]

Without objection I'll be reviewing and merging the 3 open github pull requests this week.

[yinjun111]

Hi, Jay,

I notice that there is no revision on the SimpleAlign code for the last few months. So this implementation should work without problem using the SimpleAlign2.t provided. Let me know if you need any clarification.

Cheers,
Jun

[cjfields]

We have failing Travis-CI at the moment, so hold off on a merge. We're planning on a new point release of BioPerl 1.6.x in about 1 month, we might want to wait before merging this one in.

[cjfields]

Jun, after a long long wait I'm finally getting around to reviewing these. I've pulled them into a separate branch from master and will merge back in after checking tests.

[yinjun111]

Hi, Chris,

You will have some errors from the old t/Align/SimpleAlign.t. You can try t/Align/SimpleAlign2.t, which is edited to test the new Bio::SimpleAlign

[cjfields]

I saw the errors. Do you recall whether these are failing b/c the implementation details changed, or where the tests erroneous to begin with?

[yinjun111]

These are mainly caused by different implementation of several methods. The changes are listed in the BioPerl wiki.
http://www.bioperl.org/wiki/SimpleAlign_Updates#Abstract