Commits

History for

Commits on Feb 28, 2014

fixing display problem with IDs of different length
andreasprlic
committed
884707d

Commits on Dec 17, 2013

Commits on Dec 16, 2013

Fixed issue #85.
dmyersturnbull
committed
81faa40
FractionalSimilarityScorer was actually identical to
dmyersturnbull
committed
3d919c4
Refactored alignment to allow anchored compounds for all global alignments
d-cameron
committed
f0b6981

Commits on Dec 10, 2013

Added multiple test cases for various alignment bugs including #78
d-cameron
committed
fcd8531
Compounds not included in the scoring matrix will default to the alternative case of the compound if it exists in the scoring matrix instead of the min matrix value
d-cameron
committed
6f91a9f

Commits on Oct 26, 2013

Stockholm Parser is stateless now (more tolerant but less robust)
aalhossary
committed
462bced

Commits on Oct 16, 2013

Clean up the majority of compile warnings
emckee2006
committed
8faddba

Commits on Jul 28, 2013

Made a general-purpose public method
dmyersturnbull
committed
cb9666d

Commits on Mar 2, 2013

get pariwise alignment of protein sequences
andreasprlic
committed
e76dcad

Commits on Nov 28, 2012

adding another database type constant
aalhossary
committed
ddd399f

Commits on Nov 27, 2012

Proper fixation of the bug, adding INFINITY as a constant, and documentation
aalhossary
committed
cd294f6

Commits on Nov 26, 2012

correcting a bug that takes place at the end of the file (if you reach it ;) )
aalhossary
committed
b896458

Commits on Nov 24, 2012

just doc
aalhossary
committed
a5790df

Commits on Nov 19, 2012

Changing return of parse() into List in stead of Vector
aalhossary
committed
376f82e
Adding getBioSequences(boolean ignoreCase)
aalhossary
committed
34d18af

Commits on Nov 9, 2012

Commits on Nov 7, 2012

Changing parseFile(xxx) function set into parse(xxx) and adding parseNext(int)
aalhossary
committed
e842124

Commits on Nov 6, 2012

aalhossary
committed
6eb094b
Added Stockholm Parser beta, and some test files.
aalhossary
committed
8256813

Commits on Oct 18, 2012

Refactor to use forester 1.005
markchapman
committed
28f2a11

Commits on Jul 3, 2012

demo for how to load amino acid substitution matrices
andreasprlic
committed
652cebb
an example for how to align DNA
andreasprlic
committed
ea5b48c
adding the cookbook example as a demo
andreasprlic
committed
4ca31b9

Commits on Jul 2, 2012

adding patch by Don Naki
andreasprlic
committed
466a3a6