merge v2.0#1

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pgaurav wants to merge 349 commits intoreleasefrom

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Commits on Mar 28, 2011

Commits on Apr 5, 2011

Commits on Apr 6, 2011

Commits on Apr 12, 2011

Merge remote branch 'prashant/rewrite'
ash211
committed

Commits on Apr 13, 2011

fixed bug on reading of sequence
pgaurav
committed

Commits on Apr 14, 2011

program crashed when run with unambiguous bases sequence, fixed this
pgaurav
committed

Commits on Apr 22, 2011

removed printing of seq contents
pgaurav
committed

Commits on May 4, 2011

fixed bug related to constraints
pgaurav
committed

Commits on May 7, 2011

Commits on May 17, 2011

Commits on May 18, 2011

First draft of matrix filling

Joshua Anderson
authored and
Joshua Anderson
committed
Compiles does not link
Janderson3
committed

Commits on May 20, 2011

Commits on Jun 7, 2011

Commits on Jun 8, 2011

Merge pull request #8 from pgaurav/master
shelswenson
committed

Commits on Jun 11, 2011

Bugfix in partition. Random sample now compiles, links
Janderson3
committed

Commits on Jun 16, 2011

I believe my automake is broken, but bpp theoretically re-integrated
Janderson3
committed
added new macro
Prashant Gaurav
committed
added new macro
Prashant Gaurav
committed
added -m option
Prashant Gaurav
committed
added energy functions to support unafold mode
Prashant Gaurav
committed
added function to load tstacke tstackm tstacki23 enegery values
Prashant Gaurav
committed
added change to handle unafold mode
Prashant Gaurav
committed
added changes to handle unafold mode
Prashant Gaurav
committed
merged ZS bug fix on constraints
Prashant Gaurav
committed
merged ZS changes with SHAPE
Prashant Gaurav
committed
merged ZS changes with SHAPE
Prashant Gaurav
committed
Merge pull request #10 from pgaurav/master
shelswenson
committed

Commits on Jun 17, 2011

Accessing C declarations from C++ requires the "C" extern
ash211
committed
removed Makefile
Prashant Gaurav
committed
seperate functions eL1(), eL() to handle 2x3 internal loop
Prashant Gaurav
committed
Merge pull request #12 from pgaurav/master
shelswenson
committed

Commits on Jun 19, 2011

Commits on Jun 20, 2011

--bpp option re-integrated.
Janderson3
committed
subopt related changes
Prashant Gaurav
committed
added print message
Prashant Gaurav
committed
added .dat files to base_data dir
Prashant Gaurav
committed
moved .dat files to base_data dir
Prashant Gaurav
committed
rmeoved .dat entries
Prashant Gaurav
committed
Merge branch 'master' of git://github.com/gtfold/gtfold
Prashant Gaurav
committed
Merge pull request #13 from pgaurav/master
shelswenson
committed

Commits on Jun 21, 2011

fix for contact dist
Prashant Gaurav
committed
fixed subopt, change to take value kCal
Prashant Gaurav
committed
Merge pull request #26 from pgaurav/master
shelswenson
committed

Commits on Jun 22, 2011

fix for allowable basepair
Prashant Gaurav
committed
subopt changes
Prashant Gaurav
committed
Merge pull request #27 from pgaurav/master
shelswenson
committed

Commits on Jun 23, 2011

adding UNAfold parameters
Prashant Gaurav
committed
changes to seperate unamode(--unamode), terminal mismatch(-m)
Prashant Gaurav
committed
changes to seperate unamode(--unamode), terminal mismatch(-m)
Prashant Gaurav
committed
adding file
Prashant Gaurav
committed
added print statement
Prashant Gaurav
committed

Commits on Jun 24, 2011

Merge pull request #28 from pgaurav/master
shelswenson
committed
added entry tstacke; removed sint2, sint4
Prashant Gaurav
committed
added Makefiles under UNAParams
Prashant Gaurav
committed
added entry UNAParams
Prashant Gaurav
committed
added entry UNAParams
Prashant Gaurav
committed
delete these auto generated file
Prashant Gaurav
committed
delete these auto generated file
Prashant Gaurav
committed
deleted unwanted files
Prashant Gaurav
committed
added prefilter option, rectified unamode option
Prashant Gaurav
committed
removed unwanted print statement
pgaurav
committed
added check for prefilter inputs
pgaurav
committed
Merge pull request #29 from pgaurav/master
shelswenson
committed
fixed formatting problem in help message
pgaurav
committed
added newline after Total
pgaurav
committed

Commits on Jun 26, 2011

Merge pull request #31 from pgaurav/master
shelswenson
committed

Commits on Jun 29, 2011

- changed --unamode to --unafold, - removed a debug statement
pgaurav
committed

Commits on Jul 1, 2011

Merge pull request #36 from pgaurav/master
shelswenson
committed

Commits on Jul 12, 2011

Commits on Sep 9, 2011

Fixed pseudoknot detection logic in constraint pre-processing part of the code.
iamrohitbanga
committed

Commits on Sep 10, 2011

Commits on Sep 12, 2011

Commits on Sep 16, 2011

Commits on Sep 27, 2011

Commits on Sep 30, 2011

First version of test scripts:
iamrohitbanga
committed

Commits on Oct 1, 2011

Partition Function calculation implementation completed
msoni3
committed
Merge pull request #2 from msoni3/master
pgaurav
committed
added stochastic sampling
Prashant Gaurav
committed
added stochastic sampling files
Prashant Gaurav
committed
changes related to stochastic sampling
Prashant Gaurav
committed
changed f() to be non static
Prashant Gaurav
committed

Commits on Oct 2, 2011

Partition Func overflow error due to int value resolved
msoni3
committed
Merge pull request #3 from msoni3/master
pgaurav
committed
added checks
Prashant Gaurav
committed
corrections in ML traceback
Prashant Gaurav
committed

Commits on Oct 3, 2011

Wrapper function for Ed3 and Ed5 dangling functions added
msoni3
committed

Commits on Oct 4, 2011

Merge pull request #4 from msoni3/master
pgaurav
committed

Commits on Oct 5, 2011

Commits on Oct 6, 2011

1. Merge Pseudoknot Detection Tests.
iamrohitbanga
committed

Commits on Oct 14, 2011

Commits on Oct 16, 2011

adding changes to sampling
Prashant Gaurav
committed

Commits on Oct 20, 2011

fixes to sampling algorithm
Prashant Gaurav
committed
adding fix of Eb and Ec
Prashant Gaurav
committed

Commits on Oct 21, 2011

fix RT scaling factor
Prashant Gaurav
committed
print sampling probablities
pgaurav
committed

Commits on Oct 26, 2011

Commits on Nov 2, 2011

fixed energy traceback
pgaurav
committed

Commits on Nov 4, 2011

Implementation of Unique Multiloop Decomposition
Rohit Banga
committed

Commits on Nov 11, 2011

Added a Sample Test Module
Rohit Banga
committed
Pretty Output for Suboptimal Structures Match Test. Output sent to a separate file.
Rohit Banga
committed

Commits on Nov 18, 2011