fixed issue 17, please merge #35

pgaurav · 2011-06-27T22:05:59Z

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Signed-off-by: dsokus <[email protected]>

Conflicts: gtfold-mfe/src/algorithms.c gtfold-mfe/src/main.cc gtfold-mfe/src/traceback.c

…Still can't produce structures like (...)(...)

… clear what to do with the misc loop parameters.) Signed-off-by: dsokus <[email protected]>

… algorithms.c

Shape constraints & other stuff

Fixed issue #3

…in the multiloop optimization.

…se that something is forced to pair within it

…ed verification function to check that prediction fulfills constraint criteria

Forcing constraints

…to match rna subopt.

…ture count by partition function added

"Few Bug removed from partition function and options for getting structure count by partition function added

… and verifies that they are not violated in the generated structure.

…separate file.

…red again in suboptimal traceback.

Test Framework and other code changes

zetches and others added 30 commits March 2, 2011 21:52

test

ebeea43

test text removed

06a3802

committing a small text file to test if my Github setup works.

b76b9c1

Signed-off-by: dsokus <[email protected]>

fixed constraint handling issue - forbid adjacent bp pairing

c4bbb86

place ct file in current working dir

290afc1

minor code cleanup

c4401f5

fixed bug on reading of sequence

1acf3aa

program crashed when run with unambiguous bases sequence, fixed this

51abea3

removed printing of seq contents

3f0046e

adding data files in new format

27383c2

adding script to covert data to newer format

ef501b8

support for new data format

fead43c

changes to parse datafiles compatible with UNAfold format

270f694

fixed bug related to constraints

b189299

Merge remote branch 'upstream/master' into error_est

9d4a526

Conflicts: gtfold-mfe/src/algorithms.c gtfold-mfe/src/main.cc gtfold-mfe/src/traceback.c

Commiting SHAPE support and the first attempt at fixing constraints. …

1a4dfa0

…Still can't produce structures like (...)(...)

Errors in thermodynamic paramters... commit long overdue!! (It is not…

de4982d

… clear what to do with the misc loop parameters.) Signed-off-by: dsokus <[email protected]>

Contact distance implemented + missing SHAPE header included again in…

0e3f085

… algorithms.c

Removed unnecessary output

ff9ec67

Merge pull request #2 from dsokus/shape_constraints

e7dc6b3

Shape constraints & other stuff

Fixed pseudoknotted constraint issue (issue nr. 3)

48ee2aa

Merge pull request #5 from dsokus/shape_constraints

3cd54bb

Fixed issue #3

Fix to forcing constraints, traceback error, and some small problems …

0d86566

…in the multiloop optimization.

fix to tracing W[i] even if it has positive energy, in the special ca…

e6877be

…se that something is forced to pair within it

fixed an out-of-scope reference in unconstrained predictions, and add…

4d8be8a

…ed verification function to check that prediction fulfills constraint criteria

Merge pull request #6 from dsokus/shape_constraints

e21f663

Forcing constraints

fix to prohibited constraints

ee47c24

I need to move this to another computer to go to a ballgame

42c5b93

First draft of matrix filling

83f7fe5

Compiles does not link

d814038

iamrohitbanga and others added 30 commits October 7, 2011 16:13

Rename PseudoKnotDetection Tests to ExitCode Tests.

aac4e4a

Remove pseudoknot detection sequences

8ed1a04

Test to Compare CT structure returned by GTFold and UNAFold.

7b4289c

Added meaningful names to some sequence files.

82ca1b2

Cleanup - Delete a file.

0926b47

Merge Suboptimal Structure matching test.

594093c

Output formatting for saving suboptimal structures to a file changed …

d966815

…to match rna subopt.

Few Bug removed from partition function and options for getting struc…

d069c65

…ture count by partition function added

Merge pull request #6 from msoni3/master

1367dc6

"Few Bug removed from partition function and options for getting structure count by partition function added

Constraint Verification Tests - The tests generate random constraints…

f587da4

… and verifies that they are not violated in the generated structure.

adding changes to sampling

c9ea343

fixes to sampling algorithm

c008412

adding fix of Eb and Ec

a1f5d30

fix RT scaling factor

ea00693

print sampling probablities

2d8a329

added boltzmann prob calculation

c8b8ccd

changed part func to return U

ded86f0

fixed energy traceback

3f7c982

Implementation of Unique Multiloop Decomposition

29cc807

Added a Sample Test Module

90b4481

Pretty Output for Suboptimal Structures Match Test. Output sent to a …

cdd5c97

…separate file.

adding stochastic smaplign changes

45111dc

Adding Paul Specials

99e46c4

Duplicate Structures should be reported if partial structure encounte…

7fa3ab8

…red again in suboptimal traceback.

Merge pull request #7 from iamrohitbanga/master

89c6c5d

Test Framework and other code changes

code cleanup

fb6500b

adding changes in global vars

70d4e4d

removing file

6d5a9f9

+ adding new options + script to add symlink

e492adc

added creation of symlinks

1957922

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fixed issue 17, please merge #35

fixed issue 17, please merge #35

pgaurav commented Jun 27, 2011

fixed issue 17, please merge #35

Are you sure you want to change the base?

fixed issue 17, please merge #35

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pgaurav commented Jun 27, 2011