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fixed issue 17, please merge#35

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pgaurav wants to merge 245 commits intoash211:masterash211/gtfold:masterfrom pgaurav:masterpgaurav/gtfold:masterCopy head branch name to clipboard

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Commits

Commits on Mar 3, 2011

• test

  zetches

  committed
  ebeea43

• test text removed

  zetches

  committed
  06a3802

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

  Show description for b76b9c1
  zetches

  committed
  b76b9c1

• fixed constraint handling issue - forbid adjacent bp pairing

  

  Prashant Gaurav

  authored and

  zetches

  committed
  c4bbb86

• place ct file in current working dir

  

  Prashant Gaurav

  authored and

  zetches

  committed
  290afc1

• minor code cleanup

  

  Prashant Gaurav

  authored and

  zetches

  committed
  c4401f5

Commits on Apr 13, 2011

• fixed bug on reading of sequence

  pgaurav

  committed
  1acf3aa

Commits on Apr 14, 2011

• program crashed when run with unambiguous bases sequence, fixed this

  pgaurav

  committed
  51abea3

Commits on Apr 22, 2011

• removed printing of seq contents

  pgaurav

  committed
  3f0046e

Commits on Apr 28, 2011

• adding data files in new format

  pgaurav

  committed
  27383c2

• adding script to covert data to newer format

  pgaurav

  committed
  ef501b8

• support for new data format

  pgaurav

  committed
  fead43c

• changes to parse datafiles compatible with UNAfold format

  pgaurav

  committed
  270f694

Commits on May 4, 2011

• fixed bug related to constraints

  pgaurav

  committed
  b189299

Commits on May 7, 2011

• Merge remote branch 'upstream/master' into error_est

  Show description for 9d4a526
  zetches

  committed
  9d4a526

• Commiting SHAPE support and the first attempt at fixing constraints. Still can't produce structures like (...)(...)

  zetches

  committed
  1a4dfa0

Commits on May 8, 2011

• Errors in thermodynamic paramters... commit long overdue!! (It is not clear what to do with the misc loop parameters.)

  Show description for de4982d
  zetches

  committed
  de4982d

• Contact distance implemented + missing SHAPE header included again in algorithms.c

  zetches

  committed
  0e3f085

• Removed unnecessary output

  zetches

  committed
  ff9ec67

• Merge pull request #2 from dsokus/shape_constraints

  Show description for e7dc6b3
  shelswenson

  committed
  e7dc6b3

• Fixed pseudoknotted constraint issue (issue nr. 3)

  zetches

  committed
  48ee2aa

• Merge pull request #5 from dsokus/shape_constraints

  Show description for 3cd54bb
  shelswenson

  committed
  3cd54bb

Commits on May 14, 2011

• Fix to forcing constraints, traceback error, and some small problems in the multiloop optimization.

  zetches

  committed
  0d86566

• fix to tracing W[i] even if it has positive energy, in the special case that something is forced to pair within it

  zetches

  committed
  e6877be

• fixed an out-of-scope reference in unconstrained predictions, and added verification function to check that prediction fulfills constraint criteria

  zetches

  committed
  4d8be8a

• Merge pull request #6 from dsokus/shape_constraints

  Show description for e21f663
  shelswenson

  committed
  e21f663

Commits on May 17, 2011

• fix to prohibited constraints

  zetches

  committed
  ee47c24

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

  Janderson3

  committed
  42c5b93

Commits on May 18, 2011

• First draft of matrix filling

  

  Joshua Anderson

  authored and

  Joshua Anderson

  committed
  83f7fe5

• Compiles does not link

  Janderson3

  committed
  d814038

Commits on May 20, 2011

• Finished writing all probability functions

  Janderson3

  committed
  294a556

• fixed internal loop calculation

  pgaurav

  committed
  9008ee9

Commits on May 23, 2011

• removed flag optimization

  pgaurav

  committed
  9e0612c

• added -p option to allow

  pgaurav

  committed
  b85fbaf

• added -p option to allow dir name for param files

  pgaurav

  committed
  3e117e6

• added -p option to allow dir name for param files

  pgaurav

  committed
  7e421b5

Commits on May 24, 2011

• removed unrequired header

  pgaurav

  committed
  ec8dcb9

• removed cout statement

  pgaurav

  committed
  fd23a9d

• fixed MFE and constraints. constraint check included with -v option

  zetches

  committed
  14e822e

• Fixed constraints, removed unnecessary output

  zetches

  committed
  3eee5c2

Commits on May 25, 2011

• merged Prashant's rewrite branch

  zetches

  committed
  15915e5

• Merge branch 'shape_constraints', remote branch 'prashant-rewrite/rewrite' into shape_constraints

  zetches

  committed
  1efeeb2

• Fixed merge errors, should compile now

  zetches

  committed
  da4c291

• replaced data Makefiles with Prashant's version

  zetches

  committed
  a5ebd16

• trying to commit data Makefiles again

  zetches

  committed
  b4b0055

• ...and once more..?

  zetches

  committed
  ecf119a

• fixed lost support for contact distance

  zetches

  committed
  7227e16

• Merge pull request #7 from dsokus/shape_constraints

  Show description for f4f42d6
  shelswenson

  committed
  f4f42d6

Commits on Jun 7, 2011

• testing

  pgaurav

  committed
  71de763

• change to speedup multiloop calculations

  pgaurav

  committed
  f3fdde6

Commits on Jun 8, 2011

• Merge pull request #8 from pgaurav/master

  Show description for 50d2058
  shelswenson

  committed
  50d2058

Commits on Jun 11, 2011

• Bugfix in partition. Random sample now compiles, links

  Janderson3

  committed
  7b9fe56

Commits on Jun 16, 2011

• I believe my automake is broken, but bpp theoretically re-integrated

  Janderson3

  committed
  142e6c6

• added new macro

  

  Prashant Gaurav

  committed
  b491b38

• added new macro

  

  Prashant Gaurav

  committed
  265ac33

• added -m option

  

  Prashant Gaurav

  committed
  f192620

• added energy functions to support unafold mode

  

  Prashant Gaurav

  committed
  4c9b019

• added function to load tstacke tstackm tstacki23 enegery values

  

  Prashant Gaurav

  committed
  7ff348f

• added change to handle unafold mode

  

  Prashant Gaurav

  committed
  e0ab343

• added changes to handle unafold mode

  

  Prashant Gaurav

  committed
  2ed0a64

• merged ZS bug fix on constraints

  

  Prashant Gaurav

  committed
  f9e0200

• merged ZS changes with SHAPE

  

  Prashant Gaurav

  committed
  9cb4ef7

• merged ZS changes with SHAPE

  

  Prashant Gaurav

  committed
  25b0306

• Merge pull request ash211#10 from pgaurav/master

  Show description for 5914da2
  shelswenson

  committed
  5914da2

Commits on Jun 17, 2011

• Accessing C declarations from C++ requires the "C" extern

  ash211

  committed
  69de041

• removed Makefile

  

  Prashant Gaurav

  committed
  2223754

• seperate functions eL1(), eL() to handle 2x3 internal loop

  

  Prashant Gaurav

  committed
  9262568

• Merge pull request ash211#12 from pgaurav/master

  Show description for c487f47
  shelswenson

  committed
  c487f47

Commits on Jun 19, 2011

• Pull from gtfold master

  Janderson3

  committed
  9219127

• Merged from gtfold

  Janderson3

  committed
  9e05747

Commits on Jun 20, 2011

• --bpp option re-integrated.

  Janderson3

  committed
  12b006b

• subopt related changes

  

  Prashant Gaurav

  committed
  7d7dadb

• added print message

  

  Prashant Gaurav

  committed
  0c9f170

• added .dat files to base_data dir

  

  Prashant Gaurav

  committed
  f33cfc9

• moved .dat files to base_data dir

  

  Prashant Gaurav

  committed
  6fcd379

• rmeoved .dat entries

  

  Prashant Gaurav

  committed
  cbaa6e8

• Merge branch 'master' of git://github.com/gtfold/gtfold

  

  Prashant Gaurav

  committed
  2f5af3b

• Merge pull request ash211#13 from pgaurav/master

  Show description for 2cc3a89
  shelswenson

  committed
  2cc3a89

Commits on Jun 21, 2011

• fix for contact dist

  

  Prashant Gaurav

  committed
  d2f0de2

• fixed subopt, change to take value kCal

  

  Prashant Gaurav

  committed
  4da0d65

• Merge pull request ash211#26 from pgaurav/master

  Show description for 42fc0fd
  shelswenson

  committed
  42fc0fd

Commits on Jun 22, 2011

• fix for allowable basepair

  

  Prashant Gaurav

  committed
  0ed558f

• subopt changes

  

  Prashant Gaurav

  committed
  a21bebc

• Merge pull request ash211#27 from pgaurav/master

  Show description for 57734a3
  shelswenson

  committed
  57734a3

Commits on Jun 23, 2011

• adding UNAfold parameters

  

  Prashant Gaurav

  committed
  e98313f

• changes to seperate unamode(--unamode), terminal mismatch(-m)

  

  Prashant Gaurav

  committed
  b41b459

• changes to seperate unamode(--unamode), terminal mismatch(-m)

  

  Prashant Gaurav

  committed
  bcfe005

• adding file

  

  Prashant Gaurav

  committed
  69a7bc8

• added print statement

  

  Prashant Gaurav

  committed
  4117ca8

Commits on Jun 24, 2011

• Merge pull request ash211#28 from pgaurav/master

  Show description for 3cc1c50
  shelswenson

  committed
  3cc1c50

• added entry tstacke; removed sint2, sint4

  

  Prashant Gaurav

  committed
  4d47896

• added Makefiles under UNAParams

  

  Prashant Gaurav

  committed
  bd2db40

• added entry UNAParams

  

  Prashant Gaurav

  committed
  89d7ef3

• added entry UNAParams

  

  Prashant Gaurav

  committed
  f06c44f

• delete these auto generated file

  

  Prashant Gaurav

  committed
  d9170d0

• delete these auto generated file

  

  Prashant Gaurav

  committed
  43a71ff

• deleted unwanted files

  

  Prashant Gaurav

  committed
  82bf3ec

• added prefilter option, rectified unamode option

  

  Prashant Gaurav

  committed
  ae599b4

• removed unwanted print statement

  pgaurav

  committed
  f3c2db0

• added check for prefilter inputs

  pgaurav

  committed
  d768553

• Merge pull request ash211#29 from pgaurav/master

  Show description for 65e4d90
  shelswenson

  committed
  65e4d90

• fixed formatting problem in help message

  pgaurav

  committed
  69869cc

• added newline after Total

  pgaurav

  committed
  54a21b8

Commits on Jun 26, 2011

• Merge pull request ash211#31 from pgaurav/master

  Show description for 2e72f93
  shelswenson

  committed
  2e72f93

Commits on Jun 27, 2011

• added prefix and workdir option, fixed -d option

  pgaurav

  committed
  fcb3e20

• added Vienna energy params

  pgaurav

  committed
  43b8ec5

• changes for --rnafold option

  pgaurav

  committed
  2e9862a

• Merge pull request ash211#33 from pgaurav/master

  Show description for cf4e693
  shelswenson

  committed
  cf4e693

• fixed issue 17

  pgaurav

  committed
  8d711d3

• Merge pull request ash211#34 from pgaurav/master

  Show description for 4886a32
  shelswenson

  committed
  4886a32

Commits on Jun 29, 2011

• - changed --unamode to --unafold, - removed a debug statement

  pgaurav

  committed
  f930550

Commits on Jul 1, 2011

• Merge pull request #36 from pgaurav/master

  Show description for f6efb37
  shelswenson

  committed
  f6efb37

Commits on Jul 8, 2011

• added d2 option

  pgaurav

  committed
  07ed2e6

• changed parameters for RNAfold mode

  pgaurav

  committed
  21abfb5

• removed debug mode

  pgaurav

  committed
  9b11ef9

• Merge branch 'master' of https://github.com/gtfold/gtfold

  pgaurav

  committed
  cf5d0ed

• Edited descriptions of --help message

  shelswenson

  committed
  544254c

• merged Shel's changes

  pgaurav

  committed
  f799025

• Merge pull request #43 from pgaurav/master

  Show description for 4fd11cc
  shelswenson

  committed
  4fd11cc

Commits on Jul 11, 2011

• removed debug statement

  pgaurav

  committed
  7f6c3c6

• added options for dangles, mismatch

  pgaurav

  committed
  6cbc69e

• enabled precedence of -d over -m optiom

  pgaurav

  committed
  3f2effa

• options.cc

  pgaurav

  committed
  57e86f4

• Merge pull request #44 from pgaurav/master

  Show description for 93be703
  shelswenson

  committed
  93be703

• Edited descriptions of --help message

  shelswenson

  committed
  e8c7d3e

• fixed commandline options

  pgaurav

  committed
  7959d2f

• fixed a print statement

  pgaurav

  committed
  93972e5

Commits on Jul 12, 2011

• merged changes

  pgaurav

  committed
  63fbc24

• fixed commanline options

  pgaurav

  committed
  3249482

• merged changes

  pgaurav

  committed
  58bc5a2

• Merge pull request #46 from pgaurav/master

  Show description for 3209d22
  shelswenson

  committed
  3209d22

• fixed commanline options

  pgaurav

  committed
  6b6b7ba

• Merge pull request #47 from pgaurav/master

  Show description for 80751be
  shelswenson

  committed
  80751be

• fixed minor issue

  pgaurav

  committed
  ef1b79b

• added new features list

  pgaurav

  committed
  4bfd1f8

• Merge pull request #48 from pgaurav/master

  Show description for 16e00e0
  shelswenson

  committed
  16e00e0

• updated copyright information

  shelswenson

  committed
  951612c

• corrected spelling errors in help message

  shelswenson

  committed
  6c7bdb5

• updated copyright info in README's and autor list in AUTHORS

  shelswenson

  committed
  01c1ecb

• added new header files

  pgaurav

  committed
  3b6010e

• removed TODO file

  pgaurav

  committed
  c45defa

• Merge pull request #49 from pgaurav/master

  Show description for 2d3640f
  shelswenson

  committed
  2d3640f

• removed TODO NEWS

  pgaurav

  committed
  e099009

• removing NEWS

  pgaurav

  committed
  bbe5f6d

• Merge pull request #50 from pgaurav/master

  Show description for 7a5bb17
  shelswenson

  committed
  7a5bb17

• removing NEWS

  pgaurav

  committed
  b68b49a

• Merge pull request #51 from pgaurav/master

  Show description for ad581fd
  shelswenson

  committed
  ad581fd

Commits on Jul 20, 2011

• clarified help message

  shelswenson

  committed
  d8014e1

• enable -d 2 when subopt is invoked

  pgaurav

  committed
  4e11ae5

• new subopt algorithm using -d 2 mode

  pgaurav

  committed
  4656b8b

• removed debug statement

  pgaurav

  committed
  462278d

• Merge pull request #52 from pgaurav/master

  Show description for 478ddc4
  shelswenson

  committed
  478ddc4

• clarified help message

  shelswenson

  committed
  88591d6

• added NEWS

  pgaurav

  committed
  71817d1

• fixed typos and spelling errors in README

  shelswenson

  committed
  dc12e6a

Commits on Jul 21, 2011

• added logic to read data from install dir, environ dir, current dir

  pgaurav

  committed
  2170c3f

• Merge branch 'master' of https://github.com/gtfold/gtfold

  pgaurav

  committed
  5f52ec4

• renamed environ var to GTFOLDDATADIR

  pgaurav

  committed
  5bc618a

• renamed environ var to GTFOLDDATADIR

  pgaurav

  committed
  018827a

• lookup environ var then install dir

  pgaurav

  committed
  766e66f

• Merge pull request #54 from pgaurav/master

  Show description for a575a76
  shelswenson

  committed
  a575a76

Commits on Sep 9, 2011

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

  iamrohitbanga

  committed
  a8470e3

Commits on Sep 10, 2011

• Revert "Fixed pseudoknot detection logic in constraint pre-processing part of the code."

  Show description for 8dc6951
  iamrohitbanga

  committed
  8dc6951

• Fix pseudoknot detection code.

  iamrohitbanga

  committed
  6cdf73e

Commits on Sep 12, 2011

• Corrected constraints code for handling single stranded constraints properly

  msoni3

  committed
  e9100f1

• Merge pull request #57 from iamrohitbanga/master

  Show description for 1c0c4ea
  shelswenson

  committed
  1c0c4ea

• Merge branch 'master' of https://github.com/gtfold/gtfold

  Show description for b48be6b
  msoni3

  committed
  b48be6b

Commits on Sep 14, 2011

• Merge pull request #58 from msoni3/master

  Show description for 3c2edff
  shelswenson

  committed
  3c2edff

• adding partitition function header/src files

  pgaurav

  committed
  54cfe37

• added header energy.h

  pgaurav

  committed
  17bc053

• Merge pull request #1 from pgaurav/master

  Show description for 2135309
  iamrohitbanga

  committed
  2135309

• added global vars

  pgaurav

  committed
  089d8d6

• Merge branch 'master' of https://github.com/pgaurav/gtfold

  iamrohitbanga

  committed
  6228db1

• Merge pull request #1 from pgaurav/master

  Show description for adb2665
  msoni3

  committed
  adb2665

Commits on Sep 16, 2011

• integrated partition func

  pgaurav

  committed
  f96b75f

• Merge https://github.com/pgaurav/gtfold

  msoni3

  committed
  e606b16

• Merge pull request #2 from pgaurav/master

  Show description for 5bfc440
  iamrohitbanga

  committed
  5bfc440

• Merge branch 'master' of github.com:iamrohitbanga/gtfold

  iamrohitbanga

  committed
  6f57a54

• boundary correction

  pgaurav

  committed
  a922dc6

• Merge https://github.com/pgaurav/gtfold

  msoni3

  committed
  cd7a1d7

• Merge branch 'master' of github.com:iamrohitbanga/gtfold

  iamrohitbanga

  committed
  1032965

• Merge pull request #3 from pgaurav/master

  Show description for 56170aa
  iamrohitbanga

  committed
  56170aa

• more boundary correction

  pgaurav

  committed
  42cb45d

• Merge https://github.com/pgaurav/gtfold

  msoni3

  committed
  93ea6ff

• Merge branch 'master' of github.com:iamrohitbanga/gtfold

  iamrohitbanga

  committed
  2bd6ef3

• Merge pull request #4 from pgaurav/master

  Show description for 709eda2
  iamrohitbanga

  committed
  709eda2

• more boundary correction

  pgaurav

  committed
  91e95b8

• more boundary correction

  pgaurav

  committed
  abcd9f5

• Merge https://github.com/pgaurav/gtfold

  msoni3

  committed
  881a807

• Merge pull request #5 from pgaurav/master

  Show description for 152efaf
  iamrohitbanga

  committed
  152efaf

• Merge branch 'master' of github.com:iamrohitbanga/gtfold

  iamrohitbanga

  committed
  6df8796

• Merge https://github.com/pgaurav/gtfold

  msoni3

  committed
  384554f

• debug changes

  pgaurav

  committed
  badba13

Commits on Sep 27, 2011

• Test for single stranded constraint

  msoni3

  committed
  dd34590

• Test for single stranded constraint

  msoni3

  committed
  20e64c6

Commits on Sep 30, 2011

• First version of test scripts:

  iamrohitbanga

  committed
  0ffefa5

Commits on Oct 1, 2011

• Partition Function calculation implementation completed

  msoni3

  committed
  f7923e6

• Merge pull request #2 from msoni3/master

  Show description for 53147c1
  pgaurav

  committed
  53147c1

• added stochastic sampling

  

  Prashant Gaurav

  committed
  c3fb23c

• added stochastic sampling files

  

  Prashant Gaurav

  committed
  947fa18

• changes related to stochastic sampling

  

  Prashant Gaurav

  committed
  6bf5763

• changed f() to be non static

  

  Prashant Gaurav

  committed
  d3c1e2b

Commits on Oct 2, 2011

• Partition Func overflow error due to int value resolved

  msoni3

  committed
  69d1e00

• Merge pull request #3 from msoni3/master

  Show description for ae6806e
  pgaurav

  committed
  ae6806e

• added checks

  

  Prashant Gaurav

  committed
  91e43f3

• corrections in ML traceback

  

  Prashant Gaurav

  committed
  5e349a2

Commits on Oct 3, 2011

• Wrapper function for Ed3 and Ed5 dangling functions added

  msoni3

  committed
  8c2c062

Commits on Oct 4, 2011

• Merge pull request #4 from msoni3/master

  Show description for 173d284
  pgaurav

  committed
  173d284

Commits on Oct 5, 2011

• u1d is now of length n+2 instead of length n+1 as suggested by shel

  msoni3

  committed
  e98206c

• Merge pull request #5 from msoni3/master

  Show description for 782c847
  pgaurav

  committed
  782c847

• Fix suboptimal traceback code.

  iamrohitbanga

  committed
  9d929f2

Commits on Oct 6, 2011

• 1. Merge Pseudoknot Detection Tests.

  Show description for 4b1ad01
  iamrohitbanga

  committed
  4b1ad01

Commits on Oct 7, 2011

• Fix subopt error along with constraints error.

  iamrohitbanga

  committed
  85b7ac7

• Merge the set of sequences that can be used by tests. Filtered out the ones which contain ambiguous bases.

  iamrohitbanga

  committed
  17c8e51

• Merge the README file.

  iamrohitbanga

  committed
  f5c75dd

• Rename PseudoKnotDetection Tests to ExitCode Tests.

  iamrohitbanga

  committed
  aac4e4a

• Remove pseudoknot detection sequences

  iamrohitbanga

  committed
  8ed1a04

Commits on Oct 14, 2011

• Test to Compare CT structure returned by GTFold and UNAFold.

  iamrohitbanga

  committed
  7b4289c

• Added meaningful names to some sequence files.

  iamrohitbanga

  committed
  82ca1b2

• Cleanup - Delete a file.

  iamrohitbanga

  committed
  0926b47

• Merge Suboptimal Structure matching test.

  iamrohitbanga

  committed
  594093c

• Output formatting for saving suboptimal structures to a file changed to match rna subopt.

  iamrohitbanga

  committed
  d966815

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

  msoni3

  committed
  d069c65

• Merge pull request #6 from msoni3/master

  Show description for 1367dc6
  pgaurav

  committed
  1367dc6

• Constraint Verification Tests - The tests generate random constraints and verifies that they are not violated in the generated structure.

  iamrohitbanga

  committed
  f587da4

Commits on Oct 16, 2011

• adding changes to sampling

  

  Prashant Gaurav

  committed
  c9ea343

Commits on Oct 20, 2011

• fixes to sampling algorithm

  

  Prashant Gaurav

  committed
  c008412

• adding fix of Eb and Ec

  

  Prashant Gaurav

  committed
  a1f5d30

Commits on Oct 21, 2011

• fix RT scaling factor

  

  Prashant Gaurav

  committed
  ea00693

• print sampling probablities

  pgaurav

  committed
  2d8a329

Commits on Oct 26, 2011

• added boltzmann prob calculation

  pgaurav

  committed
  c8b8ccd

• changed part func to return U

  pgaurav

  committed
  ded86f0

Commits on Nov 2, 2011

• fixed energy traceback

  pgaurav

  committed
  3f7c982

Commits on Nov 4, 2011

• Implementation of Unique Multiloop Decomposition

  

  Rohit Banga

  committed
  29cc807

Commits on Nov 11, 2011

• Added a Sample Test Module

  

  Rohit Banga

  committed
  90b4481

• Pretty Output for Suboptimal Structures Match Test. Output sent to a separate file.

  

  Rohit Banga

  committed
  cdd5c97

Commits on Nov 18, 2011

• adding stochastic smaplign changes

  pgaurav

  committed
  45111dc

• Adding Paul Specials

  

  Rohit Banga

  committed
  99e46c4

• Duplicate Structures should be reported if partial structure encountered again in suboptimal traceback.

  iamrohitbanga

  committed
  7fa3ab8

• Merge pull request #7 from iamrohitbanga/master

  Show description for 89c6c5d
  pgaurav

  committed
  89c6c5d

Commits on Dec 16, 2011

• code cleanup

  pgaurav

  committed
  fb6500b

• adding changes in global vars

  pgaurav

  committed
  70d4e4d

• removing file

  pgaurav

  committed
  6d5a9f9

• + adding new options + script to add symlink

  pgaurav

  committed
  e492adc

• added creation of symlinks

  pgaurav

  committed
  1957922