git.tuebingen.mpg.de Git - qpalma.git/log

fabio [Fri, 7 Dec 2007 16:56:33 +0000 (16:56 +0000)]

+ removed accidently checked in vim swap files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6946 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Fri, 7 Dec 2007 16:53:09 +0000 (16:53 +0000)]

+ found index bug in SWIG interface
+ added more checks
+ adapted SIQP_CPX solver from the RFP project to work with QPalma
TODO
- check newWeights -> still a +2 offset at some positions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6945 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Fri, 7 Dec 2007 13:08:45 +0000 (13:08 +0000)]

+ found bug in SWIG interface dna_len vs. dna_len-1 because of '\0' in matlab

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6941 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Thu, 6 Dec 2007 12:04:46 +0000 (12:04 +0000)]

+ changed interface array_function to array_class
+ removed bug in alignmentscores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6935 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Thu, 6 Dec 2007 12:03:46 +0000 (12:03 +0000)]

+ changed design
+ fixed variable names
+ introduced more auxiliary functions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6934 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Wed, 5 Dec 2007 17:39:01 +0000 (17:39 +0000)]

+ fixed some index bugs in the weights calculation
+ fixed array bug in SWIG interface

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6931 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Wed, 5 Dec 2007 14:34:37 +0000 (14:34 +0000)]

+ Extended C/C++ interface to return results easily
+ First running version of QPalma SWIG interface
TODO

- still some index issues remain
- add evaluation after wrong alignment generation

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6929 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Wed, 5 Dec 2007 10:10:18 +0000 (10:10 +0000)]

- python code is now checked and complete
- interface is complete
TODO

- Change logic in the myalign function
- Modify training loop accordingly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6927 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Tue, 4 Dec 2007 14:36:29 +0000 (14:36 +0000)]

+ removed several index bugs
+ added checks to compare against matlab version
+ added convenience functions
TODO
- go on with value checks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6923 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Mon, 3 Dec 2007 12:19:09 +0000 (12:19 +0000)]

+ rewrote C interface for SWIG/Python
+ extended qpalma algorithm
+ added evalutation script for alignments
TODO

- added preprocessing scripts
- create an evaluation score

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6915 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Sun, 2 Dec 2007 20:11:22 +0000 (20:11 +0000)]

+ using correct interface now
+ added some assertions for range checks
+ added two new python scripts translated from the matlab version
TODO
- dimension and range checking for all other structures/array after set_param_palma
- decide between numpy and lists for smaller arrays

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6913 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Sat, 1 Dec 2007 00:59:22 +0000 (00:59 +0000)]

+ created necessary interfaces
+ wrote some convenience python functions in set_param_palma

TODO

- complete python training loop

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6906 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Fri, 30 Nov 2007 15:53:57 +0000 (15:53 +0000)]

+ added c code from the palma project
+ added own version of the swig interface

TODO

- think about wrapper for structs / cells
user either SWIG constrcuts or native python object

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6902 e1793c9e-67f9-0310-80fc-b846ff1f7b36

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fabio [Fri, 30 Nov 2007 13:13:42 +0000 (13:13 +0000)]

+ added first converted scripts
+ SpliceAlign computation works

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6888 e1793c9e-67f9-0310-80fc-b846ff1f7b36