germs.git
12 years agoMore help output master v0.1
Michael Andreen [Wed, 19 Dec 2007 14:23:40 +0000 (15:23 +0100)]
More help output

12 years agoLicense and minor installation instructions
Michael Andreen [Wed, 19 Dec 2007 14:09:35 +0000 (15:09 +0100)]
License and minor installation instructions

12 years agoOnly build tests if we have cppunit available
Michael Andreen [Wed, 19 Dec 2007 14:00:44 +0000 (15:00 +0100)]
Only build tests if we have cppunit available

12 years agoCheck for TR1 or Boost
Michael Andreen [Wed, 19 Dec 2007 13:40:04 +0000 (14:40 +0100)]
Check for TR1 or Boost

The build system now checks for TR1 or Boost for a shared_ptr implementation
instead of assuming that TR1 is present.

12 years agoMake it possible to build statically against the included fann library.
Michael Andreen [Wed, 19 Dec 2007 13:18:03 +0000 (14:18 +0100)]
Make it possible to build statically against the included fann library.

Now checks to see if fann is installed on the system. If fann is installed
it will link dynamically to this library, otherwise a static library will
be built and linked with.

12 years agoadd an option to print the permutation
Michael Andreen [Wed, 5 Dec 2007 02:26:53 +0000 (03:26 +0100)]
add an option to print the permutation

12 years agoIntroduce -i for only identifying the model, excluding sorting.
Michael Andreen [Tue, 30 Oct 2007 08:51:08 +0000 (09:51 +0100)]
Introduce -i for only identifying the model, excluding sorting.

12 years agochanged name to GERMS
Michael Andreen [Mon, 29 Oct 2007 13:53:15 +0000 (14:53 +0100)]
changed name to GERMS

12 years agomore ignores
Michael Andreen [Mon, 29 Oct 2007 13:47:57 +0000 (14:47 +0100)]
more ignores

12 years agoSmall optimization in sort()
Michael Andreen [Mon, 29 Oct 2007 13:20:47 +0000 (13:20 +0000)]
Small optimization in sort()

safeActions() is guaranteed to only return actions that reduces the inversion
distance by one, so we don't have to compute the inversion distance at
each step.

12 years agoOnly headers and exclude tests + minor report update
Michael Andreen [Fri, 14 Sep 2007 09:14:01 +0000 (09:14 +0000)]
Only headers and exclude tests + minor report update

12 years agoAdded a Whirl model, which favors reversals, instead of using the standard
Michael Andreen [Wed, 29 Aug 2007 06:18:35 +0000 (06:18 +0000)]
Added a Whirl model, which favors reversals, instead of using the standard

12 years agoDOC: more doxygen documentation
Michael Andreen [Wed, 29 Aug 2007 06:18:34 +0000 (06:18 +0000)]
DOC: more doxygen documentation

12 years agobad testcase
Michael Andreen [Tue, 28 Aug 2007 17:07:12 +0000 (17:07 +0000)]
bad testcase

12 years agoBUGFIX: forgot to set parent to 0 on child when removing parent node
Michael Andreen [Tue, 28 Aug 2007 17:07:12 +0000 (17:07 +0000)]
BUGFIX: forgot to set parent to 0 on child when removing parent node

12 years agoAdded more doxygen documentation
Michael Andreen [Thu, 23 Aug 2007 16:59:29 +0000 (16:59 +0000)]
Added more doxygen documentation

12 years agoadded .gitignore files
Michael Andreen [Wed, 22 Aug 2007 10:39:38 +0000 (10:39 +0000)]
added .gitignore files

12 years agocalculate the proper distance, with hurdles
Michael Andreen [Thu, 16 Aug 2007 09:17:46 +0000 (09:17 +0000)]
calculate the proper distance, with hurdles

12 years agoshortBranches
Michael Andreen [Thu, 16 Aug 2007 09:17:35 +0000 (09:17 +0000)]
shortBranches

12 years agohave all tests enabled
Michael Andreen [Thu, 16 Aug 2007 08:28:13 +0000 (08:28 +0000)]
have all tests enabled

12 years agocount leaves
Michael Andreen [Thu, 16 Aug 2007 08:20:42 +0000 (08:20 +0000)]
count leaves

12 years agomake the componenttree a minimal unoriented tree
Michael Andreen [Thu, 16 Aug 2007 07:24:00 +0000 (07:24 +0000)]
make the componenttree a minimal unoriented tree

12 years agomore complete test
Michael Andreen [Wed, 15 Aug 2007 13:37:58 +0000 (13:37 +0000)]
more complete test

12 years agoinital commit of componenttree with associated changes
Michael Andreen [Wed, 15 Aug 2007 11:37:28 +0000 (11:37 +0000)]
inital commit of componenttree with associated changes

12 years agoupdated comments
Michael Andreen [Tue, 14 Aug 2007 11:45:17 +0000 (11:45 +0000)]
updated comments

12 years agopossible to chose a model
Michael Andreen [Tue, 14 Aug 2007 10:45:25 +0000 (10:45 +0000)]
possible to chose a model

12 years agomodelFactory method, to help create models
Michael Andreen [Tue, 14 Aug 2007 10:44:54 +0000 (10:44 +0000)]
modelFactory method, to help create models

12 years agoscoring function for Zipper model
Michael Andreen [Tue, 14 Aug 2007 10:43:51 +0000 (10:43 +0000)]
scoring function for Zipper model

12 years agodon't really need print the gene order
Michael Andreen [Mon, 13 Aug 2007 07:33:39 +0000 (07:33 +0000)]
don't really need print the gene order

12 years agocalculate the avg score for the model
Michael Andreen [Mon, 13 Aug 2007 07:21:17 +0000 (07:21 +0000)]
calculate the avg score for the model

12 years agosome comments
Michael Andreen [Mon, 13 Aug 2007 07:21:01 +0000 (07:21 +0000)]
some comments

12 years agogive access to reverse action members, and calculate symmetric score according to...
Michael Andreen [Fri, 3 Aug 2007 14:09:11 +0000 (14:09 +0000)]
give access to reverse action members, and calculate symmetric score according to Ajana et al.

12 years agoa little more refactoring, name might just as well return const char* since it's...
Michael Andreen [Fri, 3 Aug 2007 13:58:02 +0000 (13:58 +0000)]
a little more refactoring, name might just as well return const char* since it's a string constant, also score now takes a gene order too

12 years agogenesorter now uses models to score actions, specific actions are now derived from...
Michael Andreen [Fri, 3 Aug 2007 13:38:54 +0000 (13:38 +0000)]
genesorter now uses models to score actions, specific actions are now derived from SortActionImpl instead of SortAction, the latter is just an empty shell now

12 years agostarted a refactoring with Model class to score different sort actions
Michael Andreen [Fri, 3 Aug 2007 11:42:25 +0000 (11:42 +0000)]
started a refactoring with Model class to score different sort actions

12 years agohad a nice idea
Michael Andreen [Wed, 1 Aug 2007 15:38:04 +0000 (15:38 +0000)]
had a nice idea

12 years agoOnly show models with positive score, and convert the enum to strings
Michael Andreen [Wed, 1 Aug 2007 09:15:24 +0000 (09:15 +0000)]
Only show models with positive score, and convert the enum to strings

12 years agoadding command line options
Michael Andreen [Mon, 30 Jul 2007 10:07:13 +0000 (10:07 +0000)]
adding command line options

13 years agoa little performance tuning
Michael Andreen [Sat, 30 Jun 2007 11:18:47 +0000 (11:18 +0000)]
a little performance tuning

13 years agodon't print as much
Michael Andreen [Sat, 30 Jun 2007 11:14:38 +0000 (11:14 +0000)]
don't print as much

13 years agotoString for actions
Michael Andreen [Wed, 27 Jun 2007 06:03:23 +0000 (06:03 +0000)]
toString for actions

13 years agobetter main program
Michael Andreen [Mon, 25 Jun 2007 12:46:10 +0000 (12:46 +0000)]
better main program

13 years agocast to size_t instead of asuming unsigned long
Michael Andreen [Sun, 24 Jun 2007 21:48:16 +0000 (21:48 +0000)]
cast to size_t instead of asuming unsigned long

13 years agoadded a test case with hurdles
Michael Andreen [Sun, 24 Jun 2007 18:10:48 +0000 (18:10 +0000)]
added a test case with hurdles

13 years agorenamed a function and removed some debug output
Michael Andreen [Sun, 24 Jun 2007 18:07:10 +0000 (18:07 +0000)]
renamed a function and removed some debug output

13 years agosorting without hurdles seems to work
Michael Andreen [Sun, 24 Jun 2007 17:56:11 +0000 (17:56 +0000)]
sorting without hurdles seems to work

13 years agominor change
Michael Andreen [Sun, 24 Jun 2007 14:35:21 +0000 (14:35 +0000)]
minor change

13 years agogood to have a inversion distance function
Michael Andreen [Sun, 24 Jun 2007 14:01:54 +0000 (14:01 +0000)]
good to have a inversion distance function

13 years agominor things
Michael Andreen [Sun, 24 Jun 2007 13:42:06 +0000 (13:42 +0000)]
minor things

13 years agonicer with size_t for cycles, they can't be negative anyway
Michael Andreen [Sun, 24 Jun 2007 12:15:43 +0000 (12:15 +0000)]
nicer with size_t for cycles, they can't be negative anyway

13 years agocopy constructor and assignment constructor
Michael Andreen [Sun, 24 Jun 2007 12:15:25 +0000 (12:15 +0000)]
copy constructor and assignment constructor

13 years agobetter if SortAction takes care of the shared_ptr, makes other code easier
Michael Andreen [Sun, 24 Jun 2007 12:08:34 +0000 (12:08 +0000)]
better if SortAction takes care of the shared_ptr, makes other code easier

13 years agowe need a list of smart pointers
Michael Andreen [Sun, 24 Jun 2007 11:38:15 +0000 (11:38 +0000)]
we need a list of smart pointers

13 years agosetting up things for implementing the sorting
Michael Andreen [Sun, 24 Jun 2007 10:26:45 +0000 (10:26 +0000)]
setting up things for implementing the sorting

13 years agoModelIdentifier::identify implemented and passes test
Michael Andreen [Thu, 21 Jun 2007 12:46:22 +0000 (12:46 +0000)]
ModelIdentifier::identify implemented and passes test

13 years agoinitial commit of the modelidentifier files
Michael Andreen [Thu, 21 Jun 2007 11:57:34 +0000 (11:57 +0000)]
initial commit of the modelidentifier files

13 years agoa little cleanup and minor fix
Michael Andreen [Wed, 20 Jun 2007 09:25:07 +0000 (09:25 +0000)]
a little cleanup and minor fix

13 years agofindComponents implemented and passes test
Michael Andreen [Wed, 20 Jun 2007 09:08:42 +0000 (09:08 +0000)]
findComponents implemented and passes test

13 years agoForgot to update the comment
Michael Andreen [Wed, 20 Jun 2007 07:32:36 +0000 (07:32 +0000)]
Forgot to update the comment

13 years agofindIntervalsAtPoitns is now O(n)
Michael Andreen [Wed, 20 Jun 2007 07:32:11 +0000 (07:32 +0000)]
findIntervalsAtPoitns is now O(n)

13 years agofindIntervals is now O(n)
Michael Andreen [Wed, 20 Jun 2007 07:19:02 +0000 (07:19 +0000)]
findIntervals is now O(n)

13 years agomoved a function and added comment
Michael Andreen [Wed, 20 Jun 2007 06:57:56 +0000 (06:57 +0000)]
moved a function and added comment

13 years agofirst point in points is now a dummy so indexes matches points
Michael Andreen [Tue, 19 Jun 2007 10:59:29 +0000 (10:59 +0000)]
first point in points is now a dummy so indexes matches points

13 years agocountCycles implemented and passess test
Michael Andreen [Tue, 19 Jun 2007 10:36:11 +0000 (10:36 +0000)]
countCycles implemented and passess test

13 years agobetter use debug information at this stage
Michael Andreen [Tue, 19 Jun 2007 10:35:51 +0000 (10:35 +0000)]
better use debug information at this stage

13 years agofindIntervalAtPoints implemnted and passes test
Michael Andreen [Tue, 19 Jun 2007 10:30:11 +0000 (10:30 +0000)]
findIntervalAtPoints implemnted and passes test

13 years agofindIntervals implemented and passing test
Michael Andreen [Tue, 19 Jun 2007 09:18:53 +0000 (09:18 +0000)]
findIntervals implemented and passing test

13 years agoadding countCycles, findComponents, findIntervals declaration, with initial tests
Michael Andreen [Tue, 19 Jun 2007 08:27:42 +0000 (08:27 +0000)]
adding countCycles, findComponents, findIntervals declaration, with initial tests

13 years agolongest increasing and decreasing subsequences
Michael Andreen [Mon, 18 Jun 2007 14:54:07 +0000 (14:54 +0000)]
longest increasing and decreasing subsequences

13 years agorobinson schensted algorithm implemented
Michael Andreen [Mon, 18 Jun 2007 12:42:29 +0000 (12:42 +0000)]
robinson schensted algorithm implemented

13 years agomore documentation
Michael Andreen [Mon, 18 Jun 2007 09:58:07 +0000 (09:58 +0000)]
more documentation

13 years agoGeneOrder::reverse implemented
Michael Andreen [Mon, 18 Jun 2007 09:43:00 +0000 (09:43 +0000)]
GeneOrder::reverse implemented

13 years agosome cleanup, documentation, begin() and end() methods
Michael Andreen [Mon, 18 Jun 2007 09:01:36 +0000 (09:01 +0000)]
some cleanup, documentation, begin() and end() methods

13 years agocmake testing
Michael Andreen [Thu, 14 Jun 2007 20:35:01 +0000 (20:35 +0000)]
cmake testing

13 years agoqt tester optional
Michael Andreen [Thu, 14 Jun 2007 20:14:03 +0000 (20:14 +0000)]
qt tester optional

13 years agoneed the dir too
Michael Andreen [Thu, 14 Jun 2007 20:10:17 +0000 (20:10 +0000)]
need the dir too

13 years agolibrary path is good
Michael Andreen [Thu, 14 Jun 2007 20:10:03 +0000 (20:10 +0000)]
library path is good

13 years agoassignment works
Michael Andreen [Thu, 14 Jun 2007 20:08:45 +0000 (20:08 +0000)]
assignment works

13 years agocopy constructor works
Michael Andreen [Thu, 14 Jun 2007 20:05:36 +0000 (20:05 +0000)]
copy constructor works

13 years agoconstructor for GeneOrder done
Michael Andreen [Thu, 14 Jun 2007 19:53:56 +0000 (19:53 +0000)]
constructor for GeneOrder done

13 years agoput executables in the right place
Michael Andreen [Thu, 14 Jun 2007 14:13:15 +0000 (14:13 +0000)]
put executables in the right place

13 years agoneed a main file
Michael Andreen [Thu, 14 Jun 2007 14:01:05 +0000 (14:01 +0000)]
need a main file

13 years agoa bit nicer
Michael Andreen [Thu, 14 Jun 2007 14:00:19 +0000 (14:00 +0000)]
a bit nicer

13 years agosome more changes
Michael Andreen [Thu, 14 Jun 2007 13:55:06 +0000 (13:55 +0000)]
some more changes

13 years agosome initial tests
Michael Andreen [Thu, 14 Jun 2007 13:39:17 +0000 (13:39 +0000)]
some initial tests

13 years agolower case is nicer
Michael Andreen [Thu, 14 Jun 2007 12:39:50 +0000 (12:39 +0000)]
lower case is nicer

13 years agolink with fann
Michael Andreen [Thu, 14 Jun 2007 12:30:10 +0000 (12:30 +0000)]
link with fann

13 years agosome build tools
Michael Andreen [Thu, 14 Jun 2007 12:09:34 +0000 (12:09 +0000)]
some build tools

13 years agosome initial commits
Michael Andreen [Tue, 12 Jun 2007 10:45:47 +0000 (10:45 +0000)]
some initial commits