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Diane Trout [Wed, 22 Feb 2006 02:20:05 +0000 (02:20 +0000)]
force doxygen to look at all of our directories
Diane Trout [Wed, 22 Feb 2006 02:16:42 +0000 (02:16 +0000)]
rename some mussa_class members (ana_name to analysis_name)
also add some getters, reformat the parse_args if/else tree.
Change using character flags for analysis mode to using an enumeration.
Diane Trout [Wed, 22 Feb 2006 02:06:03 +0000 (02:06 +0000)]
test mussa class
Also the test case extension should match that of the other source
files.
Diane Trout [Wed, 22 Feb 2006 00:12:57 +0000 (00:12 +0000)]
unit test skeleton
Now we build a unit test binary, though currently there aren't any tests.
Diane Trout [Wed, 22 Feb 2006 00:07:33 +0000 (00:07 +0000)]
remove library blessings
Diane Trout [Tue, 21 Feb 2006 23:51:14 +0000 (23:51 +0000)]
break algorithm out into a subdirectory.
Diane Trout [Tue, 21 Feb 2006 23:01:44 +0000 (23:01 +0000)]
build fltk gui stuff as a library
Diane Trout [Tue, 21 Feb 2006 08:45:32 +0000 (08:45 +0000)]
we also want docs about the fltk gui code
Diane Trout [Tue, 21 Feb 2006 08:42:03 +0000 (08:42 +0000)]
add notes of what i learned about seqcomp and nway
stored notes as doxygen comments
Diane Trout [Sat, 4 Feb 2006 18:08:07 +0000 (18:08 +0000)]
add parse error exceptions for the command line args.
Diane Trout [Sat, 4 Feb 2006 18:07:25 +0000 (18:07 +0000)]
number of seqs is more informative than seq num
Diane Trout [Sat, 4 Feb 2006 00:38:24 +0000 (00:38 +0000)]
massive code move
mussa_gui_ was redundant so i moved all of those modules into
gui/
Also I used the non-recursive gnu make style build system.
And lastly there are some Doxygen compatible bits of doucmentation thrown in
here.
Diane Trout [Fri, 3 Feb 2006 02:30:04 +0000 (02:30 +0000)]
make headers less interdependent
The mussa headers all depended on including each other to get
all of the right include files. This has been broken and files are more
explicit at including what they depend on.
Also based on Accellerated C++, I followed the convention that header files
should never do a using namespace std, on the off chance that someone
wants to redefine something in the std namespace.
Diane Trout [Thu, 2 Feb 2006 23:16:38 +0000 (23:16 +0000)]
remove unnecessary member variable length.
One should trust the string.length() instead
Diane Trout [Tue, 27 Sep 2005 19:32:50 +0000 (19:32 +0000)]
[project @ 16]
Build settings for mingw32 (under cygwin)
Diane Trout [Tue, 27 Sep 2005 00:59:56 +0000 (00:59 +0000)]
[project @ 15]
As mussa is a c++ program switch from using $(CC) to $(CXX) for compilations
Diane Trout [Thu, 22 Sep 2005 00:46:01 +0000 (00:46 +0000)]
[project @ 14]
Fix save_path_base undefined error. Ticket:1
Diane Trout [Wed, 21 Sep 2005 23:26:49 +0000 (23:26 +0000)]
[project @ 13]
mussa015
Diane Trout [Wed, 21 Sep 2005 23:23:41 +0000 (23:23 +0000)]
[project @ 12]
mussa014 example
Diane Trout [Wed, 21 Sep 2005 23:22:49 +0000 (23:22 +0000)]
[project @ 11]
mussa014
Diane Trout [Wed, 21 Sep 2005 23:18:36 +0000 (23:18 +0000)]
[project @ 10]
mussa010
Diane Trout [Wed, 21 Sep 2005 23:17:51 +0000 (23:17 +0000)]
[project @ 9]
mussa009
Diane Trout [Wed, 21 Sep 2005 23:16:55 +0000 (23:16 +0000)]
[project @ 8]
mussa_008
Diane Trout [Wed, 21 Sep 2005 23:14:15 +0000 (23:14 +0000)]
[project @ 7]
mussa_pre.7
Diane Trout [Fri, 16 Sep 2005 23:08:29 +0000 (23:08 +0000)]
[project @ 6]
musssa_pre.5
Diane Trout [Fri, 16 Sep 2005 22:49:56 +0000 (22:49 +0000)]
[project @ 5]
mussa_pre.4.tar.gz
Diane Trout [Fri, 16 Sep 2005 22:45:17 +0000 (22:45 +0000)]
[project @ 4]
mussa_pI.3
Diane Trout [Fri, 16 Sep 2005 22:43:01 +0000 (22:43 +0000)]
[project @ 3]
checked in mussa_pI.2
Diane Trout [Fri, 16 Sep 2005 22:41:59 +0000 (22:41 +0000)]
[project @ 2]
Checked in mussa_pI.1