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Fix initialization of QtAssistant
[mussa.git]
/
alg
/
2006-10-12
Diane Trout
better glyph offset computation
tree
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commitdiff
2006-10-12
Diane Trout
does createLocalAlignment work for a 3 way?
tree
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commitdiff
2006-10-11
Diane Trout
add Mussa::save_motif()
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commitdiff
2006-10-11
Diane Trout
throw errors when spirit parsing fails
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commitdiff
2006-10-11
Diane Trout
a title of path("/my/silly/path") doesn't work on windows
tree
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commitdiff
2006-10-11
Diane Trout
use lines if a quad would be smaller than a pixel
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commitdiff
2006-10-10
Diane Trout
implement alphabet for sequence
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commitdiff
2006-10-05
Diane Trout
length 1 segments should be drawn as lines
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commitdiff
2006-10-05
Diane Trout
draw link lines with a width
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commitdiff
2006-10-04
Diane Trout
add --motifs
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commitdiff
2006-10-04
Diane Trout
fixes for Mussa::load_motif
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commitdiff
2006-10-04
Diane Trout
colors should default to being visible
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commitdiff
2006-10-03
Diane Trout
Add window titles
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commitdiff
2006-06-15
Diane Trout
fix wrong parent for scrollable_browser
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commitdiff
2006-10-03
Diane Trout
Death to stupid mussa pointers
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commitdiff
2006-09-19
Diane Trout
catch possible segfault with get_sequence()
tree
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commitdiff
2006-09-15
Diane Trout
use the loaded analysis path as the default save path
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commitdiff
2006-09-15
Diane Trout
keep track of a subsequences parent
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commitdiff
2006-09-15
Diane Trout
report our "start/stop" location on a subsequence
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commitdiff
2006-09-15
Diane Trout
use an enum instead of a bool for strandedness
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commitdiff
2006-09-15
Diane Trout
make our Color class serializable
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commitdiff
2006-09-14
Diane Trout
make sure we show the start of our sequence name
tree
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commitdiff
2006-09-14
Diane Trout
Implement an optional name in the motif parser
tree
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commitdiff
2006-09-12
Diane Trout
implement "typical" save and close conventions.
tree
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commitdiff
2006-09-12
Diane Trout
track where our analysis is saved and if the analysis...
tree
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commitdiff
2006-09-12
Diane Trout
add seq_forward
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commitdiff
2006-09-09
Diane Trout
make really sure load_mupa has a file to parse.
tree
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commitdiff
2006-09-08
Diane Trout
subsequences now use offsets into the shared_ptr seq_string
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commitdiff
2006-09-08
Diane Trout
catch a few more potential unchecked shared_ptr derefer...
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commitdiff
2006-09-07
Diane Trout
remove commented out string conversion
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commitdiff
2006-09-07
Diane Trout
Figured out how to serialize a shared_ptr<string>
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commitdiff
2006-09-07
Diane Trout
go back to using const char * in seqcomp
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commitdiff
2006-08-30
Diane Trout
use shared_ptr to store the sequence string
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commitdiff
2006-08-29
Diane Trout
put basepair alphabets into the Sequence class
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commitdiff
2006-08-29
Diane Trout
go back to sequence being its own class
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commitdiff
2006-08-31
Diane Trout
need to #include <cassert> if i'm going to use asserts
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commitdiff
2006-08-24
Diane Trout
start trying to figure out where the documentation is
tree
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commitdiff
2006-08-24
Diane Trout
update sequence serialization to support the xml archive
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commitdiff
2006-08-23
Diane Trout
Allow changing the name for a sequence in the sequence...
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commitdiff
2006-08-22
Diane Trout
catch the other spurious class decoration
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commitdiff
2006-08-22
Diane Trout
remove unnecessary class member decoration
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commitdiff
2006-08-12
Diane Trout
Fix merge issues with the win32 library patch
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commitdiff
2006-08-12
Brandon King
Reorder libraries for win32
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commitdiff
2006-08-12
Brandon King
Tell unittests to use native file convention for EXAMPL...
tree
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commitdiff
2006-08-10
Diane Trout
Try alpha blending the conservation paths
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commitdiff
2006-08-10
Diane Trout
Let the annotation parser skip html tags
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commitdiff
2006-08-09
Diane Trout
Implement serialize for sequence
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commitdiff
2006-08-09
Diane Trout
start breaking save out from Mussa::analyze()
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commitdiff
2006-08-09
Diane Trout
Add documentation about Mussa::soft_threshold
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commitdiff
2006-08-09
Diane Trout
add dirty flag
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commitdiff
2006-08-09
Diane Trout
change from cout to clog in some commented out debuggin...
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commitdiff
2006-07-29
Diane Trout
set mussa analysis name in MussaSetupWidget
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commitdiff
2006-07-28
Diane Trout
Use CMAKE_BINARY_DIR instead of the very wrong MUSSA_BI...
tree
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commitdiff
2006-07-27
Diane Trout
add annot and motif classes to python interface
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commitdiff
2006-07-21
Diane Trout
Build universal binaries on OS X
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commitdiff
2006-07-13
Diane Trout
start the trivial sequence filter
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commitdiff
2006-07-01
Diane Trout
SequenceLocation was being intialized with left,right
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commitdiff
2006-07-01
Diane Trout
make sure subsequences have a species name
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commitdiff
2006-07-01
Diane Trout
Implement UI for subanalysis mode
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commitdiff
2006-06-30
Diane Trout
fix boost::python sequence interface
tree
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commitdiff
2006-06-30
Diane Trout
store motifs as sequences instead of strings
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commitdiff
2006-06-29
Diane Trout
set_motifs should erase the previous motifs
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commitdiff
2006-06-29
Diane Trout
allow specifying a name for a sequence
tree
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commitdiff
2006-06-29
Diane Trout
update the annotation grammer to make species name...
tree
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commitdiff
2006-06-29
Diane Trout
break the core of add_motifs loop into a seperate function
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commitdiff
2006-06-23
Diane Trout
Getting closer to a subanalysis mode
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commitdiff
2006-06-21
Diane Trout
More progress toward subanalysis
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commitdiff
2006-06-21
Diane Trout
use a specific exception when nextTo breaks
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commitdiff
2006-06-20
Diane Trout
extend annotation names and types to allow punctuation
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commitdiff
2006-06-17
Diane Trout
make Sequence a subclass of std::string
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commitdiff
2006-06-16
Diane Trout
remove unnecessary class decoration
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commitdiff
2006-06-16
Diane Trout
ticket:104 fix some pointer problems with MussaAlignedW...
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commitdiff
2006-06-14
Diane Trout
AMD64 build support
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commitdiff
2006-06-14
Diane Trout
Make cmake happier about my target declariation order
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commitdiff
2006-06-14
Diane Trout
reformat some braces
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commitdiff
2006-06-13
Diane Trout
include the sequence coordinates when copying sequence
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commitdiff
2006-06-12
Brandon King
alg/glseqbrowser.cpp:127: error: jump to case label
tree
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commitdiff
2006-06-12
Diane Trout
Actually copy our selected sequence to the clipboard
tree
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commitdiff
2006-06-10
Diane Trout
partial implementation of sequence track copy
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commitdiff
2006-06-09
Diane Trout
More robust eol handling for Sequence::load_fasta
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commitdiff
2006-06-08
Diane Trout
improve fasta parsing
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commitdiff
2006-06-08
Diane Trout
Report error when sequence couldn't be loaded
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commitdiff
2006-06-06
Diane Trout
keep track of how far through a seqcomp we've gotten
tree
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commitdiff
2006-06-03
Diane Trout
use Qt Signals & Slots for progress tracking
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commitdiff
2006-05-27
Diane Trout
add callback for tracking analysis progress
tree
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commitdiff
2006-05-27
Diane Trout
rename [gset_soft_thres to [gs]et_soft_threshold]
tree
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commitdiff
2006-05-25
Diane Trout
add some documentation for glseqbrowser::viewport*
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commitdiff
2006-05-20
Diane Trout
turn color back on
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commitdiff
2006-05-20
Diane Trout
ticket:62 fix local alignment
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commitdiff
2006-05-18
Diane Trout
expose more of the sequence class to python
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commitdiff
2006-05-17
Diane Trout
finish implementing annotation by sequence
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commitdiff
2006-05-17
Diane Trout
switch to a character based spirit parser
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commitdiff
2006-05-17
Diane Trout
try to read fasta blocks in the annotation file
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commitdiff
2006-05-17
Diane Trout
use spirit parser for reading annot file
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commitdiff
2006-05-16
Diane Trout
add annotations by sequence string
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commitdiff
2006-05-10
Diane Trout
increase the use of python in mussa
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commitdiff
2006-04-19
Diane Trout
win32 paths need some conversion
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commitdiff
2006-04-18
Diane Trout
try to get mussagl to build on win32
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commitdiff
2006-04-13
Diane Trout
the fasta error message should include the filename
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commitdiff
2006-04-13
Diane Trout
fix ticket:83 throw an error when we don't have a fasta...
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commitdiff
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