Brandon King [Wed, 14 Feb 2007 01:39:23 +0000 (01:39 +0000)]
Added newline char at end of file to remove gcc warning
Brandon King [Wed, 14 Feb 2007 01:34:32 +0000 (01:34 +0000)]
Added new line at end of file to remove gcc warning
Brandon King [Wed, 14 Feb 2007 01:07:47 +0000 (01:07 +0000)]
Added newline char to end of line (remove compile warning)
Diane Trout [Tue, 13 Feb 2007 23:40:02 +0000 (23:40 +0000)]
IsFileValidator doesn't use signal/slots
Diane Trout [Sat, 3 Feb 2007 01:55:46 +0000 (01:55 +0000)]
detect 64bit processors and add -fPIC
this is an intermediate solution as I probably can use ADD_DEFINES()
to add the command line options for the compiler instead of fiddingly
with CMAKE variables
Props to Brandon for finding the solution in an openwengo patch.
http://dev.openwengo.org/trac/openwengo/trac.cgi/changeset/9139
Long Live CMake!
Diane Trout [Fri, 5 Jan 2007 01:49:12 +0000 (01:49 +0000)]
add some newlines at the end of some of our files
gcc 4.2 complains about this.
Diane Trout [Thu, 4 Jan 2007 22:34:37 +0000 (22:34 +0000)]
conditionally build the paircomp tests
Diane Trout [Thu, 4 Jan 2007 22:28:08 +0000 (22:28 +0000)]
paircomp used the string find_first_not_of
so i needed to add it to my sequence class. (I'm trying to keep
my sequence class to look like an immutable string).
Diane Trout [Thu, 4 Jan 2007 21:40:35 +0000 (21:40 +0000)]
split unittests into seperate executables
ticket:208
I decided it was easer to debug my unittests when they were
in smaller pieces.
Diane Trout [Thu, 21 Dec 2006 00:02:57 +0000 (00:02 +0000)]
build paircomp if available
Diane Trout [Thu, 14 Dec 2006 21:17:25 +0000 (21:17 +0000)]
len(mussa.paths()) should equal the number of found paths
ticket:244
for some reason I was returning the number of sequences instead,
that is available as sequence_count.
Renamed size_t in NwayPaths to NwayPaths::size_type
Also I exported the various types of path size counts to the python layer
Diane Trout [Wed, 13 Dec 2006 00:42:03 +0000 (00:42 +0000)]
be resistent to not creating the browser
just on the off chance that MussaWindow.browser isn't created
test the pointer before trying to call it.
(AKA some left over debugging code)
Diane Trout [Wed, 13 Dec 2006 00:40:25 +0000 (00:40 +0000)]
make mussawindow initialize icons
this is also part of the useless try to stop qobject::moveToThread
warnings, but I decided it was a good idea for when qui/mussagl.cpp:main
isn't called because we were launched from a python extension.
Diane Trout [Wed, 13 Dec 2006 00:14:00 +0000 (00:14 +0000)]
try to reduce number of moveToThread warnings
I went off on a fools errand of trying to get rid of the QObject::moveToThread
warnings that Qt was spitting out when trying to prepare an icon.
Qt does prefer widgets to be dynamically constructed and to have their
parent widget set, which is what I tried to do to cut down on the
useless chatter.
(Note the chatter only happens on OS X when the frameworks have been installed
into the application bundle).
Diane Trout [Tue, 12 Dec 2006 02:27:22 +0000 (02:27 +0000)]
fix infinite loop for absolute pathnames
and add a --prelink-only update
and update to qt 4.2.2
Diane Trout [Thu, 7 Dec 2006 23:49:39 +0000 (23:49 +0000)]
provide get_py and get_py_ptr
I didn't like (*get_py)['name' as a way of getting a python namespace
object. So I changed get_py back to returning a reference by introducing
a new function get_py_ptr which creates the python singleton and returns
a pointer to it.
Diane Trout [Thu, 7 Dec 2006 00:31:08 +0000 (00:31 +0000)]
cut down on unnecessary linking to the python library
Diane Trout [Thu, 7 Dec 2006 00:23:14 +0000 (00:23 +0000)]
Allocating objects in the constructor causes problems
What do you know, being lazy and initializing Qt GUI objects in the
constructor cause problems. (AKA a segfault when running as a test case).
This patch allocates the various GUI objects in an actual function
(which is so the different contstructors can use the same initialization
code.
It looks like another coding standard to remember.
Diane Trout [Tue, 5 Dec 2006 23:54:57 +0000 (23:54 +0000)]
make compiled in python extension initialization more flexable
Because of weird library ordering issues, my test case that tested
running python code was looking for compiled in python modules that
weren't available yet it wouldn't link properly.
I solved this by making it possible to provide a list of what
compiled-in python extensions should be initialized when you launch
the interpreter, so the mussagl program, which does have all the right
components linked in is what is specifying what modules should be
provided to the python interpreter.
Now I just need to fix the build system so you can compile mussa without
all this python crud if needed.
And maybe decide how to launch the gui from a stanard python interpreter.
Diane Trout [Tue, 5 Dec 2006 02:22:00 +0000 (02:22 +0000)]
directly build the python extension modules
I learned about SET_TARGET_PROPERTIES( ... PREFIX )
to change the starting prefix for a library, which means
that I don't need to copy the libX.so to X.so to make something
a python importable module.
Diane Trout [Tue, 5 Dec 2006 00:17:22 +0000 (00:17 +0000)]
provide python interpreter for mussa qui via a seperate thread
helps ticket:201
Since both the python read-eval-print loop and Qt have their own
event loops one can't easily have a single threaded application
provide GUI code while still having an interpreter sitting around.
Additionally due to the limitations of OS X and Windows, the main
thread needs to be the GUI thread, so I needed to start the python
interpreter in a seperate thread.
I implemented several helper classes in qui/threading to help manage
creating threads. Currently it just provides a singleton interpreter
thread. The interpreter when started in its subthread will try to
initialize ipython, and if that fails will try InteractiveConsole
(I suppose I should've caught that failing, and then finally fell back
to the fgets read-eval-looop).
The way access to the GUI layer is handled is via a signal/slot thread
specific proxy class which holds a mussa analysis object and notifies
the copy in the main thread via a signal to create a new window using
the provided mussa object.
Access to some parts of the mussa object are thread safe, because I was
so enthusiastic about marking functions as const. All the other parts
are, shall we say, "up for grabs".
The other issue is I really need to improve the CMake scripts to be
a bit more robust about deteriming if python should be linked in.
(And one of my tests breaks because of this patch).
But since it works on OS X I want to know what it'll do on linux.
I'm pretty sure since a windows GUI app doesn't have a console that
it won't work on windows. (To say nothing of the command line
argument parser crashing under windows).
Diane Trout [Thu, 30 Nov 2006 02:23:08 +0000 (02:23 +0000)]
allow adding and viewing sequences to an analysis from python
this required a way to deal with the collection of sequences
returned by Mussa::sequences()
the python wiki had some suggestions (though their code didn't compile)
http://wiki.python.org/moin/boost.python/StlContainers
Diane Trout [Wed, 29 Nov 2006 02:14:45 +0000 (02:14 +0000)]
add python interface to seqcomp
which is actually provided by the class FLP
Diane Trout [Wed, 22 Nov 2006 20:24:21 +0000 (20:24 +0000)]
Finish off setting sequence offset user interface
ticket:111
I thought it would be better for the edit sequence properties action to live
under the main edit menu, instead of the popup menu.
Also I decided to use apply/close instead of ok/cancel as it seemed better
to make fiddling with the offset interactive.
And yes I probably should implement some graphical way of aligning the
sequences instead of just typing in offsets.
Diane Trout [Tue, 21 Nov 2006 20:26:46 +0000 (20:26 +0000)]
quick option to show sequence properties window
Diane Trout [Tue, 21 Nov 2006 20:24:01 +0000 (20:24 +0000)]
rename ok/cancel to okButton/cancelButton
so I can use cancel as a function name.
Diane Trout [Tue, 21 Nov 2006 03:08:00 +0000 (03:08 +0000)]
fix bad #ifdef names
Diane Trout [Fri, 17 Nov 2006 23:19:49 +0000 (23:19 +0000)]
more fs::native for user supplied paths
ticket:237
Give boost::filesystem more hints about what filenames were entered by the
user and thus conforming to native file conventions.
Diane Trout [Thu, 2 Nov 2006 21:35:41 +0000 (21:35 +0000)]
include sequence property editor source files
sorry tristan, I forgot to add the files.
Diane Trout [Wed, 1 Nov 2006 23:55:26 +0000 (23:55 +0000)]
allow copying files into a dmg
the manual is a .html file that needed to be copied into the dmg
which required a small update to osxdist.py
Brandon King [Wed, 1 Nov 2006 18:06:07 +0000 (18:06 +0000)]
Mussagl Version number updated to 1.0
* ticket #235
Brandon King [Wed, 1 Nov 2006 18:01:36 +0000 (18:01 +0000)]
Win32 installer script update for 1.0
* Updated installer for 1.0 version of mussagl
Brandon King [Wed, 1 Nov 2006 17:51:24 +0000 (17:51 +0000)]
Mussagl Manual: 1.0 docs part 4
* Updated motif file format
* Updated UCSC Genome Broswer section slightly
Brandon King [Wed, 1 Nov 2006 17:39:10 +0000 (17:39 +0000)]
Mussagl Manual: mussa_manual.adp updated for 1.0 docs
* Updated for 1.0 documentation.
Diane Trout [Tue, 31 Oct 2006 18:43:10 +0000 (18:43 +0000)]
update CMakeLists.txt to build new SequencePropertiesWindow
Diane Trout [Tue, 31 Oct 2006 18:41:38 +0000 (18:41 +0000)]
update osxdist for qt4.2.1
Diane Trout [Mon, 30 Oct 2006 22:47:45 +0000 (22:47 +0000)]
move SubanalysisWindow code to a subdirectory
Diane Trout [Mon, 30 Oct 2006 20:49:59 +0000 (20:49 +0000)]
include filename in unparsable annotation error message
ticket:236
Diane Trout [Mon, 30 Oct 2006 20:25:21 +0000 (20:25 +0000)]
report filename for invalid fasta files
ticket:158
Diane Trout [Sat, 28 Oct 2006 01:53:48 +0000 (01:53 +0000)]
don't use staticly allocated widgets
dynamically create the widgets used in SequenceDescription
Diane Trout [Sat, 28 Oct 2006 01:53:17 +0000 (01:53 +0000)]
add include QCloseEvent to MussaWindow.hpp
wasn't needed but it was being used so this counts
as a bit more documentation
Diane Trout [Sat, 28 Oct 2006 01:47:01 +0000 (01:47 +0000)]
allow verticle scrollbar for sequence browser widget
ticket:182
if the window is smaller than the minimum useful scrollable browser
size start using a scroll bar.
Diane Trout [Sat, 28 Oct 2006 01:40:35 +0000 (01:40 +0000)]
compute the correct starting window size
ticket:233
try to compute a window size that will show the tracks as the
gl canvas decided to draw them.
Diane Trout [Fri, 27 Oct 2006 23:56:32 +0000 (23:56 +0000)]
use pointers for zoom spinbox in ZoomWidget
Brandon King [Sat, 28 Oct 2006 01:05:17 +0000 (01:05 +0000)]
Mussagl Manual: Docs 1.0 (part 3)
* Made link to SMN1 .mupa creation (ticket #170)
* Documented deselecting tracks/paths. (ticket #213)
* Fixed broken compile of rst2html from previous patch.
Brandon King [Sat, 28 Oct 2006 00:44:58 +0000 (00:44 +0000)]
Mussagl Manual: Docs 1.0 updates (part two)
* Updated Mac OS X install instruction. (ticket #168)
* Documented why sub-analysis exists (ticket: #214)
* Spelling err fix.
* Hid changelog / major updates sections for future use. (ticket: #162)
Brandon King [Sat, 28 Oct 2006 00:15:33 +0000 (00:15 +0000)]
Mussagl Manual: Updates for Docs 1.0
* Moved UCSC tutorial toward end, but linked to from Obtaining Data section.
* Added animated gif under dynamic threshold section.
* Documented command line options. (tickets: #167, #225)
* Mentioned Python existing in Mussagl. (tickets: #167, #227)
* Updated repeats documentation. (tickets: #167)
* Updated .mupa file format description.
* Added note about .mupa comment character.
* Added a create .mupa section for UCSC tutorial. (ticket:164)
* Linked to Diane's OverlappingWindow wiki page (ticket:137)
Diane Trout [Fri, 27 Oct 2006 20:40:20 +0000 (20:40 +0000)]
Use Qt4.2 openUrl to show manual
ticket:217
This function means I can link to a website without using python.
So this patch disables building the python interpreter into mussa.
I'll make it optional when I actually make some progress in
interacting with mussa via python.
Diane Trout [Fri, 27 Oct 2006 17:57:05 +0000 (17:57 +0000)]
implement set window state
ticket:194
basically works, though I need to get mussa to notice when sequence
information has been changed.
Diane Trout [Thu, 26 Oct 2006 22:51:27 +0000 (22:51 +0000)]
include icon extension for os x bundle information
Diane Trout [Thu, 26 Oct 2006 22:30:31 +0000 (22:30 +0000)]
add copy sequence as string option
ticket:215
it turned out that the reson I couldn't paste was all the invalid
characters in the fasta representation of the sequence. This adds
a copy sequence option which just copies the sequence as an undecorated
string. (which does paste).
Of course this is now confusing as there's two copy options...
Diane Trout [Thu, 26 Oct 2006 20:39:54 +0000 (20:39 +0000)]
display number of basepairs copied
ticket:211
this also provides a quick and dirty way of counting number of base pairs.
Brandon King [Thu, 26 Oct 2006 00:38:10 +0000 (00:38 +0000)]
Mussa Window Icon
* Added mussa.png icon.
* Added mussa.png to qrc file.
* Added the icon to qApplication.
Diane Trout [Tue, 24 Oct 2006 21:38:47 +0000 (21:38 +0000)]
tagged release_1.0_rc3
Brandon King [Tue, 24 Oct 2006 17:01:13 +0000 (17:01 +0000)]
Mussa Manual: spelling, wording, and grammer
Diane Trout [Tue, 24 Oct 2006 00:44:15 +0000 (00:44 +0000)]
call set_soft_threshold after subanalysis
ticket:216
this should make sure that all the match lines show up with you
first view a subanalysis. (Though perhaps not in the most
CPU efficient way.)
Diane Trout [Mon, 23 Oct 2006 22:55:44 +0000 (22:55 +0000)]
Enable Qt4 tests
ticket:207
To fix the problem generating the moc_Test files I stopped trying
to fake the .hpp file for moc, and renamed the qui/test/Test*.cpp files to
.hpp and added a very small .cpp file which included the header and
called the QTEST_MAIN or QTEST_APPLESS_MAIN macro.
APPLESS will work even if I don't have a working X server on linux, but
some parts of Qt require that the gApp be constructed.
Diane Trout [Fri, 20 Oct 2006 21:59:06 +0000 (21:59 +0000)]
add nl to end of 3 files
Diane Trout [Fri, 20 Oct 2006 01:33:10 +0000 (01:33 +0000)]
avoid multiple calls to setSoftThreshold
ticket:200
So I took the easy route and just wrapped a widet->setEnabled(false)
widget->setEnabled(true) around the setSoftThreshold code. Which should
hopefully prevent the possibility of calling setSoftThreshold before
the other call has terminated.
Diane Trout [Fri, 20 Oct 2006 01:11:36 +0000 (01:11 +0000)]
copy motifs to a new subanalysis
ticket:199
Also the second problem was that the motif_scan wasn't using the right
offsets to compute the motif start/stop locations.
Diane Trout [Thu, 19 Oct 2006 23:27:07 +0000 (23:27 +0000)]
fix motif loader under release build
tciet:163
It turns out that allocating a static class under a release build with a
static char might not be so reliable. This showed up as two problems
first was the test_algorithm unit test would fail.
The second was that the motif parser wouldn't work. In my efforts to
diagnose this I ended up moving the motif file parser to its own file
and splitting the spirit semantic actions up into multiple functors.
(functors remind me of anonmyous classes in java, useful but so annoying
synatacticaly).
Eventually I solved the problem by making the const char *alphabets
just available directly from the Alphabet class, as I couldn't figure out
a way to get the static function returning a reference to a static local
variable (which according to the C++ faq should've been allocated when called
and not before).
Diane Trout [Thu, 19 Oct 2006 00:58:47 +0000 (00:58 +0000)]
Sequence::rev_comp works on subsequences
ticket:197
Sequence::rev_comp when called on a Sequence which contained a subsequence
was actually reversing the entire sequence and not just the selected region.
To fix this I added rbegin and rend which return reverse iterators that
cover the subseq range and updated rev_comp to use them.
There's also some extra sequence unittests to make sure that rbegin/rend
work correctly. (and as a bonus loading several sequences out of one fasta
file works).
Diane Trout [Wed, 18 Oct 2006 22:49:59 +0000 (22:49 +0000)]
add to_upper_case to some sequence unittests
forcing sequences to all uppercase (though useful for doing seqcomps and
rendering) does mean that I needed to update tests to deal with the
differences from .get_sequence()
Brandon King [Wed, 18 Oct 2006 23:38:07 +0000 (23:38 +0000)]
Mussa Manual: Screenshots + Performance section
* Updated screenshots in the "view alignment" & "sub-analysis" sections.
* Removed reference to build numbers (since this is for release 1.0)
* Added an Understand Mussa section.
* Added placeholder for algorithm performance.
* Added documentation on the effects of repeats in DNA sequence on Mussa.
* Added a placeholder for Diane's overlapping windows "interesting" case.
Brandon King [Wed, 18 Oct 2006 18:47:51 +0000 (18:47 +0000)]
Mussa Manual: Deleting a Motif
* Documentation on how to delete a motif using the Motif Editor (ticket:196)
Brandon King [Wed, 18 Oct 2006 18:32:18 +0000 (18:32 +0000)]
Mussa Manual: Multiple Mussa Windows
* Documented how to view multiple analyses at one time. (ticket:179)
Brandon King [Wed, 18 Oct 2006 18:04:42 +0000 (18:04 +0000)]
Mussa Manual: save on close & save motif default behavior
* Wrote the "Save on close" section. (ticket:189)
* Documented default motif list extension, when not provided by user. (ticket:190)
* Removed old "features to implement".
Diane Trout [Tue, 17 Oct 2006 23:21:33 +0000 (23:21 +0000)]
be more forging of user provided file names
ticket:192
It turned out my use of boost::filesystem::path could toss an exception
if there were spaces in the file name on OS X. I needed to do a bit more
work to construct a safe filename for saving analyses and motifs.
Also I discovered that runtime_error was not the root exception class,
std::exception was. So I adjusted my try/catch to catch that exception
in the hope that I can provide more meaningful error messages.
Diane Trout [Tue, 17 Oct 2006 22:19:29 +0000 (22:19 +0000)]
remove old code
remove the FLTK version of mussa and the non CMake-based build systems.
Diane Trout [Tue, 17 Oct 2006 22:19:06 +0000 (22:19 +0000)]
ignore eclipse settings
Diane Trout [Tue, 17 Oct 2006 21:57:06 +0000 (21:57 +0000)]
add a manually updated version number.
Diane Trout [Tue, 17 Oct 2006 21:56:33 +0000 (21:56 +0000)]
test_mussa_python also had an unecesary QtOpenGL library link
Diane Trout [Tue, 17 Oct 2006 21:55:42 +0000 (21:55 +0000)]
attempt to make buildnum.py generate a useful header
alas I couldn't get the CMake script to work reasonably well.
Diane Trout [Tue, 17 Oct 2006 20:41:32 +0000 (20:41 +0000)]
motif save should have a default extension.
ticket:188
Diane Trout [Tue, 17 Oct 2006 20:40:17 +0000 (20:40 +0000)]
don't like QTOPENGL to python module
The only dependency the python layer should have is on QtCore so adjust
which libraries are included to only include QtCore. Otherwise when
it decides to link in QtOpenGL I get a warning about not being able to find
QtGui.
Diane Trout [Tue, 17 Oct 2006 19:05:29 +0000 (19:05 +0000)]
changing motifs should make the analysis dirty
ticket:187
though if you apply and wihtout changing anything the dirty flag will
still be set. Hopefully no one will care.
Brandon King [Tue, 17 Oct 2006 18:59:56 +0000 (18:59 +0000)]
Mussa Manual: updated motif dialog section.
* Updated text/screenshots in the motif dialog section. (ticket #191)
Diane Trout [Tue, 17 Oct 2006 18:47:49 +0000 (18:47 +0000)]
always add a blank motif
ticket:186
given the way the motif editor automatically adds motifs its important
to make sure there's a blank one for users to start editing with.
Brandon King [Tue, 17 Oct 2006 18:14:59 +0000 (18:14 +0000)]
Mussa Manual: Saving section
* Added a new saving section
* Added section template for save on close (ticket #189)
* Documented saving analysis (ticket #176)
* Documented saving analysis as (ticket #176)
* Documented saving motif lists (ticket #175)
Brandon King [Tue, 17 Oct 2006 17:29:52 +0000 (17:29 +0000)]
Mussa Manual: create/load analysis section updated
* Updated text/screenshots in the "Create new analysis" section (ticket #169)
* Updated text/screenshots in "Load a mussa parameter file" section. (ticket #181)
* Updated text/screenshots in "Load an analysis" section. (ticket #185)
Diane Trout [Tue, 17 Oct 2006 06:50:49 +0000 (06:50 +0000)]
more python interface to Sequence
Diane Trout [Tue, 17 Oct 2006 06:46:02 +0000 (06:46 +0000)]
force loaded sequence to uppercase
ticket:183
Diane Trout [Tue, 17 Oct 2006 01:36:10 +0000 (01:36 +0000)]
validate app bundle before shipping
ticket:180
This path adds some support for parsing otool results so I can test
to make sure that object files are only linked against /usr/lib,
/System/Library or @executable_path entries.
I changed it to use subprocess (which required installation on OS X
because of python2.3) and it'll also handle the uploading of packages
now.
Diane Trout [Tue, 17 Oct 2006 01:33:06 +0000 (01:33 +0000)]
don't link against X11 on OS X
the python shared library ended up picking up a link to the OS X
X11R6 libraries because it was linking against the GUI code,
if we let it link mussa will require X11 to be present on the users
system which is not always true for an OS X user.
Brandon King [Mon, 16 Oct 2006 18:51:19 +0000 (18:51 +0000)]
Mussa manual: Overview section update
* Updated all images in overview section to latest version of Mussa. (Tickets: #166, #172, #173)
* Updated text in section to match latest version of Mussa. (Tickets: #166, #172, #173)
* Removed 'Motif Toggle' button documentation. (ticket:171)
Brandon King [Mon, 16 Oct 2006 17:07:19 +0000 (17:07 +0000)]
Mussa Manual: Link to example data in UCSC genome browser section.
* Added a link to the SMN1 example data made available on our wiki.
Brandon King [Sat, 14 Oct 2006 01:06:17 +0000 (01:06 +0000)]
Mussa Manual: Save to image
* Added documentation for the save to image feature.
Diane Trout [Sat, 14 Oct 2006 01:05:05 +0000 (01:05 +0000)]
don't seqcomp sequences that are too small
ticket:151
seqcomp gets really grumpy when it trys to analyze a sequence that
is shorter than the window sequence. So instead of letting it try
to malloc all of your memory, throw a more useful exception.
Also I updated the SubanalysisWindow to catch the exception and
report it to the user.
Brandon King [Sat, 14 Oct 2006 00:28:01 +0000 (00:28 +0000)]
Fix for ticket:160
* gcc 4.0.3 didn't like assing 0 to a MussaRef, removed default value based on Diane's suggestion. That did the trick.
Brandon King [Sat, 14 Oct 2006 00:24:25 +0000 (00:24 +0000)]
Mussa Manual: motif list file masks
* Documented file masks for motif lists.
* Closes ticket:153
Diane Trout [Sat, 14 Oct 2006 00:05:43 +0000 (00:05 +0000)]
add operator< to ConservedPath
So I could sort a list of ConservedPaths it was hopefully going to
let me make simple_refine a little bit better by grouping paths
that were next to each other closer than those that were almost
next to each other execpt one match far away. Unfortunately
I didn't think it all the way through and the lists are already
sorted by that criteria. e.g.
1,1,1 < 1,1,70 < 2,2,2
when what simple refine needis is something more like
1,1,1 < 2,2,2 < 1,1,70
Brandon King [Fri, 13 Oct 2006 22:52:24 +0000 (22:52 +0000)]
Build number python script
* Reports the build number of a given darcs repository of mussa.
* In support for ticket:124.
Brandon King [Fri, 13 Oct 2006 22:07:18 +0000 (22:07 +0000)]
Save to image fix (ticket:96)
* ImageSaveDialog now uses a SequenceBrowser copy contructor to draw the image.
* glseqbrowser copy constructor was missing path_segments.
* SequenceBrowser now has a copy constructor.
* ImageSaveDialog needed to updated to use the bp per pixel zoom magnification;
meaning that when the user wants an image twice the x value of the glcanvas,
then the bps per pixel needed to halved.
* bp_per_pixel2 = ( x_1 / x_2) * bp_per_pixel_1
Diane Trout [Fri, 13 Oct 2006 05:48:13 +0000 (05:48 +0000)]
save motifs with the analysis
ticket:133
This is the last part to implement ticket:133 this hooks up the
Mussa::save and Mussa::load code to automatically try saving the motif lists
into the analysis subdirectory.
Diane Trout [Fri, 13 Oct 2006 01:31:41 +0000 (01:31 +0000)]
pass default_dir around
convert default_dir to be a shared_ptr and then pass it around
all of our windows that need to save things. Pretty much now
whenever someone saves something we'll remember that last directory
and use it as our default dir.
I hope this works on windows, if it breaks, there
might be a few fs::natives that are needed.
Diane Trout [Fri, 13 Oct 2006 00:52:08 +0000 (00:52 +0000)]
change default_dir to a QDir
from a boost::filesystem::path, this should make it
easier to pass around.
Diane Trout [Thu, 12 Oct 2006 23:52:19 +0000 (23:52 +0000)]
cleanup image save dialog aesthetics
ticket:96
one of the problems is that when people try saving an image they
couldn't find where the image was saved too. This is probably because
they didn't set a file name and no errors were thrown.
this patch ties the "save as" prompt to the save button, so once someone
gets the pixel size right they have to chose a filename.
I also fixed the problem where it wasn't loading the "lock aspect ratio"
icon out of the resource file, and made a few other aesthetics updates.
Diane Trout [Thu, 12 Oct 2006 22:58:08 +0000 (22:58 +0000)]
tabs are of the devil
Brandon King [Thu, 12 Oct 2006 22:47:45 +0000 (22:47 +0000)]
CMakeLists.txt: Added extra QT_LIBS depend to fix Qt Assistant linking.
Diane Trout [Thu, 12 Oct 2006 21:57:20 +0000 (21:57 +0000)]
Fix initialization of QtAssistant
ticket:120
I reenabled calling QtAssistant for help on windows to get around the lack
of a python standard library. However, I forgot to update the define
for initializing the QtAssistant. Needless to say an unininitialized
QtAssistantClient pointer wasn't terribly useful.