MussaGL 1.1.0

Highlight of New Features

• N's in sequence are drawing in a light gray
  • Now you can see where N's exist in your sequence.
• Scrollable main window
  • Allows for scrolling when the number of sequences is greater than the available drawing space.
• Sequence Properties ([485], [488], [489])
  • Allows for choosing the location to draw an individual sequence given an offset.
• Escape key clears sequence browser selection. (#212, [553])
• Mouse wheel now can be used to zoom in & out. (#252, [651])
• More meaningful error messages when loading annotations. (#239, [515])
• File saving and parsing improvements.

Additional New Features

• Saved analyses now save and load current soft threshold (#257, [557])
• Additional "What's This?" documentation ([518], [519])
• Qt version displayed in about box ([517])

Application Architecture Improvements

• Core sequence classes refactored.
• Annotation code refactored.
• Use of boost::shared_ptr to minimize memory leaks.
• Additional unit tests
• Started integrating paircomp by allowing mussa to build paircomp ([503])

Bug Fixes

• Sub-analysis failure to draw on init fix (#254, [524])
• Save to image crash fix (#251, [523])
• Loading saved analysis improved (#240, [554]
• More accepting of OS acceptable file names (#237, [485])
• Added -fPIC when building on 64-bit machines ([508])
• Motifs are no longer lost after closing motif window (#195, [516])
• General stabilization and other bug fixes.

Release 1.1.0 Tickets

#111

Set zero/alignment point for a sequence

#158

When unable to parse a fasta file report its name

#182

Mussa views need vertical scrolls

#194

use window feedback to show that there are unsaved changes

#195

Disable motif and closing motif editor causes loss of motifs.

#206

We need some way of indicating Ns

#210

see about removing some of the wasted border width on the sidebars

#211

Report how many basepairs are copied

#215

You should be able to paste into the motif editor

#217

Use QtDesktopServices for openURL

#226

QtTest is now a framework

#233

when first displaying mussa the tracks aren't sized to the available viewport on os x

#236

Error parsing annotation file should also include the filename in the exception.

#237

Crashing with invalid file name

#239

Report error when trying to load a directory as an annotation.

#240

When there are no matches, mussa doesn't seem to display anything

#244

len(mussa.paths()) returns number of tracks, not the number of paths found

#246

Add "What's this?" documentation to as many elements of the GUI as possible.

#247

Increase version number to 1.1.0

#248

Test latest build on all platforms

#249

darcs tag mussa_1.1.0

#250

Cmake build failure: /usr/bin/ld: cannot find -loptimized

#251

Save to image crash

#252

Make scroll wheel work

#254

Sub-analysis failing to draw paths on init

#255

Even telling cmake to use python2.3 mussa still builds against 2.5

#256

Assertion failed

#257

Saving analysis saves at current threshold

#259

New Annotations hide the sequence when you zoom to sequence view

#260

Mupa parser is cranky on windows files

#261

Mussa mupa comment character required a space

#263

Compile warnings must die!

#265

Mussa annotation file didn't work if the last sequence wasn't terminated by a newline

#266

Sub-analysis drawing bug (see attached screenshots)

#267

Sequence View soft threshold control non-responsive