Complete 2D and 3D viewing features

Full test of (almost all) 2D and 3D features:

• Viewing results in 2D mode works acceptably now (results are shown in orthographic mode).
• Overlay and side-by-side view can be toggled through an item in the View menu.
• More fixes for the mac code signing situation. Please unzip the binary and then move Athena.app to some other directory to avoid crashes at startup time. (I know, it's weird. I'm hoping to improve this in the future.)

Side-by-side view demonstration

Changes since last release:

• Inputs and outputs are now displayed side-by-side instead of superimposed. (You cannot get out of this mode right now, which is annoying. What I want is user feedback about whether this should be our preferred view, or if superimposed output is to be preferred some or all of the time.)
• Arrows are now shown in the routing view.
• The mac binary is now self-signed. This provides no useful security but does allow it to run correctly if you override the 'unknown developer' warnings.

New input files, PDBGEN, and easier output display

New features:

• The newly-organized PLY input files are present.

• The sidebars can now be hidden (use the ‘Window’ menu). This is a temporary stand-in until they can be made resizable.

• The three useful output visualizations can be shown in any combination.

• PDBGen can now be invoked.

Some notable unfinished things to be addressed in the next version:

• Side-by-side view of input and output aren’t implemented yet, so 2D mode is still not very useful. Some of the 3D input files also don’t match well in size with their outputs. (Try making the model transparent if you can't see the expected output -- it might be hidden inside.)

• I hope to try making the cylinder models (optionally) transparent, so that they can be viewed alongside the other molecular models.

• Cone display is not yet implemented (which is obvious in the routing models).

• PDBGEN does not provide any useful feedback on its progress, but halts the whole program while it runs. (After it runs, the PDBGEN log is available in the Athena log window, reachable from the View menu).

• The GUI is getting cluttered! I will attempt to simplify it in the next update.

First-draft tool output visualization

The output files of the four sequence tools can now be visualized. After running a tool, choose an output to look at from the menu in the lower-right hand corner. (The first two items in the menu aren't easy to see due to some unresolved scaling issues.)

Arrows are not yet fully implemented, and are drawn as cylinders (i.e. without their cones).

2D results aren't easy to see; focus on 3D tools for now.

FEEDBACK REQUESTED:

• Do we need to see multiple output files active a time in one frame, or is one at a time sufficient?
• Do we like having the original geometry superimposed with the output files, or should they be shown side-by-side or otherwise separately?
• Should 2D outputs be shown in fully rotatable 3D?

Bugfixes and scaffold files

Non-default scaffold files can now be selected using the file menu. The built-in m13 scaffold remains the only default that ships with Athena.

Bug fixes since v0.2.1:

• Mac Athena can now be usefully installed in /Applications (or anywhere).
• Fixed some window rendering glitches on Mac.

Move everything to sidebars

Since v0.2.0, this release offers:

• An improved tool-chooser GUI on the right side of the window. Instead of tabs, we're trying out Qt's toolbox controls.
• A complete set of rendering controls on the left side of the window -- including control of all colors.
• A new geometry selection widget, requiring fewer clicks than the old combo-box approach

As always, feedback on UI is welcome.

Draft of a new GUI arrangement

This release adds new controls for managing Athena's graphical rendering, and a single unified geometry chooser drop-down. Only relevant tools are offered to the user (PERDIX and METIS when a 2D file is open, TALOS and DAEDALUS when a 3D file is open). We are getting close to being feature-complete for a 1.0 release.

Feedback on the new GUI layout is invited, as layout and presentation decisions are the most important issue right now.

Milestone 2 Release Candidate

Since v0.1.1:

• Wireframes work correctly for all polygon shapes, even concave ones.
• Transparency is controllable (use the slider to the left of the window).
• Improve default material colors.
• Improve 2D mouse interaction.
• Fix bug where tools were not running correctly.

Improved rendering (with wireframes)

This version includes (too) many new default tests in the DAEDALUS drop-down. They provide a nice way to quickly flip through visualization of various 3d shapes.

Support all four DNA tools

Support for DAEDALUS2 and METIS has been added.