beowulfey / pylinnaeo Goto Github PK

Need to find what event is called on edge click. It does turn off if I click the title bar, but that's effectively useless.

This means that if you try and capture the output to image, it always shows the beginning. No good!
I have to save the position on the screen prior to redrawing it so that it scrolls back to the same spot on redraw.

I can try grabbing the character in the center or something, but that value will change with different sizes... might be tougher than it seems.

I save the scrollbar position when resizing, which works well, but for some reason when focus is lost then regained, the window position resets, even though it seems the position is still being saved.

Very annoying when flipping back and forth from pymol to alignment to have the scroll position reset each time!

A Sequence item consists of a sequence record with an SID, Name, and "SName" which I added. The latter is supposed to be the visible text, whereas the SID should be static per sequence.

I need to make it so changing a sequence node updates that visible text, but never forgets its original ID! That way, the sequence remains unique.

Something to explain the different color definitions; hydropathy, conservation, etc.

Maybe there's a way to attach?
If not, may have to embed a small terminal in the window?

Forgot to set "seqtype" in the reopening function. Fixed in next build.

Each time I alt-tab on windows, the amount of memory increases. Something isn't being released.

Only an issue if building from source, but not good -- without DSSP the program crashes. Need to add try/catch there.

Haven't finished Import and Export options.

Happens for sequences, but not alignments.

Right now, I'm jankily "centering" the alignments and fixing the last line manually, so that it looks left justified. This allows me to center the text but make it look left aligned within the window.

Obviously this is no good. I want it to be centered within the window. Have to find a good way to do that geometrically.

May be Windows-specific? Liberation Mono works well, but changing to a different font seems to misalign the text.

In my test.lno file there is an error with hhalign. Saw this before, now I see what's happening.

What is different about reloading? I think the problem is the saved workspace saves the alignment with dashes. This means clustalo fails during run (it needs dealign)

Similar to the scroll bar issue: sometimes on alt-tab, or other random things, the font size "forgets" what it is supposed to be (even though the setting is still there)

This is an issue with click on a subwindow (or changing tabs) not being considerd a "change active subwindow" event. So it follows through a different logic circuit.

Not sure how to debug this just yet.

Not sure why. Does not happen on v0.3.2!!

Preference pane is missing. Things I would like to add:

• Default option for tabs.
• Default theme
• Default alignment stylings (once implemented)
• Default alignment algorithm (once implemented)

Need to add a popup to modify.

It does work for sequence window titles, but not alignments.

PyOxidizer works pretty well, but I only seem to be able to use it on Windows for now (and I can't even open it on my own computer, which makes no sense). TI need to figure out how to make portable binaries for all three platforms.

I can at least run it on all three platforms... so that's good at least.

Closing issue #2 and merging it with this one, as it's related. Windows binary should be signed in addition to existing.

If I click "Get Structure", it's supposed to disable the button. It registers as disabled, but it looks active still.

Self-explanatory.

You can have two copies of the same sequence, which is no good. Should make the SeqInit check the seqlist and prevent duplicating. I already prevent duplicating alignments, so trying to make an alignment using this dupe instead of the original opens the same alignment.

Although, maybe this is good? Like if people want to have two copies of the same sequence, depending on their organization strategy?

Not sure what's going on. Observed on windows. It appears the scroll bar is on the ruler pane, and disconnecting from the alignment pane. WHAT

Seems like it isn't properly updating the list of names; won't let me change the name of something, then change it back to the original. Also, it doesn't update automatically anymore.

There's a bug in how I calculate the cursor position relative to the protein sequence -- after a certain number of lines, it resets. Prior to that, the calculator works perfectly. What?!?