appletParameters.html

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-2446 merged to spike branch

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JAL-1933 applet doc for showOccupancy parameter

I think you're trying to incorporate logic that already happens in SequenceRenderer, which is much lower level than ViewStyle. SequenceRender has a Viewport as its context. The ViewstyleI methods ...

I think you're trying to incorporate logic that already happens in SequenceRenderer, which is much lower level than ViewStyle.

SequenceRender has a Viewport as its context. The ViewstyleI methods on the viewport configure the shader, which is provided to sequence renderer. The sequence renderer also configures itself (via the Sequence canvas) directly via the viewport instance of ViewStyleI.

As each sequence is drawn, the Sequence Canvas gets a list of groups containing the sequence, and takes configuration from those groups in preference to

If this doesn't make sense, we need to sit round the table to discuss.

The problem with the suggestions is for group colouring - groups don't have a ViewStyle.

The problem with the suggestions is for group colouring - groups don't have a ViewStyle.

moved.

moved.

not clear to me if failing gracefully should be allowed here. It's an implementation error.

not clear to me if failing gracefully should be allowed here. It's an implementation error.

Removed upper-casing of consensus as it already always is.

Removed upper-casing of consensus as it already always is.

Removed upper-casing of consensus from PID and Blosum62 findColour methods.

Removed upper-casing of consensus from PID and Blosum62 findColour methods.

check added with unit test.

check added with unit test.

Done. Also disabled Conservation for nucleotide in Popup menu. Checked menu is now peptide/nucleotide sensitive *for selection created by drag in sequence panel *" " " " " " scale panel *" " " " ...

Done. Also disabled Conservation for nucleotide in Popup menu.
Checked menu is now peptide/nucleotide sensitive

  • for selection created by drag in sequence panel
  • " " " " " " scale panel
  • " " " " " " sequence ids
Just tested manually, with case-sensitive and not case-sensitive schemes saved in 2.10.1. All looked ok.

Just tested manually, with case-sensitive and not case-sensitive schemes saved in 2.10.1. All looked ok.

I can't find an issue about cascading groups, but I do remember thinking about it at the time when I introduce AnnotatedCollectionI. There are use cases - the 'make groups from' method subdivides ...

I can't find an issue about cascading groups, but I do remember thinking about it at the time when I introduce AnnotatedCollectionI.

There are use cases - the 'make groups from' method subdivides existing groups, so it could set the context to be the parent group. There are a few other avenues that need exploring with groups (named group sets, etc) - so perhaps its worth putting in the check now.

think you'll find it easiest to set context in AlignmentViewport.setSelectionGroup(..).

think you'll find it easiest to set context in AlignmentViewport.setSelectionGroup(..).

Ok I'll qualify that: toUpperCase() does not use or instantiate Locale. It does some stuff to decide if the string is already upper-case. Whether that is performance affecting would need to be meas...

Ok I'll qualify that: toUpperCase() does not use or instantiate Locale. It does some stuff to decide if the string is already upper-case. Whether that is performance affecting would need to be measured.
I ran the benchmark code from stackoverflow:
As provided (random strings):

  • String.toUpperCase() 14 seconds
  • customToUpperString() 6 seconds
    With the random strings all upper-case:
  • String.toUpperCase() 4.4 seconds
  • customToUpperString() 1.5 seconds
    So String.toUpperCase() is not the fastest.
    We could just remove this line (in PID/Blosum62ColourScheme) on the grounds that we know that the Profile consensus is always uppercase.
    This is what happens in ResidueShader.aboveThreshold() (relocated from ResidueColourScheme).
== JAL-2405. How about a new constructor SequenceGroup(AnnotatedCollectionI) which sets the context - use this constructor where the selection group is created. *applet/gui.SeqPanel.doMousePresse...

== JAL-2405.
How about a new constructor SequenceGroup(AnnotatedCollectionI) which sets the context - use this constructor where the selection group is created.

  • applet/gui.SeqPanel.doMousePressedDefineMode()
  • and many more...lots of places to change...
    Or: call SequenceGroup.setContext() in the [A]PopupMenu constructor?
Modified so that unit tests can call with parameter true or false i.e. mimic toggling the state of the menu item.

Modified so that unit tests can call with parameter true or false i.e. mimic toggling the state of the menu item.

ok - not quite sure where I saw it now, but I'm sure there was both 'background' and 'Background' in the code. Probably looked at the wrong branch.

ok - not quite sure where I saw it now, but I'm sure there was both 'background' and 'Background' in the code. Probably looked at the wrong branch.

? looks the same to me

? looks the same to me

so...

so...

ok. one day we can just have one list (or at most two - one place in code for Jalview builtins and one place in docs!)

ok. one day we can just have one list (or at most two - one place in code for Jalview builtins and one place in docs!)

this looks like it could be refactored to a UI independent interface and a Swing specific implementation. Could it ?

this looks like it could be refactored to a UI independent interface and a Swing specific implementation. Could it ?

this logic should be in jalview.viewmodel.AlignmentViewport.setViewStyle(..)

this logic should be in jalview.viewmodel.AlignmentViewport.setViewStyle(..)

you seem to have introduced a new pattern in the jbgui package where the _actionPerformed() method now takes the state parameter. Isn't that just increasing code in this package ?

you seem to have introduced a new pattern in the jbgui package where the _actionPerformed() method now takes the state parameter. Isn't that just increasing code in this package ?

We need to block out some time to work out what such a standardised pattern might be. There are lots of limitations (see JAL-1811 for e.g.) that could inform what these are, and what pattern we nee...

We need to block out some time to work out what such a standardised pattern might be. There are lots of limitations (see JAL-1811 for e.g.) that could inform what these are, and what pattern we need to avoid creating more problems in headless mode.

raiseGui didn't add the AlignFrame to the Desktop instance because the Desktop instance isn't created in headless mode. In fact, the principle reason for raiseGui was to prevent blocking in scripts by not creating file IO error dialog boxes.

Popup menu behaviour for new selection group sounds wrong by default. There already is a context - even if the group hasn't been added to the alignment - so may as well just set the context - since...

Popup menu behaviour for new selection group sounds wrong by default. There already is a context - even if the group hasn't been added to the alignment - so may as well just set the context - since it is strictly valid for a selection group

added note on JAL-1640 about reviewing interface. One blocker for unifying Group and Alignment vis settings is that some settings are traditionally viewport only (sequence feature display, colour b...

added note on JAL-1640 about reviewing interface. One blocker for unifying Group and Alignment vis settings is that some settings are traditionally viewport only (sequence feature display, colour by annotation).

um - there would be side effects if the CalcId mechanism was broken.... but no matter.

um - there would be side effects if the CalcId mechanism was broken.... but no matter.

JAL-2394 created to followup.

JAL-2394 created to followup.