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Tree exports - include user defined colours if set #630

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8 tasks done
shawnlaffan opened this issue Dec 2, 2016 · 1 comment
Closed
8 tasks done

Tree exports - include user defined colours if set #630

shawnlaffan opened this issue Dec 2, 2016 · 1 comment
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@shawnlaffan @LukedFitzpatrick
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enhancement
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Release_2.0

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@shawnlaffan
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shawnlaffan commented Dec 2, 2016 •
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If a user has assigned colours themselves (e.g. under the processes implemented in #600) then we should allow them to be exported.

This is simple for tabular trees, but nexus and newick need a bit of extra handling as we need to search for an ancestor that has a colour set.

Related to #503

Collated to do list:

  • Add tests for colour export functionality before merge
  • Option to export colours could probably be in the export metadata as a boolean.
  • Exported bootstrap blocks need to have a leading ampersand, and color keyword needs to be preceded by an exclamation mark, e.g. [&!color="#00000"] instead of ["colour"="#000000"]. Otherwise FigTree does not recognise the colours.
  • Quotes appear optional but have no apparent effect. Poss remove them if simple?
  • Needs to also apply to tabular tree. Looks like metadata just needs to be updated.
  • [[ WONTFIX - importing such data is sufficiently complex to warrant its own issue. nexus files - import annotations in node comment blocks #657 ]] Add roundtrip tests. SWL to generate some simple data using FigTree (which is the target package for colours). Currently get number format errors when reading an exported file.
  • Bootstrap block needs to go between label and number. "fred[&!color=red]:5"
  • disable for newick - figtree seems not to support it (only Nexus)
@shawnlaffan shawnlaffan added this to the Release_2.0 milestone Dec 2, 2016
LukedFitzpatrick added a commit that referenced this issue Dec 22, 2016
@LukedFitzpatrick
Tabular tree export includes user defined colours
a848dea 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Dec 22, 2016
@LukedFitzpatrick
Clean up node colour implementation in Dendrogram.pm
4ec7d03 
Updates issue #630
LukedFitzpatrick added a commit that referenced this issue Dec 22, 2016
@LukedFitzpatrick
Quick fix to previous commit
879259e 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Dec 23, 2016
@LukedFitzpatrick
Minor bug fixes
d80b2b1 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Dec 23, 2016
@LukedFitzpatrick
User defined colours in newick and nexus export. Yes/No dialog for co…
b786fca 
…lour export.

Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 1, 2017
@LukedFitzpatrick
Quick fix: default values in Export.pm
30ba5b4 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 2, 2017
@LukedFitzpatrick
Extract method for cluster_colour_mode to aid colour export down the …
ecaf53a 
…track

Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 2, 2017
@LukedFitzpatrick
Make colour export dialog only appear when in multiselect mode
d2bae1a 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 2, 2017
@LukedFitzpatrick
Minor update to tests for exporting trees
f2cbc44 
Updates #630
@LukedFitzpatrick
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LukedFitzpatrick commented Jan 2, 2017 •
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  • Add tests for colour export functionality before merge

LukedFitzpatrick added a commit that referenced this issue Jan 18, 2017
@LukedFitzpatrick
Add module to deal with boostrap blocks.
7d935a5 
Will eventually be added to each tree node, used initially to hold user defined colours.

Updates #630
LukedFitzpatrick referenced this issue Jan 19, 2017
@LukedFitzpatrick
Make colour exports work through the TreeNode bootstrap block.
6e9263c
LukedFitzpatrick added a commit that referenced this issue Jan 19, 2017
@LukedFitzpatrick
Add exclusions to bootstrap block.
ff6ac04 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 19, 2017
@LukedFitzpatrick
Put BootstrapBlock in the TreeNode space.
e9ff77d 
Updates #630
LukedFitzpatrick referenced this issue Jan 19, 2017
@LukedFitzpatrick
Merge changes from remap so we don't get too far behind
da6f4ac
LukedFitzpatrick added a commit that referenced this issue Jan 19, 2017
@LukedFitzpatrick
Change colour functions in TreeNode to just use generic bootstrap fun…
08dd186 
…ctions.

Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 19, 2017
@LukedFitzpatrick
Putting back in the proper colour format.
475916b 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 19, 2017
@LukedFitzpatrick
Fix export fail when bootstrap block not defined, and silly 'unbless'…
588341b 
… error.

Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Make exclusions actually work.
d9b6c9d 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Skeleton for unquted bootstrap block import handling.
56ef3b5 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Make the BootstrapBlock decoder deal with unquoted key/value pairs.
13b5170 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Hook up bootstrap decoding to nexus import.
3ce3da5 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Fiddly changes to make bootstrap colour export work.
50b7f15 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Make the tests pass
798c089 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 20, 2017
@LukedFitzpatrick
Roundtrip test for bootstrap import/export.
176e3d9 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 22, 2017
@LukedFitzpatrick
Fix typo in BootstrapBlock.pm
3836d9f 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 22, 2017
@LukedFitzpatrick
Add better exclusion handling mechanism to bootstrap block. Sets up f…
e7a60f5 
…or cleaner colour export system.

Updates #630
LukedFitzpatrick added a commit that referenced this issue Jan 23, 2017
@LukedFitzpatrick
Stop passing around an 'export_colours' value, instead add exclusion …
5771ca4 
…to the bootstrap block before export.

Updates #630
shawnlaffan added a commit that referenced this issue Feb 3, 2017
@shawnlaffan
Add Data::Structure::Util to the Config checklist
a4db9ed 
Updates #630
shawnlaffan added a commit that referenced this issue Feb 3, 2017
@shawnlaffan
Add Data::Structure::Util to the dependencies
c342d4a 
Updates #630
@shawnlaffan shawnlaffan mentioned this issue Feb 10, 2017
Merged
LukedFitzpatrick added a commit that referenced this issue Feb 13, 2017
@LukedFitzpatrick
Make the bootstrap block export in the form [&!key=value,!key=value].…
108e237 
… Also update tests for bootstrap block to reflect change.

Updates #630
LukedFitzpatrick added a commit that referenced this issue Feb 14, 2017
@LukedFitzpatrick
Make exclamation mark only apply to color block.
0bd21ce 
Updates #630
LukedFitzpatrick added a commit that referenced this issue Feb 14, 2017
@LukedFitzpatrick
Option to export colours is now in the export metadata. Also slight t…
20e63df 
…weaks to bootstrap block encoding/decoding.

Updates #630
shawnlaffan added a commit that referenced this issue Feb 16, 2017
@shawnlaffan
Tree exports: Move the bootstrap block to before the length
0662b97 
Also some style changes and minor inefficiencies.

Updates #630
shawnlaffan added a commit that referenced this issue Feb 17, 2017
@shawnlaffan
disable colour export in newick files, enable in text metadata
d82b078 
Updates #630
shawnlaffan added a commit that referenced this issue Feb 17, 2017
@shawnlaffan
Change a few idioms
b9ed9bf 
Updates #630
@shawnlaffan shawnlaffan mentioned this issue Feb 21, 2017
Open
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
separate the colours from the rest of the bootstrap block lists
7b28273 
Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
plain newick files do not support complex bootstrap blocks
93b7437 
updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
shift the colour reformatter into BootstrapBlock.pm
89792a3 
Also remove exclusions blocks

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
Shift the bootstrap data into a subhash, add array args methods
5e9c2c7 
The subhash makes the logic cleaner when wrangling colours and the like.
It also means we can have a label if appropriate.

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
Add a round trip test that incudes complex data structures
fdb9ce0 
This currently fails as the parser assumes json compatible strings
(which is a false assumption on my part)

[ci skip]

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
Update tests to use colour methods
9f01603 
Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
Use a non-capturing group
c37dad1 
Might make a difference when parsing very large trees

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
Miscellaneous changes
4e26ac9 
Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
set roundtrip test as todo
ebd3a60 
They can be worked on under issue #657

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
disable a failing roundtrip test
45da3a3 
It can be dealt with under #657

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
store bootstrap/comments objects under private key
4a6b141 
Otherwise they were appearing in the GUI.

Minor tweaks to methods otherwise.

Updates #630
shawnlaffan added a commit that referenced this issue Feb 21, 2017
@shawnlaffan
remove a Gtk call in the engine code
a593117 
Updates #630
shawnlaffan added a commit that referenced this issue Mar 3, 2017
@shawnlaffan
Make sure we set the branch colour properly
5596967 
This was missed in the updates to issue #630
@shawnlaffan shawnlaffan mentioned this issue Feb 9, 2018
Closed
@shawnlaffan shawnlaffan mentioned this issue May 12, 2019
Closed
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