Opened 8 years ago
Last modified 3 days ago
#787 _started defect
tree export/import cannot handle node-comment which are no bootstraps
| Reported by: | westram | Owned by: | westram |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | Libraries (multi) | Version: | SVN |
| Keywords: | tree bootstrap group newick | Cc: |
Description (last modified by westram)
Problem:
To create such comments call
- Tree/Compare topology.. in NTREE
That will generate node-comments like # 1 and # 26.
Exporting such a
leads to various names for inner nodes, e.g.
- groupname
- '# comment:groupname'
- '# comment'
When loading such a treefile, arb imports each of them as group.
Solution:
- strictly define information at inner
-nodes (in newick):
<nodeinfo> ::= <label>[':'<length>] <length> ::= length specified as <number> <label> ::= [':']<group> | <bootstrap> | <custom>':' | <remark>':'<group> <group> ::= name of group. May not match <bootstrap>! <remark> ::= <bootstrap> | <custom>- if <label> contains a :, the whole label has to be quoted.
- strictly define interpretation of <remark>s:
- <bootstrap> ::= anything that matches <number>['%'] is interpreted as support value.
where <number> is a floating point as accepted by strtod. - <custom> ::= anything else is handled as custom remark.
- may contain any character, but ':' or single quotes.
- <bootstrap> ::= anything that matches <number>['%'] is interpreted as support value.
exporter: save strict format
importer: expect + read strict format
See also https://phylipweb.github.io/phylip/newick_doc.html
Other requirements:
Provide separate, independent toggles to save
- bootstrap values and/or
- custom remarks
from GUI and CLI.
Change History (7)
comment:1 Changed 8 years ago by westram
- Description modified (diff)
comment:2 Changed 5 years ago by westram
- Description modified (diff)
- Keywords newick added
comment:3 Changed 4 years ago by westram
- Description modified (diff)
comment:4 Changed 4 weeks ago by westram
- Description modified (diff)
comment:5 Changed 5 days ago by westram
- Owner changed from devel to westram
- Status changed from new to _started
comment:6 Changed 5 days ago by westram
- Description modified (diff)
comment:7 Changed 3 days ago by westram
- Description modified (diff)
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