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 tree 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 tree-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.
  • tree exporter: save strict format
  • tree 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.


Related to #767, #838, #845

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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