Difference between revisions of "NonConformantWorkspace"

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| <ul><li>single quotes should be used to wrap internal node labels in tree description (p. 621)</li><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
| <ul><li>single quotes should be used to wrap internal node labels in tree description (p. 621)</li><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
|-
 
|-
| [http://www.molevol.org/camel/projects/nexus/NEXUS/XXXXX.nex XXXXX]
+
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-inode-labels-quoted2.nex trees-tree-bush-inode-labels-quoted2]
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
|-
 
|-
| [http://www.molevol.org/camel/projects/nexus/NEXUS/XXXXX.nex XXXXX]
+
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-inode-labels.nex trees-tree-bush-inode-labels]
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
|-
 
|-
| [http://www.molevol.org/camel/projects/nexus/NEXUS/XXXXX.nex XXXXX]
+
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-quoted-string-name1.nex trees-tree-bush-quoted-string-name1]
 +
| <ul><li>single-quoting should be used to wrap tree name with embedded spaces (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-uneven.nex trees-tree-bush-uneven]
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-ladder-cladogram.nex trees-tree-ladder-cladogram]
 +
| <ul><li>O, U and X are not valid state symbols for datatype protein (p. 620)</li><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-ladder-uneven.nex trees-tree-ladder-uneven]
 +
| <ul><li>O, U and X are not valid state symbols for datatype protein (p. 620)</li><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-ladder.nex trees-tree-ladder]
 +
| <ul><li>O, U and X are not valid state symbols for datatype protein (p. 620)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-multiple-challenges.nex trees-tree-multiple-challenges]
 +
| <ul><li>should use single quotes for wrapping tree names and internal node names</li><li>O, U and X are not valid state symbols for datatype protein (p. 620)</li><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-multiple.nex trees-tree-multiple]
 +
| <ul><li>O, U and X are not valid state symbols for datatype protein (p. 620)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-rake-cladogram.nex trees-tree-rake-cladogram]
 +
| <ul><li>hyphen not allowed in tree name without single-quoting (p. 621)</li></ul>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/UnaSmithHIV-both.nex UnaSmithHIV-both]
 +
| <ul><li>taxon label 'A1.UG.-.UG029' used for two different taxa (p. 598)</li></ul>
 
|}
 
|}
 +
 +
[[Category:NEXUS]]

Latest revision as of 11:47, 5 September 2007

Non-conformant files

Several of the test files have illegal elements, which are documented in the following table. This list allows parsers to check their error-handling capabilities. This list is not exclusive because not all files have been checked. Page numbers are from the NEXUS standard, Maddison, Swofford and Maddison (1997).

filename caveats
barns-combined
  • double-quote is not a valid gap symbol (p. 599)
  • datatype must be first in format command (p. 599)
char-interleave
  • datatype must be first in format command (p. 599)
Omland-Ravens
  • taxon names not identical across interleave pages (p. 603)
quoted-strings1
  • single (not double) quotes should be used to define tokens with embedded spaces; double-quoted tokens used in taxlabel, charlabel, matrix and tree commands (p. 621)
SPAN_Family3i
  • the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
SPAN_Family4nl
  • the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
  • hyphen not allowed inside charstate labels without single-quoting (p. 621)
SPAN_Family6iw
  • hyphen not allowed inside charstate labels without single-quoting (p. 621)
SPAN_Family7n
  • the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
  • hyphen not allowed in tree name without single-quoting (p. 621)
SPAN_Family8a
  • the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
SPAN_Family9iw
  • hyphen not allowed inside charstate labels without single-quoting (p. 621)
SPAN_Family10i
  • hyphen not allowed inside charstate labels without single-quoting (p. 621)
trees-translate
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-basal-trifurcation
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-branchlength-negative
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-branchlength-scientific
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-branchlength-zero
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-cladogram
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-extended-root-branch
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-inode-labels-partial
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-inode-labels-quoted1
  • single quotes should be used to wrap internal node labels in tree description (p. 621)
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-inode-labels-quoted2
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-inode-labels
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-bush-quoted-string-name1
  • single-quoting should be used to wrap tree name with embedded spaces (p. 621)
trees-tree-bush-uneven
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-ladder-cladogram
  • O, U and X are not valid state symbols for datatype protein (p. 620)
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-ladder-uneven
  • O, U and X are not valid state symbols for datatype protein (p. 620)
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-ladder
  • O, U and X are not valid state symbols for datatype protein (p. 620)
trees-tree-multiple-challenges
  • should use single quotes for wrapping tree names and internal node names
  • O, U and X are not valid state symbols for datatype protein (p. 620)
  • hyphen not allowed in tree name without single-quoting (p. 621)
trees-tree-multiple
  • O, U and X are not valid state symbols for datatype protein (p. 620)
trees-tree-rake-cladogram
  • hyphen not allowed in tree name without single-quoting (p. 621)
UnaSmithHIV-both
  • taxon label 'A1.UG.-.UG029' used for two different taxa (p. 598)