Difference between revisions of "NonConformantWorkspace"

From Phyloinformatics
Jump to: navigation, search
(Non-conformant files)
(Non-conformant files)
Line 64: Line 64:
 
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-inode-labels-quoted1.nex trees-tree-bush-inode-labels-quoted1]
 
| [http://www.molevol.org/camel/projects/nexus/NEXUS/trees-tree-bush-inode-labels-quoted1.nex trees-tree-bush-inode-labels-quoted1]
 
| <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/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>
 +
|-
 +
| [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>
 +
|-
 +
| [http://www.molevol.org/camel/projects/nexus/NEXUS/XXXXX.nex XXXXX]
 +
| <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]
 +
| <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]
 +
| <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/XXXXX.nex XXXXX]

Revision as of 11:26, 15 December 2006

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)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)
XXXXX
  • hyphen not allowed in tree name without single-quoting (p. 621)