Problem parsing tree with non-standard characters

Bug #1213333 reported by Jon Hill
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
Supertree Toolkit
Fix Released
High
Jon Hill

Bug Description

The tree below does not parse. The UTF “ “ do not parse in p4?

#NEXUS

[File saved Fri Aug 16 20:23:39 2013]

BEGIN TAXA;
 DIMENSIONS NTAX = 68;
 TAXLABELS
  Colletes_skinneri
  Melitta_eickworti
  Hesperapis_larreae
  'Andrena (Callandrena) sp.'
  Panurgus_calcaratus
  Calliopsis_fracta
  Calliopsis_pugionis
  Svastra_machaerantherae
  Svastra_obliqua
  Tetraloniella_sp.
  Melissodes_rustica
  Melissodes_desponsa
  Melissodes_sp.
  Dieunomia_heteropoda
  Dieunomia_nevadensis
  Chelostoma_fuliginosum
  Hoplitis_albifrons
  Hoplitis_biscutellae
  Hoplitis_pilosifrons
  Megachile_pugnata
  Coelioxys_alternata
  Paranthidium_jugatorium
  Anthidiellum_notatum
  Anthidium_oblongatum
  Anthidium_porterae
  Oreopasites_barbarae
  Holcopasites_calliopsidis
  Holcopasites_ruthae
  Nomada_maculata
  Nomada_imbricata
  Nomada_obliterta
  Leiopodus_singularis
  Xeromelecta_californica
  Zacosmia_maculata
  Paranomada_velutina
  Triopasites_penniger
  Epeolus_scutellaris
  'Triepeolus “rozeni”'
  Triepeolus_verbesinae
  Anthophora_furcata
  Anthophora_montana
  Anthophora_urbana
  Exomalopsis_completa
  Exomalopsis_rufiventris
  Ptilothrix_sp.
  Diadasia_bituberculata
  Diadasia_diminuta
  Diadasia_martialis
  Diadasia_nigrifrons
  Xylocopa_tabaniformis
  Xylocopa_virginica
  Centris_hoffmanseggiae
  Apis_dorsata
  Apis_mellifera
  Apis_nigrocincta
  Euglossa_imperialis
  Eulaema_meriana
  Eufriesea_caerulescens
  Exaerete_frontalis
  Bombus_avinoviellus
  Bombus_pensylvanicus
  Bombus_terrestris
  Melipona_sp.
  Scaptotrigona_depilis
  Lestrimelitta_limao
  Trigona_dorsalis
  Trigona_necrophaga
  Ceratina_calcarata
  ;
ENDBLOCK;

BEGIN TREES;
 TRANSLATE
  1 Colletes_skinneri,
  2 Melitta_eickworti,
  3 Hesperapis_larreae,
  4 'Andrena (Callandrena) sp.',
  5 Panurgus_calcaratus,
  6 Calliopsis_fracta,
  7 Calliopsis_pugionis,
  8 Svastra_machaerantherae,
  9 Svastra_obliqua,
  10 Tetraloniella_sp.,
  11 Melissodes_rustica,
  12 Melissodes_desponsa,
  13 Melissodes_sp.,
  14 Dieunomia_heteropoda,
  15 Dieunomia_nevadensis,
  16 Chelostoma_fuliginosum,
  17 Hoplitis_albifrons,
  18 Hoplitis_biscutellae,
  19 Hoplitis_pilosifrons,
  20 Megachile_pugnata,
  21 Coelioxys_alternata,
  22 Paranthidium_jugatorium,
  23 Anthidiellum_notatum,
  24 Anthidium_oblongatum,
  25 Anthidium_porterae,
  26 Oreopasites_barbarae,
  27 Holcopasites_calliopsidis,
  28 Holcopasites_ruthae,
  29 Nomada_maculata,
  30 Nomada_imbricata,
  31 Nomada_obliterta,
  32 Leiopodus_singularis,
  33 Xeromelecta_californica,
  34 Zacosmia_maculata,
  35 Paranomada_velutina,
  36 Triopasites_penniger,
  37 Epeolus_scutellaris,
  38 'Triepeolus “rozeni”',
  39 Triepeolus_verbesinae,
  40 Anthophora_furcata,
  41 Anthophora_montana,
  42 Anthophora_urbana,
  43 Exomalopsis_completa,
  44 Exomalopsis_rufiventris,
  45 Ptilothrix_sp.,
  46 Diadasia_bituberculata,
  47 Diadasia_diminuta,
  48 Diadasia_martialis,
  49 Diadasia_nigrifrons,
  50 Xylocopa_tabaniformis,
  51 Xylocopa_virginica,
  52 Centris_hoffmanseggiae,
  53 Apis_dorsata,
  54 Apis_mellifera,
  55 Apis_nigrocincta,
  56 Euglossa_imperialis,
  57 Eulaema_meriana,
  58 Eufriesea_caerulescens,
  59 Exaerete_frontalis,
  60 Bombus_avinoviellus,
  61 Bombus_pensylvanicus,
  62 Bombus_terrestris,
  63 Melipona_sp.,
  64 Scaptotrigona_depilis,
  65 Lestrimelitta_limao,
  66 Trigona_dorsalis,
  67 Trigona_necrophaga,
  68 Ceratina_calcarata
  ;
 UTREE * tree_1= (1,((((2,3),(4,(5,(6,7)))),((8,9),(10,(11,(12,13))))),((((14,15),((68,((16,(18,(17,19))),(20,21))),((22,23),(24,25)))),((26,((27,28),(29,(30,31)))),((32,(33,34)),((35,36),(37,(38,39)))))),((40,(41,42)),(((43,44),(45,(46,49,(47,48)))),((50,51),(52,(53,(54,55)),((56,(57,(58,59))),((60,(61,62)),(63,64,65,(66,67)))))))))));
ENDBLOCK;

Related branches

Jon Hill (jon-hill)
Changed in supertree-toolkit:
milestone: none → beta
assignee: nobody → Jon Hill (jon-hill)
importance: Undecided → High
status: New → Confirmed
Jon Hill (jon-hill)
description: updated
Jon Hill (jon-hill)
Changed in supertree-toolkit:
status: Confirmed → In Progress
Revision history for this message
Jon Hill (jon-hill) wrote :

Added a utf_replace with a dictionary of ', " and - with some latin characters too.

Changed in supertree-toolkit:
status: In Progress → Fix Committed
Jon Hill (jon-hill)
Changed in supertree-toolkit:
status: Fix Committed → Fix Released
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