NCBI C Toolkit Cross Reference

C/errmsg/indx_err.msg

  1 MODULE indx_err
  2 $$ FORMAT, 1
  3 $^   NonAsciiChar, 1, SEV_ERROR
  4 # This is a comment REJECT(LANL,EMBL,DDBJ,PIR,SP)
  5 No column of any block of the flat file in any of the formats
  6 is allowed to have a nonASCII character.  NonASCII is defined
  7 as anything greater than  decimal value 126 (`~`) or less than
  8 decimal 32 (space) except decimal 10, which is a newline.
  9 $^   MissingEnd, 2, SEV_ERROR
 10 The // line was not found after sequence was found before a line
 11 with an letter was found.  Likely to be a truncated entry.
 12 $^   MissingField, 3, SEV_ERROR
 13  Required field was not found in the flat file
 14 $^   LocusLinePosition, 4, SEV_ERROR
 15 The GenBank flat file format requires fixed column positions
 16 for a variety of fields.
 17 $^   DirSubMode, 5, SEV_WARNING
 18 Not standard EMBL format, used in DirSubMode only
 19 $^   LineTypeOrder, 6, SEV_ERROR
 20 $^   Multiple_NI, 8, SEV_ERROR
 21 $^   ContigInSegset, 9, SEV_ERROR
 22 $$ ENTRY, 2
 23 $^   ParsingSetup, 2, SEV_INFO
 24 $^   Begin, 3, SEV_ERROR
 25 Looking for valid begining according to -f arguement in command line:
 26 LOCUS for GenBank; ID for EMBL; ENTRY for PIR;
 27 $^   InvalidLineType, 6, SEV_ERROR
 28 $^   Parsed, 7, SEV_INFO
 29 $^   ParsingComplete, 8, SEV_INFO
 30 $$ ACCESSION, 3
 31 $^   BadAccessNum, 2, SEV_ERROR
 32 Accession must be upper case letter followed by 5 digits.
 33 $^   NoAccessNum, 3, SEV_ERROR
 34 No accession number could be found for this entry. The line number
 35 given is only approximate.
 36 $^   MoreAccessLine, 4, SEV_INFO
 37 More than one accession block was found.  Continuation lines with
 38 the wrong format can cause this in GenBank format.
 39 $^   ForeignAccessNum, 5, SEV_WARNING
 40 $^   DirSubTakeOver, 6, SEV_WARNING
 41 $$ LOCUS, 4
 42 $^   WrongTopology, 2, SEV_WARNING
 43 This message occurs when looking for either Circular or 'RNA' or 'DNA' in
 44 embl mode.  Anything other than this will cause this warning.
 45 $^   NoGIBBModMolType, 3, SEV_WARNING
 46  In the flat files, the only legal values are blank, RNA, pre-mRNA, mRNA,
 47  rRNA, tRNA, uRNA, ss-RNA, ds-RNA, ms-RNA, scRNA, DNA, ds-DNA, and ss-DNA
 48 $^   MayBeNewSpeciesCode, 4, SEV_WARNING
 49 Swiss-Prot specific error.  The species is not in the list of
 50 LOCUS name prefix-species pairs.
 51 $^   NoSpeciesCode, 5, SEV_WARNING
 52 Swiss-Prot error when no species can be found.
 53 $^   NoMolType, 6, SEV_WARNING
 54 Can't find Molecule type
 55 $^   BadLocusName, 7, SEV_ERROR
 56 There are multiple possible ways to get this error message.
 57 In all formats, this identifier must have either digits or
 58 uppercase letters.
 59 For Swiss-Prot, the rules are more complicated:
 60 Locus name consists of up to 10 uppercase alphanumeric characters
 61       rule: X_Y format
 62          X is a mnemonic code, up to 4 alphanumeric characters to represent
 63              the protein name.
 64          Y is a mnemonic species identification code of at most 5
 65              alphanumeric characters to representing the biological source of
 66              the protein
 67 $^   NoLocusName, 8, SEV_ERROR
 68 No token after 'LOCUS' found in GenBank format.
 69 $$ SEGMENT, 5
 70 $^   MissSegEntry, 1, SEV_WARNING
 71 The Segmented set (GenBank) that is declared has some
 72 missing members.  That is, if there 6 members declared,
 73 The set might only have:
 74  1 of 6,
 75  2 of 6,
 76  4 of 6,
 77  5 of 6 and
 78  6 of 6, and thus be missing 3 of 6.
 79    Another possible problem is there could be a line:
 80       "3 of 5", instad of "3 of 6"
 81 $^   DiffMolType, 2, SEV_WARNING
 82 A segmented set is supposed to be from the same molecule,
 83 but with some unknown regions.  It should therefore all be
 84 of the same type of molecule.  For this error to occur, there
 85 have to be different molecule types for different segments
 86 within the set.
 87 $^   BadLocusName, 3, SEV_ERROR
 88 For GenBank in a segmented set, it is an error if the segment number
 89 can not be found at the end of the LOCUS name.  So a LOCUS name
 90 in SEGMENT 2 of 10 must end in 02, as ABCD02.
 91 $^   IncompSeg, 4, SEV_ERROR
 92 There were not three blank-separated token on the SEGMENT line, in
 93 GenBank Flat File format, the segment line has to look like:
 94 SEGMENT     4 of 14
 95  for example.
 96 $^   PubMatch, 5, SEV_WARNING
 97 There were matching reference with different serial numbers in
 98 segments.
 99 $$ REFERENCE, 8
100 $^   IllegalDate, 1, SEV_WARNING
101 $$ FEATURE, 9
102 $^   NoFeatData, 1, SEV_WARNING
103 $$ SEQID, 10
104 $^   NoSeqId, 1, SEV_ERROR
105 $$ ORGANISM, 11
106 $^   Multiple, 1, SEV_ERROR
[ source navigation ] [ diff markup ] [ identifier search ] [ freetext search ] [ file search ]
This page was automatically generated by the LXR engine.
Visit the LXR main site for more information.