[med-svn] [SCM] emboss branch, master, updated. debian/6.4.0-2-15-g83042d0
Charles Plessy
plessy at debian.org
Fri Sep 14 05:31:14 UTC 2012
The following commit has been merged in the master branch:
commit 78ef855db0627065b42b4a8c22912e06ccc748e0
Author: Charles Plessy <plessy at debian.org>
Date: Fri Sep 14 14:28:22 2012 +0900
Removed upstream patch (for version 6.4.0).
diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
deleted file mode 100644
index 71f9945..0000000
--- a/debian/patches/official-upstream-patch.patch
+++ /dev/null
@@ -1,5926 +0,0 @@
-Description: Official upstream patch.
- Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c
- EMBOSS-6.4.0/emboss/dbxflat.c
- .
- 10-Aug-2011: The SwissProt description line format includes addtional
- tags which interfere with the EMBL parser used in
- previous releases. The fix replaces this with a SwissProt
- parser that strips out the extra tags. After patching the
- release, any existing SwissProt description index files
- should be reindexed. Other indexes are unchanged.
- .
- Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c
- .
- 10-Aug-2011: For databases with more than one valid format (examples
- include the EBI dbfetch server) this fix allows the
- format to be specified with a qualifier on the command
- line. In the original release only a format in the query
- string was used.
- .
- .
- Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c
- .
- 10-Aug-2011: When parsing GFF3 format input, long feature tags (for
- example extremely long translations) exceeded limits in
- regular expression parsing. Ths fix decouples testing for
- escaped quotes from the main task of finding quoted
- strings.
- .
- .
- Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat
- .
- 10-Aug-2001: The local data file used by application tcode had a missing
- parameter line.
- .
- .
- Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c
- .
- 10-Aug-2011: When sequence ranges (and possible highlighting for
- showalign) were in a list file the parser overwrote
- string values.
- .
- .
- Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c
- .
- 10-Aug-2011: Sample names in ABI format files were stored in
- incompletely defined strings. This fix corrects the
- string object. The sample name is also used as the
- sequence name.
- .
- .
- Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c
- .
- 10-Aug-2011: A future change to the format of Data Resource Catalogue
- entries in DRCAT.dat requires an update to the parsing of
- category lines. The current version is not affected.
- .
- .
- Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes
- EMBOSS-6.4.0/emboss/cacheensembl.c
- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
- EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
- EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
- .
- 10-Aug-2011: Microbial genomes use an enumerated species code which
- must be added to the query for data retrieval. This fix
- adds the species code to the comment field. In the next
- release a more complete solution will be implemented.
- .
- .
- Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h
- .
- 10-Aug-2011: Corrects the size of long integers on Windows systems only.
- .
- .
- Fix 9. EMBOSS-6.4.0/emboss/cirdna.c
- .
- 10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When
- printed outside the text scaling was too small. The text
- scale is now adjusted for the radius and sequence length
- so that labels should be readable outside the box.
- .
- .
- Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c
- .
- 10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file
- ignored the command line -mismatch qualifier for the
- first pattern. The default mismatch is now set to this
- value at the start of the pattern matching loop in the
- library.
- .
- .
- Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c
- .
- 11-Aug-2011: ajFmtScanF handled va_list incorrectly. Only noticeable by code
- developers.
- .
- .
- Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c
- .
- 18-Aug-2011: An internal string variable should be initialised as NULL.
- .
- .
- Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c
- .
- 18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment.
- This appears to be the only way to detect a protein GFF3 file.
- .
- Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein
- .
- 18-Aug-2011: In writing GFF3 protein file, uses the current term name
- from the Sequence Ontology to clear errors from the GFF3
- online validator.
- .
- Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c
- .
- 18-Aug-2011: When writing GFF3 format, tags names are explicitly
- converted to lower case as required by the GFF3
- standard. This includes EC_number and /PCR_conditions in
- EMBL/GenBank/DDBJ and several RefseqP tags. The score is
- written using g format to represent very low values.
- .
- Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c
- EMBOSS-6.4.0/ajax/core/ajseqread.c
- .
- 22-Aug-2011: When reading nexus data format with no taxlabels block
- the attempt to read the taxa (sequence names) from the
- matrix block failed.
- .
- Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c
- .
- 22-Aug-2011: The SRS access method added a stray '+' character to the
- getz command line.
- .
- Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c
- .
- 25-Aug-2011: In some cases a query using a simple identifier
- could try to test an undefined "sv" field.
- .
- .
- Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c
- .
- 02-Sep-2011: Reading "raw" sequence format failed when piped from
- standard input. In release 6.4.0 "raw" format was
- redefined as a binary format to catch binary files that
- start with one or more sequence characters followed by a
- NULL character. This fix continues to check binary files,
- but has to drop the check for data piped through standard
- input which is read as text and cannot be reread as
- binary.
- .
- Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c
- .
- 02-Sep-2011: Complex database definitions with more than one type or
- format are allowed in 6.4.0 but caused an error message
- from showdb when the type and format were tested.
- .
- Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c
- EMBOSS-6.4.0/emboss/drfindformat.c
- EMBOSS-6.4.0/emboss/drfindid.c
- EMBOSS-6.4.0/emboss/drfindresource.c
- .
- 02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype
- for data resource internals. Without -debug there was no problem.
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.gz
-Forwarded: not-needed
---- emboss-6.4.0.orig/ajax/ajaxdb/ajtextdb.c
-+++ emboss-6.4.0/ajax/ajaxdb/ajtextdb.c
-@@ -2580,9 +2580,7 @@
- {
- field = ajListIterGet(iter);
-
-- if(!nfields)
-- ajStrAppendK(&textin->Filename, '+');
-- else
-+ if(nfields)
- {
- switch(field->Link)
- {
-@@ -2684,9 +2682,7 @@
- {
- field = ajListIterGet(iter);
-
-- if(!nfields)
-- ajStrAppendK(&textin->Filename, '+');
-- else
-+ if(nfields)
- {
- switch(field->Link)
- {
---- emboss-6.4.0.orig/ajax/core/ajarch.h
-+++ emboss-6.4.0/ajax/core/ajarch.h
-@@ -137,7 +137,7 @@
-
- #ifdef WIN32
- typedef int ajint;
--typedef long ajlong; /* May need to make this long long. */
-+typedef long long ajlong;
- typedef unsigned int ajuint;
- typedef short ajshort;
- typedef unsigned short ajushort;
-@@ -159,4 +159,3 @@
- AJ_END_DECLS
-
- #endif
--
---- emboss-6.4.0.orig/ajax/core/ajfeatread.c
-+++ emboss-6.4.0/ajax/core/ajfeatread.c
-@@ -3035,7 +3035,8 @@
- AjPStr TvString = NULL;
- AjPStr tmptag = NULL;
- AjBool grpset = ajFalse;
--
-+ AjBool escapedquote = ajFalse;
-+
- /*ajDebug("featGff3oldProcessTagval '%S'\n",
- groupfield); */
-
-@@ -3050,12 +3051,19 @@
- */
-
- ajStrAssignS(&TvString, groupfield);
-+ if(ajStrFindC(TvString, "\\\"") >= 0)
-+ {
-+ escapedquote = ajTrue;
-+ ajStrExchangeCC(&TvString, "\\\"", "\001");
-+ }
-+
- while(ajStrGetLen(TvString))
- {
- if(ajRegExec(Gff3oldRegexTvTagval, TvString))
- {
- ajRegSubI(Gff3oldRegexTvTagval, 1, &tmptag);
- ajRegSubI(Gff3oldRegexTvTagval, 2, &featinValTmp);
-+
- ajStrTrimWhite(&featinValTmp);
- /*ajDebug("Gff3Tv '%S' '%S'\n", tmptag, featinValTmp);*/
- ajRegPost(Gff3oldRegexTvTagval, &TvString);
-@@ -3076,6 +3084,8 @@
- featFlagSet(gf, featinValTmp);
- else
- {
-+ if(escapedquote)
-+ ajStrExchangeCC(&featinValTmp, "\001", "\"");
- /*ajDebug("GFF3 before QuoteStrip: '%S'\n", featinValTmp);*/
- ajStrQuoteStrip(&featinValTmp);
- /*ajDebug(" GFF3 after QuoteStrip: '%S'\n", featinValTmp);*/
-@@ -5896,8 +5906,8 @@
- Gff3Regexdirective = ajRegCompC("^##(.*)");
- Gff3Regexcomment = ajRegCompC("^#(.*)");
- Gff3RegexTvTagval = ajRegCompC(" *([^ =]+)[ =]([^;]+)*(;|$)"); /* "tag name */
-- Gff3oldRegexTvTagval = ajRegCompC(" *([^ =]+)[ =]((\"(\\.|[^\\\"])*\"|"
-- "[^;]+)*)(;|$)"); /* "tag name */
-+ Gff3oldRegexTvTagval = ajRegCompC(" *([^ =]+)[ =](\"[^\"]*\"|"
-+ "[^;]+)(;|$)"); /* "tag name */
-
- FeatInitGff3 = ajTrue;
-
---- emboss-6.4.0.orig/ajax/core/ajfeatwrite.c
-+++ emboss-6.4.0/ajax/core/ajfeatwrite.c
-@@ -4134,7 +4134,7 @@
- tmpid = owner->Seqid;
-
- if(thys->Score)
-- ajFmtPrintF(file, "%S\t%S\t%S\t%d\t%d\t%.3f\t%c\t%c\t",
-+ ajFmtPrintF(file, "%S\t%S\t%S\t%d\t%d\t%.3g\t%c\t%c\t",
- tmpid,
- thys->Source,
- outtyp,
-@@ -4215,6 +4215,7 @@
- while(!ajListIterDone(iter))
- {
- tv = ajListIterGet(iter);
-+ ajStrFmtLower(&tv->Tag);
- outtag = tv->Tag;
-
- if(!outtag)
---- emboss-6.4.0.orig/ajax/core/ajfmt.c
-+++ emboss-6.4.0/ajax/core/ajfmt.c
-@@ -50,6 +50,16 @@
- #include "ajax.h"
-
-
-+#define EVF_PERCENT 1
-+#define EVF_NOCON 2
-+#define EVF_LONG 4
-+#define EVF_AJLONG 8
-+#define EVF_UNSIGNED 16
-+#define EVF_NEGATE 32
-+
-+#define EVF_BUF 128
-+
-+
- typedef void (*Fmt_T) (ajint code, VALIST ap,
- int put(int c, void *cl), void *cl,
- const ajuint* flags, ajint width, ajint precision);
-@@ -148,6 +158,8 @@
- static void cvt_u(ajint code, VALIST ap, int put(int c, void* cl), void* cl,
- const ajuint* flags, ajint width, ajint precision);
-
-+static ajint evfscanf(FILE *stream, const char *fmt, va_list ap);
-+
-
-
-
-@@ -2290,7 +2302,7 @@
- __va_copy(save_ap,ap);
- #endif
-
-- n = fscanf(file,fmt,ap);
-+ n = evfscanf(file,fmt,ap);
-
- #if defined(__amd64__) || defined(__EM64T__) || \
- defined(__PPC__) && defined(_CALL_SYSV)
-@@ -2304,6 +2316,519 @@
- }
-
-
-+
-+
-+/* @funcstatic evfscanf *******************************************************
-+**
-+** EMBOSS version of C99 vfscanf() including %S conversion
-+**
-+** @param [r] stream [FILE*] file pointer.
-+** @param [r] fmt [const char*] Format string.
-+** @param [v] ap [va_list] Variable length argument list
-+** @return [ajint] number of successful conversions
-+**
-+** @release 6.4.0
-+** @@
-+******************************************************************************/
-+
-+static ajint evfscanf(FILE *stream, const char *fmt, va_list ap)
-+{
-+ char fch = '\0';
-+ int ipc = 0;
-+ int tpc = 0;
-+
-+ ajuint uflags = 0;
-+ ajint nconv = 0;
-+ ajint width = 0;
-+ AjBool fin = ajFalse;
-+ AjBool idone = ajFalse;
-+
-+ ajulong sum = 0L;
-+
-+ ajuint nread = 0;
-+ ajint ret = EOF;
-+ ajint base = 10;
-+
-+ char *p = NULL;
-+ char fchars[] = "0123456789Ee.";
-+
-+ char buf[EVF_BUF];
-+
-+ AjPStr *str = NULL;
-+
-+ union
-+ {
-+ ajlong L;
-+ long l;
-+ unsigned long ul;
-+ ajulong uL;
-+ ajint i;
-+ ajuint u;
-+ char *c;
-+ double d;
-+ } val;
-+
-+
-+ if(feof(stream))
-+ return EOF;
-+
-+ val.ul = 0L;
-+
-+ while((fch = *fmt))
-+ {
-+ ++fmt;
-+
-+
-+ if(uflags & EVF_PERCENT)
-+ {
-+ /* If %% has been given then do a simple match */
-+ if(fch == '%')
-+ {
-+ uflags &= ~EVF_PERCENT;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++sum;
-+
-+ if(ipc != (int) fch)
-+ break;
-+
-+ continue;
-+ }
-+
-+ /* Now in the realm of format specifiers */
-+ /* First test for any width */
-+
-+ if(fch >= '0' && fch <= '0')
-+ {
-+ fch -= '0';
-+
-+ if(width == INT_MAX)
-+ width = 0;
-+ else
-+ width *= 10;
-+
-+ width += (ajint) fch;
-+
-+ continue;
-+ }
-+
-+ if((char) fch != 'S')
-+ fch = tolower(fch);
-+
-+ switch(fch)
-+ {
-+ case '*':
-+ uflags |= EVF_NOCON;
-+ continue;
-+
-+ case 'n':
-+ if(!(uflags & EVF_NOCON))
-+ *(va_arg(ap, ajint *)) = (ajint) sum;
-+
-+ break;
-+
-+ case 'c':
-+ if(!(uflags & EVF_NOCON))
-+ val.c = va_arg(ap, char *);
-+
-+ if(width == INT_MAX)
-+ width = 1;
-+
-+ while(width-- > 0)
-+ {
-+ if((ipc = getc(stream)) == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ ++nread;
-+
-+ if(!(uflags & EVF_NOCON))
-+ *val.c++ = (char) ipc;
-+ }
-+
-+ break;
-+
-+ case 'h': /* ANSI C converts shorts to ints */
-+ continue;
-+
-+ case 'l':
-+ uflags |= EVF_LONG;
-+ continue;
-+
-+ case 'L':
-+ uflags |= EVF_AJLONG;
-+ continue;
-+
-+ case 's':
-+ if(!(uflags & EVF_NOCON))
-+ val.c = va_arg(ap, char *);
-+
-+ do
-+ {
-+ ipc = getc(stream);
-+ ++sum;
-+ } while(isspace(ipc));
-+
-+ if(ipc == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ while(width-- > 0)
-+ {
-+ if(isspace(ipc))
-+ {
-+ ungetc(ipc, stream);
-+ --sum;
-+ break;
-+ }
-+
-+ if(!(uflags & EVF_NOCON))
-+ *val.c++ = (char) ipc;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++nread;
-+ }
-+
-+ if(!(uflags & EVF_NOCON))
-+ *val.c = '\0';
-+
-+ break;
-+
-+ case 'S':
-+ if(!(uflags & EVF_NOCON))
-+ {
-+ str = (AjPStr *) va_arg(ap, AjPStr *);
-+ ajStrAssignC(str,"");
-+ }
-+
-+ do
-+ {
-+ ipc = getc(stream);
-+ ++sum;
-+ } while(isspace(ipc));
-+
-+ if(ipc == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ while(width-- > 0)
-+ {
-+ if(isspace(ipc))
-+ {
-+ ungetc(ipc, stream);
-+ --sum;
-+ break;
-+ }
-+
-+ if(!(uflags & EVF_NOCON))
-+ ajStrAppendK(str, (char) ipc);
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++nread;
-+ }
-+
-+ break;
-+
-+ case 'o':
-+ base = 8;
-+ /* Fallthrough */
-+ case 'x':
-+ if(base == 10) /* To protect fallthrough from octal */
-+ base = 16;
-+ /* Fallthrough */
-+ case 'u':
-+ uflags |= EVF_UNSIGNED;
-+ /* Fallthrough */
-+ case 'd':
-+ case 'i':
-+ do
-+ {
-+ ipc = getc(stream);
-+ ++sum;
-+ } while(isspace(ipc));
-+
-+ if(ipc == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ if((char) ipc == '+' || (char) ipc == '-')
-+ {
-+ if(--width <= 0)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ if((char) ipc == '-')
-+ uflags |= EVF_NEGATE;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ ++sum;
-+ }
-+
-+ idone = ajFalse;
-+ val.uL = 0;
-+
-+ if((char) ipc == '0')
-+ {
-+ if(--width <= 0)
-+ idone = ajTrue;
-+
-+ if(!idone)
-+ if((ipc = getc(stream)) == EOF)
-+ idone = ajTrue;
-+
-+ if((char) tolower(ipc) == 'x' && !idone)
-+ {
-+ if(fch == 'o' || fch == 'd' || fch == 'u')
-+ {
-+ /* Invalid 0x */
-+ ungetc(ipc, stream);
-+ idone = ajTrue;
-+ }
-+
-+ if(!idone)
-+ base = 16;
-+
-+ if(!idone)
-+ {
-+ if((ipc = getc(stream)) == EOF)
-+ idone = ajTrue;
-+ else
-+ ++sum;
-+ }
-+ }
-+ else if(fch == 'i' && !idone)
-+ base = 8;
-+ }
-+
-+ ++nread;
-+
-+ for(;!idone;)
-+ {
-+ tpc = tolower(ipc);
-+
-+ tpc -= '0';
-+
-+ if(tpc > 9)
-+ {
-+ tpc += '0';
-+ tpc -= 'a';
-+
-+ if(tpc >= 0)
-+ tpc += 10;
-+ }
-+
-+ if(tpc < 0 || tpc >= base)
-+ {
-+ ungetc(ipc, stream);
-+ --nread;
-+ break;
-+ }
-+
-+ val.uL *= base;
-+ val.uL += tpc;
-+
-+ if(--width <= 0)
-+ break;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++nread;
-+ }
-+
-+ if((uflags & EVF_NEGATE) && !idone)
-+ val.L = -val.L;
-+
-+ if(!(uflags & EVF_NOCON))
-+ {
-+ if((uflags & (EVF_UNSIGNED | EVF_AJLONG)) ==
-+ (EVF_UNSIGNED | EVF_AJLONG))
-+ *(va_arg(ap, ajulong *)) = val.uL;
-+ else if(uflags & (EVF_AJLONG))
-+ *(va_arg(ap, ajlong *)) = val.L;
-+ else if((uflags & (EVF_UNSIGNED | EVF_LONG)) ==
-+ (EVF_UNSIGNED | EVF_LONG))
-+ *(va_arg(ap, unsigned long *)) = val.ul;
-+ else if(uflags & (EVF_LONG))
-+ *(va_arg(ap, long *)) = val.l;
-+ else if(uflags & (EVF_UNSIGNED))
-+ *(va_arg(ap, ajuint *)) = val.u;
-+ else
-+ *(va_arg(ap, ajint *)) = val.i;
-+ }
-+
-+ break;
-+
-+ case 'e':
-+ case 'f':
-+ case 'g':
-+ do
-+ {
-+ ipc = getc(stream);
-+ ++sum;
-+ } while(isspace(ipc));
-+
-+ if(ipc == EOF)
-+ {
-+ --sum;
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ if((char) ipc == '+' || (char) ipc == '-')
-+ {
-+ if((char) ipc == '-')
-+ uflags |= EVF_NEGATE;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ {
-+ fin = ajTrue;
-+ break;
-+ }
-+
-+ ++sum;
-+ }
-+
-+ val.d = 0.0;
-+
-+ ++nread;
-+
-+ for(p = buf; p < buf + EVF_BUF - 1 && width >0; --width)
-+ {
-+ if(!strchr(fchars, ipc))
-+ {
-+ ungetc(ipc, stream);
-+ --nread;
-+ break;
-+ }
-+
-+ if((char) ipc == 'e' || (char) ipc == 'E')
-+ {
-+ fchars[10] = '\0';
-+ *p++ = (char) ipc;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++nread;
-+
-+ if((char) ipc != '+' && (char) ipc != '-')
-+ continue;
-+ }
-+ else if((char) ipc == '.')
-+ fchars[12] = '\0';
-+
-+ *p++ = (char) ipc;
-+
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++nread;
-+ }
-+
-+ *p++ = '\0';
-+
-+ val.d = strtod(buf, 0);
-+
-+ if(uflags & EVF_NEGATE)
-+ val.d = -val.d;
-+
-+ fchars[10] = 'E';
-+ fchars[12] = '.';
-+
-+ *(va_arg(ap, double *)) = val.d;
-+
-+ break;
-+ }
-+
-+ if(fin)
-+ break;
-+
-+ if(nread)
-+ {
-+ if(!(uflags & EVF_NOCON))
-+ ++nconv;
-+
-+ ret = 0;
-+ sum += nread;
-+ }
-+ else if(fch != 'n' || ipc == EOF)
-+ break;
-+
-+ uflags = 0;
-+ }
-+ else if(fch == '%')
-+ {
-+ uflags = EVF_PERCENT;
-+ base = 10;
-+ nread = 0;
-+ width = INT_MAX;
-+ }
-+ else if(isspace(fch))
-+ {
-+ do
-+ {
-+ ipc = getc(stream);
-+ ++sum;
-+ } while(isspace(ipc));
-+
-+ --sum;
-+
-+ if(ipc == EOF)
-+ break;
-+
-+ ungetc(ipc, stream);
-+ }
-+ else
-+ {
-+ if((ipc = getc(stream)) == EOF)
-+ break;
-+
-+ ++sum;
-+
-+ if(ipc != (int) fch)
-+ break;
-+ }
-+
-+ }
-+
-+ if((uflags & EVF_PERCENT) && nread)
-+ {
-+ if(!(uflags & EVF_NOCON))
-+ ++nconv;
-+
-+ ret = 0;
-+ }
-+
-+ if(ipc == EOF && nconv == 0)
-+ return ret;
-+
-+
-+ return nconv;
-+}
-+
-+
-
-
- /* @funcstatic fmtVscan *******************************************************
---- emboss-6.4.0.orig/ajax/core/ajnam.c
-+++ emboss-6.4.0/ajax/core/ajnam.c
-@@ -8172,6 +8172,10 @@
- AjBool hasmethod = ajFalse;
- AjBool hastype = ajFalse;
- AjPStr name = NULL;
-+ AjPStr token = NULL;
-+ AjPStr typetoken = NULL;
-+ AjPStrTok handle = NULL;
-+ AjPStrTok typehandle = NULL;
- const AjPStr value = NULL;
- const AjPStr dbtype = NULL;
-
-@@ -8202,9 +8206,22 @@
- {
- hasformat=ajTrue;
-
-- if(!namInformatTest(value, dbtype)) /* test: dbunknowns.rc */
-- namError("Database '%S' %S: '%S' unknown",
-- entry->name, name, value);
-+ ok = ajFalse;
-+ ajStrTokenAssignC(&typehandle, dbtype, " ,;");
-+ ajStrTokenAssignC(&handle, value, " ,;");
-+
-+ while(ajStrTokenNextParse(&typehandle, &typetoken))
-+ {
-+ while(ajStrTokenNextParse(&handle, &token))
-+ {
-+ if(namInformatTest(token, typetoken))
-+ ok = ajTrue;
-+ }
-+ }
-+
-+ if(!ok) /* test: dbunknowns.rc */
-+ namError("Database '%S' %S: '%S' unknown",
-+ entry->name, name, value);
- }
-
- if(ajStrPrefixC(name, "method"))
-@@ -8221,9 +8238,13 @@
- hastype=ajTrue;
- oktype = ajFalse;
-
-- for(k=0; namDbTypes[k].Name; k++)
-- if(ajStrMatchCaseC(value, namDbTypes[k].Name))
-- oktype = ajTrue;
-+ ajStrTokenAssignC(&typehandle, value, " ,;");
-+ while(ajStrTokenNextParse(&typehandle, &typetoken))
-+ {
-+ for(k=0; namDbTypes[k].Name; k++)
-+ if(ajStrMatchCaseC(typetoken, namDbTypes[k].Name))
-+ oktype = ajTrue;
-+ }
-
- if(!oktype) /* test: dbunknowns.rc */
- namError("Database '%S' %S: '%S' unknown",
-@@ -8260,6 +8281,10 @@
- }
-
- ajStrDel(&name);
-+ ajStrTokenDel(&handle);
-+ ajStrTokenDel(&typehandle);
-+ ajStrDel(&token);
-+ ajStrDel(&typetoken);
-
- return ok;
- }
---- emboss-6.4.0.orig/ajax/core/ajnexus.c
-+++ emboss-6.4.0/ajax/core/ajnexus.c
-@@ -2,23 +2,25 @@
- ** @source AJAX nexus file parsing functions
- **
- ** @author Copyright (C) 2003 Peter Rice
--** @version 1.0
-+** @version $Revision: 1.20 $
-+** @modified $Date: 2011/08/09 12:03:22 $ by $Author: rice $
- ** @@
- **
- ** This library is free software; you can redistribute it and/or
--** modify it under the terms of the GNU Library General Public
-+** modify it under the terms of the GNU Lesser General Public
- ** License as published by the Free Software Foundation; either
--** version 2 of the License, or (at your option) any later version.
-+** version 2.1 of the License, or (at your option) any later version.
- **
- ** This library is distributed in the hope that it will be useful,
- ** but WITHOUT ANY WARRANTY; without even the implied warranty of
- ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
--** Library General Public License for more details.
-+** Lesser General Public License for more details.
-+**
-+** You should have received a copy of the GNU Lesser General Public
-+** License along with this library; if not, write to the Free Software
-+** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-+** MA 02110-1301, USA.
- **
--** You should have received a copy of the GNU Library General Public
--** License along with this library; if not, write to the
--** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
--** Boston, MA 02111-1307, USA.
- ******************************************************************************/
-
- #include "ajax.h"
-@@ -152,6 +154,8 @@
- **
- ** @param [u] buff [AjPFilebuff] Input buffered file
- ** @return [AjPNexus] Nexus data object
-+**
-+** @release 2.8.0
- ** @@
- ******************************************************************************/
-
-@@ -197,6 +201,7 @@
- if(!ajStrPrefixCaseC(rdline, "#NEXUS"))
- { /* first line test */
- ajFilebuffReset(buff);
-+ ajStrDel(&rdline);
-
- return NULL;
- }
-@@ -205,7 +210,10 @@
-
- ok = ajBuffreadLine(buff, &rdline);
- if(!ok)
-+ {
-+ ajStrDel(&rdline);
- return NULL;
-+ }
-
- block = ajFalse;
- commentlevel = 0;
-@@ -254,7 +262,11 @@
- else if (block && ajRegExec(endexp, rdline)) /* end line */
- {
- if (!nexusBlockSave(ret, blocklist, blockname))
-+ {
-+ ajStrDel(&rdline);
-+ ajStrDel(&blockname);
- return NULL;
-+ }
-
- ajStrAssignClear(&blockname);
- block = ajFalse;
-@@ -266,9 +278,8 @@
- if (ajStrGetLen(rdline))
- {
- ajListstrPushAppend(blocklist, rdline);
-+ rdline = NULL;
- }
--
-- rdline = NULL;
- }
-
- ok = ajBuffreadLine(buff, &rdline);
-@@ -277,11 +288,16 @@
- if (block)
- {
- ajDebug("ajNexusParse unclosed block '%S'\n", blockname);
--
-+ ajStrDel(&rdline);
-+ ajStrDel(&blockname);
- return NULL;
- }
-
- ajNexusTrace(ret);
-+ ajStrDel(&rdline);
-+ ajStrDel(&blockname);
-+
-+ ajListFree(&blocklist);
-
- return ret;
- }
-@@ -295,6 +311,8 @@
- **
- ** @return [AjPNexus] New AjPNexus object
- ** @category new [AjPNexus] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- AjPNexus ajNexusNew(void)
-@@ -309,12 +327,14 @@
-
-
-
--/* @funcstatic nexusTaxaNew ***********************************************
-+/* @funcstatic nexusTaxaNew ***************************************************
- **
- ** Constructor for AjPNexusTaxa
- **
- ** @return [AjPNexusTaxa] New AjPNexusTaxa object
- ** @category new [AjPNexusTaxa] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusTaxa nexusTaxaNew(void)
-@@ -335,6 +355,8 @@
- **
- ** @return [AjPNexusCharacters] New AjPNexusCharacters object
- ** @category new [AjPNexusCharacters] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusCharacters nexusCharactersNew(void)
-@@ -363,6 +385,8 @@
- **
- ** @return [AjPNexusUnaligned] New AjPNexusUnaligned object
- ** @category new [AjPNexusUnaligned] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusUnaligned nexusUnalignedNew(void)
-@@ -389,6 +413,8 @@
- **
- ** @return [AjPNexusDistances] New AjPNexusDistances object
- ** @category new [AjPNexusDistances] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusDistances nexusDistancesNew(void)
-@@ -409,12 +435,14 @@
-
-
-
--/* @funcstatic nexusSetsNew ***********************************************
-+/* @funcstatic nexusSetsNew ***************************************************
- **
- ** Constructor for AjPNexusSets
- **
- ** @return [AjPNexusSets] New AjPNexusSets object
- ** @category new [AjPNexusSets] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusSets nexusSetsNew(void)
-@@ -435,6 +463,8 @@
- **
- ** @return [AjPNexusAssumptions] New AjPNexusAssumptions object
- ** @category new [AjPNexusAssumptions] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusAssumptions nexusAssumptionsNew(void)
-@@ -452,12 +482,14 @@
-
-
-
--/* @funcstatic nexusCodonsNew ***********************************************
-+/* @funcstatic nexusCodonsNew *************************************************
- **
- ** Constructor for AjPNexusCodons
- **
- ** @return [AjPNexusCodons] New AjPNexusCodons object
- ** @category new [AjPNexusCodons] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusCodons nexusCodonsNew(void)
-@@ -472,12 +504,14 @@
-
-
-
--/* @funcstatic nexusTreesNew ***********************************************
-+/* @funcstatic nexusTreesNew **************************************************
- **
- ** Constructor for AjPNexusTrees
- **
- ** @return [AjPNexusTrees] New AjPNexusTrees object
- ** @category new [AjPNexusTrees] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusTrees nexusTreesNew(void)
-@@ -492,12 +526,14 @@
-
-
-
--/* @funcstatic nexusNotesNew ***********************************************
-+/* @funcstatic nexusNotesNew **************************************************
- **
- ** Constructor for AjPNexusNotes
- **
- ** @return [AjPNexusNotes] New AjPNexusNotes object
- ** @category new [AjPNexusNotes] Default constructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjPNexusNotes nexusNotesNew(void)
-@@ -519,6 +555,8 @@
- ** @param [d] pthys [AjPNexus*] AjPNexus object
- ** @return [void]
- ** @category delete [AjPNexus] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- void ajNexusDel(AjPNexus* pthys)
-@@ -553,6 +591,8 @@
- ** @param [d] pthys [AjPNexusTaxa*] AjPNexusTaxa object
- ** @return [void]
- ** @category delete [AjPNexusTaxa] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusTaxaDel(AjPNexusTaxa* pthys)
-@@ -579,6 +619,8 @@
- ** @param [d] pthys [AjPNexusCharacters*] AjPNexusCharacters object
- ** @return [void]
- ** @category delete [AjPNexusCharacters] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusCharactersDel(AjPNexusCharacters* pthys)
-@@ -618,6 +660,8 @@
- ** @param [d] pthys [AjPNexusUnaligned*] AjPNexusUnaligned object
- ** @return [void]
- ** @category delete [AjPNexusUnaligned] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusUnalignedDel(AjPNexusUnaligned* pthys)
-@@ -650,6 +694,8 @@
- ** @param [d] pthys [AjPNexusDistances*] AjPNexusDistances object
- ** @return [void]
- ** @category delete [AjPNexusDistances] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusDistancesDel(AjPNexusDistances* pthys)
-@@ -680,6 +726,8 @@
- ** @param [d] pthys [AjPNexusSets*] AjPNexusSets object
- ** @return [void]
- ** @category delete [AjPNexusSets] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusSetsDel(AjPNexusSets* pthys)
-@@ -715,6 +763,8 @@
- ** @param [d] pthys [AjPNexusAssumptions*] AjPNexuAssumptionss object
- ** @return [void]
- ** @category delete [AjPNexusAssumptions] Default destructor
-+**
-+** @release 2.9.0
- ******************************************************************************/
-
- static void nexusAssumptionsDel(AjPNexusAssumptions* pthys)
-@@ -750,6 +800,8 @@
- ** @param [d] pthys [AjPNexusCodons*] AjPNexusCodons object
- ** @return [void]
- ** @category delete [AjPNexusCodons] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusCodonsDel(AjPNexusCodons* pthys)
-@@ -780,6 +832,8 @@
- ** @param [d] pthys [AjPNexusTrees*] AjPNexusTrees object
- ** @return [void]
- ** @category delete [AjPNexusTrees] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusTreesDel(AjPNexusTrees* pthys)
-@@ -802,13 +856,15 @@
-
-
-
--/* @funcstatic nexusNotesDel ************************************************
-+/* @funcstatic nexusNotesDel **************************************************
- **
- ** Destructor for AjPNexusNotes
- **
- ** @param [d] pthys [AjPNexusNotes*] AjPNexusNotes object
- ** @return [void]
- ** @category delete [AjPNexusNotes] Default destructor
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static void nexusNotesDel(AjPNexusNotes* pthys)
-@@ -841,6 +897,8 @@
- ** @param [w] list [AjPList] List of block records
- ** @param [r] blockname [const AjPStr] Block name
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusBlockSave(AjPNexus thys, AjPList list,
-@@ -905,7 +963,7 @@
-
-
-
--/* @funcstatic nexusCommand ********************************************
-+/* @funcstatic nexusCommand ***************************************************
- **
- ** Finds the next command and command string in a block
- **
-@@ -913,6 +971,8 @@
- ** @param [w] command [AjPStr*] Command name
- ** @param [w] cmdstr [AjPStr*] Command string
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusCommand(AjPList list, AjPStr* command, AjPStr* cmdstr)
-@@ -944,6 +1004,8 @@
- {
- ajRegPre(endcommand, &tmpstr);
- ajStrAssignS(cmdstr, tmpstr);
-+ ajStrDel(&tmpstr);
-+ ajStrDel(&rdline);
-
- return ajTrue;
- }
-@@ -957,6 +1019,8 @@
- {
- ajRegPre(endcommand, &tmpstr);
- ajStrAppendS(cmdstr, tmpstr);
-+ ajStrDel(&tmpstr);
-+ ajStrDel(&rdline);
-
- return ajTrue;
- }
-@@ -970,19 +1034,23 @@
- }
- }
-
-+ ajStrDel(&rdline);
-+
- return ajFalse;
- }
-
-
-
-
--/* @funcstatic nexusParseTaxa ********************************************
-+/* @funcstatic nexusParseTaxa *************************************************
- **
- ** Parses Nexus commands for a Taxa block
- **
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseTaxa(AjPNexus thys, AjPList list)
-@@ -1024,6 +1092,8 @@
- if (!thys->Taxa->Ntax)
- {
- ajDebug("nexusParseTaxa failed: dimension Ntax not found\n");
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-
- return ajFalse;
- }
-@@ -1034,12 +1104,17 @@
- {
- ajDebug("nexusParseTaxa failed: Ntax %d read %d TaxLabels\n",
- thys->Taxa->Ntax, i);
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-
- return ajFalse;
- }
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- if (!thys->Taxa->Ntax)
- {
- ajDebug("nexusParseTaxa failed: taxa data not found\n");
-@@ -1061,6 +1136,8 @@
- ** @param [u] list [AjPList] List of block records
- ** @param [r] newtaxa [AjBool] If true, set NewTaxa
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseCharacters(AjPNexus thys, AjPList list, AjBool newtaxa)
-@@ -1145,6 +1222,8 @@
- if(!nexusGetInt(cmdstr, dimexp3, 1, &thys->Characters->Nchar))
- {
- ajDebug("nexusParseCharacters failed: nchar undefined\n");
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
- return ajFalse;
- }
- }
-@@ -1197,6 +1276,8 @@
- ajDebug("nexusParseCharacters "
- "failed: Ntax %d read %d TaxLabels\n",
- thys->Taxa->Ntax, i);
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-
- return ajFalse;
- }
-@@ -1238,6 +1319,9 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- if (!thys->Characters->Nchar)
- {
- ajDebug("nexusParseCharacters failed: dimension nchar undefined\n");
-@@ -1258,6 +1342,8 @@
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseUnaligned(AjPNexus thys, AjPList list)
-@@ -1336,6 +1422,9 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-@@ -1349,6 +1438,8 @@
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseDistances(AjPNexus thys, AjPList list)
-@@ -1447,19 +1538,24 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-
-
-
--/* @funcstatic nexusParseSets ********************************************
-+/* @funcstatic nexusParseSets *************************************************
- **
- ** Parses Nexus commands for a Sets block
- **
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseSets(AjPNexus thys, AjPList list)
-@@ -1505,6 +1601,9 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-@@ -1518,6 +1617,8 @@
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseAssumptions(AjPNexus thys, AjPList list)
-@@ -1594,19 +1695,24 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-
-
-
--/* @funcstatic nexusParseCodons ********************************************
-+/* @funcstatic nexusParseCodons ***********************************************
- **
- ** Parses Nexus commands for a Codons block
- **
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseCodons(AjPNexus thys, AjPList list)
-@@ -1640,19 +1746,24 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-
-
-
--/* @funcstatic nexusParseTrees ********************************************
-+/* @funcstatic nexusParseTrees ************************************************
- **
- ** Parses Nexus commands for a Trees block
- **
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseTrees(AjPNexus thys, AjPList list)
-@@ -1681,19 +1792,24 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-
-
-
--/* @funcstatic nexusParseNotes ********************************************
-+/* @funcstatic nexusParseNotes ************************************************
- **
- ** Parses Nexus commands for a Notes block
- **
- ** @param [w] thys [AjPNexus] Nexus object
- ** @param [u] list [AjPList] List of block records
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusParseNotes(AjPNexus thys, AjPList list)
-@@ -1722,6 +1838,9 @@
- }
- }
-
-+ ajStrDel(&command);
-+ ajStrDel(&cmdstr);
-+
- return ajTrue;
- }
-
-@@ -1737,6 +1856,8 @@
- ** @param [u] exp [AjPRegexp] Compiled regular expression for parsing
- ** @param [w] dest [AjPStr**] Array generated
- ** @return [ajint] Number of strings returned
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static ajint nexusGetArray(AjPStr src, AjPRegexp exp,
-@@ -1779,6 +1900,8 @@
- ** @param [r] isub [ajint] Substring number to extract
- ** @param [w] dest [AjPStr*] String generated
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusGetStr(AjPStr src, AjPRegexp exp, ajint isub, AjPStr* dest)
-@@ -1805,6 +1928,8 @@
- ** @param [r] isub [ajint] Substring number to extract
- ** @param [w] dest [char*] String generated
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusGetChar(AjPStr src, AjPRegexp exp, ajint isub, char* dest)
-@@ -1841,6 +1966,8 @@
- ** @param [r] isub [ajint] Substring number to extract
- ** @param [w] dest [ajuint*] Integer generated
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusGetInt(AjPStr src, AjPRegexp exp, ajint isub, ajuint* dest)
-@@ -1860,7 +1987,7 @@
-
-
-
--/* @funcstatic nexusGetBool **************************************************
-+/* @funcstatic nexusGetBool ***************************************************
- **
- ** Sets a nexus bool from a parsed nexus command in the form [no]name.
- ** We know name is found, we test for the "no" part.
-@@ -1870,6 +1997,8 @@
- ** @param [r] isub [ajint] Substring number to extract
- ** @param [w] dest [AjBool*] Boolean generated
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusGetBool(AjPStr src, AjPRegexp exp, ajint isub, AjBool* dest)
-@@ -1893,7 +2022,7 @@
-
-
-
--/* @funcstatic nexusVocab ***************************************************
-+/* @funcstatic nexusVocab *****************************************************
- **
- ** Tests a string against a controlled vocabulary
- **
-@@ -1901,6 +2030,8 @@
- ** @param [r] src [const AjPStr] String to be tested
- ** @param [r] vocab [const char* []] List of known values, ending in a NULL
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusVocab(const char* title, const AjPStr src,
-@@ -1927,6 +2058,8 @@
- **
- ** @param [r] thys [const AjPNexus] nexus object
- ** @return [void]
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- void ajNexusTrace(const AjPNexus thys)
-@@ -2430,6 +2563,8 @@
- **
- ** @param [r] thys [const AjPNexus] Nexus object
- ** @return [AjPStr*] taxa string array, NULL terminated, read only
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- AjPStr* ajNexusGetTaxa(const AjPNexus thys)
-@@ -2452,6 +2587,8 @@
- **
- ** @param [r] thys [const AjPNexus] Nexus object
- ** @return [ajuint] Number of taxa
-+**
-+** @release 2.8.0
- ** @@
- ******************************************************************************/
-
-@@ -2478,6 +2615,8 @@
- **
- ** @param [u] thys [AjPNexus] Nexus object
- ** @return [AjPStr*] taxa string array, NULL terminated, read only
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- AjPStr* ajNexusGetSequences(AjPNexus thys)
-@@ -2502,6 +2641,8 @@
- **
- ** @param [u] thys [AjPNexus] Nexus object
- ** @return [AjBool] ajTrue on success
-+**
-+** @release 2.8.0
- ******************************************************************************/
-
- static AjBool nexusSetSequences(AjPNexus thys)
-@@ -2591,7 +2732,7 @@
-
- for (i=0; thys->Taxa->TaxLabels[i]; i++)
- {
-- seqstr = ajStrNewRes(thys->Characters->Nchar+1);
-+ seqstr = ajStrNewRes(thys->Characters->Nchar+1);
- ajTablePut(seqtab, thys->Taxa->TaxLabels[i], seqstr);
- seqstr = NULL;
- }
-@@ -2599,6 +2740,7 @@
- else
- {
- AJCNEW0(thys->Taxa->TaxLabels, (thys->Ntax+1));
-+ ajDebug("thys->Taxa->TaxLabels 0..%u\n", (thys->Ntax+1));
- }
-
- taxlabel = NULL;
-@@ -2609,6 +2751,7 @@
- ajStrAssignS(&rdline, thys->Characters->Matrix[i]);
- ajStrRemoveWhiteExcess(&rdline);
-
-+ ajDebug("rdline: '%S'\n", rdline);
- if (!taxlabel || thys->Characters->Interleave ||
- (ajStrGetLen(seqstr) >= thys->Characters->Nchar))
- { /* next tax label */
-@@ -2617,13 +2760,23 @@
-
- ajRegSubI(word, 0, &taxlabel);
- ajRegPost(word, &tmpstr);
-+ ajDebug("taxlabel '%S' rest '%S'\n", taxlabel, tmpstr);
- ajStrAssignS(&rdline, tmpstr);
- ajStrQuoteStripAll(&taxlabel);
-+ ajDebug("unquoted taxlabel %p '%S'\n", taxlabel, taxlabel);
-
- if (!havetaxa)
- {
-+ ajDebug("ajTablePut itax.%u label %p '%S'\n",
-+ itax,
-+ thys->Taxa->TaxLabels[itax],
-+ thys->Taxa->TaxLabels[itax]);
- ajStrAssignS(&thys->Taxa->TaxLabels[itax], taxlabel);
- seqstr = ajStrNewRes(thys->Characters->Nchar+1);
-+ ajDebug("ajTablePut itax %u label %p '%S'\n",
-+ itax,
-+ thys->Taxa->TaxLabels[itax],
-+ thys->Taxa->TaxLabels[itax]);
- ajTablePut(seqtab, thys->Taxa->TaxLabels[itax], seqstr);
- seqstr = NULL;
- itax++;
-@@ -2631,8 +2784,10 @@
- havetaxa = ajTrue;
- }
-
-+ ajDebug("havetaxa: %B taxlabel '%S'\n", havetaxa, taxlabel);
- seqstr = ajTableFetchmodS(seqtab, taxlabel);
-
-+ ajDebug("seqstr '%S'\n", seqstr);
- if (!seqstr)
- {
- ajErr("Unknown taxon '%S' in nexus data", taxlabel);
-@@ -2650,12 +2805,12 @@
- {
- ajRegSubI(word, 0, &tmpstr);
- ajStrAppendS(&seqstr, tmpstr);
-- ajTablePut(seqtab, taxlabel, seqstr); /* just to make sure */
- ajRegPost(word, &tmpstr);
- ajStrAssignS(&rdline, tmpstr);
- }
-
- ajStrExchangeKK(&seqstr, gapch, '-');
-+ ajDebug("seqstr updated '%S'\n", seqstr);
- }
-
- ajRegFree(&word);
-@@ -2683,6 +2838,8 @@
- }
-
- ajTableFree(&seqtab);
-+ ajStrDel(&firstseq);
-+ ajStrDel(&taxlabel);
-
- return ajTrue;
- }
-@@ -2700,6 +2857,8 @@
- ** @param [d] pthis [AjPStr**] Pointer to the string array to be deleted.
- ** The pointer is always deleted.
- ** @return [void]
-+**
-+** @release 4.0.0
- ** @@
- ******************************************************************************/
-
---- emboss-6.4.0.orig/ajax/core/ajpat.c
-+++ emboss-6.4.0/ajax/core/ajpat.c
-@@ -752,6 +752,8 @@
- default:
- mismreg = ajRegCompC("<mismatch=(\\d+)>");
-
-+ mismatch=mismatches; /* set for first pattern */
-+
- while (ajBuffreadLineTrim(infile,&line))
- {
- if (ajStrGetCharFirst(line) == '>')
-@@ -762,7 +764,7 @@
- mismatch);
- ajStrSetClear(&name);
- ajStrSetClear(&pat);
-- mismatch=mismatches;
-+ mismatch=mismatches; /* reset for next pattern */
- }
-
- ajStrCutStart(&line,1);
---- emboss-6.4.0.orig/ajax/core/ajquery.c
-+++ emboss-6.4.0/ajax/core/ajquery.c
-@@ -1609,7 +1609,14 @@
- fmtstat = ajRegExec(queryRegFmt, *Pqry);
-
- if(!fmtstat)
-+ {
-+ if(ajStrGetLen(textin->Formatstr))
-+ {
-+ if(findformat(textin->Formatstr, &textin->Format))
-+ ajStrAssignS(&qry->Formatstr, textin->Formatstr);
-+ }
- return NULL;
-+ }
-
- ajRegSubI(queryRegFmt, 1, &queryFormat);
- ajRegSubI(queryRegFmt, 2, Pqry);
-@@ -2716,15 +2723,21 @@
- ajDebug("ajQueryAddFieldOrC.i '%s' '%S'\n",
- "id", qrystring);
-
-- ajQueryAddFieldElseC(qry, "acc",
-- MAJSTRGETPTR(qrystring));
-- ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
-- "acc", qrystring);
-+ if(qry->HasAcc && ajQueryKnownFieldC(qry, "acc"))
-+ {
-+ ajQueryAddFieldElseC(qry, "acc",
-+ MAJSTRGETPTR(qrystring));
-+ ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
-+ "acc", qrystring);
-+ }
-
-- ajQueryAddFieldElseC(qry, "sv",
-- MAJSTRGETPTR(qrystring));
-- ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
-- "sv", qrystring);
-+ if(ajQueryKnownFieldC(qry, "sv"))
-+ {
-+ ajQueryAddFieldElseC(qry, "sv",
-+ MAJSTRGETPTR(qrystring));
-+ ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
-+ "sv", qrystring);
-+ }
- }
- ajStrAssignS(&lastoper, operstr);
- ajStrTrimWhite(&lastoper);
---- emboss-6.4.0.orig/ajax/core/ajrange.c
-+++ emboss-6.4.0/ajax/core/ajrange.c
-@@ -179,7 +179,7 @@
- ajuint minsize, ajuint size)
- {
- AjPRange ret = NULL;
-- AjPFile infile;
-+ AjPFile infile = NULL;
- AjPStr line = NULL;
- char whiteSpace[] = " \t\n\r";
- char notSpace[] = "\n\r";
-@@ -189,9 +189,9 @@
- ajuint numone;
- ajuint numtwo;
-
-- AjPStr one;
-- AjPStr two;
-- AjPStr text;
-+ AjPStr one = NULL;
-+ AjPStr two = NULL;
-+ AjPStr text = NULL;
-
- AjPList onelist;
- AjPList twolist;
-@@ -229,13 +229,17 @@
- one = ajStrNew();
- ajStrTokenNextParse(&tokens, &one);
- ajListstrPushAppend(onelist, one);
-+ one = NULL;
-
- two = ajStrNew();
- ajStrTokenNextParse(&tokens, &two);
-
- if(ajStrGetLen(two))
-- ajListstrPushAppend(twolist, two);
-- else
-+ {
-+ ajListstrPushAppend(twolist, two);
-+ two = NULL;
-+ }
-+ else
- {
- ajWarn("Odd integer(s) in range specification:\n%S\n", line);
-
-@@ -247,10 +251,14 @@
- ajStrTokenNextParseC(&tokens, notSpace, &text);
- ajStrTrimWhite(&text);
- ajListstrPushAppend(textlist, text);
-+ text = NULL;
-
- ajStrTokenDel( &tokens);
- }
-
-+ ajFileClose(&infile);
-+ ajStrDel(&line);
-+
- /* now we know how many pairs of numbers to store, create ajRange object */
- n = ajListstrGetLength(onelist);
- if(size)
-@@ -331,6 +339,7 @@
- /* do the text */
- ajListstrPop(textlist, &text);
- ret->text[k] = text;
-+ text = NULL;
- }
-
-
---- emboss-6.4.0.orig/ajax/core/ajseqabi.c
-+++ emboss-6.4.0/ajax/core/ajseqabi.c
-@@ -181,6 +181,7 @@
- *machine = ajStrNewRes(l+1);
- ajReadbinBinary(fp,1,l,(void*)ajStrGetuniquePtr(machine));
- *(ajStrGetuniquePtr(machine)+l)='\0';
-+ ajStrSetValid(machine);
- }
- else
- return ajFalse;
-@@ -961,6 +962,7 @@
- *sample = ajStrNewRes(l+1);
- ajReadbinBinary(fp,1,l,(void*)ajStrGetuniquePtr(sample));
- *(ajStrGetuniquePtr(sample)+l)='\0';
-+ ajStrSetValid(sample);
- }
-
- return ajTrue;
---- emboss-6.4.0.orig/ajax/core/ajseqread.c
-+++ emboss-6.4.0/ajax/core/ajseqread.c
-@@ -5497,6 +5497,7 @@
- static AjBool seqReadRaw(AjPSeq thys, AjPSeqin seqin)
- {
- AjPFilebuff buff;
-+ const char* cp;
- AjPFile fp;
- AjBool ok = ajFalse;
- ajulong filestat = 0L;
-@@ -5506,83 +5507,139 @@
- AjPStr buf = NULL;
- char *cbuf;
- AjPStr tmpseq = NULL;
--
-- if(!seqRegRawNonseq)
-- seqRegRawNonseq = ajRegCompC("[^A-Za-z0-9 \t\n\r*-]");
-+ size_t iread;
-+
-+ ajDebug("seqReadRaw\n");
-
- buff = seqin->Input->Filebuff;
- fp = ajFilebuffGetFile(buff);
-
-- ajDebug("seqReadRaw\n");
-+ if(!seqRegRawNonseq)
-+ seqRegRawNonseq = ajRegCompC("[^A-Za-z0-9 \t\n\r*-]");
-
- if(ajFilebuffIsEnded(buff))
- return ajFalse;
-
-- buf = ajStrNewRes(4096);
-- ajStrSetValidLen(&buf, inc);
-- cbuf = ajStrGetuniquePtr(&buf);
--
-- filestat = ajFileSeek(fp, 0L, SEEK_END);
-- filesize = ajFileResetPos(fp);
-- filestat = ajFileSeek(fp, (ajlong) filestat, 0);
-+ filestat = ajFileSeek(fp, 0L, SEEK_CUR);
-
-- ok = ajTrue;
-+ if(filestat)
-+ {
-+ /* not a file - cannot use binary, so we can only read the buffer */
-+ while(ajBuffreadLineStore(buff, &seqReadLine,
-+ seqin->Input->Text, &thys->TextPtr))
-+ {
-+ ajDebug("read '%S'\n", seqReadLine);
-
-- for(i=0; i < filesize; i += inc)
-+ cp = ajStrGetPtr(seqReadLine);
-+ if(strlen(cp) != ajStrGetLen(seqReadLine))
-+ {
-+ ajDebug("seqReadRaw: Null character found in line: %S\n",
-+ seqReadLine);
-+ ajFilebuffResetStore(buff, seqin->Input->Text, &thys->TextPtr);
-+ ajStrAssignClear(&thys->Seq);
-+
-+ return ajFalse;
-+ }
-+
-+ if(ajRegExec(seqRegRawNonseq, seqReadLine))
-+ {
-+ ajDebug("seqReadRaw: Bad character found in line: %S\n",
-+ seqReadLine);
-+ ajFilebuffResetStore(buff, seqin->Input->Text, &thys->TextPtr);
-+ ajStrAssignClear(&thys->Seq);
-+
-+ return ajFalse;
-+ }
-+ seqAppend(&thys->Seq, seqReadLine);
-+ seqin->Input->Records++;
-+ ajDebug("read %d lines\n", seqin->Input->Records);
-+ }
-+ }
-+ else
- {
-- if((i+inc) > filesize)
-+ if(ajFilebuffIsEnded(buff))
- {
-- inc = (ajuint) (filesize - i);
-- ajStrSetValidLen(&buf, inc);
-+ ajFileSeek(fp, 0L, SEEK_END);
-+ return ajFalse;
- }
-
-- ajReadbinBinary(fp, inc, 1, cbuf);
-- cbuf[inc] = '\0';
-+ buf = ajStrNewRes(4096);
-+ ajStrSetValidLen(&buf, inc);
-+ cbuf = ajStrGetuniquePtr(&buf);
-+
-+ filestat = ajFileSeek(fp, 0L, SEEK_END);
-+ filesize = ajFileResetPos(fp);
-+ filestat = ajFileSeek(fp, 0L, SEEK_SET);
-
-- if(strlen(cbuf) != inc)
-+ if(!filesize)
- {
-- ajDebug("seqReadRaw: Null character found in line: %s\n",
-- cbuf);
-- ok = ajFalse;
-- break;
-+ ajFileSeek(fp,(ajlong) filesize, SEEK_SET);
-+ return ajFalse;
- }
-+
-+ ok = ajTrue;
-
-- if(ajRegExec(seqRegRawNonseq, buf))
-- {
-- ajDebug("seqReadRaw: Bad character found in line: %s\n",
-- cbuf);
-- ok = ajFalse;
-- break;
-- }
-+ for(i=0; i < filesize; i += inc)
-+ {
-+ if((i+inc) > filesize)
-+ {
-+ inc = (ajuint) (filesize - i);
-+ ajStrSetValidLen(&buf, inc);
-+ }
-
-- ajStrAssignC(&tmpseq, cbuf);
-+ iread = ajReadbinBinary(fp, inc, 1, cbuf);
-+ cbuf[inc] = '\0';
-
-- if(seqin->Input->Text)
-- ajStrAppendS(&thys->TextPtr, tmpseq);
-+ if(strlen(cbuf) != iread)
-+ {
-+ ajDebug("seqReadRaw: Null character found in line: %s\n",
-+ cbuf);
-+ ok = ajFalse;
-+ break;
-+ }
-
-- seqAppend(&thys->Seq, tmpseq);
-- seqin->Input->Records++;
-- ajDebug("read %d lines\n", seqin->Input->Records);
-- }
-+ if(ajRegExec(seqRegRawNonseq, buf))
-+ {
-+ ajDebug("seqReadRaw: Bad character found in line: %S\n",
-+ seqReadLine);
-+ ok = ajFalse;
-+ break;
-+ }
-
-- ajStrDel(&buf);
-- ajStrDel(&tmpseq);
-+ ajStrAssignC(&tmpseq, cbuf);
-
-- if(!ok)
-- {
-- ajFileSeek(fp,(ajlong) filestat,0);
-+ if(seqin->Input->Text)
-+ ajStrAppendS(&thys->TextPtr, tmpseq);
-+
-+ seqAppend(&thys->Seq, tmpseq);
-+ seqin->Input->Records++;
-+ ajDebug("read %d lines\n", seqin->Input->Records);
-+ }
-
-- if(seqin->Input->Text)
-- ajStrAssignC(&thys->TextPtr, "");
-+ ajStrDel(&buf);
-+ ajStrDel(&tmpseq);
-+
-+ if(!ok)
-+ {
-+ ajFileSeek(fp,(ajlong) filestat,0);
-+
-+ if(seqin->Input->Text)
-+ ajStrAssignC(&thys->TextPtr, "");
-+
-+ ajFilebuffResetPos(buff);
-+
-+ return ajFalse;
-+ }
-
-- ajFilebuffResetPos(buff);
-
-- return ajFalse;
- }
-
- ajFilebuffClear(buff, -1);
- buff->File->End=ajTrue;
-
-+ if(!seqin->Input->Records)
-+ return ajFalse;
-+
- return ajTrue;
- }
-
-@@ -7898,6 +7955,7 @@
- ajuint j;
- AjPFilebuff buff;
- AjPStr* seqs = NULL;
-+ AjPStr* names = NULL;
- AjPNexus nexus = NULL;
-
- SeqPMsfData phydata = NULL;
-@@ -7953,8 +8011,11 @@
- seqs = ajNexusGetTaxa(phydata->Nexus);
- phydata->Names = AJCALLOC(phydata->Nseq, sizeof(*phydata->Names));
-
-- for(j=0;j<phydata->Nseq;j++)
-- ajStrAssignS(&phydata->Names[j], seqs[j]);
-+ if(seqs)
-+ {
-+ for(j=0;j<phydata->Nseq;j++)
-+ ajStrAssignS(&phydata->Names[j], seqs[j]);
-+ }
-
- seqin->SeqData = phydata;
- ajDebug("Nexus parsed %d sequences\n", phydata->Nseq);
-@@ -7974,22 +8035,23 @@
- return ajFalse;
- }
-
-- if (!phydata->Names) /* finally set from the sequences */
-- {
-- seqs = ajNexusGetTaxa(phydata->Nexus);
-+ thys->Weight = 1.0;
-+ ajStrAssignS(&thys->Seq, seqs[i]);
-+
-+ if (!phydata->Names)
- phydata->Names = AJCALLOC(phydata->Nseq, sizeof(*phydata->Names));
-
-+ if (!phydata->Names[0]) /* finally set from the sequences */
-+ {
-+ names = ajNexusGetTaxa(phydata->Nexus);
- for(j=0;j<phydata->Nseq;j++)
-- ajStrAssignS(&phydata->Names[j], seqs[j]);
-+ ajStrAssignS(&phydata->Names[j], names[j]);
- }
-
- ajDebug("returning [%d] '%S'\n", i, phydata->Names[i]);
-
- ajStrAssignS(&thys->Name, phydata->Names[i]);
-
-- thys->Weight = 1.0;
-- ajStrAssignS(&thys->Seq, seqs[i]);
--
- phydata->Count++;
-
- if(phydata->Count >= phydata->Nseq)
-@@ -13827,7 +13889,7 @@
- ajStrAssignC(&seqFtFmtGff, "gff3");
-
- if(!seqRegGff3Typ)
-- seqRegGff3Typ = ajRegCompC("^#!(.*)");
-+ seqRegGff3Typ = ajRegCompC("^#!Type (.*)");
-
- ok = ajBuffreadLineStore(buff, &seqReadLine,
- seqin->Input->Text, &thys->TextPtr);
-@@ -13885,7 +13947,8 @@
-
- if(ajRegExec(seqRegGff3Typ, seqReadLine))
- {
-- ajFmtPrintS(&outstr, "%S\n", seqReadLine);
-+ ajRegSubI(seqRegGff3Typ, 1, &typstr);
-+ ajFmtPrintS(&outstr, "#!Type %S", typstr);
- }
-
- ok = ajBuffreadLineStore(buff, &seqReadLine,
-@@ -13966,7 +14029,7 @@
- ajFeattabinDel(&seqin->Ftquery);
- seqin->Ftquery = ajFeattabinNewSSF(seqFtFmtGff, thys->Name,
- ajStrGetPtr(seqin->Type), ftfile);
-- ajDebug("GFF FEAT TabIn %x\n", seqin->Ftquery);
-+ ajDebug("GFF3 FEAT TabIn %x\n", seqin->Ftquery);
- ftfile = NULL;
- ajFeattableDel(&seqin->Fttable);
- ajFeattableDel(&thys->Fttable);
---- emboss-6.4.0.orig/ajax/ensembl/ensdatabaseadaptor.c
-+++ emboss-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
-@@ -156,8 +156,8 @@
- ** @argrule Ini dbc [EnsPDatabaseconnection] Ensembl Database Connection
- ** @argrule Ini database [AjPStr] Database name
- ** @argrule Ini species [AjPStr] Species
--** @argrule Ini dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
--** enumeration
-+** @argrule Ini dbag [EnsEDatabaseadaptorGroup]
-+** Ensembl Database Adaptor Group enumeration
- ** @argrule Ini multi [AjBool] Multiple species
- ** @argrule Ini identifier [ajuint] Species identifier
- ** @argrule Url url [const AjPStr] Uniform Resource Locator
-@@ -239,7 +239,7 @@
- return NULL;
-
- collectionre =
-- ajRegCompC("^\\w+_collection_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
-+ ajRegCompC("^(\\w+)_collection_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
-
- multire =
- ajRegCompC("^ensembl_([a-z]+)(_\\w+?)*?(?:_\\d+)?_(\\d+)$");
-@@ -254,10 +254,12 @@
- /* Ensembl Collection databases have to be matched first. */
-
- group = ajStrNew();
-+ prefix = ajStrNew();
- swversion = ajStrNew();
-
-- ajRegSubI(collectionre, 1, &group);
-- ajRegSubI(collectionre, 2, &swversion);
-+ ajRegSubI(collectionre, 1, &prefix);
-+ ajRegSubI(collectionre, 2, &group);
-+ ajRegSubI(collectionre, 3, &swversion);
-
- if(ajStrMatchCaseC(swversion, ensSoftwareVersion))
- {
-@@ -290,6 +292,7 @@
- }
-
- ajStrDel(&group);
-+ ajStrDel(&prefix);
- ajStrDel(&swversion);
- }
- else if(ajRegExec(multire, database))
-@@ -417,6 +420,9 @@
- **
- ** Constructor for an Ensembl Database Adaptor with initial values.
- **
-+** If a database name has not been provided, the database name of the
-+** Ensembl Database Connection will be used.
-+**
- ** Ensembl Database Adaptors are singleton objects in the sense that a single
- ** instance of an Ensembl Database Adaptor connected to a particular database
- ** is sufficient to instantiate any number of Ensembl Object Adaptors from the
-@@ -430,12 +436,10 @@
- **
- ** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::new
- ** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
--** @param [u] database [AjPStr] Database name (optional). If not provided, the
--** database name in the Database Connection will
--** be used.
-+** @param [uN] database [AjPStr] Database name
- ** @param [u] species [AjPStr] Species
--** @param [u] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
--** enumeration
-+** @param [u] dbag [EnsEDatabaseadaptorGroup]
-+** Ensembl Database Adaptor Group enumeration
- ** @param [r] multi [AjBool] Multiple species
- ** @param [r] identifier [ajuint] Species identifier
- **
-@@ -555,15 +559,15 @@
-
- /* @section destructors *******************************************************
- **
--** Destruction destroys all internal data structures and frees the
--** memory allocated for an Ensembl Database Adaptor object.
-+** Destruction destroys all internal data structures and frees the memory
-+** allocated for an Ensembl Database Adaptor object.
- **
- ** @fdata [EnsPDatabaseadaptor]
- **
--** @nam3rule Del Destroy (free) an Ensembl Database Adaptor object
-+** @nam3rule Del Destroy (free) an Ensembl Database Adaptor
- **
--** @argrule * Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor
--** object address
-+** @argrule * Pdba [EnsPDatabaseadaptor*]
-+** Ensembl Database Adaptor address
- **
- ** @valrule * [void]
- **
-@@ -586,8 +590,7 @@
- ** @see ensExit
- ** @see ensRegistryExit
- **
--** @param [d] Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor
--** object address
-+** @param [d] Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor address
- **
- ** @return [void]
- ** @@
-@@ -652,8 +655,8 @@
- ** @valrule Databaseconnection [EnsPDatabaseconnection]
- ** Ensembl Database Connection or NULL
- ** @valrule Species [AjPStr] Species or NULL
--** @valrule Group [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
--** enumeration or ensEDatabaseadaptorGroupNULL
-+** @valrule Group [EnsEDatabaseadaptorGroup]
-+** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
- ** @valrule Multispecies [AjBool] Multiple species or ajFalse
- ** @valrule Identifier [ajuint] Species identifier or 0
- **
-@@ -693,8 +696,8 @@
- ** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::group
- ** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
- **
--** @return [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
--** enumeration or ensEDatabaseadaptorGroupNULL
-+** @return [EnsEDatabaseadaptorGroup]
-+** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
- ** @@
- ******************************************************************************/
-
-@@ -793,10 +796,10 @@
- ** @nam4rule Species Set the species
- **
- ** @argrule * dba [EnsPDatabaseadaptor] Ensembl Database Adaptor object
--** @argrule Databaseconnection dbc [EnsPDatabaseconnection] Ensembl Database
--** Connection
--** @argrule Group dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor
--** Group enumeration
-+** @argrule Databaseconnection dbc [EnsPDatabaseconnection]
-+** Ensembl Database Connection
-+** @argrule Group dbag [EnsEDatabaseadaptorGroup]
-+** Ensembl Database Adaptor Group enumeration
- ** @argrule Identifier identifier [ajuint] Species identifier
- ** @argrule Multispecies multi [AjBool] Multi-species attribute
- ** @argrule Species species [AjPStr] Species
---- emboss-6.4.0.orig/ajax/ensembl/ensdatabaseadaptor.h
-+++ emboss-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
-@@ -121,7 +121,7 @@
-
- EnsPDatabaseadaptor ensRegistryGetDatabaseadaptor(
- EnsEDatabaseadaptorGroup dbag,
-- const AjPStr alias);
-+ AjPStr alias);
-
- EnsPDatabaseadaptor ensRegistryGetReferenceadaptor(EnsPDatabaseadaptor dba);
-
---- emboss-6.4.0.orig/ajax/ensembl/ensregistry.c
-+++ emboss-6.4.0/ajax/ensembl/ensregistry.c
-@@ -569,8 +569,6 @@
- const RegistryPQualityCheck rqc,
- ajuint level);
-
--static AjPStr registryAliasRegister(const AjPStr alias);
--
- static AjBool registryAliasLoadDatabaseconnection(
- EnsPDatabaseconnection dbc,
- EnsPDatabaseadaptor dba);
-@@ -2029,6 +2027,8 @@
-
- AjBool ensRegistryLoadServername(AjPStr servername)
- {
-+ ajuint dbid = 0;
-+
- AjBool debug = AJFALSE;
- AjBool registered = AJFALSE;
-
-@@ -2037,6 +2037,9 @@
- AjPList svrnames = NULL;
- AjPList dbnames = NULL;
-
-+ AjPRegexp dbidre = NULL;
-+
-+ AjPStr dbidstr = NULL;
- AjPStr dbname = NULL;
- AjPStr source = NULL;
- AjPStr svrname = NULL;
-@@ -2059,6 +2062,8 @@
- ** List objects must be re-created and freed for each server.
- */
-
-+ dbidre = ajRegCompC("SpeciesIdentifier=(\\d+)");
-+
- value = ajStrNew();
-
- svrnames = ajListstrNew();
-@@ -2103,17 +2108,15 @@
-
- registrySourceRegister(source, ®istered);
-
-+ if((debug == ajTrue) && (registered == ajTrue))
-+ ajDebug("ensRegistryLoadServername '%S' already "
-+ "registered via source '%S'.\n",
-+ svrname, source);
-+
- ajStrDel(&source);
-
- if(registered == ajTrue)
-- {
-- if(debug)
-- ajDebug("ensRegistryLoadServername '%S' already "
-- "registered.\n",
-- svrname);
--
- continue;
-- }
-
- /*
- ** Create an Ensembl Database Connection to the AJAX Server for
-@@ -2150,40 +2153,64 @@
-
- dba = ensDatabaseadaptorNewUrl(value);
-
-- if((ensDatabaseadaptorGetMultispecies(dba) == ajTrue) &&
-- (ensDatabaseadaptorGetIdentifier(dba) == 0))
-+ if(ensDatabaseadaptorGetMultispecies(dba) == ajTrue)
- {
- /*
-- ** Expand an Ensembl Database Adaptor representing a
-- ** collection database into species-specific
-- ** Ensembl Database Adaptor objects before registering.
-- ** Delete the Ensembl Database Adaptor for the collection.
-+ ** For Ensembl Database Adaptors representing collection
-+ ** databases, the species name needs resetting to the AJAX
-+ ** database name and the species identifier needs parsing
-+ ** from the comment field of the AJAX database definition.
- */
-
-- registryEntryLoadCollection(
-- dbc,
-- ensDatabaseconnectionGetDatabasename(
-- ensDatabaseadaptorGetDatabaseconnection(dba)),
-- ensDatabaseadaptorGetGroup(dba));
-+ ensDatabaseadaptorSetSpecies(dba, dbname);
-
-- ensDatabaseadaptorDel(&dba);
-- }
-- else
-- {
-- /*
-- ** Register Ensembl Database Adaptor objects for
-- ** multi-species and species-specific databases.
-- ** Add the species as alias if registered or delete the
-- ** Ensembl Database Adaptor if not registered,
-- ** successfully.
-- */
-+ ajNamSvrGetdbAttrC(svrname, dbname, "comment", &value);
-
-- if(ensRegistryAddDatabaseadaptor(dba))
-- ensRegistryAliasAdd(ensDatabaseadaptorGetSpecies(dba),
-- ensDatabaseadaptorGetSpecies(dba));
-+ if(ajRegExec(dbidre, value))
-+ {
-+ dbid = 0;
-+ dbidstr = ajStrNew();
-+
-+ ajRegSubI(dbidre, 1, &dbidstr);
-+
-+ if(ajStrToUint(dbidstr, &dbid))
-+ {
-+ ensDatabaseadaptorSetIdentifier(dba, dbid);
-+
-+ ajStrDel(&dbidstr);
-+ }
-+ else
-+ {
-+ ajDebug("ensRegistryLoadServer could not parse a "
-+ "valid unsigned integer from the "
-+ "'SpeciesIdentifer=INTEGER' expression in "
-+ "the comment field of AJAX database "
-+ "definition for Ensembl collection "
-+ "database '%S'.\n", dbname);
-+
-+ ajStrDel(&dbidstr);
-+
-+ ensDatabaseadaptorDel(&dba);
-+
-+ continue;
-+ }
-+ }
- else
-+ {
-+ ajDebug("ensRegistryLoadServer could not find a "
-+ "'SpeciesIdentifer=INTEGER' entry in the "
-+ "comment field of AJAX database "
-+ "definition for Ensembl collection "
-+ "database '%S'.\n", dbname);
-+
- ensDatabaseadaptorDel(&dba);
-+
-+ continue;
-+ }
- }
-+
-+ if(ensRegistryAddDatabaseadaptor(dba) == ajFalse)
-+ ensDatabaseadaptorDel(&dba);
- }
-
- ajListIterDel(&dbniter);
-@@ -2196,6 +2223,8 @@
- ajListIterDel(&svriter);
- ajListstrFree(&svrnames);
-
-+ ajRegFree(&dbidre);
-+
- ajStrDel(&value);
-
- if(debug)
-@@ -2370,70 +2399,6 @@
-
-
-
--/* @funcstatic registryAliasRegister ******************************************
--**
--** Check, whether an alias name can be resolved directly or after replacing
--** underscore characters into a species name. If not, register the alias
--** without underscore characters and set the alias with underscores as alias.
--**
--** @param [r] alias [const AjPStr] Alias name
--**
--** @return [AjPStr] Species name or NULL
--** @@
--******************************************************************************/
--
--static AjPStr registryAliasRegister(const AjPStr alias)
--{
-- AjPStr species = NULL;
-- AjPStr unalias = NULL;
--
-- if(!(alias && ajStrGetLen(alias)))
-- return NULL;
--
-- /* Resolve an eventual alias to the species name. */
--
-- ensRegistryAliasResolve(alias, &species);
--
-- if(!species)
-- {
-- /*
-- ** If this alias has not been registered before, test if it has been
-- ** registered without underscores.
-- */
--
-- unalias = ajStrNewS(alias);
--
-- /*
-- ** FIXME: Since EMBOSS DBNAMES cannot cope with spaces species names
-- ** must include underscores.
-- ajStrExchangeCC(&unalias, "_", " ");
-- */
--
-- ensRegistryAliasResolve(unalias, &species);
--
-- if(!species)
-- {
-- /*
-- ** If the alias without underscores has also not been registered
-- ** before, register it as species before registering the one
-- ** with underscores as alias.
-- */
--
-- ensRegistryAliasAdd(unalias, unalias);
-- ensRegistryAliasAdd(unalias, alias);
--
-- ensRegistryAliasResolve(alias, &species);
-- }
--
-- ajStrDel(&unalias);
-- }
--
-- return species;
--}
--
--
--
--
- /* @func ensRegistryAliasAdd **************************************************
- **
- ** Add a Registry Alias entry to the Ensembl Registry.
-@@ -2861,8 +2826,6 @@
-
- ajStrAssignS(&species, line);
-
-- ensRegistryAliasAdd(species, species);
--
- block = ajTrue;
- }
- }
-@@ -3387,8 +3350,6 @@
- ajSqlcolumnToUint(sqlr, &identifier);
- ajSqlcolumnToStr(sqlr, &species);
-
-- ensRegistryAliasAdd(species, species);
--
- dba = ensRegistryNewDatabaseadaptor(dbc,
- dbname,
- species,
-@@ -3699,7 +3660,10 @@
- if(!alias)
- return NULL;
-
-- species = registryAliasRegister(alias);
-+ ensRegistryAliasResolve(alias, &species);
-+
-+ if(species == NULL)
-+ species = alias;
-
- dba = ensDatabaseadaptorNewIni(dbc,
- database,
-@@ -3801,7 +3765,10 @@
- if(!alias)
- return NULL;
-
-- species = registryAliasRegister(alias);
-+ ensRegistryAliasResolve(alias, &species);
-+
-+ if(species == NULL)
-+ species = alias;
-
- rsa = ensDatabaseadaptorNewIni(dbc,
- database,
-@@ -4517,13 +4484,13 @@
- **
- ** @argrule AllDatabaseadaptors dbag [EnsEDatabaseadaptorGroup]
- ** Ensembl Database Adaptor Group enumeration
--** @argrule AllDatabaseadaptors alias [const AjPStr]
-+** @argrule AllDatabaseadaptors alias [AjPStr]
- ** Ensembl Database Adaptor alias name or species name
- ** @argrule AllDatabaseadaptors dbas [AjPList] AJAX List of
- ** Ensembl Database Adaptor objects
- ** @argrule Databaseadaptor dbag [EnsEDatabaseadaptorGroup]
- ** Ensembl Database Adaptor Group enumeration
--** @argrule Databaseadaptor alias [const AjPStr]
-+** @argrule Databaseadaptor alias [AjPStr]
- ** Ensembl Database Adaptor alias name or species name
- ** @argrule Referenceadaptor dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
- **
-@@ -4549,7 +4516,7 @@
- **
- ** @param [uN] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
- ** enumeration
--** @param [rN] alias [const AjPStr] Ensembl Database Adaptor alias name or
-+** @param [rN] alias [AjPStr] Ensembl Database Adaptor alias name or
- ** species name
- ** @param [u] dbas [AjPList] AJAX List of Ensembl Database Adaptor objects
- **
-@@ -4558,7 +4525,7 @@
- ******************************************************************************/
-
- AjBool ensRegistryGetAllDatabaseadaptors(EnsEDatabaseadaptorGroup dbag,
-- const AjPStr alias,
-+ AjPStr alias,
- AjPList dbas)
- {
- void** keyarray = NULL;
-@@ -4593,8 +4560,17 @@
- if(!dbas)
- return ajFalse;
-
-+ /*
-+ ** Resolve an alias name into a valid species name. If the alias did not
-+ ** resolve into a species name, use the alias directly. If an alias was
-+ ** not passed in, it is still NULL, implying all species.
-+ */
-+
- ensRegistryAliasResolve(alias, &species);
-
-+ if(species == NULL)
-+ species = alias;
-+
- ajTableToarrayKeysValues(registryEntry, &keyarray, &valarray);
-
- for(i = 0; keyarray[i]; i++)
-@@ -4761,7 +4737,7 @@
- ** @cc Bio::EnsEMBL::Registry::get_DBAdaptor
- ** @param [u] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
- ** enumeration
--** @param [r] alias [const AjPStr] Scientific species name or alias name
-+** @param [r] alias [AjPStr] Scientific species name or alias name
- **
- ** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
- ** @@
-@@ -4769,7 +4745,7 @@
-
- EnsPDatabaseadaptor ensRegistryGetDatabaseadaptor(
- EnsEDatabaseadaptorGroup dbag,
-- const AjPStr alias)
-+ AjPStr alias)
- {
- AjBool debug = AJFALSE;
-
-@@ -4797,8 +4773,16 @@
- if(!alias)
- return NULL;
-
-+ /*
-+ ** Resolve an alias name into a valid species name. If the alias did not
-+ ** resolve into a species name, use the alias directly.
-+ */
-+
- ensRegistryAliasResolve(alias, &species);
-
-+ if(species == NULL)
-+ species = alias;
-+
- if(debug)
- ajDebug("ensRegistryGetDatabaseadaptor alias '%S' -> species '%S'\n",
- alias, species);
---- emboss-6.4.0.orig/ajax/ensembl/ensregistry.h
-+++ emboss-6.4.0/ajax/ensembl/ensregistry.h
-@@ -116,7 +116,7 @@
- AjBool ensRegistryRemoveDatabaseadaptor(EnsPDatabaseadaptor* Pdba);
-
- AjBool ensRegistryGetAllDatabaseadaptors(EnsEDatabaseadaptorGroup dbag,
-- const AjPStr alias,
-+ AjPStr alias,
- AjPList dbas);
-
- AjPStr ensRegistryGetStableidentifierprefix(EnsPDatabaseadaptor dba);
---- emboss-6.4.0.orig/emboss/cacheensembl.c
-+++ emboss-6.4.0/emboss/cacheensembl.c
-@@ -181,6 +181,11 @@
- ajFmtPrintF(outf, "%S\n", dbname);
-
- ajFmtPrintF(cachef, "DBNAME %S [\n", dbname);
-+
-+ if(ensDatabaseadaptorGetMultispecies(dba) == ajTrue)
-+ ajFmtPrintF(cachef, " comment: \"SpeciesIdentifier=%u\"\n",
-+ ensDatabaseadaptorGetIdentifier(dba));
-+
- ajFmtPrintF(cachef, " release: \"%s\"\n", ensSoftwareGetVersion());
- ajFmtPrintF(cachef, " server: \"%S\"\n", svrname);
- ajFmtPrintF(cachef, " url: \"%S\"\n", dbcurl);
---- emboss-6.4.0.orig/emboss/cirdna.c
-+++ emboss-6.4.0/emboss/cirdna.c
-@@ -970,7 +970,7 @@
- {
- token = ajStrParseC(Name2, ";");
- /*ajStrExchangeCC(&Name2, ";", " ");*/
-- stringLength = ajGraphicsCalcTextlengthS(token);
-+ stringLength = mmtolen * ajGraphicsCalcTextlengthS(token);
- xy1 = ajGraphicsCalcCoord(xDraw, yDraw, r2Ticks+postext, Angle);
- xy2 = ajGraphicsCalcCoord(xDraw, yDraw, r2Ticks+postext+stringLength,
- Angle);
-@@ -1029,6 +1029,10 @@
- float stringHeight;
- float r1Blocks;
- float r2Blocks;
-+ float mmtolen;
-+
-+ /* radius is 2pi*radius in mm, RealLength in bases */
-+ mmtolen = RealLength/(Radius * (float) 2.0 * (float) 3.1416);
-
- r1Blocks = Radius+((float)1.0*BlockHeight/(float)2);
- r2Blocks = r1Blocks-BlockHeight;
-@@ -1053,15 +1057,17 @@
- ajGraphicsSetFgcolour(Colour);
- }
-
-- stringLength = cirdna_HorTextPileLengthMax(Name2, NumNames);
-+ stringLength = mmtolen * cirdna_HorTextPileLengthMax(Name2, NumNames);
- stringHeight = ajGraphicsCalcTextheight();
-- StartAngle = cirdna_ComputeAngle(RealLength, (To+From)/2+stringLength/2,
-+ StartAngle = cirdna_ComputeAngle(RealLength,
-+ (To+From)/2 + stringLength/2,
- OriginAngle);
-- EndAngle = cirdna_ComputeAngle(RealLength, (To+From)/2-stringLength/2,
-+ EndAngle = cirdna_ComputeAngle(RealLength,
-+ (To+From)/2 - stringLength/2,
- OriginAngle);
-
- if(ajStrMatchCaseC(PosBlocks, "Out") )
-- cirdna_HorTextPile(xDraw, yDraw, r1Blocks+(Adjust*postext), StartAngle,
-+ cirdna_HorTextPile(xDraw, yDraw, r1Blocks+Adjust*postext, StartAngle,
- EndAngle, Name2, postext, 1);
- else
- cirdna_HorTextPile(xDraw, yDraw,
---- emboss-6.4.0.orig/emboss/data/Efeatures.gff3protein
-+++ emboss-6.4.0/emboss/data/Efeatures.gff3protein
-@@ -193,7 +193,7 @@
-
- # METAL - Binding site for a metal ion.
-
--metal_binding SO:0001092 SO:0001092_metal
-+polypeptide_metal_contact SO:0001092 SO:0001092_metal
- /note
- /comment
-
-@@ -215,11 +215,7 @@
- # internal cyclic lactam
- #SULFATATION Generally of tyrosine
-
--protein_modification_categorized_by_chemical_process MOD:01156
-- /note
-- /comment
--
--post_translational_modification SO:0001089
-+post_translationally_modified_region MOD:01156 SO:0001089
- /note
- /comment
-
-@@ -351,7 +347,7 @@
-
- # TURN - DSSP secondary structure
-
--turn SO:0001128
-+polypeptide_turn_motif SO:0001128
- /note
- /comment
-
-@@ -371,7 +367,7 @@
- # /comment
- /ftid
-
--natural_variant SO:0001147 SO:0001147_variant
-+natural_variant_site SO:0001147 SO:0001147_variant
- /note
- /comment
- /ftid
---- emboss-6.4.0.orig/emboss/data/Etcode.dat
-+++ emboss-6.4.0/emboss/data/Etcode.dat
-@@ -22,6 +22,7 @@
- 0.25
- 0.23
- 0.21
-+0.19
- 0.17
- 0.00
- #
---- emboss-6.4.0.orig/emboss/dbiflat.c
-+++ emboss-6.4.0/emboss/dbiflat.c
-@@ -91,6 +91,10 @@
-
- static AjPList* fdl = NULL;
-
-+static AjBool dbiflat_ParseSwiss(AjPFile libr, AjPFile* alistfile,
-+ AjBool systemsort, AjPStr* fields,
-+ ajint* maxFieldLen, ajuint* countfield,
-+ ajint *dpos, AjPStr* myid, AjPList* acl);
- static AjBool dbiflat_ParseEmbl(AjPFile libr, AjPFile* alistfile,
- AjBool systemsort, AjPStr* fields,
- ajint* maxFieldLen, ajuint* countfield,
-@@ -135,7 +139,7 @@
- static DbiflatOParser parser[] =
- {
- {"EMBL", dbiflat_ParseEmbl},
-- {"SWISS", dbiflat_ParseEmbl},
-+ {"SWISS", dbiflat_ParseSwiss},
- {"GB", dbiflat_ParseGenbank},
- {"REFSEQ", dbiflat_ParseRefseq},
- {NULL, NULL}
-@@ -594,6 +598,385 @@
- }
-
-
-+
-+
-+/* @funcstatic dbiflat_ParseSwiss *********************************************
-+**
-+** Parse the ID, accession from a SwissProt or UniProtKB entry.
-+**
-+** Reads to the end of the entry and then returns.
-+**
-+** @param [u] libr [AjPFile] Input database file
-+** @param [u] alistfile [AjPFile*] field data files array
-+** @param [r] systemsort [AjBool] If ajTrue use system sort, else internal sort
-+** @param [w] fields [AjPStr*] Fields required
-+** @param [w] maxFieldLen [ajint*] Maximum token length for each field
-+** @param [w] countfield [ajuint*] Number of tokens for each field
-+** @param [w] dpos [ajint*] Byte offset
-+** @param [w] myid [AjPStr*] ID
-+** @param [w] myfdl [AjPList*] Lists of field values
-+** @return [AjBool] ajTrue on success.
-+** @@
-+******************************************************************************/
-+
-+static AjBool dbiflat_ParseSwiss(AjPFile libr, AjPFile* alistfile,
-+ AjBool systemsort, AjPStr* fields,
-+ ajint* maxFieldLen, ajuint* countfield,
-+ ajint* dpos, AjPStr* myid,
-+ AjPList* myfdl)
-+{
-+ AjPStr tmpacnum = NULL;
-+ char* fd;
-+ ajint lineType;
-+ static ajint numFields;
-+ static ajint accfield = -1;
-+ static ajint desfield = -1;
-+ static ajint keyfield = -1;
-+ static ajint taxfield = -1;
-+ static ajint svnfield = -1;
-+ static AjBool reset = AJTRUE;
-+ AjBool svndone = ajFalse;
-+ AjBool done = ajFalse;
-+ ajint i;
-+ ajint lo;
-+ ajint hi;
-+ ajint fieldwidth;
-+ AjPStr tmpac = NULL;
-+ AjPStr format = NULL;
-+ AjPStr prefix = NULL;
-+ const char* p;
-+ const char* q;
-+ const char* swissprefix[] = {
-+ "RecName: ", "AltName: ", "SubName: ",
-+ "Includes:", "Contains:", "Flags: ",
-+ "Full=", "Short=", "EC=",
-+ "Allergen=", "Biotech=", "CD_antigen=", "INN=",
-+ NULL
-+ };
-+ ajuint j;
-+
-+ if(!fields)
-+ {
-+ reset = ajTrue;
-+ accfield = svnfield = desfield = keyfield = taxfield = -1;
-+ return ajFalse;
-+ }
-+
-+ if(reset)
-+ {
-+ numFields = 0;
-+ while(fields[numFields])
-+ {
-+ countfield[numFields]=0;
-+ if(ajStrMatchCaseC(fields[numFields], "acc"))
-+ accfield=numFields;
-+ else if(ajStrMatchCaseC(fields[numFields], "sv"))
-+ svnfield=numFields;
-+ else if(ajStrMatchCaseC(fields[numFields], "des"))
-+ desfield=numFields;
-+ else if(ajStrMatchCaseC(fields[numFields], "key"))
-+ keyfield=numFields;
-+ else if(ajStrMatchCaseC(fields[numFields], "org"))
-+ taxfield=numFields;
-+ else
-+ ajWarn("EMBL parsing unknown field '%S' ignored",
-+ fields[numFields]);
-+ numFields++;
-+ }
-+
-+ reset = ajFalse;
-+ }
-+
-+ if(!regEmblType)
-+ regEmblType = ajRegCompC("^([A-Z][A-Z]) +");
-+
-+ if(!regEmblAcc)
-+ regEmblAcc = ajRegCompC("([A-Za-z0-9-]+)");
-+
-+ if(!regEmblWrd)
-+ regEmblWrd = ajRegCompC("([A-Za-z0-9_]+)");
-+
-+ if(!regEmblVer)
-+ regEmblVer = ajRegCompC("([A-Za-z0-9_.]+)");
-+
-+ if(!regEmblPhr)
-+ regEmblPhr = ajRegCompC(" *([^;.\n\r]+)");
-+
-+ if(!regEmblTax)
-+ regEmblTax = ajRegCompC(" *([^;.\n\r()]+)");
-+
-+ if(!regEmblId)
-+ regEmblId = ajRegCompC("^ID ([^\\s;]+)(;\\s+SV\\s+(\\d+))?");
-+
-+ if(!regEmblEnd)
-+ regEmblEnd = ajRegCompC("^//");
-+
-+ *dpos = (ajint) ajFileResetPos(libr); /* Lossy cast */
-+
-+ while(ajReadline(libr, &rline))
-+ {
-+ if(ajRegExec(regEmblEnd, rline))
-+ {
-+ done = ajTrue;
-+ break;
-+ }
-+
-+ if(ajRegExec(regEmblType, rline))
-+ {
-+ ajRegSubI(regEmblType, 1, &typStr);
-+ if(ajStrMatchC(typStr, "ID"))
-+ lineType = FLATTYPE_ID;
-+ else if(ajStrMatchC(typStr, "SV") ||
-+ ajStrMatchC(typStr, "IV")) /* emblcds database */
-+ lineType = FLATTYPE_VER;
-+ else if(ajStrMatchC(typStr, "AC") ||
-+ ajStrMatchC(typStr, "PA")) /* emblcds database */
-+ lineType = FLATTYPE_ACC;
-+ else if(ajStrMatchC(typStr, "DE"))
-+ lineType = FLATTYPE_DES;
-+ else if(ajStrMatchC(typStr, "KW"))
-+ lineType = FLATTYPE_KEY;
-+ else if(ajStrMatchC(typStr, "OS"))
-+ lineType = FLATTYPE_TAX;
-+ else if(ajStrMatchC(typStr, "OC"))
-+ lineType = FLATTYPE_TAX;
-+ else
-+ lineType=FLATTYPE_OTHER;
-+
-+ if(lineType != FLATTYPE_OTHER)
-+ ajRegPost(regEmblType, &tmpline);
-+ }
-+ else
-+ lineType = FLATTYPE_OTHER;
-+
-+ if(lineType == FLATTYPE_ID)
-+ {
-+ ajRegExec(regEmblId, rline);
-+ ajRegSubI(regEmblId, 1, myid);
-+ ajStrFmtUpper(myid);
-+ ajDebug("++id '%S'\n", *myid);
-+ ajRegSubI(regEmblId, 3, &tmpfd);
-+ if(svnfield >= 0 && ajStrGetLen(tmpfd))
-+ {
-+ ajStrFmtUpper(&tmpfd);
-+ ajStrInsertK(&tmpfd, 0, '.');
-+ ajStrInsertS(&tmpfd, 0, *myid);
-+ /*ajDebug("++sv '%S'\n", tmpfd);*/
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
-+
-+ countfield[svnfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[svnfield], fd);
-+ }
-+ svndone = ajTrue;
-+ }
-+ continue;
-+ }
-+
-+ if(lineType == FLATTYPE_ACC && accfield >= 0)
-+ {
-+ while(ajRegExec(regEmblAcc, tmpline))
-+ {
-+ ajRegSubI(regEmblAcc, 1, &tmpfd);
-+ ajStrFmtUpper(&tmpfd);
-+ /*ajDebug("++acc '%S'\n", tmpfd);*/
-+
-+ if(!tmpacnum)
-+ ajStrAssignS(&tmpacnum, tmpfd);
-+
-+ if((p=strchr(MAJSTRGETPTR(tmpfd),(int)'-')))
-+ {
-+ q = p;
-+ while(isdigit((int)*(--q)));
-+ ++q;
-+ ajStrAssignSubC(&tmpstr,q,0,(ajint)(p-q-1));
-+ ajStrToInt(tmpstr,&lo);
-+ fieldwidth = (ajint) (p-q);
-+ ajFmtPrintS(&format,"%%S%%0%dd",fieldwidth);
-+
-+ ++p;
-+ q = p;
-+ while(!isdigit((int)*q))
-+ ++q;
-+ sscanf(q,"%d",&hi);
-+ ajStrAssignSubC(&prefix,p,0,(ajint)(q-p-1));
-+
-+ if(systemsort)
-+ {
-+ for(i=lo;i<=hi;++i)
-+ {
-+ ajFmtPrintS(&tmpac,MAJSTRGETPTR(format),prefix,i);
-+ embDbiMaxlen(&tmpac, &maxFieldLen[accfield]);
-+ countfield[accfield]++;
-+ ajFmtPrintF(alistfile[accfield],
-+ "%S %S\n", *myid, tmpac);
-+ }
-+ ajStrDel(&tmpac);
-+ }
-+ else
-+ {
-+ for(i=lo;i<=hi;++i)
-+ {
-+ ajFmtPrintS(&tmpac,MAJSTRGETPTR(format),prefix,i);
-+ embDbiMaxlen(&tmpac, &maxFieldLen[accfield]);
-+ countfield[accfield]++;
-+ fd = ajCharNewS(tmpac);
-+ ajListPushAppend(myfdl[accfield], fd);
-+ }
-+ ajStrDel(&tmpac);
-+ }
-+ ajStrDel(&format);
-+ ajStrDel(&prefix);
-+ }
-+ else {
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[accfield]);
-+
-+ countfield[accfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[accfield],
-+ "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[accfield], fd);
-+ }
-+ }
-+ ajRegPost(regEmblAcc, &tmpstr);
-+ ajStrAssignS(&tmpline, tmpstr);
-+ }
-+ continue;
-+ }
-+ else if(lineType == FLATTYPE_DES && desfield >= 0)
-+ {
-+ ajStrTrimWhiteStart(&tmpline);
-+ for(j=0; swissprefix[j]; j++)
-+ {
-+ if(ajStrPrefixC(tmpline, swissprefix[j]))
-+ ajStrCutStart(&tmpline, strlen(swissprefix[j]));
-+ }
-+ while(ajRegExec(regEmblWrd, tmpline))
-+ {
-+ ajRegSubI(regEmblWrd, 1, &tmpfd);
-+ ajStrFmtUpper(&tmpfd);
-+ /*ajDebug("++des '%S'\n", tmpfd);*/
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[desfield]);
-+
-+ countfield[desfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[desfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[desfield], fd);
-+ }
-+ ajRegPost(regEmblWrd, &tmpstr);
-+ ajStrAssignS(&tmpline, tmpstr);
-+ }
-+ continue;
-+ }
-+ else if(lineType == FLATTYPE_VER && svnfield >= 0)
-+ {
-+ while(ajRegExec(regEmblVer, tmpline))
-+ {
-+ ajRegSubI(regEmblVer, 1, &tmpfd);
-+ ajStrFmtUpper(&tmpfd);
-+ /*ajDebug("++sv '%S'\n", tmpfd);*/
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
-+
-+ countfield[svnfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[svnfield], fd);
-+ }
-+ ajRegPost(regEmblVer, &tmpstr);
-+ ajStrAssignS(&tmpline, tmpstr);
-+ }
-+ svndone = ajTrue;
-+ continue;
-+ }
-+ else if(lineType == FLATTYPE_KEY && keyfield >= 0)
-+ {
-+ while(ajRegExec(regEmblPhr, tmpline))
-+ {
-+ ajRegSubI(regEmblPhr, 1, &tmpfd);
-+ ajRegPost(regEmblPhr, &tmpstr);
-+ ajStrAssignS(&tmpline, tmpstr);
-+ ajStrTrimWhiteEnd(&tmpfd);
-+ if(!ajStrGetLen(tmpfd))
-+ continue;
-+ ajStrFmtUpper(&tmpfd);
-+ /*ajDebug("++key '%S'\n", tmpfd);*/
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[keyfield]);
-+
-+ countfield[keyfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[keyfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[keyfield], fd);
-+ }
-+ }
-+ continue;
-+ }
-+ else if(lineType == FLATTYPE_TAX && taxfield >= 0)
-+ {
-+ while(ajRegExec(regEmblTax, tmpline))
-+ {
-+ ajRegSubI(regEmblTax, 1, &tmpfd);
-+ ajRegPost(regEmblTax, &tmpstr);
-+ ajStrAssignS(&tmpline, tmpstr);
-+ ajStrFmtUpper(&tmpfd);
-+ ajStrTrimWhiteEnd(&tmpfd);
-+ if(!ajStrGetLen(tmpfd))
-+ continue;
-+ /*ajDebug("++tax '%S'\n", tmpfd);*/
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[taxfield]);
-+
-+ countfield[taxfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[taxfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[taxfield], fd);
-+ }
-+ }
-+ continue;
-+ }
-+ }
-+
-+ if(!done)
-+ return ajFalse;
-+
-+ if(svnfield >= 0 && !svndone && tmpacnum)
-+ {
-+ ajFmtPrintS(&tmpfd, "%S.0", tmpacnum);
-+ embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
-+
-+ countfield[svnfield]++;
-+ if(systemsort)
-+ ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
-+ else
-+ {
-+ fd = ajCharNewS(tmpfd);
-+ ajListPushAppend(myfdl[svnfield], fd);
-+ }
-+ }
-+
-+ ajStrDel(&tmpacnum);
-+
-+ return ajTrue;
-+}
-+
-+
-
-
- /* @funcstatic dbiflat_ParseEmbl **********************************************
---- emboss-6.4.0.orig/emboss/dbxflat.c
-+++ emboss-6.4.0/emboss/dbxflat.c
-@@ -32,6 +32,7 @@
- static AjBool dbxflat_ParseFastq(EmbPBtreeEntry entry, AjPFile inf);
- static AjBool dbxflat_ParseEmbl(EmbPBtreeEntry entry, AjPFile inf);
- static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf);
-+static AjBool dbxflat_ParseSwiss(EmbPBtreeEntry entry, AjPFile inf);
-
- static AjBool dbxflat_NextEntry(EmbPBtreeEntry entry, AjPFile inf);
-
-@@ -76,7 +77,7 @@
- static DbxflatOParser parser[] =
- {
- {"EMBL", dbxflat_ParseEmbl},
-- {"SWISS", dbxflat_ParseEmbl},
-+ {"SWISS", dbxflat_ParseSwiss},
- {"GB", dbxflat_ParseGenbank},
- {"REFSEQ", dbxflat_ParseGenbank},
- {"FASTQ", dbxflat_ParseFastq},
-@@ -715,6 +716,101 @@
-
-
-
-+
-+/* @funcstatic dbxflat_ParseSwiss *********************************************
-+**
-+** Parse the ID, accession from a SwissProt or UniProtKB entry.
-+**
-+** Reads to the end of the entry and then returns.
-+**
-+** @param [w] entry [EmbPBtreeEntry] entry
-+** @param [u] inf [AjPFile] Input file
-+**
-+** @return [AjBool] ajTrue on success.
-+** @@
-+******************************************************************************/
-+
-+static AjBool dbxflat_ParseSwiss(EmbPBtreeEntry entry, AjPFile inf)
-+{
-+ AjPStr line = NULL;
-+ ajlong pos = 0L;
-+ const char* swissprefix[] = {
-+ "RecName: ", "AltName: ", "SubName: ",
-+ "Includes:", "Contains:", "Flags: ",
-+ "Full=", "Short=", "EC=",
-+ "Allergen=", "Biotech=", "CD_antigen=", "INN=",
-+ NULL
-+ };
-+ ajuint i;
-+
-+ if(!dbxflat_wrdexp)
-+ dbxflat_wrdexp = ajRegCompC("([A-Za-z0-9_-]+)");
-+
-+ line = ajStrNewC("");
-+
-+ while(!ajStrPrefixC(line,"//"))
-+ {
-+ pos = ajFileResetPos(inf);
-+
-+ if(!ajReadlineTrim(inf,&line))
-+ {
-+ ajStrDel(&line);
-+ return ajFalse;
-+ }
-+ if(ajStrPrefixC(line,"ID"))
-+ {
-+ entry->fpos = pos;
-+ ajFmtScanS(line,"%*S%S",&entry->id);
-+ ajStrTrimEndC(&entry->id, ";");
-+/*
-+ ++global;
-+ printf("%d. %s\n",global,ajStrGetPtr(entry->id));
-+*/
-+ if(svfield)
-+ embBtreeEmblSV(line,svfield->data);
-+ }
-+
-+
-+ if(svfield)
-+ if(ajStrPrefixC(line,"SV") ||
-+ ajStrPrefixC(line,"IV")) /* emblcds database format */
-+ embBtreeEmblAC(line,svfield->data);
-+
-+ if(accfield)
-+ if(ajStrPrefixC(line,"AC") ||
-+ ajStrPrefixC(line,"PA")) /* emblcds database format */
-+ embBtreeEmblAC(line,accfield->data);
-+
-+ if(keyfield)
-+ if(ajStrPrefixC(line,"KW"))
-+ embBtreeEmblKW(line,keyfield->data,keyfield->len);
-+
-+ if(desfield)
-+ if(ajStrPrefixC(line,"DE"))
-+ {
-+ ajStrCutStart(&line, 5);
-+ ajStrTrimWhiteStart(&line);
-+ for(i=0; swissprefix[i]; i++)
-+ {
-+ if(ajStrPrefixC(line, swissprefix[i]))
-+ ajStrCutStart(&line, strlen(swissprefix[i]));
-+ }
-+ embBtreeParseField(line,dbxflat_wrdexp, desfield);
-+ }
-+
-+ if(orgfield)
-+ if(ajStrPrefixC(line,"OC") || ajStrPrefixC(line,"OS"))
-+ embBtreeEmblTX(line,orgfield->data,orgfield->len);
-+ }
-+
-+
-+ ajStrDel(&line);
-+
-+ return ajTrue;
-+}
-+
-+
-+
-
- /* @funcstatic dbxflat_NextEntry ********************************************
- **
---- emboss-6.4.0.orig/emboss/dbxresource.c
-+++ emboss-6.4.0/emboss/dbxresource.c
-@@ -535,6 +535,19 @@
- if(urlfield && !ajStrMatchC(rest, "None"))
- embBtreeParseField(rest, dbxresource_wrdexp, urlfield);
- }
-+ else if(ajStrMatchC(name, "NARCat"))
-+ {
-+ if(catfield && !ajStrMatchC(rest, "None"))
-+ {
-+ handle = ajStrTokenNewC(rest, "|");
-+ while(ajStrTokenNextParse(&handle, &token))
-+ {
-+ ajStrRemoveWhiteExcess(&token);
-+ ajListstrPush(catfield->data,ajStrNewS(token));
-+ }
-+ ajStrTokenDel(&handle);
-+ }
-+ }
- else if(ajStrSuffixC(name, "Cat"))
- {
- if(catfield && !ajStrMatchC(rest, "None"))
---- emboss-6.4.0.orig/emboss/drfinddata.c
-+++ emboss-6.4.0/emboss/drfinddata.c
-@@ -155,8 +155,9 @@
- {
- if(!ajTableMatchS(foundtable, resource->Id))
- {
-- ajDebug("drcat id '%S' category '%S'\n",
-- resource->Id, resource->Cat);
-+ ajDebug("drcat id '%S' categories %u\n",
-+ resource->Id,
-+ ajListGetLength(resource->Cat));
- ajResourceoutWrite(outfile, resource);
- ajTablePut(foundtable, ajStrNewS(resource->Id),
- (void *) 1);
---- emboss-6.4.0.orig/emboss/drfindformat.c
-+++ emboss-6.4.0/emboss/drfindformat.c
-@@ -152,8 +152,9 @@
- {
- if(!ajTableMatchS(foundtable, resource->Id))
- {
-- ajDebug("drcat id '%S' category '%S'\n",
-- resource->Id, resource->Cat);
-+ ajDebug("drcat id '%S' categories %u\n",
-+ resource->Id,
-+ ajListGetLength(resource->Cat));
- ajResourceoutWrite(outfile, resource);
- ajTablePut(foundtable, ajStrNewS(resource->Id),
- (void *) 1);
---- emboss-6.4.0.orig/emboss/drfindid.c
-+++ emboss-6.4.0/emboss/drfindid.c
-@@ -152,8 +152,9 @@
- {
- if(!ajTableMatchS(foundtable, resource->Id))
- {
-- ajDebug("drcat id '%S' category '%S'\n",
-- resource->Id, resource->Cat);
-+ ajDebug("drcat id '%S' categories %u\n",
-+ resource->Id,
-+ ajListGetLength(resource->Cat));
- ajResourceoutWrite(outfile, resource);
- ajTablePut(foundtable, ajStrNewS(resource->Id),
- (void *) 1);
---- emboss-6.4.0.orig/emboss/drfindresource.c
-+++ emboss-6.4.0/emboss/drfindresource.c
-@@ -162,9 +162,10 @@
- {
- if(!ajTableMatchS(foundtable, resource->Id))
- {
-- ajDebug("drcat id '%S' category '%S'\n",
-- resource->Id, resource->Cat);
-- ajResourceoutWrite(outfile, resource);
-+ ajDebug("drcat id '%S' categories %u\n",
-+ resource->Id,
-+ ajListGetLength(resource->Cat));
-+ ajResourceoutWrite(outfile, resource);
- ajTablePut(foundtable, ajStrNewS(resource->Id),
- (void *) 1);
- }
---- emboss-6.4.0.orig/emboss/server.ensemblgenomes
-+++ emboss-6.4.0/emboss/server.ensemblgenomes
-@@ -1,4 +1,4 @@
--# server.ensemblgenomes 2011-07-05 00:00:00
-+# server.ensemblgenomes 2011-07-27 00:00:00
- # Automatically generated by cacheensembl for server 'ensemblgenomes'.
-
- DBNAME acyrthosiphon_pisum [
-@@ -194,6 +194,7 @@
- ALIAS 15368 brachypodium_distachyon
-
- DBNAME b_afzelii [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -202,6 +203,7 @@
- ALIAS 390236 b_afzelii
-
- DBNAME b_amyloliquefaciens [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -210,6 +212,7 @@
- ALIAS 326423 b_amyloliquefaciens
-
- DBNAME b_anthracis_a0248 [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -218,6 +221,7 @@
- ALIAS 592021 b_anthracis_a0248
-
- DBNAME b_anthracis_ames [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -226,6 +230,7 @@
- ALIAS 198094 b_anthracis_ames
-
- DBNAME b_anthracis_ames_ancestor [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -234,6 +239,7 @@
- ALIAS 261594 b_anthracis_ames_ancestor
-
- DBNAME b_anthracis_cdc_684 [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -242,6 +248,7 @@
- ALIAS 568206 b_anthracis_cdc_684
-
- DBNAME b_anthracis_sterne [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -250,6 +257,7 @@
- ALIAS 260799 b_anthracis_sterne
-
- DBNAME b_aphidicola_5a [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -258,6 +266,7 @@
- ALIAS 563178 b_aphidicola_5a
-
- DBNAME b_aphidicola_baizongia [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -266,6 +275,7 @@
- ALIAS 224915 b_aphidicola_baizongia
-
- DBNAME b_aphidicola_cinara [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -274,6 +284,7 @@
- ALIAS 372461 b_aphidicola_cinara
-
- DBNAME b_aphidicola_schizaphis [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -282,6 +293,7 @@
- ALIAS 198804 b_aphidicola_schizaphis
-
- DBNAME b_aphidicola_tokyo_1998 [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -290,6 +302,7 @@
- ALIAS 107806 b_aphidicola_tokyo_1998
-
- DBNAME b_aphidicola_tuc7 [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
-@@ -298,6 +311,7 @@
- ALIAS 561501 b_aphidicola_tuc7
-
- DBNAME b_burgdorferi_dsm_4680 [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -306,6 +320,7 @@
- ALIAS 224326 b_burgdorferi_dsm_4680
-
- DBNAME b_burgdorferi_zs7 [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -314,6 +329,7 @@
- ALIAS 445985 b_burgdorferi_zs7
-
- DBNAME b_cereus_03bb102 [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -322,6 +338,7 @@
- ALIAS 572264 b_cereus_03bb102
-
- DBNAME b_cereus_172560w [
-+ comment: "SpeciesIdentifier=50"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -330,6 +347,7 @@
- ALIAS 526967 b_cereus_172560w
-
- DBNAME b_cereus_95_8201 [
-+ comment: "SpeciesIdentifier=36"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -338,6 +356,7 @@
- ALIAS 526979 b_cereus_95_8201
-
- DBNAME b_cereus_ah1271 [
-+ comment: "SpeciesIdentifier=71"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -346,6 +365,7 @@
- ALIAS 526992 b_cereus_ah1271
-
- DBNAME b_cereus_ah1272 [
-+ comment: "SpeciesIdentifier=53"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -354,6 +374,7 @@
- ALIAS 526993 b_cereus_ah1272
-
- DBNAME b_cereus_ah1273 [
-+ comment: "SpeciesIdentifier=43"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -362,6 +383,7 @@
- ALIAS 526994 b_cereus_ah1273
-
- DBNAME b_cereus_ah187 [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -370,6 +392,7 @@
- ALIAS 405534 b_cereus_ah187
-
- DBNAME b_cereus_ah603 [
-+ comment: "SpeciesIdentifier=49"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -378,6 +401,7 @@
- ALIAS 526990 b_cereus_ah603
-
- DBNAME b_cereus_ah621 [
-+ comment: "SpeciesIdentifier=46"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -386,6 +410,7 @@
- ALIAS 526972 b_cereus_ah621
-
- DBNAME b_cereus_ah676 [
-+ comment: "SpeciesIdentifier=38"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -394,6 +419,7 @@
- ALIAS 526991 b_cereus_ah676
-
- DBNAME b_cereus_ah820 [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -402,6 +428,7 @@
- ALIAS 405535 b_cereus_ah820
-
- DBNAME b_cereus_atcc_10876 [
-+ comment: "SpeciesIdentifier=70"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -410,6 +437,7 @@
- ALIAS 526980 b_cereus_atcc_10876
-
- DBNAME b_cereus_atcc_10987 [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -418,6 +446,7 @@
- ALIAS 222523 b_cereus_atcc_10987
-
- DBNAME b_cereus_atcc_14579 [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -426,6 +455,7 @@
- ALIAS 226900 b_cereus_atcc_14579
-
- DBNAME b_cereus_atcc_4342 [
-+ comment: "SpeciesIdentifier=72"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -434,6 +464,7 @@
- ALIAS 526977 b_cereus_atcc_4342
-
- DBNAME b_cereus_b4264 [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -442,6 +473,7 @@
- ALIAS 405532 b_cereus_b4264
-
- DBNAME b_cereus_bdrd_bcer4 [
-+ comment: "SpeciesIdentifier=62"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -450,6 +482,7 @@
- ALIAS 526978 b_cereus_bdrd_bcer4
-
- DBNAME b_cereus_bdrd_st196 [
-+ comment: "SpeciesIdentifier=34"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -458,6 +491,7 @@
- ALIAS 526976 b_cereus_bdrd_st196
-
- DBNAME b_cereus_bdrd_st24 [
-+ comment: "SpeciesIdentifier=37"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -466,6 +500,7 @@
- ALIAS 526974 b_cereus_bdrd_st24
-
- DBNAME b_cereus_bdrd_st26 [
-+ comment: "SpeciesIdentifier=39"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -474,6 +509,7 @@
- ALIAS 526975 b_cereus_bdrd_st26
-
- DBNAME b_cereus_bgsc_6e1 [
-+ comment: "SpeciesIdentifier=67"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -482,6 +518,7 @@
- ALIAS 526970 b_cereus_bgsc_6e1
-
- DBNAME b_cereus_cytotoxis [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -490,6 +527,7 @@
- ALIAS 315749 b_cereus_cytotoxis
-
- DBNAME b_cereus_f65185 [
-+ comment: "SpeciesIdentifier=30"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -498,6 +536,7 @@
- ALIAS 526989 b_cereus_f65185
-
- DBNAME b_cereus_g9842 [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -506,6 +545,7 @@
- ALIAS 405531 b_cereus_g9842
-
- DBNAME b_cereus_m1293 [
-+ comment: "SpeciesIdentifier=40"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -514,6 +554,7 @@
- ALIAS 526973 b_cereus_m1293
-
- DBNAME b_cereus_mm1550 [
-+ comment: "SpeciesIdentifier=65"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -522,6 +563,7 @@
- ALIAS 526969 b_cereus_mm1550
-
- DBNAME b_cereus_mm3 [
-+ comment: "SpeciesIdentifier=52"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -530,6 +572,7 @@
- ALIAS 526971 b_cereus_mm3
-
- DBNAME b_cereus_q1 [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -538,6 +581,7 @@
- ALIAS 361100 b_cereus_q1
-
- DBNAME b_cereus_r309803 [
-+ comment: "SpeciesIdentifier=33"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -546,6 +590,7 @@
- ALIAS 526968 b_cereus_r309803
-
- DBNAME b_cereus_rock1_15 [
-+ comment: "SpeciesIdentifier=42"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -554,6 +599,7 @@
- ALIAS 526982 b_cereus_rock1_15
-
- DBNAME b_cereus_rock1_3 [
-+ comment: "SpeciesIdentifier=78"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -562,6 +608,7 @@
- ALIAS 526981 b_cereus_rock1_3
-
- DBNAME b_cereus_rock3_28 [
-+ comment: "SpeciesIdentifier=57"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -570,6 +617,7 @@
- ALIAS 526983 b_cereus_rock3_28
-
- DBNAME b_cereus_rock3_29 [
-+ comment: "SpeciesIdentifier=51"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -578,6 +626,7 @@
- ALIAS 526984 b_cereus_rock3_29
-
- DBNAME b_cereus_rock3_42 [
-+ comment: "SpeciesIdentifier=77"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -586,6 +635,7 @@
- ALIAS 526985 b_cereus_rock3_42
-
- DBNAME b_cereus_rock3_44 [
-+ comment: "SpeciesIdentifier=48"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -594,6 +644,7 @@
- ALIAS 526986 b_cereus_rock3_44
-
- DBNAME b_cereus_rock4_18 [
-+ comment: "SpeciesIdentifier=55"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -602,6 +653,7 @@
- ALIAS 526988 b_cereus_rock4_18
-
- DBNAME b_cereus_rock4_2 [
-+ comment: "SpeciesIdentifier=76"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -610,6 +662,7 @@
- ALIAS 526987 b_cereus_rock4_2
-
- DBNAME b_cereus_var_anthracis [
-+ comment: "SpeciesIdentifier=69"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -618,6 +671,7 @@
- ALIAS 637380 b_cereus_var_anthracis
-
- DBNAME b_cereus_zk [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -626,6 +680,7 @@
- ALIAS 288681 b_cereus_zk
-
- DBNAME b_clausii [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -634,6 +689,7 @@
- ALIAS 66692 b_clausii
-
- DBNAME b_duttonii [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -642,6 +698,7 @@
- ALIAS 412419 b_duttonii
-
- DBNAME b_garinii [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -650,6 +707,7 @@
- ALIAS 290434 b_garinii
-
- DBNAME b_halodurans [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -658,6 +716,7 @@
- ALIAS 272558 b_halodurans
-
- DBNAME b_hermsii [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -666,6 +725,7 @@
- ALIAS 314723 b_hermsii
-
- DBNAME b_licheniformis_goettingen [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -674,6 +734,7 @@
- ALIAS 279010 b_licheniformis_goettingen
-
- DBNAME b_licheniformis_novozymes [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -681,6 +742,7 @@
-
-
- DBNAME b_megaterium_atcc_12872 [
-+ comment: "SpeciesIdentifier=73"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -689,6 +751,7 @@
- ALIAS 545693 b_megaterium_atcc_12872
-
- DBNAME b_megaterium_dsm_319 [
-+ comment: "SpeciesIdentifier=80"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -697,6 +760,7 @@
- ALIAS 592022 b_megaterium_dsm_319
-
- DBNAME b_mycoides_dsm_2048 [
-+ comment: "SpeciesIdentifier=47"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -705,6 +769,7 @@
- ALIAS 526997 b_mycoides_dsm_2048
-
- DBNAME b_mycoides_rock1_4 [
-+ comment: "SpeciesIdentifier=28"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -713,6 +778,7 @@
- ALIAS 526998 b_mycoides_rock1_4
-
- DBNAME b_mycoides_rock3_17 [
-+ comment: "SpeciesIdentifier=59"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -721,6 +787,7 @@
- ALIAS 526999 b_mycoides_rock3_17
-
- DBNAME b_pseudofirmus [
-+ comment: "SpeciesIdentifier=54"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -729,6 +796,7 @@
- ALIAS 398511 b_pseudofirmus
-
- DBNAME b_pseudomycoides [
-+ comment: "SpeciesIdentifier=58"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -737,6 +805,7 @@
- ALIAS 527000 b_pseudomycoides
-
- DBNAME b_pumilus [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -745,6 +814,7 @@
- ALIAS 315750 b_pumilus
-
- DBNAME b_recurrentis [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -753,6 +823,7 @@
- ALIAS 412418 b_recurrentis
-
- DBNAME b_selenitireducens [
-+ comment: "SpeciesIdentifier=32"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -761,6 +832,7 @@
- ALIAS 439292 b_selenitireducens
-
- DBNAME b_subtilis [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -769,6 +841,7 @@
- ALIAS 224308 b_subtilis
-
- DBNAME b_thuringiensis [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -777,6 +850,7 @@
- ALIAS 412694 b_thuringiensis
-
- DBNAME b_thuringiensis_atcc_10792 [
-+ comment: "SpeciesIdentifier=41"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -785,6 +859,7 @@
- ALIAS 527031 b_thuringiensis_atcc_10792
-
- DBNAME b_thuringiensis_bgsc_4aj1 [
-+ comment: "SpeciesIdentifier=75"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -793,6 +868,7 @@
- ALIAS 527022 b_thuringiensis_bgsc_4aj1
-
- DBNAME b_thuringiensis_bgsc_4aw1_andalous [
-+ comment: "SpeciesIdentifier=56"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -801,6 +877,7 @@
- ALIAS 527032 b_thuringiensis_bgsc_4aw1_andalous
-
- DBNAME b_thuringiensis_bgsc_4ba1_pondicheri [
-+ comment: "SpeciesIdentifier=29"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -809,6 +886,7 @@
- ALIAS 527029 b_thuringiensis_bgsc_4ba1_pondicheri
-
- DBNAME b_thuringiensis_bgsc_4bd1_huazhong [
-+ comment: "SpeciesIdentifier=31"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -817,6 +895,7 @@
- ALIAS 527030 b_thuringiensis_bgsc_4bd1_huazhong
-
- DBNAME b_thuringiensis_bgsc_4cc1_pulsiensis [
-+ comment: "SpeciesIdentifier=35"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -825,6 +904,7 @@
- ALIAS 527028 b_thuringiensis_bgsc_4cc1_pulsiensis
-
- DBNAME b_thuringiensis_bgsc_4y1_tochigiensis [
-+ comment: "SpeciesIdentifier=44"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -833,6 +913,7 @@
- ALIAS 527024 b_thuringiensis_bgsc_4y1_tochigiensis
-
- DBNAME b_thuringiensis_bmb171 [
-+ comment: "SpeciesIdentifier=68"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -841,6 +922,7 @@
- ALIAS 714359 b_thuringiensis_bmb171
-
- DBNAME b_thuringiensis_bt407 [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -849,6 +931,7 @@
- ALIAS 527021 b_thuringiensis_bt407
-
- DBNAME b_thuringiensis_ibl200 [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -857,6 +940,7 @@
- ALIAS 527019 b_thuringiensis_ibl200
-
- DBNAME b_thuringiensis_ibl4222 [
-+ comment: "SpeciesIdentifier=64"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -865,6 +949,7 @@
- ALIAS 527020 b_thuringiensis_ibl4222
-
- DBNAME b_thuringiensis_konkukian [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -873,6 +958,7 @@
- ALIAS 281309 b_thuringiensis_konkukian
-
- DBNAME b_thuringiensis_t01001 [
-+ comment: "SpeciesIdentifier=60"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -881,6 +967,7 @@
- ALIAS 527025 b_thuringiensis_t01001
-
- DBNAME b_thuringiensis_t03a001_kurstaki [
-+ comment: "SpeciesIdentifier=63"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -889,6 +976,7 @@
- ALIAS 527023 b_thuringiensis_t03a001_kurstaki
-
- DBNAME b_thuringiensis_t04001_sotto [
-+ comment: "SpeciesIdentifier=61"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -897,6 +985,7 @@
- ALIAS 527026 b_thuringiensis_t04001_sotto
-
- DBNAME b_thuringiensis_t13001_pakistani [
-+ comment: "SpeciesIdentifier=45"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -905,6 +994,7 @@
- ALIAS 527027 b_thuringiensis_t13001_pakistani
-
- DBNAME b_turicatae [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
-@@ -913,6 +1003,7 @@
- ALIAS 314724 b_turicatae
-
- DBNAME b_tusciae [
-+ comment: "SpeciesIdentifier=79"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -921,6 +1012,7 @@
- ALIAS 562970 b_tusciae
-
- DBNAME b_weihenstephanensis [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
-@@ -1221,6 +1313,7 @@
- ]
-
- DBNAME e_coli_042 [
-+ comment: "SpeciesIdentifier=43"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1229,12 +1322,14 @@
- ALIAS 216592 e_coli_042
-
- DBNAME e_coli_042_funcgen [
-+ comment: "SpeciesIdentifier=43"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_55989 [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1243,12 +1338,14 @@
- ALIAS 585055 e_coli_55989
-
- DBNAME e_coli_55989_funcgen [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_atcc_27325 [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1257,12 +1354,14 @@
- ALIAS 316407 e_coli_atcc_27325
-
- DBNAME e_coli_atcc_27325_funcgen [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_atcc_33849 [
-+ comment: "SpeciesIdentifier=39"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1271,12 +1370,14 @@
- ALIAS 536056 e_coli_atcc_33849
-
- DBNAME e_coli_atcc_33849_funcgen [
-+ comment: "SpeciesIdentifier=39"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_atcc_8739 [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1285,12 +1386,14 @@
- ALIAS 481805 e_coli_atcc_8739
-
- DBNAME e_coli_atcc_8739_funcgen [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_bl21 [
-+ comment: "SpeciesIdentifier=32"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1299,12 +1402,14 @@
- ALIAS 511693 e_coli_bl21
-
- DBNAME e_coli_bl21_funcgen [
-+ comment: "SpeciesIdentifier=32"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_bl21_de3_jgi [
-+ comment: "SpeciesIdentifier=40"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1313,12 +1418,14 @@
- ALIAS 866768 e_coli_bl21_de3_jgi
-
- DBNAME e_coli_bl21_de3_jgi_funcgen [
-+ comment: "SpeciesIdentifier=40"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_bl21_de3_kribb [
-+ comment: "SpeciesIdentifier=38"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1327,12 +1434,14 @@
- ALIAS 469008 e_coli_bl21_de3_kribb
-
- DBNAME e_coli_bl21_de3_kribb_funcgen [
-+ comment: "SpeciesIdentifier=38"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_bw2952 [
-+ comment: "SpeciesIdentifier=31"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1341,12 +1450,14 @@
- ALIAS 595496 e_coli_bw2952
-
- DBNAME e_coli_bw2952_funcgen [
-+ comment: "SpeciesIdentifier=31"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_dh10b [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1355,12 +1466,14 @@
- ALIAS 316385 e_coli_dh10b
-
- DBNAME e_coli_dh10b_funcgen [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_ec4115 [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1369,12 +1482,14 @@
- ALIAS 444450 e_coli_ec4115
-
- DBNAME e_coli_ec4115_funcgen [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_edl933 [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1383,12 +1498,14 @@
- ALIAS 155864 e_coli_edl933
-
- DBNAME e_coli_edl933_funcgen [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_k12 [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1397,12 +1514,14 @@
- ALIAS 511145 e_coli_k12
-
- DBNAME e_coli_k12_funcgen [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o103_h2 [
-+ comment: "SpeciesIdentifier=36"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1411,12 +1530,14 @@
- ALIAS 585395 e_coli_o103_h2
-
- DBNAME e_coli_o103_h2_funcgen [
-+ comment: "SpeciesIdentifier=36"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o111_h_ [
-+ comment: "SpeciesIdentifier=37"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1425,12 +1546,14 @@
- ALIAS 585396 e_coli_o111_h_
-
- DBNAME e_coli_o111_h__funcgen [
-+ comment: "SpeciesIdentifier=37"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o127_h6 [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1439,12 +1562,14 @@
- ALIAS 574521 e_coli_o127_h6
-
- DBNAME e_coli_o127_h6_funcgen [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o139_h28 [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1453,12 +1578,14 @@
- ALIAS 331111 e_coli_o139_h28
-
- DBNAME e_coli_o139_h28_funcgen [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o157_h7_tw14588 [
-+ comment: "SpeciesIdentifier=45"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1467,12 +1594,14 @@
- ALIAS 502346 e_coli_o157_h7_tw14588
-
- DBNAME e_coli_o157_h7_tw14588_funcgen [
-+ comment: "SpeciesIdentifier=45"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o17_k52_h18 [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1481,12 +1610,14 @@
- ALIAS 585056 e_coli_o17_k52_h18
-
- DBNAME e_coli_o17_k52_h18_funcgen [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o18_k1_h7 [
-+ comment: "SpeciesIdentifier=46"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1495,12 +1626,14 @@
- ALIAS 714962 e_coli_o18_k1_h7
-
- DBNAME e_coli_o18_k1_h7_funcgen [
-+ comment: "SpeciesIdentifier=46"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o1_k1_apec [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1509,12 +1642,14 @@
- ALIAS 405955 e_coli_o1_k1_apec
-
- DBNAME e_coli_o1_k1_apec_funcgen [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o26_h11 [
-+ comment: "SpeciesIdentifier=35"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1523,12 +1658,14 @@
- ALIAS 573235 e_coli_o26_h11
-
- DBNAME e_coli_o26_h11_funcgen [
-+ comment: "SpeciesIdentifier=35"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o45_k1 [
-+ comment: "SpeciesIdentifier=28"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1537,12 +1674,14 @@
- ALIAS 585035 e_coli_o45_k1
-
- DBNAME e_coli_o45_k1_funcgen [
-+ comment: "SpeciesIdentifier=28"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o55_h7 [
-+ comment: "SpeciesIdentifier=44"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1551,12 +1690,14 @@
- ALIAS 701177 e_coli_o55_h7
-
- DBNAME e_coli_o55_h7_funcgen [
-+ comment: "SpeciesIdentifier=44"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o6 [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1565,12 +1706,14 @@
- ALIAS 217992 e_coli_o6
-
- DBNAME e_coli_o6_funcgen [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o6_k15_h31 [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1579,12 +1722,14 @@
- ALIAS 362663 e_coli_o6_k15_h31
-
- DBNAME e_coli_o6_k15_h31_funcgen [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o7_k1 [
-+ comment: "SpeciesIdentifier=30"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1593,12 +1738,14 @@
- ALIAS 585057 e_coli_o7_k1
-
- DBNAME e_coli_o7_k1_funcgen [
-+ comment: "SpeciesIdentifier=30"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o8 [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1607,12 +1754,14 @@
- ALIAS 585034 e_coli_o8
-
- DBNAME e_coli_o8_funcgen [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o81 [
-+ comment: "SpeciesIdentifier=29"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1621,12 +1770,14 @@
- ALIAS 585397 e_coli_o81
-
- DBNAME e_coli_o81_funcgen [
-+ comment: "SpeciesIdentifier=29"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_o9_h4 [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1635,12 +1786,14 @@
- ALIAS 331112 e_coli_o9_h4
-
- DBNAME e_coli_o9_h4_funcgen [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_rel606 [
-+ comment: "SpeciesIdentifier=33"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1649,12 +1802,14 @@
- ALIAS 413997 e_coli_rel606
-
- DBNAME e_coli_rel606_funcgen [
-+ comment: "SpeciesIdentifier=33"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_sakai [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1663,12 +1818,14 @@
- ALIAS 386585 e_coli_sakai
-
- DBNAME e_coli_sakai_funcgen [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_se11 [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1677,12 +1834,14 @@
- ALIAS 409438 e_coli_se11
-
- DBNAME e_coli_se11_funcgen [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_se15 [
-+ comment: "SpeciesIdentifier=42"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1691,12 +1850,14 @@
- ALIAS 431946 e_coli_se15
-
- DBNAME e_coli_se15_funcgen [
-+ comment: "SpeciesIdentifier=42"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_sms_3_5 [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1705,12 +1866,14 @@
- ALIAS 439855 e_coli_sms_3_5
-
- DBNAME e_coli_sms_3_5_funcgen [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_tw14359 [
-+ comment: "SpeciesIdentifier=34"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1719,12 +1882,14 @@
- ALIAS 544404 e_coli_tw14359
-
- DBNAME e_coli_tw14359_funcgen [
-+ comment: "SpeciesIdentifier=34"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_coli_uti89 [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1733,12 +1898,14 @@
- ALIAS 364106 e_coli_uti89
-
- DBNAME e_coli_uti89_funcgen [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME e_fergusonii [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -1747,6 +1914,7 @@
- ALIAS 585054 e_fergusonii
-
- DBNAME e_fergusonii_funcgen [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
-@@ -1843,6 +2011,7 @@
- ]
-
- DBNAME mycobacterium_sp_jls [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1851,6 +2020,7 @@
- ALIAS 164757 mycobacterium_sp_jls
-
- DBNAME mycobacterium_sp_kms [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1859,6 +2029,7 @@
- ALIAS 189918 mycobacterium_sp_kms
-
- DBNAME mycobacterium_sp_mcs [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1867,6 +2038,7 @@
- ALIAS 164756 mycobacterium_sp_mcs
-
- DBNAME m_abscessus [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1875,6 +2047,7 @@
- ALIAS 36809 m_abscessus
-
- DBNAME m_avium [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1883,6 +2056,7 @@
- ALIAS 243243 m_avium
-
- DBNAME m_bovis_af2122_97 [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1891,6 +2065,7 @@
- ALIAS 233413 m_bovis_af2122_97
-
- DBNAME m_bovis_pasteur_1173p2 [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1899,6 +2074,7 @@
- ALIAS 410289 m_bovis_pasteur_1173p2
-
- DBNAME m_bovis_tokyo_172 [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1907,6 +2083,7 @@
- ALIAS 561275 m_bovis_tokyo_172
-
- DBNAME m_gilvum [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1915,6 +2092,7 @@
- ALIAS 350054 m_gilvum
-
- DBNAME m_leprae_br4923 [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1923,6 +2101,7 @@
- ALIAS 561304 m_leprae_br4923
-
- DBNAME m_leprae_tn [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1931,6 +2110,7 @@
- ALIAS 272631 m_leprae_tn
-
- DBNAME m_marinum [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1939,6 +2119,7 @@
- ALIAS 216594 m_marinum
-
- DBNAME m_paratuberculosis [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1947,6 +2128,7 @@
- ALIAS 262316 m_paratuberculosis
-
- DBNAME m_smegmatis [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1955,6 +2137,7 @@
- ALIAS 246196 m_smegmatis
-
- DBNAME m_tuberculosis_atcc_25177 [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1963,6 +2146,7 @@
- ALIAS 419947 m_tuberculosis_atcc_25177
-
- DBNAME m_tuberculosis_cdc1551 [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1971,6 +2155,7 @@
- ALIAS 83331 m_tuberculosis_cdc1551
-
- DBNAME m_tuberculosis_h37rv [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1979,6 +2164,7 @@
- ALIAS 83332 m_tuberculosis_h37rv
-
- DBNAME m_tuberculosis_kzn_1435 [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1987,6 +2173,7 @@
- ALIAS 478434 m_tuberculosis_kzn_1435
-
- DBNAME m_ulcerans [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -1995,6 +2182,7 @@
- ALIAS 362242 m_ulcerans
-
- DBNAME m_vanbaalenii [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
-@@ -2030,6 +2218,7 @@
- ALIAS n_crassa neurospora_crassa
-
- DBNAME n_gonorrhoeae_atcc_700825 [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2038,6 +2227,7 @@
- ALIAS 242231 n_gonorrhoeae_atcc_700825
-
- DBNAME n_gonorrhoeae_nccp11945 [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2046,6 +2236,7 @@
- ALIAS 521006 n_gonorrhoeae_nccp11945
-
- DBNAME n_meningitidis_053442 [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2054,6 +2245,7 @@
- ALIAS 374833 n_meningitidis_053442
-
- DBNAME n_meningitidis_2a [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2062,6 +2254,7 @@
- ALIAS 272831 n_meningitidis_2a
-
- DBNAME n_meningitidis_8013 [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2070,6 +2263,7 @@
- ALIAS 604162 n_meningitidis_8013
-
- DBNAME n_meningitidis_a [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2078,6 +2272,7 @@
- ALIAS 122587 n_meningitidis_a
-
- DBNAME n_meningitidis_alpha14 [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2086,6 +2281,7 @@
- ALIAS 487 n_meningitidis_alpha14
-
- DBNAME n_meningitidis_b [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
-@@ -2330,6 +2526,7 @@
- ]
-
- DBNAME p_abyssi [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
-@@ -2338,6 +2535,7 @@
- ALIAS 272844 p_abyssi
-
- DBNAME p_furiosus [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
-@@ -2346,6 +2544,7 @@
- ALIAS 186497 p_furiosus
-
- DBNAME p_horikoshii [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
-@@ -2354,6 +2553,7 @@
- ALIAS 70601 p_horikoshii
-
- DBNAME p_kodakaraensis [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
-@@ -2428,6 +2628,7 @@
- ALIAS 7668 strongylocentrotus_purpuratus
-
- DBNAME s_agalactiae_ia [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2436,6 +2637,7 @@
- ALIAS 205921 s_agalactiae_ia
-
- DBNAME s_agalactiae_iii [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2444,6 +2646,7 @@
- ALIAS 211110 s_agalactiae_iii
-
- DBNAME s_agalactiae_v [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2452,6 +2655,7 @@
- ALIAS 208435 s_agalactiae_v
-
- DBNAME s_aureus_04_02981 [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2460,12 +2664,14 @@
- ALIAS 703339 s_aureus_04_02981
-
- DBNAME s_aureus_04_02981_funcgen [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_bovine_rf122 [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2474,12 +2680,14 @@
- ALIAS 273036 s_aureus_bovine_rf122
-
- DBNAME s_aureus_bovine_rf122_funcgen [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_col [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2488,12 +2696,14 @@
- ALIAS 93062 s_aureus_col
-
- DBNAME s_aureus_col_funcgen [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_ed133 [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2502,12 +2712,14 @@
- ALIAS 685039 s_aureus_ed133
-
- DBNAME s_aureus_ed133_funcgen [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_ed98 [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2516,12 +2728,14 @@
- ALIAS 681288 s_aureus_ed98
-
- DBNAME s_aureus_ed98_funcgen [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_jh1 [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2530,12 +2744,14 @@
- ALIAS 359787 s_aureus_jh1
-
- DBNAME s_aureus_jh1_funcgen [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_jh9 [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2544,12 +2760,14 @@
- ALIAS 359786 s_aureus_jh9
-
- DBNAME s_aureus_jh9_funcgen [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_jkd6008 [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2558,12 +2776,14 @@
- ALIAS 546342 s_aureus_jkd6008
-
- DBNAME s_aureus_jkd6008_funcgen [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_jkd6159 [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2572,12 +2792,14 @@
- ALIAS 869816 s_aureus_jkd6159
-
- DBNAME s_aureus_jkd6159_funcgen [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_mrsa252 [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2586,12 +2808,14 @@
- ALIAS 282458 s_aureus_mrsa252
-
- DBNAME s_aureus_mrsa252_funcgen [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_mssa476 [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2600,12 +2824,14 @@
- ALIAS 282459 s_aureus_mssa476
-
- DBNAME s_aureus_mssa476_funcgen [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_mu3 [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2614,12 +2840,14 @@
- ALIAS 418127 s_aureus_mu3
-
- DBNAME s_aureus_mu3_funcgen [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_mu50 [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2628,12 +2856,14 @@
- ALIAS 158878 s_aureus_mu50
-
- DBNAME s_aureus_mu50_funcgen [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_mw2 [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2642,12 +2872,14 @@
- ALIAS 196620 s_aureus_mw2
-
- DBNAME s_aureus_mw2_funcgen [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_n315 [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2656,12 +2888,14 @@
- ALIAS 158879 s_aureus_n315
-
- DBNAME s_aureus_n315_funcgen [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_nctc_8325 [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2670,12 +2904,14 @@
- ALIAS 93061 s_aureus_nctc_8325
-
- DBNAME s_aureus_nctc_8325_funcgen [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_newman [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2684,12 +2920,14 @@
- ALIAS 426430 s_aureus_newman
-
- DBNAME s_aureus_newman_funcgen [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_st398 [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2698,12 +2936,14 @@
- ALIAS 523796 s_aureus_st398
-
- DBNAME s_aureus_st398_funcgen [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_tch1516 [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2712,12 +2952,14 @@
- ALIAS 451516 s_aureus_tch1516
-
- DBNAME s_aureus_tch1516_funcgen [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_tw20 [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2726,12 +2968,14 @@
- ALIAS 663951 s_aureus_tw20
-
- DBNAME s_aureus_tw20_funcgen [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_aureus_usa300 [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2740,12 +2984,14 @@
- ALIAS 451515 s_aureus_usa300
-
- DBNAME s_aureus_usa300_funcgen [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_boydii_18 [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2754,12 +3000,14 @@
- ALIAS 344609 s_boydii_18
-
- DBNAME s_boydii_18_funcgen [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_boydii_4 [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2768,12 +3016,14 @@
- ALIAS 300268 s_boydii_4
-
- DBNAME s_boydii_4_funcgen [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_carnosus [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2782,12 +3032,14 @@
- ALIAS 396513 s_carnosus
-
- DBNAME s_carnosus_funcgen [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_dysenteriae [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2796,12 +3048,14 @@
- ALIAS 300267 s_dysenteriae
-
- DBNAME s_dysenteriae_funcgen [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_dysgalactiae [
-+ comment: "SpeciesIdentifier=40"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2810,6 +3064,7 @@
- ALIAS 486410 s_dysgalactiae
-
- DBNAME s_epidermidis_atcc_12228 [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2818,12 +3073,14 @@
- ALIAS 176280 s_epidermidis_atcc_12228
-
- DBNAME s_epidermidis_atcc_12228_funcgen [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_epidermidis_atcc_35984 [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2832,12 +3089,14 @@
- ALIAS 176279 s_epidermidis_atcc_35984
-
- DBNAME s_epidermidis_atcc_35984_funcgen [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_equi [
-+ comment: "SpeciesIdentifier=33"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2846,6 +3105,7 @@
- ALIAS 553482 s_equi
-
- DBNAME s_equi_mgcs10565 [
-+ comment: "SpeciesIdentifier=5"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2854,6 +3114,7 @@
- ALIAS 552526 s_equi_mgcs10565
-
- DBNAME s_equi_zooepidemicus [
-+ comment: "SpeciesIdentifier=32"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2862,6 +3123,7 @@
- ALIAS 40041 s_equi_zooepidemicus
-
- DBNAME s_flexneri_2457t [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2870,12 +3132,14 @@
- ALIAS 198215 s_flexneri_2457t
-
- DBNAME s_flexneri_2457t_funcgen [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_flexneri_301 [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2884,12 +3148,14 @@
- ALIAS 198214 s_flexneri_301
-
- DBNAME s_flexneri_301_funcgen [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_flexneri_5b [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2898,12 +3164,14 @@
- ALIAS 373384 s_flexneri_5b
-
- DBNAME s_flexneri_5b_funcgen [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_flexneri_x [
-+ comment: "SpeciesIdentifier=41"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -2912,12 +3180,14 @@
- ALIAS 591020 s_flexneri_x
-
- DBNAME s_flexneri_x_funcgen [
-+ comment: "SpeciesIdentifier=41"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_gallolyticus [
-+ comment: "SpeciesIdentifier=45"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2926,6 +3196,7 @@
- ALIAS 637909 s_gallolyticus
-
- DBNAME s_gordonii [
-+ comment: "SpeciesIdentifier=6"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2934,6 +3205,7 @@
- ALIAS 467705 s_gordonii
-
- DBNAME s_haemolyticus [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2942,12 +3214,14 @@
- ALIAS 279808 s_haemolyticus
-
- DBNAME s_haemolyticus_funcgen [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_lugdunensis [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -2956,12 +3230,14 @@
- ALIAS 698737 s_lugdunensis
-
- DBNAME s_lugdunensis_funcgen [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_mitis [
-+ comment: "SpeciesIdentifier=48"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2970,6 +3246,7 @@
- ALIAS 365659 s_mitis
-
- DBNAME s_mutans_atcc_700610 [
-+ comment: "SpeciesIdentifier=7"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2978,6 +3255,7 @@
- ALIAS 210007 s_mutans_atcc_700610
-
- DBNAME s_mutans_nn2025 [
-+ comment: "SpeciesIdentifier=44"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2986,6 +3264,7 @@
- ALIAS 511691 s_mutans_nn2025
-
- DBNAME s_pneumoniae_70585 [
-+ comment: "SpeciesIdentifier=34"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -2994,6 +3273,7 @@
- ALIAS 488221 s_pneumoniae_70585
-
- DBNAME s_pneumoniae_a19 [
-+ comment: "SpeciesIdentifier=49"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3002,6 +3282,7 @@
- ALIAS 525381 s_pneumoniae_a19
-
- DBNAME s_pneumoniae_atcc_700669 [
-+ comment: "SpeciesIdentifier=39"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3010,6 +3291,7 @@
- ALIAS 561276 s_pneumoniae_atcc_700669
-
- DBNAME s_pneumoniae_atcc_baa_255 [
-+ comment: "SpeciesIdentifier=8"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3018,6 +3300,7 @@
- ALIAS 171101 s_pneumoniae_atcc_baa_255
-
- DBNAME s_pneumoniae_cgsp14 [
-+ comment: "SpeciesIdentifier=9"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3026,6 +3309,7 @@
- ALIAS 516950 s_pneumoniae_cgsp14
-
- DBNAME s_pneumoniae_d39 [
-+ comment: "SpeciesIdentifier=10"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3034,6 +3318,7 @@
- ALIAS 373153 s_pneumoniae_d39
-
- DBNAME s_pneumoniae_g54 [
-+ comment: "SpeciesIdentifier=11"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3042,6 +3327,7 @@
- ALIAS 512566 s_pneumoniae_g54
-
- DBNAME s_pneumoniae_hungary19a_6 [
-+ comment: "SpeciesIdentifier=12"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3050,6 +3336,7 @@
- ALIAS 487214 s_pneumoniae_hungary19a_6
-
- DBNAME s_pneumoniae_jja [
-+ comment: "SpeciesIdentifier=35"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3058,6 +3345,7 @@
- ALIAS 488222 s_pneumoniae_jja
-
- DBNAME s_pneumoniae_p1031 [
-+ comment: "SpeciesIdentifier=37"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3066,6 +3354,7 @@
- ALIAS 488223 s_pneumoniae_p1031
-
- DBNAME s_pneumoniae_taiwan19f_14 [
-+ comment: "SpeciesIdentifier=36"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3074,6 +3363,7 @@
- ALIAS 487213 s_pneumoniae_taiwan19f_14
-
- DBNAME s_pneumoniae_tigr4 [
-+ comment: "SpeciesIdentifier=13"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3082,6 +3372,7 @@
- ALIAS 170187 s_pneumoniae_tigr4
-
- DBNAME s_pyogenes_atcc_baa_595 [
-+ comment: "SpeciesIdentifier=17"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3090,6 +3381,7 @@
- ALIAS 198466 s_pyogenes_atcc_baa_595
-
- DBNAME s_pyogenes_m18 [
-+ comment: "SpeciesIdentifier=15"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3098,6 +3390,7 @@
- ALIAS 186103 s_pyogenes_m18
-
- DBNAME s_pyogenes_m2 [
-+ comment: "SpeciesIdentifier=20"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3106,6 +3399,7 @@
- ALIAS 370552 s_pyogenes_m2
-
- DBNAME s_pyogenes_m28 [
-+ comment: "SpeciesIdentifier=16"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3114,6 +3408,7 @@
- ALIAS 319701 s_pyogenes_m28
-
- DBNAME s_pyogenes_m4 [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3122,6 +3417,7 @@
- ALIAS 370554 s_pyogenes_m4
-
- DBNAME s_pyogenes_m49 [
-+ comment: "SpeciesIdentifier=25"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3130,6 +3426,7 @@
- ALIAS 471876 s_pyogenes_m49
-
- DBNAME s_pyogenes_m5 [
-+ comment: "SpeciesIdentifier=24"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3138,6 +3435,7 @@
- ALIAS 160491 s_pyogenes_m5
-
- DBNAME s_pyogenes_m6 [
-+ comment: "SpeciesIdentifier=19"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3146,6 +3444,7 @@
- ALIAS 286636 s_pyogenes_m6
-
- DBNAME s_pyogenes_mgas2096 [
-+ comment: "SpeciesIdentifier=22"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3154,6 +3453,7 @@
- ALIAS 370553 s_pyogenes_mgas2096
-
- DBNAME s_pyogenes_mgas5005 [
-+ comment: "SpeciesIdentifier=14"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3162,6 +3462,7 @@
- ALIAS 293653 s_pyogenes_mgas5005
-
- DBNAME s_pyogenes_mgas9429 [
-+ comment: "SpeciesIdentifier=23"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3170,6 +3471,7 @@
- ALIAS 370551 s_pyogenes_mgas9429
-
- DBNAME s_pyogenes_sf370 [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3178,6 +3480,7 @@
- ALIAS 160490 s_pyogenes_sf370
-
- DBNAME s_pyogenes_ssi_1 [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3186,6 +3489,7 @@
- ALIAS 193567 s_pyogenes_ssi_1
-
- DBNAME s_sanguinis [
-+ comment: "SpeciesIdentifier=26"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3194,6 +3498,7 @@
- ALIAS 388919 s_sanguinis
-
- DBNAME s_saprophyticus [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
-@@ -3202,12 +3507,14 @@
- ALIAS 342451 s_saprophyticus
-
- DBNAME s_saprophyticus_funcgen [
-+ comment: "SpeciesIdentifier=18"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
- ]
-
- DBNAME s_sonnei [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
-@@ -3216,12 +3523,14 @@
- ALIAS 300269 s_sonnei
-
- DBNAME s_sonnei_funcgen [
-+ comment: "SpeciesIdentifier=21"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
- ]
-
- DBNAME s_suis_05zyh33 [
-+ comment: "SpeciesIdentifier=27"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3230,6 +3539,7 @@
- ALIAS 391295 s_suis_05zyh33
-
- DBNAME s_suis_98hah33 [
-+ comment: "SpeciesIdentifier=28"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3238,6 +3548,7 @@
- ALIAS 391296 s_suis_98hah33
-
- DBNAME s_suis_bm407 [
-+ comment: "SpeciesIdentifier=42"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3246,6 +3557,7 @@
- ALIAS 568814 s_suis_bm407
-
- DBNAME s_suis_gz1 [
-+ comment: "SpeciesIdentifier=50"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3254,6 +3566,7 @@
- ALIAS 423211 s_suis_gz1
-
- DBNAME s_suis_p1_7 [
-+ comment: "SpeciesIdentifier=43"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3262,6 +3575,7 @@
- ALIAS 218494 s_suis_p1_7
-
- DBNAME s_suis_sc84 [
-+ comment: "SpeciesIdentifier=41"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3270,6 +3584,7 @@
- ALIAS 568813 s_suis_sc84
-
- DBNAME s_thermophilus_atcc_baa_250 [
-+ comment: "SpeciesIdentifier=29"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3278,6 +3593,7 @@
- ALIAS 264199 s_thermophilus_atcc_baa_250
-
- DBNAME s_thermophilus_atcc_baa_491 [
-+ comment: "SpeciesIdentifier=30"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3286,6 +3602,7 @@
- ALIAS 322159 s_thermophilus_atcc_baa_491
-
- DBNAME s_thermophilus_cnrz_1066 [
-+ comment: "SpeciesIdentifier=31"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3294,6 +3611,7 @@
- ALIAS 299768 s_thermophilus_cnrz_1066
-
- DBNAME s_uberis [
-+ comment: "SpeciesIdentifier=38"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
-@@ -3350,6 +3668,7 @@
- ]
-
- DBNAME wolbachia_sp_brugia_malayi [
-+ comment: "SpeciesIdentifier=3"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
-@@ -3358,6 +3677,7 @@
- ALIAS 292805 wolbachia_sp_brugia_malayi
-
- DBNAME wolbachia_sp_drosophila_simulans [
-+ comment: "SpeciesIdentifier=2"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
-@@ -3366,6 +3686,7 @@
- ALIAS 66084 wolbachia_sp_drosophila_simulans
-
- DBNAME w_pipientis_culex_pipiens [
-+ comment: "SpeciesIdentifier=1"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
-@@ -3374,6 +3695,7 @@
- ALIAS 570417 w_pipientis_culex_pipiens
-
- DBNAME w_pipientis_wmel [
-+ comment: "SpeciesIdentifier=4"
- release: "62"
- server: "ensemblgenomes"
- url: "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
---- emboss-6.4.0.orig/nucleus/embgroup.c
-+++ emboss-6.4.0/nucleus/embgroup.c
-@@ -1173,7 +1173,7 @@
- AjPStr tail;
- AjPStr revhead;
- AjPStr revtail;
-- AjPStr dummy; /* dummy string for ajListstrPop() */
-+ AjPStr dummy = NULL; /* dummy string for ajListstrPop() */
-
-
- len = ajListstrToarray(sublist, &sub);
diff --git a/debian/patches/series b/debian/patches/series
index fab8c5d..f9ff02d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-official-upstream-patch.patch
using-pager-in-tfm.patch
tfm-html.patch
fix-postgresql-macro.patch
--
The European Molecular Biology Open Software Suite.
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