[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, &registered);
- 
-+            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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