the Fink project is an effort to port
popular Unix programs to Mac OS X
Package: emboss
Version: 5.0.0
Revision: 8
#Distribution: 10.4
Depends: %N-ajax5-shlibs (>= %v-%r), %N-nucleus5-shlibs (>= %v-%r), %N-plplot5-shlibs (>= %v-%r), x11, x11-shlibs, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, system-java14
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev, freetype219, fontconfig2-dev, expat1
#Replaces: emboss (<< 5.0.0)
Source: mirror:custom:EMBOSS-%v.tar.gz
CustomMirror: <<
Primary: ftp://emboss.open-bio.org/pub/EMBOSS/
<<
Source-MD5: be4c895220ad34afd65d450ba7d8e34b
#SetCPPFLAGS: -Dstat64=stat
Patch: %n.patch
ConfigureParams: --with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home --with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include --disable-dependency-tracking --libdir=%p/lib/EMBOSS
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/include/EMBOSS
mv %i/include/*.* %i/include/EMBOSS/
ln -s EMBOSS/lib{ajax,ajaxg,nucleus,eplplot}.dylib %i/lib
mv %i/lib/EMBOSS/*.*a %i/lib
<<
SplitOff10: <<
Package: %N-ajax5-shlibs
Depends: %N-plplot5-shlibs (>= %v-%r), libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, libiconv
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libajax.5*.dylib
lib/EMBOSS/libajaxg.5*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libajax.5.dylib 6.0.0 %n (>= 5.0.0-3)
%p/lib/EMBOSS/libajaxg.5.dylib 6.0.0 %n (>= 5.0.0-3)
<<
<<
SplitOff11: <<
Package: %N-ajax5-dev
Depends: %N-ajax5-shlibs (= %v-%r)
Conflicts: %N-dev, %N-ajax4-dev
Replaces: %N-dev
DocFiles: ChangeLog COPYING README
Files: <<
lib/libajax*
lib/EMBOSS/libajax*
include/EMBOSS/aj*.h
include/EMBOSS/pcre*
<<
BuildDependsOnly: True
<<
SplitOff20: <<
Package: %N-nucleus5-shlibs
Depends: %N-ajax5-shlibs (>= %v-%r)
Replaces: %N (<< 5.0.0-3)
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libnucleus.5*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libnucleus.5.dylib 6.0.0 %n (>= 5.0.0-3)
<<
<<
SplitOff21: <<
Package: %N-nucleus5-dev
Depends: %N-nucleus5-shlibs (= %v-%r)
Conflicts: %N-dev, %N-nucleus4-dev
Replaces: %N-dev, %N (<< 5.0.0-3)
DocFiles: ChangeLog COPYING README
Files: <<
lib/libnucleus*
lib/EMBOSS/libnucleus*
include/EMBOSS/em*.h
<<
BuildDependsOnly: True
<<
SplitOff30: <<
Package: %N-plplot5-shlibs
Depends: libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, libiconv, x11-shlibs
Replaces: %N (<< 5.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libeplplot.3*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libeplplot.3.dylib 6.0.0 %n (>= 3.0.0-4)
<<
<<
SplitOff31: <<
Package: %N-plplot5-dev
Depends: %N-plplot5-shlibs (= %v-%r)
Conflicts: %N-dev, %N-plplot5-dev (<< 5.0.0-3)
Replaces: %N-dev, %N (<< 5.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/libeplplot*
lib/EMBOSS/libeplplot*
include/eplplot/*.h
<<
BuildDependsOnly: True
<<
RunTimeVars: <<
# PLPLOT_LIB: %p/share/EMBOSS/
EMBOSS_DATA: %p/share/EMBOSS/data
<<
DocFiles: <<
AUTHORS ChangeLog COMPAT COPYING FAQ INSTALL KNOWN_BUGS LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from the
web. Also, as extensive libraries are provided with the package, it is a
platform to allow other scientists to develop and release software in
true open source spirit. EMBOSS also integrates a range of currently
available packages and tools for sequence analysis into a seamless
whole.
<<
DescUsage: <<
See the README file for other environment variables you may need to
configure. See http://emboss.sourceforge.net/Jemboss/ for
information on using the Jemboss GUI for EMBOSS. To prevent conflicts,
the headers are located in %p/include/EMBOSS instead of %p/include.
Install emboss-kaptain for a GUI that works with X-Windows.
<<
DescPort: <<
dmacks added explicit linking to libs that supply symbols used by
the shared libraries here. This prevents things that link against
the shared libraries from having to know to pass additional flags
when the linker requires all symbols be defined.
dmacks overhauled splitoff layout so that lib versions can float
against each other and patched to assure use of EMBOSS's own pcre
headers (libpcre doesn't understand ABI compatibility rules:(
<<
Maintainer: Koen van der Drift
Homepage: http://emboss.sourceforge.net
License: GPL
diff -Naur EMBOSS-5.0.0/ajax/Makefile.in EMBOSS-5.0.0-patched/ajax/Makefile.in
--- EMBOSS-5.0.0/ajax/Makefile.in 2007-07-12 06:53:32.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/Makefile.in 2007-12-03 20:09:43.000000000 -0500
@@ -55,7 +55,8 @@
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
libLTLIBRARIES_INSTALL = $(INSTALL)
LTLIBRARIES = $(lib_LTLIBRARIES)
-libajax_la_LIBADD =
+#libajax_la_LIBADD =
+libajaxg_la_LIBADD = libajax.la ../plplot/libeplplot.la
am__libajax_la_SOURCES_DIST = ajacd.c ajalign.c ajarr.c ajassert.c \
ajbase.c ajcall.c ajcod.c ajdan.c ajdmx.c ajdom.c ajdomain.c \
ajexcept.c ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajindex.c \
@@ -85,7 +86,9 @@
$(libajax_la_LDFLAGS) $(LDFLAGS) -o $@
@ISCYGWIN_FALSE@am_libajax_la_rpath = -rpath $(libdir)
@ISCYGWIN_TRUE@am_libajax_la_rpath = -rpath $(libdir)
-libajaxg_la_LIBADD =
+#libajaxg_la_LIBADD =
+libajaxg_la_LIBADD = libajax.la ../plplot/libeplplot.la
+libajaxg_la_DEPENDENCIES = libajax.la ../plplot/libeplplot.la
am__libajaxg_la_SOURCES_DIST = ajgraph.c ajhist.c
@ISCYGWIN_FALSE@am_libajaxg_la_OBJECTS = $(am__objects_2)
libajaxg_la_OBJECTS = $(am_libajaxg_la_OBJECTS)
diff -Naur EMBOSS-5.0.0/ajax/ajindex.c EMBOSS-5.0.0-patched/ajax/ajindex.c
--- EMBOSS-5.0.0/ajax/ajindex.c 2007-07-06 08:18:48.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/ajindex.c 2008-03-06 05:47:31.000000000 -0500
@@ -1364,7 +1364,7 @@
{
id = bucket->Ids[i];
len = BT_BUCKIDLEN(id->id);
- if((lptr-buf+1)+len > cache->pagesize) /* overflow */
+ if((lptr-buf+1) + (len+1+BT_DDOFFROFF) > cache->pagesize) /* overflow */
{
ajDebug("WriteBucket: Overflow\n");
if(!overflow) /* No overflow buckets yet */
@@ -1986,6 +1986,9 @@
ajlong blockno = 0L;
ajlong rblockno = 0L;
ajlong lblockno = 0L;
+ ajlong ibn = 0L;
+
+
AjPStr mediankey = NULL;
ajlong medianless = 0L;
ajlong mediangtr = 0L;
@@ -2139,10 +2142,12 @@
}
- ipage = rpage;
+ ibn = rblockno;
if(strcmp(key->Ptr,mediankey->Ptr)<0)
- ipage = lpage;
+ ibn = lblockno;
+ ipage = ajBtreeCacheRead(cache,ibn);
+
btreeInsertNonFull(cache,ipage,key,less,greater);
@@ -2516,7 +2521,14 @@
static ajint btreeNumIdCompare(const void *a, const void *b)
{
- return (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
+ ajlong val;
+
+ val = (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
+
+ if(!val)
+ return 0;
+
+ return (val < 0L) ? -1 : 1;
}
@@ -9895,7 +9907,7 @@
/* @funcstatic btreeInsertKeySec *****************************************
**
-** Insert a secpndary key into a potentially full node
+** Insert a secondary key into a potentially full node
**
** @param [u] cache [AjPBtcache] cache
** @param [u] page [AjPBtpage] original page
@@ -9936,7 +9948,8 @@
ajlong blockno = 0L;
ajlong rblockno = 0L;
ajlong lblockno = 0L;
-
+ ajlong ibn = 0L;
+
AjPStr mediankey = NULL;
ajlong medianless = 0L;
ajlong mediangtr = 0L;
@@ -10090,10 +10103,12 @@
}
- ipage = rpage;
+ ibn = rblockno;
if(strcmp(key->Ptr,mediankey->Ptr)<0)
- ipage = lpage;
+ ibn = lblockno;
+ ipage = ajBtreeCacheRead(cache,ibn);
+
btreeInsertNonFullSec(cache,ipage,key,less,greater);
@@ -10258,7 +10273,7 @@
btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
i = 0;
@@ -10355,7 +10370,7 @@
btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
i = 0;
@@ -10668,7 +10683,7 @@
btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
page = ajBtreeCacheRead(cache,pSarray[skeys]);
@@ -10726,7 +10741,7 @@
btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
page = ajBtreeCacheRead(cache,pSarray[0]);
@@ -11956,8 +11971,14 @@
static ajint btreeOffsetCompare(const void *a, const void *b)
{
- return (*(AjPBtId const *)a)->offset -
- (*(AjPBtId const *)b)->offset;
+ ajlong val;
+
+ val = (*(AjPBtId const *)a)->offset - (*(AjPBtId const *)b)->offset;
+
+ if(!val)
+ return 0;
+
+ return (val < 0L) ? -1 : 1;
}
@@ -13386,6 +13407,8 @@
ajlong blockno = 0L;
ajlong rblockno = 0L;
ajlong lblockno = 0L;
+ ajlong ibn = 0L;
+
AjPStr mediankey = NULL;
ajlong medianless = 0L;
ajlong mediangtr = 0L;
@@ -13534,13 +13557,15 @@
}
- ipage = rpage;
+ ibn = rblockno;
if(strcmp(key->Ptr,mediankey->Ptr)<0)
- ipage = lpage;
+ ibn = lblockno;
lpage->dirty = BT_DIRTY;
rpage->dirty = BT_DIRTY;
+ ipage = ajBtreeCacheRead(cache,ibn);
+
btreeInsertNonFull(cache,ipage,key,less,greater);
@@ -15020,6 +15045,8 @@
ajlong blockno = 0L;
ajlong rblockno = 0L;
ajlong lblockno = 0L;
+ ajlong ibn = 0L;
+
ajlong mediankey = 0L;
ajlong medianless = 0L;
ajlong mediangtr = 0L;
@@ -15162,12 +15189,14 @@
}
- ipage = rpage;
+ ibn = rblockno;
if(key < mediankey)
- ipage = lpage;
+ ibn = lblockno;
lpage->dirty = BT_DIRTY;
rpage->dirty = BT_DIRTY;
+
+ ipage = ajBtreeCacheRead(cache,ibn);
btreeNumInsertNonFull(cache,ipage,key,less,greater);
@@ -15502,7 +15531,7 @@
btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
page = ajBtreeCacheRead(cache,pSarray[skeys]);
@@ -15551,7 +15580,7 @@
btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
page = ajBtreeCacheRead(cache,pSarray[0]);
@@ -15727,7 +15756,7 @@
btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
i = 0;
@@ -15817,7 +15846,7 @@
btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
- if(!ppage->pageno)
+ if(ppage->pageno == cache->secrootblock)
ppage->dirty = BT_LOCK;
i = 0;
diff -Naur EMBOSS-5.0.0/ajax/ajindex.h EMBOSS-5.0.0-patched/ajax/ajindex.h
--- EMBOSS-5.0.0/ajax/ajindex.h 2007-07-11 12:07:25.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/ajindex.h 2008-03-06 05:47:38.000000000 -0500
@@ -38,6 +38,66 @@
#define TX_EXTENSION "xtx"
+/* Useful page filling values */
+
+/*
+ * Length of integers after the ID string in a primary bucket
+ * i.e. dbno + dups + offset + refoffset
+ */
+#define BT_DDOFFROFF (sizeof(ajint) + sizeof(ajint) + sizeof(ajlong) + \
+ sizeof(ajlong))
+
+/*
+ * Preamble before key lengths in an internal node
+ * i.e. nodetype+blocknumber+nkeys+totlen+left+right+overflow+prev
+ */
+#define BT_NODEPREAMBLE (sizeof(ajint) + sizeof(ajlong) + sizeof(ajint) + \
+ sizeof(ajint) + sizeof(ajlong) + sizeof(ajlong) + sizeof(ajlong) + \
+ sizeof(ajlong))
+
+/*
+ * This is the length of extra pointer required in primary index
+ * page space calculations i.e. the total space taken by
+ * key/pointer pairs in an internal page is:
+ * BT_PTRLEN + ((keylenmax + sizeof(long))*nkeys)
+ * This is because there is one more pointer than the
+ * value of 'order' in a B+ tree.
+ */
+#define BT_PTRLEN sizeof(ajlong)
+
+
+/*
+ * Length of extra space, on top of a key string, taken up by a
+ * key in an internal node. This is an ajint holding the length
+ * of a string plus the length of a block pointer (ajlong)
+ */
+#define BT_IDKEYEXTRA (sizeof(ajint) + sizeof(ajlong))
+
+
+/*
+ * Preamble before key lengths in an id bucket
+ * i.e. nodetype+nentries+overflow
+ */
+#define BT_BUCKPREAMBLE (sizeof(ajint) + sizeof(ajint) + sizeof(ajlong))
+
+
+/*
+ * Size of a key in a key length table block in an internal node or bucket
+ */
+#define BT_KEYLENENTRY sizeof(ajint)
+
+/*
+ * Size of an offset key
+ */
+#define BT_OFFKEYLEN sizeof(ajlong)
+
+/*
+ * Length of integers per entry in a num bucket
+ * i.e. dbno + offset + refoffset
+ */
+#define BT_DOFFROFF (sizeof(ajint) + sizeof(ajlong) + sizeof(ajlong))
+
+
/* @data AjPBtNode ***********************************************************
diff -Naur EMBOSS-5.0.0/ajax/ajseqdb.c EMBOSS-5.0.0-patched/ajax/ajseqdb.c
--- EMBOSS-5.0.0/ajax/ajseqdb.c 2007-07-06 08:22:40.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/ajseqdb.c 2008-02-29 12:14:48.000000000 -0500
@@ -4314,7 +4314,7 @@
if(!seqRegGcgId)
{
- seqRegGcgId =ajRegCompC("^>...([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
+ seqRegGcgId =ajRegCompC("^>...([^ ]+) +(Dummy Header|[^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
}
@@ -4352,7 +4352,7 @@
else if(ajRegExec(seqRegGcgId2, line))
{
ajStrAssignC(&gcgtype, "ASCII");
- ajRegSubI(seqRegGcgId, 1, &tmpstr);
+ ajRegSubI(seqRegGcgId2, 1, &tmpstr);
ispir = ajTrue;
}
else
@@ -5546,7 +5546,7 @@
if(!seqRegGcgId)
{
- seqRegGcgId =ajRegCompC("^>...([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
+ seqRegGcgId =ajRegCompC("^>...([^ ]+) +(Dummy Header|[^ ]+) +([^ ]+) +([^ ]+) +([0-9]+)");
seqRegGcgId2=ajRegCompC("^>[PF]1;([^ ]+)");
}
@@ -5584,7 +5584,7 @@
else if(ajRegExec(seqRegGcgId2, line))
{
ajStrAssignC(&gcgtype, "ASCII");
- ajRegSubI(seqRegGcgId, 1, &tmpstr);
+ ajRegSubI(seqRegGcgId2, 1, &tmpstr);
ispir = ajTrue;
}
else
diff -Naur EMBOSS-5.0.0/ajax/ajseqread.c EMBOSS-5.0.0-patched/ajax/ajseqread.c
--- EMBOSS-5.0.0/ajax/ajseqread.c 2007-07-11 08:09:51.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/ajseqread.c 2008-02-29 12:14:49.000000000 -0500
@@ -604,7 +604,7 @@
/* Feature Gap, ReadFunction, Multiset, Padding */
{"unknown", "Unknown format",
AJFALSE, AJFALSE, AJTRUE, AJTRUE,
- AJTRUE, AJTRUE, seqReadText, AJTRUE, 0}, /* alias for text */
+ AJTRUE, AJTRUE, seqReadText, AJFALSE, 0}, /* alias for text */
{"gcg", "GCG sequence format",
AJFALSE, AJTRUE, AJTRUE, AJTRUE,
AJFALSE, AJTRUE, seqReadGcg, AJFALSE, 0}, /* do first, headers mislead */
@@ -6637,6 +6637,7 @@
else /* test for a SwissProt/SpTrEMBL entry */
{
if(ajStrFindC(seqReadLine, " PRT; ")>= 0 ||
+ ajStrFindC(seqReadLine, " Unreviewed; ") >= 0 ||
ajStrFindC(seqReadLine, " Reviewed; ") >= 0 ||
ajStrFindC(seqReadLine, " Preliminary; ") >= 0
)
@@ -6650,7 +6651,7 @@
ok = ajFileBuffGetStore(buff, &seqReadLine, seqin->Text, &thys->TextPtr);
- while(ok && !ajStrPrefixC(seqReadLine, "SQ "))
+ while(ok && !ajStrPrefixC(seqReadLine, "SQ"))
{
bufflines++;
@@ -7028,6 +7029,17 @@
}
}
+ if(!ajSeqIsNuc(thys))
+ {
+ ajFileBuffReset(buff);
+ ajStrDel(&tmpstr);
+ ajStrDel(&token);
+ ajStrDel(&datestr);
+ ajStrDel(&relstr);
+ ajStrTokenDel(&handle);
+ return ajFalse;
+ }
+
ajSeqSetNuc(thys);
ajFileBuffClear(buff, 0);
@@ -7830,8 +7842,10 @@
if(ajStrMatchC(typstr, "Protein"))
ajSeqSetProt(thys);
- else
+ else if(ajSeqIsNuc(thys))
ajSeqSetNuc(thys);
+ else
+ ajSeqSetProt(thys);
ajFileBuffClear(buff, 0);
diff -Naur EMBOSS-5.0.0/ajax/ajseqtype.c EMBOSS-5.0.0-patched/ajax/ajseqtype.c
--- EMBOSS-5.0.0/ajax/ajseqtype.c 2007-02-09 13:30:59.000000000 -0500
+++ EMBOSS-5.0.0-patched/ajax/ajseqtype.c 2008-02-29 12:14:49.000000000 -0500
@@ -160,7 +160,7 @@
** - Phylip and some alignment output
** ~ GCG for gaps at ends
** * Staden for DNA but stop for protein (fix on input?)
-** O Phylip (fix on input?)
+** O Phylip (fix on input?) - no longer possible: O is pyrrolysine in proteins
*/
@@ -174,14 +174,14 @@
char seqCharNuc[] = "ACGTUBDHKMNRSVWXY?";
char seqCharNucPure[] = "ACGTU";
char seqCharNucAmbig[] = "BDHKMNRSVWXY?";
-char seqCharGap[] = ".~O-"; /* phylip uses O */
+char seqCharGap[] = ".~-"; /* phylip uses O */
char seqCharNucDna[] = "ACGTBDHKMNRSVWXY?";
char seqCharNucRna[] = "ACGUBDHKMNRSVWXY?";
-char seqCharGapany[] = ".~O-"; /* phylip uses O */
+char seqCharGapany[] = ".~-"; /* phylip uses O */
char seqCharGapdash[] = "-";
char seqCharGapdot[] = ".";
char seqGap = '-'; /* the (only) EMBOSS gap character */
-char seqCharGapTest[] = " .~O-"; /* phylip uses O - don't forget space */
+char seqCharGapTest[] = " .~-"; /* phylip uses O - don't forget space */
char seqCharPhylo[] = "?"; /* phylip uses ? for unknown or gap */
diff -Naur EMBOSS-5.0.0/ajax/ajseqwrite.c EMBOSS-5.0.0-patched/ajax/ajseqwrite.c
--- EMBOSS-5.0.0/ajax/ajseqwrite.c 2007-07-06 08:10:46.000000000 -0400
+++ EMBOSS-5.0.0-patched/ajax/ajseqwrite.c 2008-02-29 12:14:50.000000000 -0500
@@ -2788,18 +2788,18 @@
{
if(ilen + ajStrGetLen(cur) > 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "AC ", cur);
+ ajFmtPrintF(outseq->File, "AC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
@@ -2808,7 +2808,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
}
if(ajStrGetLen(outseq->Sv))
@@ -2827,25 +2827,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KW ", cur);
+ ajFmtPrintF(outseq->File, "KW ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajStrGetLen(outseq->Tax))
@@ -2859,25 +2859,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "OC ", cur);
+ ajFmtPrintF(outseq->File, "OC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(seqoutUfoLocal(outseq))
@@ -2973,18 +2973,18 @@
{
if(ilen + ajStrGetLen(cur) > 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "AC ", cur);
+ ajFmtPrintF(outseq->File, "AC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
@@ -2993,7 +2993,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
}
if(ajStrGetLen(outseq->Sv))
@@ -3021,25 +3021,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KW ", cur);
+ ajFmtPrintF(outseq->File, "KW ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajStrGetLen(outseq->Tax))
@@ -3053,25 +3053,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "OC ", cur);
+ ajFmtPrintF(outseq->File, "OC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(seqoutUfoLocal(outseq))
@@ -3209,7 +3209,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ";\nXX\n", cur);
+ ajFmtPrintF(outseq->File, ";\nXX\n");
}
/* no SV line in the new format - see the ID line */
@@ -3237,7 +3237,7 @@
"DT %D (Rel. %S, Last updated, Version %S)\n",
outseq->Date->ModDate, outseq->Date->ModRel,
outseq->Date->ModVer);
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
}
if(ajStrGetLen(outseq->Desc))
@@ -3250,7 +3250,7 @@
ajFmtPrintF(outseq->File, "DE %S\n", tmpline);
tmpline = ajStrParseC(NULL, "\n");
}
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
}
if(ajListGetLength(outseq->Keylist))
@@ -3261,25 +3261,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KW ", cur);
+ ajFmtPrintF(outseq->File, "KW ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\nXX\n", cur);
+ ajFmtPrintF(outseq->File, ".\nXX\n");
}
if(ajStrGetLen(outseq->Tax))
@@ -3293,25 +3293,25 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "OC ", cur);
+ ajFmtPrintF(outseq->File, "OC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajStrGetLen(outseq->Organelle))
ajFmtPrintF(outseq->File, "OG %S\n", outseq->Organelle);
@@ -3319,7 +3319,7 @@
if(ajStrGetLen(outseq->Tax) ||
ajStrGetLen(outseq->Organelle) ||
ajListGetLength(outseq->Taxlist) > 1)
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
if(ajListGetLength(outseq->Reflist))
{
@@ -3438,7 +3438,7 @@
}
}
ajListIterDel(&it);
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
}
if(ajListGetLength(outseq->Cmtlist))
@@ -3457,7 +3457,7 @@
ajFmtPrintF(outseq->File, "CC %S\n", tmpline);
tmpline = ajStrParseC(NULL, "\n");
}
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
}
ajListIterDel(&it);
}
@@ -3471,7 +3471,7 @@
if(!ajFeatWrite(outseq->Ftquery, outseq->Fttable))
ajWarn("seqWriteEmbl features output failed UFO: '%S'",
outseq->Ufo);
- ajFmtPrintF(outseq->File, "XX\n", cur);
+ ajFmtPrintF(outseq->File, "XX\n");
}
ajSeqoutGetBasecount(outseq, b);
@@ -3541,18 +3541,18 @@
{
if(ilen + ajStrGetLen(cur) > 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "AC ", cur);
+ ajFmtPrintF(outseq->File, "AC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
@@ -3562,7 +3562,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
}
if(ajStrGetLen(outseq->Desc))
@@ -3579,18 +3579,18 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "OC ", cur);
+ ajFmtPrintF(outseq->File, "OC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
@@ -3598,7 +3598,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajListGetLength(outseq->Keylist))
@@ -3609,18 +3609,18 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KW ", cur);
+ ajFmtPrintF(outseq->File, "KW ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
@@ -3628,7 +3628,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(seqoutUfoLocal(outseq))
@@ -3708,18 +3708,18 @@
{
if(ilen + ajStrGetLen(cur) > 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "AC ", cur);
+ ajFmtPrintF(outseq->File, "AC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
@@ -3729,7 +3729,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
}
if(ajStrGetLen(outseq->Desc))
@@ -3746,18 +3746,18 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "OC ", cur);
+ ajFmtPrintF(outseq->File, "OC ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
@@ -3765,7 +3765,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajListGetLength(outseq->Keylist))
@@ -3776,18 +3776,18 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KW ", cur);
+ ajFmtPrintF(outseq->File, "KW ");
ilen = 6;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
@@ -3795,7 +3795,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(seqoutUfoLocal(outseq))
@@ -3918,23 +3918,20 @@
it = ajListIterNewread(outseq->Acclist);
while((cur = (AjPStr) ajListIterGet(it)))
{
- if(ilen + ajStrGetLen(cur) > 79)
- {
- ajFmtPrintF(outseq->File, "\n", cur);
- ilen = 0;
- }
-
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "ACCESSION ", cur);
- ilen = 12;
+ ajFmtPrintF(outseq->File, "ACCESSION ");
+ ilen = 11;
}
- else
+ if(ilen + ajStrGetLen(cur) > 79)
{
- ajFmtPrintF(outseq->File, " ", cur);
- ilen += 1;
+ ajFmtPrintF(outseq->File, "\n ");
+ ilen = 11;
}
+ ajFmtPrintF(outseq->File, " ");
+ ilen += 1;
+
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
@@ -3942,7 +3939,7 @@
ajListIterDel(&it) ;
if(ilen > 0)
- ajFmtPrintF(outseq->File, "\n", cur);
+ ajFmtPrintF(outseq->File, "\n");
}
if(ajStrGetLen(outseq->Sv))
@@ -3960,28 +3957,26 @@
it = ajListIterNewread(outseq->Keylist);
while((cur = (AjPStr) ajListIterGet(it)))
{
- if(ilen+ajStrGetLen(cur) >= 79)
- {
- ajFmtPrintF(outseq->File, ";\n", cur);
- ilen = 0;
- }
-
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, "KEYWORDS ", cur);
- ilen = 12;
+ ajFmtPrintF(outseq->File, "KEYWORDS ");
+ ilen = 11;
}
- else
+ if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, "; ", cur);
- ilen += 2;
+ ajFmtPrintF(outseq->File, ";\n ");
+ ilen = 11;
}
+
+ ajFmtPrintF(outseq->File, "; ");
+ ilen += 2;
+
ajFmtPrintF(outseq->File, "%S", cur);
ilen += ajStrGetLen(cur);
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
if(ajStrGetLen(outseq->Tax))
@@ -3997,18 +3992,18 @@
{
if(ilen+ajStrGetLen(cur) >= 79)
{
- ajFmtPrintF(outseq->File, ";\n", cur);
+ ajFmtPrintF(outseq->File, ";\n");
ilen = 0;
}
if(ilen == 0)
{
- ajFmtPrintF(outseq->File, " ", cur);
+ ajFmtPrintF(outseq->File, " ");
ilen = 12;
}
else
{
- ajFmtPrintF(outseq->File, "; ", cur);
+ ajFmtPrintF(outseq->File, "; ");
ilen += 2;
}
ajFmtPrintF(outseq->File, "%S", cur);
@@ -4016,7 +4011,7 @@
}
ajListIterDel(&it) ;
- ajFmtPrintF(outseq->File, ".\n", cur);
+ ajFmtPrintF(outseq->File, ".\n");
}
}
diff -Naur EMBOSS-5.0.0/emboss/dbxfasta.c EMBOSS-5.0.0-patched/emboss/dbxfasta.c
--- EMBOSS-5.0.0/emboss/dbxfasta.c 2007-07-06 08:15:29.000000000 -0400
+++ EMBOSS-5.0.0-patched/emboss/dbxfasta.c 2008-02-29 12:17:19.000000000 -0500
@@ -34,6 +34,8 @@
static AjPRegexp dbxfasta_wrdexp = NULL;
+static ajuint maxidlen = 0;
+static ajuint idtrunc = 0;
static AjBool dbxfasta_NextEntry(EmbPBtreeEntry entry, AjPFile inf,
AjPRegexp typeexp, ajint idtype);
@@ -187,7 +189,9 @@
embBtreeDumpParameters(entry);
embBtreeCloseCaches(entry);
-
+ if(maxidlen)
+ ajUser("Resource idlen truncated %u IDs. Maximum ID length was %u.",
+ idtrunc, maxidlen);
embBtreeEntryDel(&entry);
ajStrDel(&tmpstr);
ajStrDel(&filename);
@@ -431,12 +435,27 @@
return ajFalse;
}
+ if(ajStrGetLen(entry->id) > entry->idlen)
+ {
+ if(ajStrGetLen(entry->id) > maxidlen)
+ {
+ ajWarn("id '%S' too long, truncating to idlen %d",
+ entry->id, entry->idlen);
+ maxidlen = ajStrGetLen(entry->id);
+ }
+ idtrunc++;
+ ajStrKeepRange(&entry->id,0,entry->idlen-1);
+ }
+
ajStrFmtLower(&entry->id);
if(entry->do_accession && ajStrGetLen(ac))
{
str = ajStrNew();
- ajStrAssignS(&str,ac);
+ if(ajStrGetLen(ac) > entry->aclen)
+ ajStrAssignSubS(&str,ac,0,entry->aclen-1);
+ else
+ ajStrAssignS(&str,ac);
ajListPush(entry->ac,(void *)str);
}
@@ -444,13 +463,17 @@
ajStrAssignS(&sv,gi);
if(entry->do_sv && ajStrGetLen(sv))
+ embBtreeFastaDE(sv, entry->sv, entry->svlen);
+/*
{
str = ajStrNew();
ajStrAssignS(&str,sv);
ajListPush(entry->ac,(void *)str);
}
-
+*/
if(entry->do_description && ajStrGetLen(de))
+ embBtreeFastaDE(de, entry->de, entry->delen);
+/*
while(ajRegExec(dbxfasta_wrdexp,de))
{
ajRegSubI(dbxfasta_wrdexp, 1, &tmpfd);
@@ -459,7 +482,7 @@
ajListPush(entry->de,(void *)str);
ajRegPost(dbxfasta_wrdexp, &de);
}
-
+*/
ajStrDel(&de);
ajStrDel(&ac);
diff -Naur EMBOSS-5.0.0/emboss/psiphi.c EMBOSS-5.0.0-patched/emboss/psiphi.c
--- EMBOSS-5.0.0/emboss/psiphi.c 2007-07-06 08:15:29.000000000 -0400
+++ EMBOSS-5.0.0-patched/emboss/psiphi.c 2007-07-27 05:28:27.000000000 -0400
@@ -160,7 +160,7 @@
finishres = ajAcdGetInt("finishresiduenumber");
/* reserve memory for and read in structure */
- /* JISON */ pdb = ajPdbReadoldNew(pdbfile);
+ /* JISON */ pdb = ajPdbReadNew(pdbfile,0);
/* check and set number of chain to be analysed */
highest = pdb->Nchn;
@@ -440,6 +440,9 @@
ajint lowestres = 0;
AjPAtom inlist = NULL;
+
+ if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
+ ajFatal("Chain %d has no atoms",myindex+1);
/* read first atom in list into memory, but keep it on list */
ajListPeek(pdb->Chains[myindex]->Atoms,
diff -Naur EMBOSS-5.0.0/nucleus/embindex.c EMBOSS-5.0.0-patched/nucleus/embindex.c
--- EMBOSS-5.0.0/nucleus/embindex.c 2007-07-06 08:15:00.000000000 -0400
+++ EMBOSS-5.0.0-patched/nucleus/embindex.c 2008-03-06 05:47:44.000000000 -0500
@@ -24,6 +24,12 @@
#define KWLIMIT 12
+static AjPStr embindexLine = NULL;
+static AjPStr embindexToken = NULL;
+static AjPStr embindexTstr = NULL;
+static AjPStr embindexPrefix = NULL;
+static AjPStr embindexFormat = NULL;
+static AjPStrTok embindexHandle = NULL;
static AjPFile btreeCreateFile(const AjPStr idirectory, const AjPStr dbname,
@@ -51,12 +57,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(kwline)[5]);
+ ajStrAssignSubS(&line, kwline, 5, -1);
- handle = ajStrTokenNewC(line,"\n;");
+ handle = ajStrTokenNewC(line,"\n\r;");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -64,7 +67,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -77,6 +79,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(kwlist,(void *)str);
+ str = NULL;
}
}
@@ -109,12 +112,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(txline)[5]);
+ ajStrAssignSubS(&line, txline, 5, -1);
- handle = ajStrTokenNewC(line,"\n;()");
+ handle = ajStrTokenNewC(line,"\n\r;()");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -123,7 +123,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -136,6 +135,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(txlist,(void *)str);
+ str = NULL;
}
}
@@ -162,72 +162,54 @@
void embBtreeEmblAC(const AjPStr acline, AjPList aclist)
{
- AjPStr line = NULL;
- AjPStrTok handle = NULL;
- AjPStr token = NULL;
- AjPStr str = NULL;
- AjPStr tstr = NULL;
- AjPStr prefix = NULL;
- AjPStr format = NULL;
char *p = NULL;
char *q = NULL;
ajuint lo = 0;
ajuint hi = 0;
ajuint field = 0;
ajuint i;
+ AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
- tstr = ajStrNew();
- prefix = ajStrNew();
- format = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(acline)[5]);
+ ajStrAssignSubS(&embindexLine, acline, 5, -1);
- handle = ajStrTokenNewC(line,"\n;");
+ ajStrTokenAssignC(&embindexHandle,embindexLine,"\n\r;");
- while(ajStrTokenNextParse(&handle,&token))
+ while(ajStrTokenNextParse(&embindexHandle,&embindexToken))
{
- ajStrTrimWhite(&token);
- if((p=strchr(MAJSTRGETPTR(token),(int)'-')))
+ ajStrTrimWhite(&embindexToken);
+ if((p=strchr(MAJSTRGETPTR(embindexToken),(int)'-')))
{
q = p;
while(isdigit((int)*(--q)));
++q;
- ajStrAssignSubC(&tstr,q,0,(ajuint)(p-q-1));
- ajStrToUint(tstr,&lo);
+ ajStrAssignSubC(&embindexTstr,q,0,(ajuint)(p-q-1));
+ ajStrToUint(embindexTstr,&lo);
field = (ajuint) (p-q);
- ajFmtPrintS(&format,"%%S%%0%uu",field);
+ ajFmtPrintS(&embindexFormat,"%%S%%0%uu",field);
++p;
q = p;
while(!isdigit((int)*q))
++q;
sscanf(q,"%u",&hi);
- ajStrAssignSubC(&prefix,p,0,(ajuint)(q-p-1));
+ ajStrAssignSubC(&embindexPrefix,p,0,(ajuint)(q-p-1));
for(i=lo;i<=hi;++i)
{
- str = ajStrNew();
- ajFmtPrintS(&str,MAJSTRGETPTR(format),prefix,i);
+ ajFmtPrintS(&str,MAJSTRGETPTR(embindexFormat),
+ embindexPrefix,i);
ajListPush(aclist,(void *)str);
+ str = NULL;
}
}
else
{
- str = ajStrNew();
- ajStrAssignS(&str,token);
+ ajStrAssignS(&str,embindexToken);
ajListPush(aclist,(void *)str);
+ str = NULL;
}
}
- ajStrDel(&tstr);
- ajStrDel(&prefix);
- ajStrDel(&format);
- ajStrDel(&token);
- ajStrTokenDel(&handle);
- ajStrDel(&line);
-
return;
}
@@ -253,16 +235,10 @@
AjPStr idstr = NULL;
AjPStr svstr = NULL;
- line = ajStrNew();
- token = ajStrNew();
- idstr = ajStrNew();
- svstr = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(idline)[5]);
+ ajStrAssignSubS(&line, idline, 5, -1);
- handle = ajStrTokenNewC(line," \t\n;");
+ handle = ajStrTokenNewC(line," \t\n\r;");
- str = ajStrNew();
if(!ajStrTokenNextParse(&handle,&idstr))
return;
if(!ajStrTokenNextParse(&handle,&token))
@@ -273,10 +249,13 @@
if(!ajStrMatchC(token, "SV"))
return;
+ str = ajStrNewRes(MAJSTRGETLEN(idstr)+MAJSTRGETLEN(svstr)+2);
+
ajFmtPrintS(&str,"%S.%S", idstr, svstr);
ajListPush(svlist,(void *)str);
-
+ str = NULL;
+
ajStrDel(&idstr);
ajStrDel(&svstr);
ajStrDel(&token);
@@ -308,12 +287,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(deline)[5]);
+ ajStrAssignSubS(&line, deline, 5, -1);
- handle = ajStrTokenNewC(line,"\n \t()");
+ handle = ajStrTokenNewC(line,"\n\r \t()");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -321,7 +297,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -334,6 +309,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(delist,(void *)str);
+ str = NULL;
}
}
@@ -373,16 +349,10 @@
ajuint hi = 0;
ajuint field = 0;
ajuint i;
-
- line = ajStrNew();
- token = ajStrNew();
- tstr = ajStrNew();
- prefix = ajStrNew();
- format = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(acline)[12]);
- handle = ajStrTokenNewC(line,"\n ");
+ ajStrAssignSubS(&line, acline, 12, -1);
+
+ handle = ajStrTokenNewC(line,"\n\r ");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -406,16 +376,16 @@
for(i=lo;i<=hi;++i)
{
- str = ajStrNew();
ajFmtPrintS(&str,MAJSTRGETPTR(format),prefix,i);
ajListPush(aclist,(void *)str);
+ str = NULL;
}
}
else
{
- str = ajStrNew();
ajStrAssignS(&str,token);
ajListPush(aclist,(void *)str);
+ str = NULL;
}
}
@@ -451,12 +421,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(kwline)[8]);
+ ajStrAssignSubS(&line, kwline, 8, -1);
- handle = ajStrTokenNewC(line,"\n;");
+ handle = ajStrTokenNewC(line,"\n\r;");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -464,7 +431,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -477,6 +443,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(kwlist,(void *)str);
+ str = NULL;
}
}
@@ -509,12 +476,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(kwline)[10]);
+ ajStrAssignSubS(&line, kwline, 10, -1);
- handle = ajStrTokenNewC(line,"\n \t()");
+ handle = ajStrTokenNewC(line,"\n\r \t()");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -522,7 +486,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -535,6 +498,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(kwlist,(void *)str);
+ str = NULL;
}
}
@@ -567,12 +531,9 @@
AjPStr token = NULL;
AjPStr str = NULL;
- line = ajStrNew();
- token = ajStrNew();
-
- ajStrAssignC(&line, &MAJSTRGETPTR(kwline)[9]);
+ ajStrAssignSubS(&line, kwline, 9, -1);
- handle = ajStrTokenNewC(line,"\n;()");
+ handle = ajStrTokenNewC(line,"\n\r;()");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -581,7 +542,6 @@
ajStrTrimWhite(&token);
if(ajStrGetLen(token))
{
- str = ajStrNew();
if(maxlen)
{
if(ajStrGetLen(token) > maxlen)
@@ -594,6 +554,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(kwlist,(void *)str);
+ str = NULL;
}
}
@@ -625,9 +586,7 @@
AjPStr token = NULL;
AjPStr str = NULL;
- token = ajStrNew();
-
- handle = ajStrTokenNewC(kwline,"\n ");
+ handle = ajStrTokenNewC(kwline,"\n\r ");
while(ajStrTokenNextParse(&handle,&token))
{
@@ -648,6 +607,7 @@
ajStrAssignS(&str,token);
ajStrFmtLower(&str);
ajListPush(kwlist,(void *)str);
+ str = NULL;
}
}
@@ -1156,11 +1116,16 @@
}
if(!ajNamGetValueC("CACHESIZE",&value))
+ {
entry->cachesize = BTREE_DEF_CACHESIZE;
+ ajUser("CACHESIZE defaults to %d", entry->cachesize);
+ }
else
{
if(ajStrToUint(value,&n))
+ {
entry->cachesize = n;
+ }
else
{
ajErr("Bad value for environment variable 'CACHESIZE'");
@@ -1169,11 +1134,16 @@
}
if(!ajNamGetValueC("PAGESIZE",&value))
+ {
entry->pagesize = BTREE_DEF_PAGESIZE;
+ ajUser("PAGESIZE defaults to %d", entry->pagesize);
+ }
else
{
if(ajStrToUint(value,&n))
+ {
entry->pagesize = n;
+ }
else
{
ajErr("Bad value for environment variable 'PAGESIZE'");
@@ -1182,37 +1152,83 @@
}
- entry->idorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
- entry->idfill = (entry->pagesize - 16) / (entry->idlen + 28);
- entry->acorder = (entry->pagesize - 60) / ((entry->aclen + 1) + 12);
- entry->acfill = (entry->pagesize - 16) / (entry->aclen + 28);
- entry->svorder = (entry->pagesize - 60) / ((entry->svlen + 1) + 12);
- entry->svfill = (entry->pagesize - 16) / (entry->svlen + 28);
-
- entry->kworder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
- entry->kwfill = (entry->pagesize - 16) / (entry->kwlen + 28);
- entry->deorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
- entry->defill = (entry->pagesize - 16) / (entry->delen + 28);
- entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
- entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
-
- entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
- entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
- entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-
- entry->kwsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
- entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
- entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+ entry->idorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->idlen + 1) + BT_IDKEYEXTRA);
- entry->idsecorder = (entry->pagesize - 60) / 24;
- entry->idsecfill = (entry->pagesize - 60) / 20;
+ entry->idfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->idlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
- entry->acsecorder = (entry->pagesize - 60) / 24;
- entry->acsecfill = (entry->pagesize - 60) / 20;
+ entry->acorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->aclen + 1) + BT_IDKEYEXTRA);
+
+ entry->acfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->aclen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
+
+ entry->svorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->svlen + 1) + BT_IDKEYEXTRA);
+
+ entry->svfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->svlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
+
+ entry->kworder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->kwlen + 1) + BT_IDKEYEXTRA);
+
+ entry->kwfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->kwlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
+
+ entry->deorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->delen + 1) + BT_IDKEYEXTRA);
+
+ entry->defill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->delen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
+
+ entry->txorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->txlen + 1) + BT_IDKEYEXTRA);
+
+ entry->txfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->txlen + 1) + BT_KEYLENENTRY + BT_DDOFFROFF);
+
+
+ entry->idsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ (BT_OFFKEYLEN + BT_IDKEYEXTRA);
+
+ entry->acsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ (BT_OFFKEYLEN + BT_IDKEYEXTRA);
+
+ entry->svsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ (BT_OFFKEYLEN + BT_IDKEYEXTRA);
+
+
+ entry->idsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ BT_DOFFROFF;
+
+ entry->acsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ BT_DOFFROFF;
+
+ entry->svsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ BT_DOFFROFF;
+
+
+ /*
+ * The secondary tree keys are the IDs of the entries containing
+ * the keywords
+ */
+
+ entry->kwsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->idlen + 1) + BT_IDKEYEXTRA);
+ entry->desecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->idlen + 1) + BT_IDKEYEXTRA);
+ entry->txsecorder = (entry->pagesize - (BT_NODEPREAMBLE + BT_PTRLEN)) /
+ ((entry->idlen + 1) + BT_IDKEYEXTRA);
+
+
+ entry->kwsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->idlen + 1) + BT_KEYLENENTRY);
+ entry->desecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->idlen + 1) + BT_KEYLENENTRY);
+ entry->txsecfill = (entry->pagesize - BT_BUCKPREAMBLE) /
+ ((entry->idlen + 1) + BT_KEYLENENTRY);
- entry->svsecorder = (entry->pagesize - 60) / 24;
- entry->svsecfill = (entry->pagesize - 60) / 20;
-
ajStrDel(&value);
return;
@@ -1251,7 +1267,7 @@
entry->cachesize,
entry->idsecorder, slevel,
entry->idsecfill, count,
- entry->kwlen);
+ entry->idlen);
if(!entry->idcache)
ajFatal("Cannot open ID index");
@@ -1267,7 +1283,7 @@
entry->cachesize,
entry->acsecorder, slevel,
entry->acsecfill, count,
- entry->kwlen);
+ entry->aclen);
if(!entry->accache)
ajFatal("Cannot open ACC index");
@@ -1282,7 +1298,7 @@
entry->cachesize,
entry->svsecorder, slevel,
entry->svsecfill, count,
- entry->kwlen);
+ entry->svlen);
if(!entry->svcache)
ajFatal("Cannot open SV index");
@@ -1414,6 +1430,44 @@
+#if 0
+
+/* @func embBtreeProbeCaches ***********************************************
+**
+** Close index files
+**
+** @param [u] entry [EmbPBtreeEntry] database data
+**
+** @return [AjBool] true on success
+** @@
+******************************************************************************/
+
+AjBool embBtreeProbeCaches(EmbPBtreeEntry entry)
+{
+
+ if(entry->do_id)
+ {
+ ajBtreeProbePriArray(entry->idcache);
+ ajBtreeProbeSecArray(entry->idcache);
+ }
+
+ if(entry->do_accession)
+ {
+ ajBtreeProbePriArray(entry->accache);
+ ajBtreeProbeSecArray(entry->accache);
+ }
+
+ if(entry->do_sv)
+ {
+ ajBtreeProbePriArray(entry->svcache);
+ ajBtreeProbeSecArray(entry->svcache);
+ }
+
+ return ajTrue;
+}
+
+#endif
+
/* @func embBtreeDumpParameters ***********************************************
**
@@ -1454,3 +1508,23 @@
return ajTrue;
}
+
+
+/* @func embIndexExit **********************************************************
+**
+** Cleanup indexing internals on exit
+**
+** @return [void]
+******************************************************************************/
+
+void embIndexExit(void)
+{
+ ajStrDel(&embindexLine);
+ ajStrDel(&embindexToken);
+ ajStrDel(&embindexTstr);
+ ajStrDel(&embindexPrefix);
+ ajStrDel(&embindexFormat);
+ ajStrTokenDel(&embindexHandle);
+
+ return;
+}
Package: emboss
Version: 6.0.1
Revision: 2
#Distribution: 10.4
Depends: %N-ajax6-shlibs (>= %v-%r), %N-nucleus6-shlibs (>= %v-%r), %N-plplot6-shlibs (>= %v-%r), x11, x11-shlibs, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, system-java14, expat1-shlibs, fontconfig2-shlibs
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev, freetype219, expat1, fontconfig2-dev
#Replaces: emboss (<< 5.0.0)
Source: mirror:custom:EMBOSS-%v.tar.gz
CustomMirror: <<
Primary: ftp://emboss.open-bio.org/pub/EMBOSS/
<<
Source-MD5: 2182b148dace6bea403deed8facae40d
#SetCPPFLAGS: -Dstat64=stat
#Patch: %n.patch
ConfigureParams: --with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home --with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include --disable-dependency-tracking --libdir=%p/lib/EMBOSS
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/include/EMBOSS
mv %i/include/*.* %i/include/EMBOSS/
ln -s EMBOSS/lib{ajax,ajaxg,nucleus,eplplot}.dylib %i/lib
mv %i/lib/EMBOSS/*.*a %i/lib
<<
SplitOff10: <<
Package: %N-ajax6-shlibs
Depends: %N-plplot6-shlibs (>= %v-%r), libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, libiconv
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libajax.6*.dylib
lib/EMBOSS/libajaxg.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libajax.6.dylib 7.0.0 %n (>= 5.0.0-3)
%p/lib/EMBOSS/libajaxg.6.dylib 7.0.0 %n (>= 5.0.0-3)
<<
<<
SplitOff11: <<
Package: %N-ajax6-dev
Depends: %N-ajax6-shlibs (= %v-%r)
Conflicts: %N-dev, %N-ajax4-dev, %N-ajax5-dev
Replaces: %N-dev
DocFiles: ChangeLog COPYING README
Files: <<
lib/libajax*
lib/EMBOSS/libajax*
include/EMBOSS/aj*.h
include/EMBOSS/pcre*
<<
BuildDependsOnly: True
<<
SplitOff20: <<
Package: %N-nucleus6-shlibs
Depends: %N-ajax6-shlibs (>= %v-%r)
Replaces: %N (<< 6.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libnucleus.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libnucleus.6.dylib 7.0.0 %n (>= 5.0.0-3)
<<
<<
SplitOff21: <<
Package: %N-nucleus6-dev
Depends: %N-nucleus6-shlibs (= %v-%r)
Conflicts: %N-dev, %N-nucleus4-dev, %N-nucleus5-dev
Replaces: %N-dev, %N (<< 5.0.0-3)
DocFiles: ChangeLog COPYING README
Files: <<
lib/libnucleus*
lib/EMBOSS/libnucleus*
include/EMBOSS/em*.h
<<
BuildDependsOnly: True
<<
SplitOff30: <<
Package: %N-plplot6-shlibs
Depends: libpng3-shlibs, libjpeg-shlibs, gd2-shlibs, libiconv, x11-shlibs
Replaces: %N (<< 5.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libeplplot.3*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libeplplot.3.dylib 6.0.0 %n (>= 3.0.0-4)
<<
<<
SplitOff31: <<
Package: %N-plplot6-dev
Depends: %N-plplot6-shlibs (= %v-%r)
Conflicts: %N-dev, %N-plplot5-dev (<< 6.0.0-1)
Replaces: %N-dev, %N (<< 6.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/libeplplot*
lib/EMBOSS/libeplplot*
include/eplplot/*.h
<<
BuildDependsOnly: True
<<
RunTimeVars: <<
# PLPLOT_LIB: %p/share/EMBOSS/
EMBOSS_DATA: %p/share/EMBOSS/data
<<
DocFiles: <<
AUTHORS ChangeLog COMPAT COPYING FAQ INSTALL KNOWN_BUGS LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from the
web. Also, as extensive libraries are provided with the package, it is a
platform to allow other scientists to develop and release software in
true open source spirit. EMBOSS also integrates a range of currently
available packages and tools for sequence analysis into a seamless
whole.
<<
DescUsage: <<
See the README file for other environment variables you may need to
configure. See http://emboss.sourceforge.net/Jemboss/ for
information on using the Jemboss GUI for EMBOSS. To prevent conflicts,
the headers are located in %p/include/EMBOSS instead of %p/include.
Install emboss-kaptain for a GUI that works with X-Windows.
<<
DescPort: <<
dmacks added explicit linking to libs that supply symbols used by
the shared libraries here. This prevents things that link against
the shared libraries from having to know to pass additional flags
when the linker requires all symbols be defined.
dmacks overhauled splitoff layout so that lib versions can float
against each other and patched to assure use of EMBOSS's own pcre
headers (libpcre doesn't understand ABI compatibility rules:(
<<
Maintainer: Koen van der Drift
Homepage: http://emboss.sourceforge.net
License: GPL