Update to emboss 1.1.0, fixing some style bugs too.

PR:		ports/20519
Submitted by:	Johann Visagie <johann@egenetics.com> (maintainer)

1 files changed, 257 insertions, 4 deletions

diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 0f02fc99752..dd8d44bd023 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -15,6 +15,7 @@ bin/cusp
 bin/cutseq
 bin/dan
 bin/dbiblast
+bin/dbifasta
 bin/dbiflat
 bin/dbigcg
 bin/descseq
@@ -102,6 +103,7 @@ bin/supermatcher
 bin/syco
 bin/textsearch
 bin/tfextract
+bin/tfm
 bin/tfscan
 bin/tmap
 bin/transeq
@@ -111,6 +113,7 @@ bin/wobble
 bin/wordcount
 bin/wordmatch
 bin/wossname
+etc/emboss.default.sample
 lib/libplplot.so.4
 lib/libplplot.so
 lib/libplplot.a
@@ -123,6 +126,248 @@ lib/libajaxg.a
 lib/libnucleus.so.1
 lib/libnucleus.so
 lib/libnucleus.a
+share/doc/EMBOSS/manuals/Makefile
+share/doc/EMBOSS/manuals/Makefile.am
+share/doc/EMBOSS/manuals/Makefile.in
+share/doc/EMBOSS/manuals/Makefile.in.orig
+share/doc/EMBOSS/programs/html/Makefile
+share/doc/EMBOSS/programs/html/Makefile.am
+share/doc/EMBOSS/programs/html/Makefile.in
+share/doc/EMBOSS/programs/html/Makefile.in.orig
+share/doc/EMBOSS/programs/html/antigenic.html
+share/doc/EMBOSS/programs/html/backtranseq.html
+share/doc/EMBOSS/programs/html/banana.html
+share/doc/EMBOSS/programs/html/chaos.html
+share/doc/EMBOSS/programs/html/checktrans.html
+share/doc/EMBOSS/programs/html/chips.html
+share/doc/EMBOSS/programs/html/cirdna.html
+share/doc/EMBOSS/programs/html/codcmp.html
+share/doc/EMBOSS/programs/html/complex.html
+share/doc/EMBOSS/programs/html/compseq.html
+share/doc/EMBOSS/programs/html/cpgplot.html
+share/doc/EMBOSS/programs/html/cpgreport.html
+share/doc/EMBOSS/programs/html/cusp.html
+share/doc/EMBOSS/programs/html/cutseq.html
+share/doc/EMBOSS/programs/html/dan.html
+share/doc/EMBOSS/programs/html/dbiblast.html
+share/doc/EMBOSS/programs/html/dbifasta.html
+share/doc/EMBOSS/programs/html/dbigcg.html
+share/doc/EMBOSS/programs/html/dbiflat.html
+share/doc/EMBOSS/programs/html/descseq.html
+share/doc/EMBOSS/programs/html/digest.html
+share/doc/EMBOSS/programs/html/dotmatcher.html
+share/doc/EMBOSS/programs/html/dottup.html
+share/doc/EMBOSS/programs/html/dreg.html
+share/doc/EMBOSS/programs/html/einverted.html
+share/doc/EMBOSS/programs/html/embossdata.html
+share/doc/EMBOSS/programs/html/emma.html
+share/doc/EMBOSS/programs/html/equicktandem.html
+share/doc/EMBOSS/programs/html/est2genome.html
+share/doc/EMBOSS/programs/html/etandem.html
+share/doc/EMBOSS/programs/html/extractseq.html
+share/doc/EMBOSS/programs/html/findkm.html
+share/doc/EMBOSS/programs/html/freak.html
+share/doc/EMBOSS/programs/html/fuzznuc.html
+share/doc/EMBOSS/programs/html/fuzzpro.html
+share/doc/EMBOSS/programs/html/fuzztran.html
+share/doc/EMBOSS/programs/html/garnier.html
+share/doc/EMBOSS/programs/html/geecee.html
+share/doc/EMBOSS/programs/html/getorf.html
+share/doc/EMBOSS/programs/html/helixturnhelix.html
+share/doc/EMBOSS/programs/html/iep.html
+share/doc/EMBOSS/programs/html/infoseq.html
+share/doc/EMBOSS/programs/html/isochore.html
+share/doc/EMBOSS/programs/html/lindna.html
+share/doc/EMBOSS/programs/html/maskfeat.html
+share/doc/EMBOSS/programs/html/maskseq.html
+share/doc/EMBOSS/programs/html/matcher.html
+share/doc/EMBOSS/programs/html/merger.html
+share/doc/EMBOSS/programs/html/msbar.html
+share/doc/EMBOSS/programs/html/needle.html
+share/doc/EMBOSS/programs/html/newcpgreport.html
+share/doc/EMBOSS/programs/html/newcpgseek.html
+share/doc/EMBOSS/programs/html/newseq.html
+share/doc/EMBOSS/programs/html/noreturn.html
+share/doc/EMBOSS/programs/html/nthseq.html
+share/doc/EMBOSS/programs/html/octanol.html
+share/doc/EMBOSS/programs/html/oddcomp.html
+share/doc/EMBOSS/programs/html/palindrome.html
+share/doc/EMBOSS/programs/html/pasteseq.html
+share/doc/EMBOSS/programs/html/patmatdb.html
+share/doc/EMBOSS/programs/html/patmatmotifs.html
+share/doc/EMBOSS/programs/html/pepcoil.html
+share/doc/EMBOSS/programs/html/pepinfo.html
+share/doc/EMBOSS/programs/html/pepnet.html
+share/doc/EMBOSS/programs/html/pepstats.html
+share/doc/EMBOSS/programs/html/pepwheel.html
+share/doc/EMBOSS/programs/html/pepwindow.html
+share/doc/EMBOSS/programs/html/pepwindowall.html
+share/doc/EMBOSS/programs/html/plotorf.html
+share/doc/EMBOSS/programs/html/polydot.html
+share/doc/EMBOSS/programs/html/preg.html
+share/doc/EMBOSS/programs/html/prettyplot.html
+share/doc/EMBOSS/programs/html/prettyseq.html
+share/doc/EMBOSS/programs/html/prima.html
+share/doc/EMBOSS/programs/html/printsextract.html
+share/doc/EMBOSS/programs/html/profit.html
+share/doc/EMBOSS/programs/html/prophecy.html
+share/doc/EMBOSS/programs/html/prophet.html
+share/doc/EMBOSS/programs/html/prosextract.html
+share/doc/EMBOSS/programs/html/pscan.html
+share/doc/EMBOSS/programs/html/rebaseextract.html
+share/doc/EMBOSS/programs/html/redata.html
+share/doc/EMBOSS/programs/html/remap.html
+share/doc/EMBOSS/programs/html/revseq.html
+share/doc/EMBOSS/programs/html/restrict.html
+share/doc/EMBOSS/programs/html/seealso.html
+share/doc/EMBOSS/programs/html/seqmatchall.html
+share/doc/EMBOSS/programs/html/seqret.html
+share/doc/EMBOSS/programs/html/seqretall.html
+share/doc/EMBOSS/programs/html/seqretset.html
+share/doc/EMBOSS/programs/html/showdb.html
+share/doc/EMBOSS/programs/html/showfeat.html
+share/doc/EMBOSS/programs/html/showorf.html
+share/doc/EMBOSS/programs/html/showseq.html
+share/doc/EMBOSS/programs/html/shuffleseq.html
+share/doc/EMBOSS/programs/html/sigcleave.html
+share/doc/EMBOSS/programs/html/splitter.html
+share/doc/EMBOSS/programs/html/stretcher.html
+share/doc/EMBOSS/programs/html/stssearch.html
+share/doc/EMBOSS/programs/html/supermatcher.html
+share/doc/EMBOSS/programs/html/syco.html
+share/doc/EMBOSS/programs/html/textsearch.html
+share/doc/EMBOSS/programs/html/tfextract.html
+share/doc/EMBOSS/programs/html/tfm.html
+share/doc/EMBOSS/programs/html/tfscan.html
+share/doc/EMBOSS/programs/html/tmap.html
+share/doc/EMBOSS/programs/html/transeq.html
+share/doc/EMBOSS/programs/html/trimseq.html
+share/doc/EMBOSS/programs/html/water.html
+share/doc/EMBOSS/programs/html/wobble.html
+share/doc/EMBOSS/programs/html/wordcount.html
+share/doc/EMBOSS/programs/html/wordmatch.html
+share/doc/EMBOSS/programs/html/wossname.html
+share/doc/EMBOSS/programs/text/Makefile
+share/doc/EMBOSS/programs/text/Makefile.am
+share/doc/EMBOSS/programs/text/Makefile.in
+share/doc/EMBOSS/programs/text/Makefile.in.orig
+share/doc/EMBOSS/programs/text/antigenic.txt
+share/doc/EMBOSS/programs/text/backtranseq.txt
+share/doc/EMBOSS/programs/text/banana.txt
+share/doc/EMBOSS/programs/text/chaos.txt
+share/doc/EMBOSS/programs/text/checktrans.txt
+share/doc/EMBOSS/programs/text/chips.txt
+share/doc/EMBOSS/programs/text/cirdna.txt
+share/doc/EMBOSS/programs/text/codcmp.txt
+share/doc/EMBOSS/programs/text/complex.txt
+share/doc/EMBOSS/programs/text/compseq.txt
+share/doc/EMBOSS/programs/text/cpgplot.txt
+share/doc/EMBOSS/programs/text/cpgreport.txt
+share/doc/EMBOSS/programs/text/cusp.txt
+share/doc/EMBOSS/programs/text/cutseq.txt
+share/doc/EMBOSS/programs/text/dan.txt
+share/doc/EMBOSS/programs/text/dbiblast.txt
+share/doc/EMBOSS/programs/text/dbifasta.txt
+share/doc/EMBOSS/programs/text/dbiflat.txt
+share/doc/EMBOSS/programs/text/dbigcg.txt
+share/doc/EMBOSS/programs/text/descseq.txt
+share/doc/EMBOSS/programs/text/digest.txt
+share/doc/EMBOSS/programs/text/dotmatcher.txt
+share/doc/EMBOSS/programs/text/dottup.txt
+share/doc/EMBOSS/programs/text/dreg.txt
+share/doc/EMBOSS/programs/text/einverted.txt
+share/doc/EMBOSS/programs/text/embossdata.txt
+share/doc/EMBOSS/programs/text/emma.txt
+share/doc/EMBOSS/programs/text/equicktandem.txt
+share/doc/EMBOSS/programs/text/est2genome.txt
+share/doc/EMBOSS/programs/text/etandem.txt
+share/doc/EMBOSS/programs/text/extractseq.txt
+share/doc/EMBOSS/programs/text/findkm.txt
+share/doc/EMBOSS/programs/text/freak.txt
+share/doc/EMBOSS/programs/text/fuzznuc.txt
+share/doc/EMBOSS/programs/text/fuzzpro.txt
+share/doc/EMBOSS/programs/text/fuzztran.txt
+share/doc/EMBOSS/programs/text/garnier.txt
+share/doc/EMBOSS/programs/text/geecee.txt
+share/doc/EMBOSS/programs/text/getorf.txt
+share/doc/EMBOSS/programs/text/helixturnhelix.txt
+share/doc/EMBOSS/programs/text/iep.txt
+share/doc/EMBOSS/programs/text/infoseq.txt
+share/doc/EMBOSS/programs/text/tfm.txt
+share/doc/EMBOSS/programs/text/isochore.txt
+share/doc/EMBOSS/programs/text/lindna.txt
+share/doc/EMBOSS/programs/text/maskfeat.txt
+share/doc/EMBOSS/programs/text/maskseq.txt
+share/doc/EMBOSS/programs/text/matcher.txt
+share/doc/EMBOSS/programs/text/merger.txt
+share/doc/EMBOSS/programs/text/msbar.txt
+share/doc/EMBOSS/programs/text/needle.txt
+share/doc/EMBOSS/programs/text/newcpgreport.txt
+share/doc/EMBOSS/programs/text/newcpgseek.txt
+share/doc/EMBOSS/programs/text/newseq.txt
+share/doc/EMBOSS/programs/text/noreturn.txt
+share/doc/EMBOSS/programs/text/nthseq.txt
+share/doc/EMBOSS/programs/text/octanol.txt
+share/doc/EMBOSS/programs/text/oddcomp.txt
+share/doc/EMBOSS/programs/text/palindrome.txt
+share/doc/EMBOSS/programs/text/pasteseq.txt
+share/doc/EMBOSS/programs/text/patmatdb.txt
+share/doc/EMBOSS/programs/text/patmatmotifs.txt
+share/doc/EMBOSS/programs/text/pepcoil.txt
+share/doc/EMBOSS/programs/text/pepinfo.txt
+share/doc/EMBOSS/programs/text/pepnet.txt
+share/doc/EMBOSS/programs/text/pepstats.txt
+share/doc/EMBOSS/programs/text/pepwheel.txt
+share/doc/EMBOSS/programs/text/pepwindow.txt
+share/doc/EMBOSS/programs/text/pepwindowall.txt
+share/doc/EMBOSS/programs/text/plotorf.txt
+share/doc/EMBOSS/programs/text/polydot.txt
+share/doc/EMBOSS/programs/text/preg.txt
+share/doc/EMBOSS/programs/text/prettyplot.txt
+share/doc/EMBOSS/programs/text/prettyseq.txt
+share/doc/EMBOSS/programs/text/prima.txt
+share/doc/EMBOSS/programs/text/printsextract.txt
+share/doc/EMBOSS/programs/text/profit.txt
+share/doc/EMBOSS/programs/text/prophecy.txt
+share/doc/EMBOSS/programs/text/prophet.txt
+share/doc/EMBOSS/programs/text/prosextract.txt
+share/doc/EMBOSS/programs/text/pscan.txt
+share/doc/EMBOSS/programs/text/rebaseextract.txt
+share/doc/EMBOSS/programs/text/redata.txt
+share/doc/EMBOSS/programs/text/remap.txt
+share/doc/EMBOSS/programs/text/restrict.txt
+share/doc/EMBOSS/programs/text/revseq.txt
+share/doc/EMBOSS/programs/text/seealso.txt
+share/doc/EMBOSS/programs/text/seqmatchall.txt
+share/doc/EMBOSS/programs/text/seqret.txt
+share/doc/EMBOSS/programs/text/seqretall.txt
+share/doc/EMBOSS/programs/text/seqretset.txt
+share/doc/EMBOSS/programs/text/showdb.txt
+share/doc/EMBOSS/programs/text/showfeat.txt
+share/doc/EMBOSS/programs/text/showorf.txt
+share/doc/EMBOSS/programs/text/showseq.txt
+share/doc/EMBOSS/programs/text/shuffleseq.txt
+share/doc/EMBOSS/programs/text/sigcleave.txt
+share/doc/EMBOSS/programs/text/splitter.txt
+share/doc/EMBOSS/programs/text/stretcher.txt
+share/doc/EMBOSS/programs/text/stssearch.txt
+share/doc/EMBOSS/programs/text/supermatcher.txt
+share/doc/EMBOSS/programs/text/syco.txt
+share/doc/EMBOSS/programs/text/textsearch.txt
+share/doc/EMBOSS/programs/text/tfextract.txt
+share/doc/EMBOSS/programs/text/tfscan.txt
+share/doc/EMBOSS/programs/text/tmap.txt
+share/doc/EMBOSS/programs/text/transeq.txt
+share/doc/EMBOSS/programs/text/trimseq.txt
+share/doc/EMBOSS/programs/text/water.txt
+share/doc/EMBOSS/programs/text/wobble.txt
+share/doc/EMBOSS/programs/text/wordcount.txt
+share/doc/EMBOSS/programs/text/wordmatch.txt
+share/doc/EMBOSS/programs/text/wossname.txt
+share/doc/EMBOSS/tutorials/Makefile
+share/doc/EMBOSS/tutorials/Makefile.am
+share/doc/EMBOSS/tutorials/Makefile.in
+share/doc/EMBOSS/tutorials/Makefile.in.orig
 share/EMBOSS/plstnd5.fnt
 share/EMBOSS/plxtnd5.fnt
 share/EMBOSS/acd/ajbad.acd
@@ -163,12 +408,13 @@ share/EMBOSS/acd/cusp.acd
 share/EMBOSS/acd/cutseq.acd
 share/EMBOSS/acd/dan.acd
 share/EMBOSS/acd/dbiblast.acd
+share/EMBOSS/acd/dbifasta.acd
 share/EMBOSS/acd/dbiflat.acd
 share/EMBOSS/acd/dbigcg.acd
 share/EMBOSS/acd/descseq.acd
 share/EMBOSS/acd/digest.acd
-share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dottup.acd
+share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dreg.acd
 share/EMBOSS/acd/einverted.acd
 share/EMBOSS/acd/embossdata.acd
@@ -213,8 +459,8 @@ share/EMBOSS/acd/pepnet.acd
 share/EMBOSS/acd/pepstats.acd
 share/EMBOSS/acd/pepwheel.acd
 share/EMBOSS/acd/pepwindow.acd
-share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/plotorf.acd
+share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
@@ -236,8 +482,8 @@ share/EMBOSS/acd/seqret.acd
 share/EMBOSS/acd/seqretall.acd
 share/EMBOSS/acd/seqretset.acd
 share/EMBOSS/acd/seqretsplit.acd
-share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/seqrettype.acd
+share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/showfeat.acd
 share/EMBOSS/acd/showorf.acd
 share/EMBOSS/acd/showseq.acd
@@ -250,6 +496,7 @@ share/EMBOSS/acd/supermatcher.acd
 share/EMBOSS/acd/syco.acd
 share/EMBOSS/acd/textsearch.acd
 share/EMBOSS/acd/tfextract.acd
+share/EMBOSS/acd/tfm.acd
 share/EMBOSS/acd/tfscan.acd
 share/EMBOSS/acd/tmap.acd
 share/EMBOSS/acd/transeq.acd
@@ -640,12 +887,18 @@ share/EMBOSS/test/wormpep/acnum.trg
 share/EMBOSS/test/wormpep/division.lkp
 share/EMBOSS/test/wormpep/entrynam.idx
 share/EMBOSS/test/wormpep/wormpep
+@dirrm share/doc/EMBOSS/manuals
+@dirrm share/doc/EMBOSS/programs/html
+@dirrm share/doc/EMBOSS/programs/text
+@dirrm share/doc/EMBOSS/programs
+@dirrm share/doc/EMBOSS/tutorials
+@dirrm share/doc/EMBOSS
+@dirrm share/EMBOSS/acd
 @dirrm share/EMBOSS/data/CODONS
 @dirrm share/EMBOSS/data/REBASE
 @dirrm share/EMBOSS/data/PRINTS
 @dirrm share/EMBOSS/data/PROSITE
 @dirrm share/EMBOSS/data
-@dirrm share/EMBOSS/acd
 @dirrm share/EMBOSS/test/data
 @dirrm share/EMBOSS/test/embl
 @dirrm share/EMBOSS/test/pir