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- Update to 5.0.0

Browse Source 
PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
This commit is contained in:
Rong-En Fan 2008-04-13 07:22:42 +00:00
parent a0ab9c0e54
commit 6098818ed4
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=211152
17 changed files with 707 additions and 6851 deletions
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22
biology/embassy/Makefile
View File

@ -7,19 +7,16 @@
#
PORTNAME= embassy
PORTVERSION= 3.0.0
PORTREVISION= 2
PORTVERSION= 5.0.0
CATEGORIES= biology
MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \
ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DIST_SUBDIR= emboss
MAINTAINER= fernan@iib.unsam.edu.ar
COMMENT= A collection of contributed EMBOSS applications
LIB_DEPENDS= nucleus.3:${PORTSDIR}/biology/emboss
LIB_DEPENDS= nucleus.5:${PORTSDIR}/biology/emboss
PREFIX?= ${LOCALBASE}/emboss
NO_MTREE= yes
@ -27,7 +24,9 @@ USE_SUBMAKE= yes
USE_ICONV= yes
USE_GMAKE= yes
GNU_CONFIGURE= yes
USE_XORG= x11
USE_MOTIF= yes
USE_LDCONFIG= yes
OPTIONS= DOMAINATRIX "Protein domain apps" on \
DOMALIGN "Protein domain apps" on \
@ -41,7 +40,8 @@ OPTIONS= DOMAINATRIX "Protein domain apps" on \
MSE "A multiple sequence screen editor" on \
MYEMBOSS "Examples for developers of EMBOSS apps" on \
PHYLIP "Phylogeny inference" on \
TOPO "Transmembrane display" on
TOPO "Transmembrane display" on \
VIENNA "RNA folding" on
CONFIGURE_ENV+= CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
@ -50,8 +50,8 @@ EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
DOMAINATRIX_VERSION= 0.1.0
EMNU_VERSION= 1.05
ESIM4_VERSION= 1.0.0
HMMER_VERSION= 2.1.1
MEME_VERSION= 2.3.1
HMMER_VERSION= 2.3.2
MEME_VERSION= 0.1.0
MSE_VERSION= 1.0.0
TOPO_VERSION= 1.0.0
PHYLIP_VERSION= 3.6b
@ -60,8 +60,10 @@ DOMSEARCH_VERSION= 0.1.0
SIGNATURE_VERSION= 0.1.0
STRUCTURE_VERSION= 0.1.0
MYEMBOSS_VERSION= 3.0.0
EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \
DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS
VIENNA_VERSION= 1.6
EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP \
TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \
VIENNA
.include <bsd.port.pre.mk>

81
biology/embassy/distinfo
View File

@ -1,39 +1,42 @@
MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 655f6ec58e0b9dfdac111fd9481359cb
SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 6bc374c5275dead68ef09d8273bf4d73a03bc56990e795d6eddcee4de25c12a0
SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 349882
MD5 (emboss/EMNU-1.05.tar.gz) = b3a7fc11e46f7166ddeec11f2fe03d9b
SHA256 (emboss/EMNU-1.05.tar.gz) = d7261d615d6547a9824d3d9e3f82ff756c0db5786e8356bc54cc5fa0c516b26f
SIZE (emboss/EMNU-1.05.tar.gz) = 348924
MD5 (emboss/ESIM4-1.0.0.tar.gz) = 835393b3246eb4543a694362c6f335ff
SHA256 (emboss/ESIM4-1.0.0.tar.gz) = f8241c9e37ccc17dbd29df2d9c90063ba7caf4e64cc5c368b6878c3aa3895620
SIZE (emboss/ESIM4-1.0.0.tar.gz) = 384396
MD5 (emboss/HMMER-2.1.1.tar.gz) = 382594654e45a7e8d5872b4b1016a494
SHA256 (emboss/HMMER-2.1.1.tar.gz) = 78647dfb7841e8b52b4c3de34400c68d17a877b698956ac9a5ee5e030569cca6
SIZE (emboss/HMMER-2.1.1.tar.gz) = 561289
MD5 (emboss/MEME-2.3.1.tar.gz) = 6f4e516e413582268a34e91fb12e21c3
SHA256 (emboss/MEME-2.3.1.tar.gz) = bec2c8002b8b551ef9c639bcb58633499060cd8a1bfe4754db5ed201a6a0dffa
SIZE (emboss/MEME-2.3.1.tar.gz) = 423966
MD5 (emboss/MSE-1.0.0.tar.gz) = 3b9810e870937ec32220b5c9fe7a83cd
SHA256 (emboss/MSE-1.0.0.tar.gz) = ddf9092721666d64c56733d9b6d04e749957848cafa8ba4ec6eee083a0ffcab3
SIZE (emboss/MSE-1.0.0.tar.gz) = 415051
MD5 (emboss/PHYLIP-3.6b.tar.gz) = 6f2c10438d788acf4a1dff23441b2a2c
SHA256 (emboss/PHYLIP-3.6b.tar.gz) = 32aba94d0be011ee304e974657db11544297c008e53341cd000a1f412eb874e2
SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1136746
MD5 (emboss/TOPO-1.0.0.tar.gz) = 7b3355570ba36f7daf57dcbc717215ce
SHA256 (emboss/TOPO-1.0.0.tar.gz) = ff10378b4ecad69ddb374cd47a7d3c7fa5975d6695057f05ea264940258ebaa3
SIZE (emboss/TOPO-1.0.0.tar.gz) = 351796
MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 4332d7de49b27f257b58a90510223eb7
SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = de66ddfdb72ccf7291be614c9a83fd8fc47363191cb2c045b372de5cc334a594
SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 347672
MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = c62f9b69a9ed9580d4489a8de9ea4863
SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = f4933b62e19ee6b23a78b70c3cf2d5a9a18eff1d7532f92e2d33b1d683877916
SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 352793
MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 1e30e12048609a468b7b4d4affb177cf
SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = c6bb252beaccac5256d99301933b15da6ef90af3f20d7f92fed1f78b271785ee
SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 400125
MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6efc35eb2855738252e0537198f5225d
SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 7142e207987da46cd85c81088ea475abb866da90ff57e4c3ca1c63bd8f209b64
SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 362563
MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 15d5bc7b0ce9dfb113777c06c4e18906
SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = 0a19ebbe52da849fb87799edaea2281a1bf235e6045725789b9b29e58f0a0dc5
SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 323628
MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0be3c59550e1e22924ea2540b11af275
SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = b81fde3ab329ab75482b341568ef2965d99803765438f3825688a0d2abc05ca6
SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420051
MD5 (emboss/EMNU-1.05.tar.gz) = 64d8b9c2cd1a566aebb3355eb684bd35
SHA256 (emboss/EMNU-1.05.tar.gz) = 56a55f336b0083ecfd2fd2dae0613f46e802eacb3214c16fc1966e6516795b95
SIZE (emboss/EMNU-1.05.tar.gz) = 389665
MD5 (emboss/ESIM4-1.0.0.tar.gz) = ee65d0da0f2d75959f370b13f2218c1c
SHA256 (emboss/ESIM4-1.0.0.tar.gz) = eee1cc8fef40e19fab74b16f1c1cb0883a49561eb9fdc2075f428085c6722bda
SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431329
MD5 (emboss/HMMER-2.3.2.tar.gz) = 3aa5707db81854f2674bf27aaeb1362e
SHA256 (emboss/HMMER-2.3.2.tar.gz) = 31bbcca1f71b82170a65c4438f9cb9f1dfe3d4e066037a852060b010e3e39b5b
SIZE (emboss/HMMER-2.3.2.tar.gz) = 565223
MD5 (emboss/MEME-0.1.0.tar.gz) = d304f3b8a8e15af4dfa7b295655d80ec
SHA256 (emboss/MEME-0.1.0.tar.gz) = ed4c02010af036515203661c28776b5e773e77eccad59990b7ac1410399d45ef
SIZE (emboss/MEME-0.1.0.tar.gz) = 448413
MD5 (emboss/MSE-1.0.0.tar.gz) = 3978a06e3651104f622a5834523c45de
SHA256 (emboss/MSE-1.0.0.tar.gz) = e35560310ece8bb2dec7eeb88e99f39f313bf7366afc445e3b074b687e7f36b2
SIZE (emboss/MSE-1.0.0.tar.gz) = 445013
MD5 (emboss/PHYLIP-3.6b.tar.gz) = 760a90bea49872aba95fd7dd2b67570c
SHA256 (emboss/PHYLIP-3.6b.tar.gz) = c2397937f4b827844192a33b31f13271a3560c81045543d912a9c28eb6ad894f
SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1594433
MD5 (emboss/TOPO-1.0.0.tar.gz) = d45602a1b1f22da50a775c41df5fe672
SHA256 (emboss/TOPO-1.0.0.tar.gz) = ed1921e92d1bbd9fcc16ab36f2fcbafca9e60cc0d4b4fd1da77660ffd3e7b2f2
SIZE (emboss/TOPO-1.0.0.tar.gz) = 379381
MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = e5d004c1223116abaebb6657ae4a80fa
SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = aa61cfc6da3cc478dd7f476537cdc6d966b00b90e2adedc709eb75e39e840c5c
SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 460530
MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = 778ab15bce09a6440fc6859b3a27157d
SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = 23e069161ec56df5eab5fc491ca3493c056cfee42f2e05f1b5ef258498792a87
SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 469776
MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 26deae308cc5aac3dee5dd03df2ae9e8
SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 9b0529befdbe5d56b3370cfffe0a4b4cc523f350b50ddd4a61dd24776a1770e8
SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 573992
MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6736b4741b15d4cba488a5422fcfaee1
SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 3ed8ea5373232cd80302ff3b8727838b4de2f6b39aa263ab9530bbbe71d730c1
SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 530874
MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 9c3d6ea80166f62cd6ee63dfcb7e57a4
SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = dc21b1772c2d76ed1c717eba6f8443b86cdf2e3cbcf71e056cdb9723138e4440
SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 354179
MD5 (emboss/VIENNA-1.6.tar.gz) = 282ed7ac9c1741160fcb1e8d48539311
SHA256 (emboss/VIENNA-1.6.tar.gz) = 04c4a57486e23c2cc8ef396d9012c396519b2ab1b13b2500199e6457a34cfa58
SIZE (emboss/VIENNA-1.6.tar.gz) = 635638

322
biology/embassy/pkg-plist
View File

@ -12,6 +12,21 @@
%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/index.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/cathparse.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainnr.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainreso.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainseqs.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainsse.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/scopparse.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/ssematch.html
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/cathparse.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainnr.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainreso.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainseqs.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainsse.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/scopparse.txt
%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/ssematch.txt
%%PLIST_DOMALIGN%%bin/allversusall
%%PLIST_DOMALIGN%%bin/domainalign
%%PLIST_DOMALIGN%%bin/domainrep
@ -20,63 +35,112 @@
%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd
%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd
%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd
%%PLIST_DOMSEARCH%%bin/seqfraggle
%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/index.html
%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/allversusall.html
%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainalign.html
%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainrep.html
%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/seqalign.html
%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/allversusall.txt
%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainalign.txt
%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainrep.txt
%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/seqalign.txt
%%PLIST_DOMSEARCH%%bin/seqnr
%%PLIST_DOMSEARCH%%bin/seqsearch
%%PLIST_DOMSEARCH%%bin/seqfraggle
%%PLIST_DOMSEARCH%%bin/seqsort
%%PLIST_DOMSEARCH%%bin/seqwords
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/index.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqfraggle.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqnr.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsearch.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsort.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqwords.html
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqfraggle.txt
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqnr.txt
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsearch.txt
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsort.txt
%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqwords.txt
%%PLIST_EMNU%%bin/emnu
%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
%%PLIST_HMMER%%bin/ealistat
%%PLIST_HMMER%%bin/ehmmalign
%%PLIST_HMMER%%bin/ehmmbuild
%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/index.html
%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/emnu.html
%%PLIST_EMNU%%share/EMBOSS/doc/programs/text/emnu.txt
%%PLIST_ESIM4%%bin/esim4
%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/index.html
%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/esim4.html
%%PLIST_ESIM4%%share/EMBOSS/doc/programs/text/esim4.txt
%%PLIST_HMMER%%bin/ehmmcalibrate
%%PLIST_HMMER%%bin/ehmmconvert
%%PLIST_HMMER%%bin/ehmmemit
%%PLIST_HMMER%%bin/ehmmfetch
%%PLIST_HMMER%%bin/ehmmindex
%%PLIST_HMMER%%bin/ehmmbuild
%%PLIST_HMMER%%bin/ehmmalign
%%PLIST_HMMER%%bin/ehmmpfam
%%PLIST_HMMER%%bin/ehmmsearch
%%PLIST_HMMER%%lib/libhmmer.a
%%PLIST_HMMER%%lib/libhmmer.la
%%PLIST_HMMER%%lib/libhmmer.so
%%PLIST_HMMER%%lib/libhmmer.so.2
%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
%%PLIST_MEME%%bin/meme
%%PLIST_MEME%%lib/libmeme.a
%%PLIST_MEME%%lib/libmeme.la
%%PLIST_MEME%%lib/libmeme.so
%%PLIST_MEME%%lib/libmeme.so.2
%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/index.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmalign.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmbuild.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmcalibrate.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmconvert.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmemit.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmfetch.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmindex.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmpfam.html
%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmsearch.html
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmalign.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmbuild.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmcalibrate.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmconvert.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmemit.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmfetch.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmindex.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmpfam.txt
%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmsearch.txt
%%PLIST_MEME%%bin/emast
%%PLIST_MEME%%bin/ememe
%%PLIST_MEME%%share/EMBOSS/acd/emast.acd
%%PLIST_MEME%%share/EMBOSS/acd/ememe.acd
%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/index.html
%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/emast.html
%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/ememe.html
%%PLIST_MEME%%share/EMBOSS/doc/programs/text/emast.txt
%%PLIST_MEME%%share/EMBOSS/doc/programs/text/ememe.txt
%%PLIST_MSE%%bin/mse
%%PLIST_MSE%%lib/libckit.a
%%PLIST_MSE%%lib/libckit.la
%%PLIST_MSE%%lib/libckit.so
%%PLIST_MSE%%lib/libckit.so.1
%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
%%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html
%%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/mse.html
%%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt
%%PLIST_MSE%%lib/libckit.so.1
%%PLIST_MSE%%lib/libckit.so
%%PLIST_MSE%%lib/libckit.la
%%PLIST_MSE%%lib/libckit.a
%%PLIST_MYEMBOSS%%bin/myseq
%%PLIST_MYEMBOSS%%bin/mytest
%%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd
%%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd
%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myseq/index.html
%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myseq/myseq.html
%%PLIST_MYEMBOSS%%share/EMBOSS/doc/programs/text/myseq.txt
%%PLIST_PHYLIP%%bin/fclique
%%PLIST_PHYLIP%%bin/fconsense
%%PLIST_PHYLIP%%bin/fcontml
%%PLIST_PHYLIP%%bin/fcontrast
%%PLIST_PHYLIP%%bin/fdiscboot
%%PLIST_PHYLIP%%bin/fdnacomp
%%PLIST_PHYLIP%%bin/fdnadist
%%PLIST_PHYLIP%%bin/fdnainvar
@ -85,14 +149,13 @@
%%PLIST_PHYLIP%%bin/fdnamove
%%PLIST_PHYLIP%%bin/fdnapars
%%PLIST_PHYLIP%%bin/fdnapenny
%%PLIST_PHYLIP%%bin/fdollop
%%PLIST_PHYLIP%%bin/fdolmove
%%PLIST_PHYLIP%%bin/fdollop
%%PLIST_PHYLIP%%bin/fdolpenny
%%PLIST_PHYLIP%%bin/fdrawgram
%%PLIST_PHYLIP%%bin/fdrawtree
%%PLIST_PHYLIP%%bin/ffactor
%%PLIST_PHYLIP%%bin/ffitch
%%PLIST_PHYLIP%%bin/ffreqboot
%%PLIST_PHYLIP%%bin/fgendist
%%PLIST_PHYLIP%%bin/fkitsch
%%PLIST_PHYLIP%%bin/fmix
@ -104,10 +167,12 @@
%%PLIST_PHYLIP%%bin/fpromlk
%%PLIST_PHYLIP%%bin/fprotdist
%%PLIST_PHYLIP%%bin/fprotpars
%%PLIST_PHYLIP%%bin/frestboot
%%PLIST_PHYLIP%%bin/frestdist
%%PLIST_PHYLIP%%bin/frestml
%%PLIST_PHYLIP%%bin/fretree
%%PLIST_PHYLIP%%bin/fdiscboot
%%PLIST_PHYLIP%%bin/ffreqboot
%%PLIST_PHYLIP%%bin/frestboot
%%PLIST_PHYLIP%%bin/fseqboot
%%PLIST_PHYLIP%%bin/fseqbootall
%%PLIST_PHYLIP%%bin/ftreedist
@ -152,6 +217,81 @@
%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqbootall.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedistpair.acd
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/index.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fclique.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fconsense.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fcontml.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fcontrast.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdiscboot.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnacomp.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnadist.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnainvar.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnaml.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnamlk.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnapars.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnapenny.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdollop.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdolpenny.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdrawgram.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdrawtree.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffactor.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffitch.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffreqboot.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fmix.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fgendist.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fkitsch.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fmove.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fneighbor.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpars.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpenny.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fproml.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpromlk.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fprotdist.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fprotpars.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/frestboot.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/frestml.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fretree.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fseqboot.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fseqbootall.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ftreedist.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ftreedistpair.html
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fclique.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fconsense.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fcontml.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fcontrast.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdiscboot.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnacomp.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnadist.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnainvar.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnaml.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnamlk.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnapars.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnapenny.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdollop.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdolpenny.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdrawgram.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdrawtree.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffactor.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffitch.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffreqboot.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fgendist.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fkitsch.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fmix.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fmove.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fneighbor.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpars.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpenny.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fproml.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpromlk.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fprotdist.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fprotpars.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/frestboot.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/frestml.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fretree.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fseqboot.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fseqbootall.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ftreedist.txt
%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ftreedistpair.txt
%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font1
%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font2
%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font3
@ -163,22 +303,37 @@
%%PLIST_PHYLIP%%@dirrm share/PHYLIP
%%PLIST_SIGNATURE%%bin/libgen
%%PLIST_SIGNATURE%%bin/matgen3d
%%PLIST_SIGNATURE%%bin/rocon
%%PLIST_SIGNATURE%%bin/rocplot
%%PLIST_SIGNATURE%%bin/rocon
%%PLIST_SIGNATURE%%bin/siggen
%%PLIST_SIGNATURE%%bin/siggenlig
%%PLIST_SIGNATURE%%bin/sigscan
%%PLIST_SIGNATURE%%bin/sigscanlig
%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd
%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd
%%PLIST_ESIM4%%bin/esim4
%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/index.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/libgen.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/matgen3d.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocon.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocplot.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggen.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggenlig.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscan.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscanlig.html
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/libgen.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/matgen3d.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocon.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocplot.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggen.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggenlig.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscan.txt
%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscanlig.txt
%%PLIST_STRUCTURE%%bin/contacts
%%PLIST_STRUCTURE%%bin/domainer
%%PLIST_STRUCTURE%%bin/hetparse
@ -195,7 +350,110 @@
%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd
%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd
%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/index.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/contacts.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/domainer.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/hetparse.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/interface.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbparse.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbplus.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbtosp.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/sites.html
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/contacts.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/domainer.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/hetparse.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/interface.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbparse.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbplus.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbtosp.txt
%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/sites.txt
%%PLIST_TOPO%%bin/topo
%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
@dirrmtry share/EMBOSS/acd
@dirrmtry share/EMBOSS
%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/index.html
%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.html
%%PLIST_TOPO%%share/EMBOSS/doc/programs/text/topo.txt
%%PLIST_VIENNA%%bin/vrnaalifold
%%PLIST_VIENNA%%bin/vrnacofoldpf
%%PLIST_VIENNA%%bin/vrnaevalpair
%%PLIST_VIENNA%%bin/vrnainverse
%%PLIST_VIENNA%%bin/vrnaalifoldpf
%%PLIST_VIENNA%%bin/vrnadistance
%%PLIST_VIENNA%%bin/vrnafold
%%PLIST_VIENNA%%bin/vrnalfold
%%PLIST_VIENNA%%bin/vrnacofold
%%PLIST_VIENNA%%bin/vrnaduplex
%%PLIST_VIENNA%%bin/vrnafoldpf
%%PLIST_VIENNA%%bin/vrnaplot
%%PLIST_VIENNA%%bin/vrnacofoldconc
%%PLIST_VIENNA%%bin/vrnaeval
%%PLIST_VIENNA%%bin/vrnaheat
%%PLIST_VIENNA%%bin/vrnasubopt
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifold.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnadistance.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnafoldpf.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaplot.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifoldpf.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaduplex.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaheat.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnasubopt.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofold.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaeval.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnainverse.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofoldconc.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaevalpair.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnalfold.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofoldpf.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnafold.acd
%%PLIST_VIENNA%%share/EMBOSS/acd/vrnapaln.acd
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/index.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaalifold.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaalifoldpf.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofold.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofoldconc.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofoldpf.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnadistance.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaduplex.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaeval.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaevalpair.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnafold.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnafoldpf.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaheat.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnainverse.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnalfold.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaplot.html
%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnasubopt.html
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaalifold.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaalifoldpf.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofold.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofoldconc.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofoldpf.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnadistance.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaduplex.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaeval.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaevalpair.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnafold.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnafoldpf.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaheat.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnainverse.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnalfold.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaplot.txt
%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnasubopt.txt
%%PLIST_VIENNA%%lib/libviennarna.so.1
%%PLIST_VIENNA%%lib/libviennarna.so
%%PLIST_VIENNA%%lib/libviennarna.la
%%PLIST_VIENNA%%lib/libviennarna.a
@dirrmtry share/EMBOSS/doc/html/embassy/vienna
@dirrmtry share/EMBOSS/doc/html/embassy/topo
@dirrmtry share/EMBOSS/doc/html/embassy/structure
@dirrmtry share/EMBOSS/doc/html/embassy/signature
@dirrmtry share/EMBOSS/doc/html/embassy/phylipnew
@dirrmtry share/EMBOSS/doc/html/embassy/myseq
@dirrmtry share/EMBOSS/doc/html/embassy/mse
@dirrmtry share/EMBOSS/doc/html/embassy/memenew
@dirrmtry share/EMBOSS/doc/html/embassy/hmmernew
@dirrmtry share/EMBOSS/doc/html/embassy/esim4
@dirrmtry share/EMBOSS/doc/html/embassy/emnu
@dirrmtry share/EMBOSS/doc/html/embassy/domsearch
@dirrmtry share/EMBOSS/doc/html/embassy/domalign
@dirrmtry share/EMBOSS/doc/html/embassy/domainatrix
@dirrmtry share/EMBOSS/doc/html/embassy

36
biology/emboss/Makefile
View File

@ -6,15 +6,11 @@
#
PORTNAME= emboss
PORTVERSION= 3.0.0
PORTREVISION= 2
PORTVERSION= 5.0.0
RELEASE= ${PORTNAME:U}-${PORTVERSION}
CATEGORIES= biology
MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \
ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTNAME= ${PORTNAME:U}-${PORTVERSION}
DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
MASTER_SITES= SF
DISTNAME= ${RELEASE}
DIST_SUBDIR= ${PORTNAME}
MAINTAINER= fernan@iib.unsam.edu.ar
@ -33,26 +29,28 @@ USE_SUBMAKE= yes
USE_GMAKE= yes
GNU_CONFIGURE= yes
USE_AUTOTOOLS= libtool:15
INSTALLS_SHLIB= yes
USE_LDCONFIG= yes
USE_MOTIF= yes
SUB_FILES= pkg-message
SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR}
DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U}
DOCSDIR= ${PREFIX}/share/${PORTNAME:U}/doc
DATADIR= ${PREFIX}/share/${PORTNAME:U}
CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
.if !defined(WITHOUT_X11)
USE_XORG= x11
USE_MOTIF= yes
LIB_DEPENDS+= gd.4:${PORTSDIR}/graphics/gd \
png.5:${PORTSDIR}/graphics/png
.else
CONFIGURE_ARGS+= --without-x
.endif
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template
post-patch:
.if !defined(NOPORTDOCS)
.for DIR in ${DOC_DIRS}
@ ${REINPLACE_CMD} -e \
's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
${WRKSRC}/${DIR}/Makefile.in
.endfor
.endif
pre-install:
@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}

6
biology/emboss/distinfo
View File

@ -1,3 +1,3 @@
MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b
SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560

5134
biology/emboss/files/patch-ajindex.c
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File diff suppressed because it is too large Load Diff

170
biology/emboss/files/patch-ajindex.h
View File

@ -1,170 +0,0 @@
--- ajax/ajindex.h.orig Mon Jan 23 12:17:10 2006
+++ ajax/ajindex.h Thu Dec 22 13:12:32 2005
@@ -67,6 +67,23 @@
} AjOBtNode;
#define AjPBtNode AjOBtNode*
+
+
+
+typedef struct AjSBtMem
+{
+ struct AjSBtMem *next;
+ struct AjSBtMem *prev;
+ AjPStr *karray;
+ ajlong *parray;
+ ajlong *overflows;
+ AjBool used;
+} AjOBtMem;
+#define AjPBtMem AjOBtMem*
+
+
+
+
/* @data AjPBtId ***************************************************
**
** Btree ID
@@ -137,6 +154,54 @@
+/* @data AjPBtNumId ***************************************************
+**
+** Btree ID
+**
+** @attr id [AjPStr] Unique ID
+** @attr dbno [ajint] Database file number
+** @attr dups [ajint] Duplicates
+** @attr offset [ajlong] Offset within database file (ftello)
+** @attr refoffset [ajlong] Offset within reference database file (ftello)
+******************************************************************************/
+
+typedef struct AjSBtNumId
+{
+ ajint dbno;
+ ajlong offset;
+ ajlong refoffset;
+} AjOBtNumId;
+#define AjPBtNumId AjOBtNumId*
+
+
+
+
+/* @data AjPNumBucket ***************************************************
+**
+** Offset bucket structure on disc
+**
+** Key, filenumber, ftell ID, subkey page (char*, ajint, ajlong, ajlong)
+**
+** @attr NodeType [ajint] Node type
+** @attr Nentries [ajint] Number of entries
+** @attr Overflow [ajlong] Offset to overflow block
+** @attr offset [ajlong*] file offsets
+** @attr refoffset [ajlong*] ref file offsets
+** @attr offset [ajint*] database numbers
+******************************************************************************/
+
+typedef struct AjSNumBucket
+{
+ ajint NodeType;
+ ajint Nentries;
+ ajlong Overflow;
+ AjPBtNumId *NumId;
+} AjONumBucket;
+#define AjPNumBucket AjONumBucket*
+
+
+
+
/* Database file name structure
**
** ajint order Order of B+tree
@@ -387,6 +452,10 @@
** @attr snperbucket [ajint] Undocumented
** @attr secrootblock [ajlong] secondary tree root block
** @attr kwlimit [ajint] Max length of secondary key
+** @attr bmem [AjPBtMem] primary memory allocation MRU bottom
+** @attr bsmem [AjPBtMem] secondary memory allocation MRU bottom
+** @attr tmem [AjPBtMem] primary memory allocation MRU top
+** @attr tsmem [AjPBtMem] secondary memory allocation MRU top
******************************************************************************/
typedef struct AjSBtCache
@@ -409,6 +478,12 @@
ajint snperbucket;
ajlong secrootblock;
ajint kwlimit;
+
+ AjPBtMem bmem;
+ AjPBtMem tmem;
+ AjPBtMem bsmem;
+ AjPBtMem tsmem;
+
} AjOBtcache;
#define AjPBtcache AjOBtcache*
@@ -511,6 +586,32 @@
+/* @data AjPBtHybrid ***************************************************
+**
+** Btree ID
+**
+** @attr key1 [AjPStr] Unique ID
+** @attr dbno [ajint] Database file number
+** @attr dups [ajint] Duplicates
+** @attr offset [ajlong] Offset within database file (ftello)** @attr refoffset [ajlong] Offset within reference database file (ftello)
+** @attr refoffset [ajlong] Offset within reference database file (ftello)
+** @attr treeblock [ajlong] Secondary tree root page
+******************************************************************************/
+
+typedef struct AjSBtHybrid
+{
+ AjPStr key1;
+ ajint dbno;
+ ajint dups;
+ ajlong offset;
+ ajlong refoffset;
+ ajlong treeblock;
+} AjOBtHybrid;
+#define AjPBtHybrid AjOBtHybrid*
+
+
+
+
AjPBtcache ajBtreeCacheNewC(const char *file, const char *ext,
const char *idir, const char *mode,
ajint pagesize, ajint order, ajint fill,
@@ -553,7 +654,8 @@
AjBool ajBtreeReplaceId(AjPBtcache cache, const AjPBtId rid);
ajint ajBtreeReadEntries(const char *filename, const char *indexdir,
- AjPStr **seqfiles, AjPStr **reffiles);
+ const char *directory,
+ AjPStr **seqfiles, AjPStr **reffiles);
void ajBtreeInsertDupId(AjPBtcache cache, AjPBtId id);
AjPList ajBtreeDupFromKey(AjPBtcache cache, const char *key);
@@ -580,6 +682,21 @@
void ajBtreeInsertKeyword(AjPBtcache cache, const AjPBtPri pri);
void ajBtreeLockTest(AjPBtcache cache);
+
+
+
+AjPBtpage ajBtreeHybFindInsert(AjPBtcache cache, const char *key);
+AjPBtpage ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key);
+
+void ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page);
+void ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb);
+AjPBtHybrid ajBtreeHybNew(void);
+void ajBtreeHybDel(AjPBtHybrid *thys);
+void ajBtreeFreePriArray(AjPBtcache cache);
+void ajBtreeFreeSecArray(AjPBtcache cache);
+void ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock,
+ AjPStr idname, AjPList list);
+
#endif

67
biology/emboss/files/patch-ajpdb.c
View File

@ -1,67 +0,0 @@
--- ajax/ajpdb.c.orig Mon Jan 23 12:19:22 2006
+++ ajax/ajpdb.c Fri Aug 19 13:49:12 2005
@@ -1198,7 +1198,7 @@
osstr = ajStrNew();
xstr = ajStrNew();
- /* Start of main application loop */
+ /* Start of main loop */
while(ajFileReadLine(inf,&line))
{
if(ajStrPrefixC(line,"XX"))
@@ -1313,6 +1313,8 @@
(ret)->Nchn = ncha;
(ret)->Ngp = ngrp;
+
+ continue;
}
@@ -1382,7 +1384,11 @@
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&mod);
if((mode == 0) && (mod!=1))
- break;
+ {
+ /* break; */
+ /* Discard remaining AT lines */
+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"AT"));
+ }
/* Chain number */
ajStrToken(&token,&handle,NULL);
@@ -1463,7 +1469,10 @@
"jison@hgmp.mrc.ac.uk");
}
else
+ {
ajListPushApp((ret)->Chains[chn-1]->Atoms,(void *)atom);
+ }
+ continue;
}
/* Parse residue line */
@@ -1479,8 +1488,11 @@
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&mod);
if((mode == 0) && (mod!=1))
- break;
-
+ {
+ /* break;*/
+ /* Discard remaining RE lines */
+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"RE"));
+ }
/* Chain number */
ajStrToken(&token,&handle,NULL);
ajStrToInt(token,&chn);
@@ -1585,6 +1597,8 @@
ajStrToFloat(token,&residue->pol_rel);
ajListPushApp((ret)->Chains[chn-1]->Residues,(void *)residue);
+
+ continue;
}
}
/* End of main application loop */

195
biology/emboss/files/patch-ajseqdb.c
View File

@ -1,195 +0,0 @@
--- ajax/ajseqdb.c.orig Mon Jan 23 12:20:25 2006
+++ ajax/ajseqdb.c Thu Dec 22 13:12:57 2005
@@ -27,8 +27,7 @@
******************************************************************************/
#include "ajax.h"
-#include "ajmem.h"
-#include "ajfile.h"
+
#include "limits.h"
#include <stdarg.h>
#include <sys/types.h>
@@ -3055,13 +3054,13 @@
if(qryd->do_id)
- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
if(qryd->do_ac)
- seqEmbossOpenCache(qry,AC_EXTENSION,&qryd->accache);
+ seqEmbossOpenSecCache(qry,AC_EXTENSION,&qryd->accache);
if(qryd->do_sv)
- seqEmbossOpenCache(qry,SV_EXTENSION,&qryd->svcache);
+ seqEmbossOpenSecCache(qry,SV_EXTENSION,&qryd->svcache);
if(qryd->do_kw)
{
@@ -3073,14 +3072,14 @@
if(qryd->do_de)
{
if(!qryd->idcache)
- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
seqEmbossOpenSecCache(qry,DE_EXTENSION,&qryd->decache);
}
if(qryd->do_tx)
{
if(!qryd->idcache)
- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
seqEmbossOpenSecCache(qry,TX_EXTENSION,&qryd->txcache);
}
@@ -3149,6 +3148,7 @@
if(qryd->nentries == -1)
qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
ajStrStr(qry->IndexDir),
+ ajStrStr(qry->Directory),
&qryd->files,&qryd->reffiles);
*cache = ajBtreeCacheNewC(ajStrStr(qry->DbAlias),ext,
@@ -3209,6 +3209,7 @@
if(qryd->nentries == -1)
qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
ajStrStr(qry->IndexDir),
+ ajStrStr(qry->Directory),
&qryd->files,&qryd->reffiles);
@@ -3270,6 +3271,7 @@
n = ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
+ qry->Directory->Ptr,
&filestrings,&reffilestrings);
@@ -3365,7 +3367,13 @@
{
entry = ajBtreeIdFromKey(qryd->idcache,ajStrStr(qry->Id));
if(entry)
- ajListPushApp(qryd->List,(void *)entry);
+ {
+ if(!entry->dups)
+ ajListPushApp(qryd->List,(void *)entry);
+ else
+ ajBtreeHybLeafList(qryd->idcache,entry->offset,
+ entry->id,qryd->List);
+ }
}
@@ -3373,14 +3381,26 @@
{
entry = ajBtreeIdFromKey(qryd->accache,ajStrStr(qry->Acc));
if(entry)
- ajListPushApp(qryd->List,(void *)entry);
+ {
+ if(!entry->dups)
+ ajListPushApp(qryd->List,(void *)entry);
+ else
+ ajBtreeHybLeafList(qryd->accache,entry->offset,
+ entry->id,qryd->List);
+ }
}
if((qryd->do_sv && !entry) && (qryd->do_sv && qryd->svcache))
{
entry = ajBtreeIdFromKey(qryd->svcache,ajStrStr(qry->Gi));
if(entry)
- ajListPushApp(qryd->List,(void *)entry);
+ {
+ if(!entry->dups)
+ ajListPushApp(qryd->List,(void *)entry);
+ else
+ ajBtreeHybLeafList(qryd->svcache,entry->offset,
+ entry->id,qryd->List);
+ }
}
if(!ajListLength(qryd->List))
@@ -3512,13 +3532,25 @@
qryd = qry->QryData;
if(qryd->do_id && qryd->idcache)
+ {
+ ajBtreeFreeSecArray(qryd->idcache);
ajBtreeCacheDel(&qryd->idcache);
+ }
+
if(qryd->do_ac && qryd->accache)
+ {
+ ajBtreeFreeSecArray(qryd->accache);
ajBtreeCacheDel(&qryd->accache);
+ }
+
if(qryd->do_sv && qryd->svcache)
+ {
+ ajBtreeFreeSecArray(qryd->svcache);
ajBtreeCacheDel(&qryd->svcache);
+ }
+
if(qryd->do_kw && qryd->kwcache)
ajBtreeCacheDel(&qryd->kwcache);
@@ -3608,7 +3640,14 @@
ajStrToLower(&kwid);
id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
if(id)
- ajListPushApp(qryd->List,(void *)id);
+ {
+ if(!id->dups)
+ ajListPushApp(qryd->List,(void *)id);
+ else
+ ajBtreeHybLeafList(qryd->idcache,id->offset,
+ id->id,qryd->List);
+ }
+ ajStrDel(&kwid);
}
ajListDel(&tlist);
ajBtreePriDel(&pri);
@@ -3637,7 +3676,13 @@
ajStrToLower(&kwid);
id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
if(id)
- ajListPushApp(qryd->List,(void *)id);
+ {
+ if(!id->dups)
+ ajListPushApp(qryd->List,(void *)id);
+ else
+ ajBtreeHybLeafList(qryd->idcache,id->offset,
+ id->id,qryd->List);
+ }
ajStrDel(&kwid);
}
ajListDel(&tlist);
@@ -3667,7 +3712,14 @@
ajStrToLower(&kwid);
id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
if(id)
- ajListPushApp(qryd->List,(void *)id);
+ {
+ if(!id->dups)
+ ajListPushApp(qryd->List,(void *)id);
+ else
+ ajBtreeHybLeafList(qryd->idcache,id->offset,
+ id->id,qryd->List);
+ }
+ ajStrDel(&kwid);
}
ajListDel(&tlist);
ajBtreePriDel(&pri);
@@ -3832,6 +3884,7 @@
qryd = qry->QryData;
i = -1;
ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
+ qry->Directory->Ptr,
&qryd->files,&qryd->reffiles);
seqin->Single = ajTrue;

89
biology/emboss/files/patch-dbxfasta.c
View File

@ -1,89 +0,0 @@
--- emboss/dbxfasta.c.orig Mon Jan 23 12:22:12 2006
+++ emboss/dbxfasta.c Wed Jan 4 16:31:37 2006
@@ -2,7 +2,7 @@
**
** Index flatfile databases
**
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
** @@
**
** This program is free software; you can redistribute it and/or
@@ -77,6 +77,7 @@
AjPBtId idobj = NULL;
AjPBtPri priobj = NULL;
+ AjPBtHybrid hyb = NULL;
AjPRegexp typeexp = NULL;
@@ -102,7 +103,8 @@
idobj = ajBtreeIdNew();
priobj = ajBtreePriNew();
-
+ hyb = ajBtreeHybNew();
+
nfields = embBtreeSetFields(entry,fieldarray);
embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -134,22 +136,22 @@
if(entry->do_id)
{
ajStrToLower(&entry->id);
- ajStrAssS(&idobj->id,entry->id);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->idcache,idobj);
+ ajStrAssS(&hyb->key1,entry->id);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->idcache,hyb);
}
if(entry->do_accession)
while(ajListPop(entry->ac,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->accache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->accache,hyb);
ajStrDel(&word);
}
@@ -157,11 +159,11 @@
while(ajListPop(entry->sv,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->svcache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->svcache,hyb);
ajStrDel(&word);
}
@@ -197,7 +199,8 @@
ajBtreeIdDel(&idobj);
ajBtreePriDel(&priobj);
-
+ ajBtreeHybDel(&hyb);
+
ajExit();
return 0;

146
biology/emboss/files/patch-dbxflat.c
View File

@ -1,146 +0,0 @@
--- emboss/dbxflat.c.orig Mon Jan 23 12:22:23 2006
+++ emboss/dbxflat.c Sun Jan 1 07:29:09 2006
@@ -2,7 +2,7 @@
**
** Index flatfile databases
**
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
** @@
**
** This program is free software; you can redistribute it and/or
@@ -106,6 +106,7 @@
AjPBtId idobj = NULL;
AjPBtPri priobj = NULL;
+ AjPBtHybrid hyb = NULL;
embInit("dbxflat", argc, argv);
@@ -126,7 +127,8 @@
idobj = ajBtreeIdNew();
priobj = ajBtreePriNew();
-
+ hyb = ajBtreeHybNew();
+
nfields = embBtreeSetFields(entry,fieldarray);
embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -156,11 +158,11 @@
if(entry->do_id)
{
ajStrToLower(&entry->id);
- ajStrAssS(&idobj->id,entry->id);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->idcache,idobj);
+ ajStrAssS(&hyb->key1,entry->id);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->idcache,hyb);
}
if(entry->do_accession)
@@ -168,11 +170,11 @@
while(ajListPop(entry->ac,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->accache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->accache,hyb);
ajStrDel(&word);
}
}
@@ -182,11 +184,11 @@
while(ajListPop(entry->sv,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->svcache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->svcache,hyb);
ajStrDel(&word);
}
}
@@ -231,15 +233,11 @@
}
}
-
-
-
-
-
ajFileClose(&inf);
}
+
embBtreeDumpParameters(entry);
embBtreeCloseCaches(entry);
@@ -256,7 +254,8 @@
ajBtreeIdDel(&idobj);
ajBtreePriDel(&priobj);
-
+ ajBtreeHybDel(&hyb);
+
ajExit();
return 0;
@@ -306,11 +305,13 @@
}
if(entry->do_sv)
- if(ajStrPrefixC(line,"SV"))
+ if(ajStrPrefixC(line,"SV") ||
+ ajStrPrefixC(line,"IV")) /* emblcds database format */
embBtreeEmblAC(line,entry->sv);
if(entry->do_accession)
- if(ajStrPrefixC(line,"AC"))
+ if(ajStrPrefixC(line,"AC") ||
+ ajStrPrefixC(line,"PA")) /* emblcds database format */
embBtreeEmblAC(line,entry->ac);
if(entry->do_keyword)
@@ -356,12 +357,10 @@
line = ajStrNewC("");
sumline = ajStrNew();
+
while(!ajStrPrefixC(line,"//") && ret)
{
- pos = ajFileTell(inf);
-
-
if(ajStrPrefixC(line,"LOCUS"))
{
entry->fpos = pos;
@@ -423,7 +422,7 @@
}
-
+ pos = ajFileTell(inf);
if(!ajFileReadLine(inf,&line))
ret = ajFalse;

96
biology/emboss/files/patch-dbxgcg.c
View File

@ -1,96 +0,0 @@
--- emboss/dbxgcg.c.orig Mon Jan 23 12:22:30 2006
+++ emboss/dbxgcg.c Thu Dec 22 13:13:18 2005
@@ -2,7 +2,7 @@
**
** Index flatfile databases
**
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
** @@
**
** This program is free software; you can redistribute it and/or
@@ -136,6 +136,7 @@
AjPBtId idobj = NULL;
AjPBtPri priobj = NULL;
+ AjPBtHybrid hyb = NULL;
embInit("dbxgcg", argc, argv);
@@ -156,7 +157,8 @@
idobj = ajBtreeIdNew();
priobj = ajBtreePriNew();
-
+ hyb = ajBtreeHybNew();
+
nfields = embBtreeSetFields(entry,fieldarray);
embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -204,12 +206,12 @@
if(entry->do_id)
{
ajStrToLower(&entry->id);
- ajStrAssS(&idobj->id,entry->id);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->refoffset = entry->reffpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->idcache,idobj);
+ ajStrAssS(&hyb->key1,entry->id);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->refoffset = entry->reffpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->idcache,hyb);
}
if(entry->do_accession)
@@ -217,12 +219,12 @@
while(ajListPop(entry->ac,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->refoffset = entry->reffpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->accache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->refoffset = entry->reffpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->accache,hyb);
ajStrDel(&word);
}
}
@@ -232,12 +234,12 @@
while(ajListPop(entry->sv,(void **)&word))
{
ajStrToLower(&word);
- ajStrAssS(&idobj->id,word);
- idobj->dbno = i;
- idobj->offset = entry->fpos;
- idobj->refoffset = entry->reffpos;
- idobj->dups = 0;
- ajBtreeInsertId(entry->svcache,idobj);
+ ajStrAssS(&hyb->key1,word);
+ hyb->dbno = i;
+ hyb->offset = entry->fpos;
+ hyb->refoffset = entry->reffpos;
+ hyb->dups = 0;
+ ajBtreeHybInsertId(entry->svcache,hyb);
ajStrDel(&word);
}
}
@@ -303,7 +305,8 @@
ajBtreeIdDel(&idobj);
ajBtreePriDel(&priobj);
-
+ ajBtreeHybDel(&hyb);
+
ajExit();
return 0;

115
biology/emboss/files/patch-embindex.c
View File

@ -1,115 +0,0 @@
--- nucleus/embindex.c.orig Mon Jan 23 12:24:54 2006
+++ nucleus/embindex.c Thu Dec 22 13:12:38 2005
@@ -973,15 +973,14 @@
if(!do_ref)
{
ajListPop(entry->files,(void **)&tmpstr);
- ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
+ ajFmtPrintF(entfile,"%S\n",tmpstr);
ajListPushApp(entry->files,(void *)tmpstr);
}
else
{
ajListPop(entry->files,(void **)&tmpstr);
ajListPop(entry->reffiles,(void **)&refstr);
- ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
- entry->directory,refstr);
+ ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
ajListPushApp(entry->files,(void *)tmpstr);
ajListPushApp(entry->reffiles,(void *)refstr);
}
@@ -1150,7 +1149,15 @@
entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+ entry->idsecorder = (entry->pagesize - 60) / 24;
+ entry->idsecfill = (entry->pagesize - 60) / 20;
+ entry->acsecorder = (entry->pagesize - 60) / 24;
+ entry->acsecfill = (entry->pagesize - 60) / 20;
+
+ entry->svsecorder = (entry->pagesize - 60) / 24;
+ entry->svsecfill = (entry->pagesize - 60) / 20;
+
ajStrDel(&value);
return;
@@ -1183,28 +1190,38 @@
if(entry->do_id)
{
- entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
- entry->pagesize, entry->idorder,
- entry->idfill, level,
- entry->cachesize);
+ entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
+ entry->pagesize, entry->idorder,
+ entry->idfill, level,
+ entry->cachesize,
+ entry->idsecorder, slevel,
+ entry->idsecfill, count,
+ entry->kwlen);
ajBtreeCreateRootNode(entry->idcache,0L);
}
if(entry->do_accession)
{
- entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
- entry->pagesize, entry->acorder,
- entry->acfill, level,
- entry->cachesize);
+ entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
+ entry->pagesize,
+ entry->acorder, entry->acfill,
+ level,
+ entry->cachesize,
+ entry->acsecorder, slevel,
+ entry->acsecfill, count,
+ entry->kwlen);
ajBtreeCreateRootNode(entry->accache,0L);
}
if(entry->do_sv)
{
- entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
- entry->pagesize, entry->svorder,
- entry->svfill, level,
- entry->cachesize);
+ entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
+ entry->pagesize, entry->svorder,
+ entry->svfill, level,
+ entry->cachesize,
+ entry->svsecorder, slevel,
+ entry->svsecfill, count,
+ entry->kwlen);
ajBtreeCreateRootNode(entry->svcache,0L);
}
@@ -1270,18 +1287,27 @@
if(entry->do_id)
{
+ ajBtreeFreePriArray(entry->idcache);
+ ajBtreeFreeSecArray(entry->idcache);
+
ajBtreeCacheSync(entry->idcache,0L);
ajBtreeCacheDel(&entry->idcache);
}
if(entry->do_accession)
{
+ ajBtreeFreePriArray(entry->accache);
+ ajBtreeFreeSecArray(entry->accache);
+
ajBtreeCacheSync(entry->accache,0L);
ajBtreeCacheDel(&entry->accache);
}
if(entry->do_sv)
{
+ ajBtreeFreePriArray(entry->svcache);
+ ajBtreeFreeSecArray(entry->svcache);
+
ajBtreeCacheSync(entry->svcache,0L);
ajBtreeCacheDel(&entry->svcache);
}

96
biology/emboss/files/patch-embindex.h
View File

@ -1,96 +0,0 @@
--- nucleus/embindex.h.orig Mon Jan 23 12:24:46 2006
+++ nucleus/embindex.h Thu Dec 22 13:12:44 2005
@@ -16,6 +16,76 @@
#define BTREE_DEF_CACHESIZE 100
#define BTREE_DEF_PAGESIZE 2048
+/* @data EmbPBtreeEntry *******************************************************
+**
+** Index tree entries
+**
+** @alias EmbSBtreeEntry
+**
+** @attr do_id [AjBool] Undocumented
+** @attr do_accession [AjBool] Undocumented
+** @attr do_sv [AjBool] Undocumented
+** @attr do_description [AjBool] Undocumented
+** @attr do_keyword [AjBool] Undocumented
+** @attr do_taxonomy [AjBool] Undocumented
+** @attr dbname [AjPStr] Undocumented
+** @attr dbrs [AjPStr] Undocumented
+** @attr release [AjPStr] Undocumented
+** @attr date [AjPStr] Undocumented
+** @attr dbtype [AjPStr] Undocumented
+** @attr directory [AjPStr] Undocumented
+** @attr idirectory [AjPStr] Undocumented
+** @attr files [AjPList] Undocumented
+** @attr reffiles [AjPList] Undocumented
+** @attr nfiles [ajint] Undocumented
+** @attr cachesize [ajint] Undocumented
+** @attr pagesize [ajint] Undocumented
+** @attr idlen [ajint] Undocumented
+** @attr aclen [ajint] Undocumented
+** @attr svlen [ajint] Undocumented
+** @attr kwlen [ajint] Undocumented
+** @attr delen [ajint] Undocumented
+** @attr txlen [ajint] Undocumented
+** @attr idorder [ajint] Undocumented
+** @attr idfill [ajint] Undocumented
+** @attr idsecorder [ajint] Undocumented
+** @attr idsecfill [ajint] Undocumented
+** @attr acorder [ajint] Undocumented
+** @attr acfill [ajint] Undocumented
+** @attr acsecorder [ajint] Undocumented
+** @attr acsecfill [ajint] Undocumented
+** @attr svorder [ajint] Undocumented
+** @attr svfill [ajint] Undocumented
+** @attr svsecorder [ajint] Undocumented
+** @attr svsecfill [ajint] Undocumented
+** @attr kworder [ajint] Undocumented
+** @attr kwfill [ajint] Undocumented
+** @attr kwsecorder [ajint] Undocumented
+** @attr kwsecfill [ajint] Undocumented
+** @attr deorder [ajint] Undocumented
+** @attr defill [ajint] Undocumented
+** @attr desecorder [ajint] Undocumented
+** @attr desecfill [ajint] Undocumented
+** @attr txorder [ajint] Undocumented
+** @attr txfill [ajint] Undocumented
+** @attr txsecorder [ajint] Undocumented
+** @attr txsecfill [ajint] Undocumented
+** @attr idcache [AjPBtcache] Undocumented
+** @attr accache [AjPBtcache] Undocumented
+** @attr svcache [AjPBtcache] Undocumented
+** @attr kwcache [AjPBtcache] Undocumented
+** @attr decache [AjPBtcache] Undocumented
+** @attr txcache [AjPBtcache] Undocumented
+** @attr fpos [ajlong] Undocumented
+** @attr reffpos [ajlong] Undocumented
+** @attr id [AjPStr] Undocumented
+** @attr ac [AjPList] Undocumented
+** @attr sv [AjPList] Undocumented
+** @attr tx [AjPList] Undocumented
+** @attr kw [AjPList] Undocumented
+** @attr de [AjPList] Undocumented
+******************************************************************************/
+
typedef struct EmbSBtreeEntry
{
AjBool do_id;
@@ -48,10 +118,16 @@
ajint idorder;
ajint idfill;
+ ajint idsecorder;
+ ajint idsecfill;
ajint acorder;
ajint acfill;
+ ajint acsecorder;
+ ajint acsecfill;
ajint svorder;
ajint svfill;
+ ajint svsecorder;
+ ajint svsecfill;
ajint kworder;
ajint kwfill;

72
biology/emboss/files/patch-marscan.c
View File

@ -1,72 +0,0 @@
--- emboss/marscan.c.orig Mon Jan 23 11:36:36 2006
+++ emboss/marscan.c Mon Jan 23 08:56:35 2006
@@ -1,7 +1,7 @@
/* @source marscan application
**
** Finds MAR/SAR sites in nucleic sequences
-** @author: Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
+** @author Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
** @@
**
** This program is free software; you can redistribute it and/or
@@ -249,33 +249,41 @@
amino8rev, carboxyl8rev, buf8rev, off8rev,
sotable8rev, solimit8rev, regexp8rev, skipm8rev,
&hits8rev, m8rev, &tidy8rev);
+ ajDebug("Marscan '%S' hits %d:%d %d:%d\n", seqname,
+ hits16, hits16rev,
+ hits8, hits8rev);
+
+ /* initialise the output feature table */
+ tab = ajFeattableNewDna(seqname);
+
+ /*
+ ** append reverse lists to forward lists and sort them by match
+ ** position
+ */
- if((hits16 || hits16rev) && (hits8 || hits8rev))
+ if(hits8 || hits8rev)
{
- /*
- ** append reverse lists to forward lists and sort them by match
- ** position
- */
ajListPushList(l8, &l8rev);
ajListSort(l8, embPatRestrictStartCompare);
-
+ }
+ if((hits16 || hits16rev))
+ {
ajListPushList(l16, &l16rev);
ajListSort(l16, embPatRestrictStartCompare);
- /* initialise the output feature table */
- if(!tab)
- tab = ajFeattableNewDna(seqname);
-
- /*
- ** find pairs of hits within the required distance and output
- ** the results
- */
- marscan_stepdown(l16, l8, &tab);
-
- /* write features and tidy up */
- ajReportWrite(report, tab, seq);
- ajFeattableDel(&tab);
}
+
+
+ /*
+ ** find pairs of hits within the required distance and output
+ ** the results
+ */
+ marscan_stepdown(l16, l8, &tab);
+
+ ajDebug("Marscan reportwrite '%S'\n", seqname);
+ /* write features and tidy up */
+ ajReportWrite(report, tab, seq);
+ ajFeattableDel(&tab);
while(ajListPop(l16,(void **)&aptr))
embMatMatchDel(&aptr);

8
biology/emboss/pkg-descr
View File

@ -12,12 +12,8 @@ core libraries which are under the LGPL.
EMBASSY packages are third party applications which have been integrated with
the EMBOSS suite, but which are not included in the base EMBOSS distribution
for licensing or other reasons. This port includes the currently available
EMBASSY applications. During an interactive install the user will be asked
to choose which of these will be installed (default: all). Note that the
EMBASSY versions of PHYLIP and HMMER should not clash with the standalone
versions (also in ports/biology) due to the fact that their binaries have been
renamed.
for licensing or other reasons. The EMBASSY packages live in the
biology/embassy port.
WWW: http://www.emboss.org/

903
biology/emboss/pkg-plist
View File

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