Updated to bioperl-0.7.0.

Revision history for Bioperl core modules

0.7  Large number of changes, including refactoring of the
     Object system, new parsers, new functionality and
     all round better system. Highlights are:


     o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
       Bio::Root::IO for I/O and file/handle capabilities.

     o Imported BPlite modules from Ian Korf for BLAST
       parsing. This is considered the supported BLAST parser;
       Bio::Tools::Blast.pm will eventually phase out due to lack of support.

     o Improved Sequence Feature model. Added complete location
       modelling (with fuzzy and compound locations).  See
       Bio::LocationI and the modules under Bio/Location.  Added
       support in Genbank/EMBL format parsing to completely parse
       feature tables for complex locations.

     o Moved special support for databanks etc to specialized modules under
       Bio/Seq/. One of these supports very large sequences through
       a temporary file as a backend.

     o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
       CDS retrieval and exon shuffling.

     o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF

     o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
       DB/GDB (the latter has platform-specific limitations).

     o New analysis parser framework for HT sequence annotation (see
       Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)

     o New Alignment IO framework

     o New Index modules (Swissprot)

     o New modules for running Blast within perl
       (Bio::Tools::Run::StandAloneBlast). Added modules for running
       Multiple Sequence Alignment tools ClustalW and TCoffee
       (Bio::Tools::Run::Alignment).

     o New Cookbook-style tutorial (see bptutorial.pl). Improved
       documentation across the package.

     o Much improved cross platform support. Many known incompatibilities
       have been fixed; however, NT and Mac do not work across the entire
       setup (see PLATFORMS).

     o Many bug fixes, code restructuring, etc. Overall stability and
       maintainability benefit a lot.

     o A total of 957 automatic tests


0.6.2

   There are very few functionality changes but a large
   number of software improvements/bug fixes across the package.

   o The EMBL/GenBank parsing are improved.

   o The Swissprot reading is improved. Swissprot writing
     is disabled as it doesn't work at all. This needs to
     wait for 0.7 release

   o BLAST reports with no hits are correctly parsed.

   o Several other bugs of the BLAST parser (regular expressions, ...)
     fixed.

   o Old syntax calls have been replaced with more modern syntax

   o Modules that did not work at all, in particular the Sim4
     set have been removed

   o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
     have improved compliance with interface specs and documentation

   o Mailing list documentation updated throughout the distribution

   o Most minor bug fixes have happened.

   o The scripts in /examples now work and have the modern syntax
     rather than the deprecated syntax


0.6.1  Sun April 2 2000

   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are
     provided

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved, with better PSI-BLAST
     support and better overall behaviour.

   o Flat file indexed databases provide both random access
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.

    The 0.6 release also has improved software engineering

   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of
     bioperl.

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).



0.05.1 Tue Jun 29 05:30:44 1999
        - Central distribution now requires Perl 5.004. This was
          done to get around 5.003-based problems in Bio/Index/*
          and SimpleAlign.
        - Various bug fixes in the Bio::Tools::Blast modules
          including better exception handling and PSI-Blast
          support. See Bio/Tools/Blast/CHANGES for more.
        - Fixed the Parse mechanism in Seq.pm to use readseq.
	  Follow the instructions in README for how to install
	  it (basically, you have to edit Parse.pm).
        - Improved documentation of Seq.pm, indicating where
          objects are returned and where strings are returned.
        - Fixed uninitialized warnings in Bio::Root::Object.pm
          and Bio::Tools::SeqPattern.pm.
        - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.

0.05  Sun Apr 25 01:14:11 1999
        - Bio::Tools::Blast modules have less memory problems
          and faster parsing. Webblast uses LWP and supports
          more functionality. See Bio/Tools/Blast/CHANGES for more.
        - The Bio::SeqIO system has been started, moving the
          sequence reformatting code out of the sequence object
        - The Bio::Index:: system has been started, providing
          generic index capabilities and specifically works for
          Fasta formatted databases and EMBL .dat formatted
	  databases
        - The Bio::DB:: system started, providing access to
          databases, both via flat file + index (see above) and
          via http to NCBI
        - The scripts/ directory, where industrial strength scripts
          are put has been started.
        - Many changes - a better distribution all round.

7 files changed, 40 insertions, 93 deletions

diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile
index 1b46c91af2c..fcea148fbb7 100644
--- a/biology/bioperl/Makefile
+++ b/biology/bioperl/Makefile
@@ -1,32 +1,21 @@
-# $NetBSD: Makefile,v 1.3 2001/02/16 13:41:26 wiz Exp $
+# $NetBSD: Makefile,v 1.4 2001/04/05 21:48:40 jtb Exp $
 #
 
-DISTNAME=		bioperl-0.04.4
+DISTNAME=		bioperl-0.7.0
 CATEGORIES=		biology
-MASTER_SITES=		ftp://bio.perl.org/pub/DIST/
+MASTER_SITES=		http://bioperl.org/Core/Latest/
 
 MAINTAINER=		packages@netbsd.org
-HOMEPAGE=		http://bio.perl.org/
+HOMEPAGE=		http://bioperl.org/
 COMMENT=		Perl tools for computational molecular biology
 
 USE_PERL5=		# defined
 PERL5_PACKLIST=		${PERL5_SITEARCH}/auto/Bio/.packlist
-PERL5_PACKLIST+=	${PERL5_SITEARCH}/auto/bp_sw/.packlist
 
 do-configure:
-	cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
-	cd ${WRKSRC}/Compile/SW; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
-
-pre-build:
-	cd ${WRKSRC}/Compile/SW/libs; ${MAKE_PROGRAM}
-
-post-build:
-	cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM}
-	cd ${WRKSRC}; ${MAKE_PROGRAM} test
-	cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} test
+	@cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
 
 post-install:
-	cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} install
 	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/bioperl
 	cd ${WRKSRC}/examples; ${GTAR} cf - . \
 		| (cd ${PREFIX}/share/examples/bioperl; ${GTAR} xf -)
diff --git a/biology/bioperl/files/md5 b/biology/bioperl/files/md5
index 41efd041385..d97ecad284c 100644
--- a/biology/bioperl/files/md5
+++ b/biology/bioperl/files/md5
@@ -1,3 +1,3 @@
-$NetBSD: md5,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $
+$NetBSD: md5,v 1.2 2001/04/05 21:48:40 jtb Exp $
 
-MD5 (bioperl-0.04.4.tar.gz) = e131dfd837423ec0fc746a3b83e68020
+SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6
diff --git a/biology/bioperl/files/patch-sum b/biology/bioperl/files/patch-sum
index 1cfc5723524..24b54b7806f 100644
--- a/biology/bioperl/files/patch-sum
+++ b/biology/bioperl/files/patch-sum
@@ -1,5 +1,6 @@
-$NetBSD: patch-sum,v 1.2 2000/08/26 03:36:38 jlam Exp $
+$NetBSD: patch-sum,v 1.3 2001/04/05 21:48:40 jtb Exp $
 
-MD5 (patch-aa) = c18e708c55eeae44ac7ec7a860d67f00
-MD5 (patch-ab) = cf3fd5491b9aac607ed516ce4cf0213c
-MD5 (patch-ac) = 4de5755319b2d54ce180633847275c92
+This placeholder file is generated by the ``makepatchsum'' target
+whenever the patches directory is empty or missing. Its purpose
+is to ensure that the presence of any obsolete patches will cause
+the proper error to be emitted at build time.
diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa
deleted file mode 100644
index 704b8fdc216..00000000000
--- a/biology/bioperl/patches/patch-aa
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $
-
---- Compile/SW/Makefile.PL.orig	Fri Dec 11 08:24:25 1998
-+++ Compile/SW/Makefile.PL	Mon Mar  1 11:37:15 1999
-@@ -13,9 +13,9 @@
- 
- sub MY::postamble{
- '
--$(MYEXTLIB): libs/libsw$(LIB_EXT)
-+$(MYEXTLIB):
- 	DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; export DEFINE INC CC; \
--	cd libs && $(MAKE) libsw.a -e
-+	cd libs && $(MAKE) libsw$(LIB_EXT) -e
- 
- ';
- }
diff --git a/biology/bioperl/patches/patch-ab b/biology/bioperl/patches/patch-ab
deleted file mode 100644
index b76fbbaa9b0..00000000000
--- a/biology/bioperl/patches/patch-ab
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $
-
---- Compile/SW/libs/makefile.orig	Fri Dec 11 16:24:29 1998
-+++ Compile/SW/libs/makefile	Sat Apr 10 21:45:14 1999
-@@ -1,5 +1,4 @@
--
--
-+CFLAGS+=-fPIC
- 
- OBJS =	aln.o\
- 	alnconvert.o\
-@@ -52,7 +51,5 @@
- 	ar ru libsw.a $(OBJS)
- 
- wisefile.o : wisefile.c
--	$(CC) $(CFLAGS) -DNOERROR wisefile.c
-+	${CC} ${CFLAGS} -c -DNOERROR wisefile.c
- 
--CFLAGS = -c -O
--CC     = cc
diff --git a/biology/bioperl/patches/patch-ac b/biology/bioperl/patches/patch-ac
deleted file mode 100644
index 064961c8ae6..00000000000
--- a/biology/bioperl/patches/patch-ac
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ac,v 1.1 2000/08/26 03:36:45 jlam Exp $
-
---- Bio/Root/Err.pm.orig	Thu Feb  4 03:06:35 1999
-+++ Bio/Root/Err.pm
-@@ -984,7 +984,7 @@
-            : This method is an alternative to Bio::Root::Object::throw()
-            : and is not as well developed or documented as that method.
- 
--See Also   : L<warning>(), B<Bio::Root::Object::throw()>, B<Bio::Root::Global::strictness()
-+See Also   : L<warning>(), B<Bio::Root::Object::throw()>, B<Bio::Root::Global::strictness()>
- 
- =cut
- 
diff --git a/biology/bioperl/pkg/PLIST b/biology/bioperl/pkg/PLIST
index 4e429081653..99571fe9ec6 100644
--- a/biology/bioperl/pkg/PLIST
+++ b/biology/bioperl/pkg/PLIST
@@ -1,9 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2000/08/27 07:10:59 jlam Exp $
-share/examples/bioperl/blast/blast_config.pl
-share/examples/bioperl/blast/blast_seq.pl
-share/examples/bioperl/blast/example.table1
-share/examples/bioperl/blast/example.table2
-share/examples/bioperl/blast/html.pl
+@comment $NetBSD: PLIST,v 1.3 2001/04/05 21:48:41 jtb Exp $
 share/examples/bioperl/blast/out/blastn.2.gz
 share/examples/bioperl/blast/out/blastn.2.wu.gz
 share/examples/bioperl/blast/out/blastp.1.gcg.gz
@@ -19,26 +14,44 @@ share/examples/bioperl/blast/out/blastx.2
 share/examples/bioperl/blast/out/blastx.2.email.gz
 share/examples/bioperl/blast/out/blastx.208.gz
 share/examples/bioperl/blast/out/tblastn.206.out.gz
-share/examples/bioperl/blast/parse.pl
-share/examples/bioperl/blast/parse2.pl
-share/examples/bioperl/blast/parse_multi.pl
-share/examples/bioperl/blast/parse_positions.pl
-share/examples/bioperl/blast/parse_stream.pl
-share/examples/bioperl/blast/print_blasts.pl
-share/examples/bioperl/blast/run.pl
 share/examples/bioperl/blast/seq/acc1.dna.fasta
 share/examples/bioperl/blast/seq/seqs.fasta
 share/examples/bioperl/blast/seq/yal011w.dna.fasta
 share/examples/bioperl/blast/seq/yel009c.fasta
 share/examples/bioperl/blast/seq/ymr284w.fasta
+share/examples/bioperl/blast/blast_config.pl
+share/examples/bioperl/blast/blast_seq.pl
+share/examples/bioperl/blast/example.table1
+share/examples/bioperl/blast/example.table2
+share/examples/bioperl/blast/html.pl
+share/examples/bioperl/blast/parse_blast.pl
+share/examples/bioperl/blast/parse_blast2.pl
+share/examples/bioperl/blast/parse_multi.pl
+share/examples/bioperl/blast/parse_positions.pl
+share/examples/bioperl/blast/print_blasts.pl
+share/examples/bioperl/blast/retrieve_blast.pl
+share/examples/bioperl/blast/run_blast_remote.pl
 share/examples/bioperl/blosum62.bla
+share/examples/bioperl/change_gene.pl
+share/examples/bioperl/clustalw.pl
+share/examples/bioperl/getGenBank.pl
 share/examples/bioperl/gon250.bla
+share/examples/bioperl/gsequence
+share/examples/bioperl/hitdisplay.pl
 share/examples/bioperl/psw.pl
 share/examples/bioperl/restriction.pl
 share/examples/bioperl/rev_and_trans.pl
+share/examples/bioperl/seq_pattern.pl
+share/examples/bioperl/simplealign.pl
+share/examples/bioperl/standaloneblast.pl
+share/examples/bioperl/test-genscan.pl
+share/examples/bioperl/root_object/Outer.pm
 share/examples/bioperl/root_object/Bar.pm
 share/examples/bioperl/root_object/Foo.pm
-share/examples/bioperl/root_object/Outer.pm
+share/examples/bioperl/root_object/vector/Person.pm
+share/examples/bioperl/root_object/vector/PersonManager.pm
+share/examples/bioperl/root_object/vector/vector.out
+share/examples/bioperl/root_object/vector/vector.pl
 share/examples/bioperl/root_object/destroy.pl
 share/examples/bioperl/root_object/error.out
 share/examples/bioperl/root_object/error.pl
@@ -51,21 +64,14 @@ share/examples/bioperl/root_object/read.test
 share/examples/bioperl/root_object/read.test2
 share/examples/bioperl/root_object/read.test3
 share/examples/bioperl/root_object/utilities.pl
-share/examples/bioperl/root_object/vector/Person.pm
-share/examples/bioperl/root_object/vector/PersonManager.pm
-share/examples/bioperl/root_object/vector/vector.out
-share/examples/bioperl/root_object/vector/vector.pl
-share/examples/bioperl/seq/id.list
 share/examples/bioperl/seq/seq.fasta.gz
+share/examples/bioperl/seq/id.list
 share/examples/bioperl/seq/seq1.fasta
 share/examples/bioperl/seq/seq2.fasta
 share/examples/bioperl/seq/seqs1.pl
 share/examples/bioperl/seq/seqs2.pl
 share/examples/bioperl/seq/seqs3.pl
-share/examples/bioperl/seq/seqs4.pl
 share/examples/bioperl/seq/seqtools.pl
-share/examples/bioperl/seq_pattern.pl
-share/examples/bioperl/simplealign.pl
 @dirrm share/examples/bioperl/seq
 @dirrm share/examples/bioperl/root_object/vector
 @dirrm share/examples/bioperl/root_object