From 44ffcb2663242671a2406529b7e24c91ca712f8d Mon Sep 17 00:00:00 2001
From: birney <birney@bioperl.org>
Date: Sun, 19 Sep 1999 16:13:44 +0000
Subject: [PATCH] fixed index bugs, and fixed makefile

svn path=/bioperl-live/branches/stable-0-05-new/; revision=1069
---
 Bio/Index/EMBL.pm      | 13 ++++++--
 Bio/Index/Fasta.pm     | 13 ++++++--
 Bio/Index/SwissPfam.pm | 12 ++++++--
 MANIFEST               | 84 +-------------------------------------------------
 4 files changed, 31 insertions(+), 91 deletions(-)

diff --git a/Bio/Index/EMBL.pm b/Bio/Index/EMBL.pm
index 53d848840..e44fc7cef 100644
--- a/Bio/Index/EMBL.pm
+++ b/Bio/Index/EMBL.pm
@@ -97,11 +97,18 @@ sub _type_stamp {
     return '__EMBL_FLAT__'; # What kind of index are we?
 }
 
-sub _version {
-    return 0.1;
+#
+# Suggested fix by Michael G Schwern <schwern@pobox.com> to
+# get around a clash with CPAN shell...
+#
+
+BEGIN {
+    $VERSION = 0.1;
 }
-$VERSION = _version();
 
+sub _version {
+    return $VERSION;
+}
 
 
 =head2 _initialize
diff --git a/Bio/Index/Fasta.pm b/Bio/Index/Fasta.pm
index 3432eb8db..0f4464f0b 100644
--- a/Bio/Index/Fasta.pm
+++ b/Bio/Index/Fasta.pm
@@ -97,11 +97,18 @@ sub _type_stamp {
     return '__FASTA__'; # What kind of index are we?
 }
 
-sub _version {
-    return 0.2;
+#
+# Suggested fix by Michael G Schwern <schwern@pobox.com> to
+# get around a clash with CPAN shell...
+#
+
+BEGIN { 
+    $VERSION = 0.2;
 }
-$VERSION = _version();
 
+sub _version {
+    return $VERSION;
+}
 
 
 =head2 _initialize
diff --git a/Bio/Index/SwissPfam.pm b/Bio/Index/SwissPfam.pm
index b612ff40d..33afecc92 100644
--- a/Bio/Index/SwissPfam.pm
+++ b/Bio/Index/SwissPfam.pm
@@ -94,10 +94,18 @@ sub _type_stamp {
     return '__SWISSPFAM__'; # What kind of index are we?
 }
 
+#
+# Suggested fix by Michael G Schwern <schwern@pobox.com> to
+# get around a clash with CPAN shell...
+#
+
+BEGIN {
+    $VERSION = 0.1;
+}
+
 sub _version {
-    return 0.1;
+    return $VERSION;
 }
-$VERSION = _version();
 
 
 
diff --git a/MANIFEST b/MANIFEST
index f0862d2d3..45ae26b3f 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,5 +1,5 @@
 # Bioperl Manifest List
-# $Id: MANIFEST,v 1.12 1999-04-06 16:57:36 birney Exp $
+# $Id: MANIFEST,v 1.12.6.1 1999-09-19 16:13:44 birney Exp $
 #
 MANIFEST
 Makefile.PL
@@ -82,88 +82,6 @@ examples/root_object/read.pl
 examples/root_object/read.test
 examples/root_object/read.test2
 examples/root_object/read.test3
-Compile/SW/Makefile.PL
-Compile/SW/bp_sw.pm
-Compile/SW/bp_sw.xs
-Compile/SW/libs/aln.c
-Compile/SW/libs/aln.h
-Compile/SW/libs/alnconvert.c
-Compile/SW/libs/alnconvert.h
-Compile/SW/libs/alnrange.c
-Compile/SW/libs/alnrange.h
-Compile/SW/libs/asciibtcanvas.c
-Compile/SW/libs/asciibtcanvas.h
-Compile/SW/libs/basematrix.c
-Compile/SW/libs/basematrix.h
-Compile/SW/libs/btcanvas.c
-Compile/SW/libs/btcanvas.h
-Compile/SW/libs/codon.c
-Compile/SW/libs/codon.h
-Compile/SW/libs/commandline.c
-Compile/SW/libs/commandline.h
-Compile/SW/libs/complexconsensi.c
-Compile/SW/libs/complexconsensi.h
-Compile/SW/libs/complexevalset.c
-Compile/SW/libs/complexevalset.h
-Compile/SW/libs/complexsequence.c
-Compile/SW/libs/complexsequence.h
-Compile/SW/libs/compmat.c
-Compile/SW/libs/compmat.h
-Compile/SW/libs/database.h
-Compile/SW/libs/dna.c
-Compile/SW/libs/dna.h
-Compile/SW/libs/dnamatrix.c
-Compile/SW/libs/dnamatrix.h
-Compile/SW/libs/dpenvelope.c
-Compile/SW/libs/dpenvelope.h
-Compile/SW/libs/dyna.h
-Compile/SW/libs/dynlibcross.c
-Compile/SW/libs/dynlibcross.h
-Compile/SW/libs/histogram.c
-Compile/SW/libs/histogram.h
-Compile/SW/libs/hscore.c
-Compile/SW/libs/hscore.h
-Compile/SW/libs/linesubs.c
-Compile/SW/libs/linesubs.h
-Compile/SW/libs/makefile
-Compile/SW/libs/packaln.c
-Compile/SW/libs/packaln.h
-Compile/SW/libs/probability.c
-Compile/SW/libs/probability.h
-Compile/SW/libs/protein.c
-Compile/SW/libs/protein.h
-Compile/SW/libs/proteindb.c
-Compile/SW/libs/proteindb.h
-Compile/SW/libs/proteinsw.c
-Compile/SW/libs/proteinsw.h
-Compile/SW/libs/seqaligndisplay.c
-Compile/SW/libs/seqaligndisplay.h
-Compile/SW/libs/sequence.c
-Compile/SW/libs/sequence.h
-Compile/SW/libs/sequencedb.c
-Compile/SW/libs/sequencedb.h
-Compile/SW/libs/sw.h
-Compile/SW/libs/sw_wrap.c
-Compile/SW/libs/sw_wrap.h
-Compile/SW/libs/wisebase.h
-Compile/SW/libs/wiseconfig.c
-Compile/SW/libs/wiseconfig.h
-Compile/SW/libs/wiseerror.c
-Compile/SW/libs/wiseerror.h
-Compile/SW/libs/wisefile.c
-Compile/SW/libs/wisefile.h
-Compile/SW/libs/wisememman.c
-Compile/SW/libs/wisememman.h
-Compile/SW/libs/wiseoverlay.c
-Compile/SW/libs/wiseoverlay.h
-Compile/SW/libs/wiserandom.c
-Compile/SW/libs/wiserandom.h
-Compile/SW/libs/wisestring.c
-Compile/SW/libs/wisestring.h
-Compile/SW/libs/wisetime.c
-Compile/SW/libs/wisetime.h
-Compile/SW/test.pl
-Compile/SW/typemap
 
 
 
-- 
2.11.4.GIT