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academic/bpp1.9-phyl: Added (Bio++ 1.9 Phyl Library)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
This commit is contained in:
Petar Petrov
Dave Woodfall
parent
15bcc39c2b
commit
1f0ff62f35
5 changed files with 197 additions and 0 deletions
10
academic/bpp1.9-phyl/README
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10
academic/bpp1.9-phyl/README
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence
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analysis, phylogenetics, molecular evolution and population genetics.
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Bio++ is Object Oriented and is designed to be both easy to use and
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computer efficient. Bio++ intends to help programmers to write
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computer expensive programs, by providing them a set of re-usable
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tools.
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This contains the Bio++ 1.9 (April 2010) Phyl Library. It can be
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installed along the current Bio++ suite libraries, however they better
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not be present at compile time.
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119
academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
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119
academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
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#!/bin/bash
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# Slackware build script for bpp1.9-phyl
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# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=bpp1.9-phyl
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SRCNAM=bpp-phyl
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VERSION=${VERSION:-1.9.0}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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cd $SRCNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# CAPS wants TreeTemplateTools to be modified a bit...
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patch -p1 -i $CWD/caps_TreeTemplateTools.patch
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# Use custom install place, so libs can coexist with latest bpp
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export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH"
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sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl.spec
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source /etc/profile.d/gcc5.sh
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mkdir -p build
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cd build
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cmake \
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-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \
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-DCMAKE_INSTALL_PREFIX=/usr \
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-DCMAKE_BUILD_TYPE=Release ..
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sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl/cmake_install.cmake
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sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Phyl/cmake_install.cmake
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make
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make DESTDIR=$PKG install
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cd ..
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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chmod 0644 AUTHORS ChangeLog COPYING
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cp -a \
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AUTHORS ChangeLog COPYING \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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10
academic/bpp1.9-phyl/bpp1.9-phyl.info
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10
academic/bpp1.9-phyl/bpp1.9-phyl.info
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PRGNAM="bpp1.9-phyl"
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VERSION="1.9.0"
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HOMEPAGE="http://biopp.univ-montp2.fr/"
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DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-phyl-1.9.0.tar.gz"
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MD5SUM="1b100b688faca52419e9f782798b8add"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="bpp1.9-seq"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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39
academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
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39
academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
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diff -pruN orig/Phyl/TreeTemplateTools.h new/Phyl/TreeTemplateTools.h
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--- orig/Phyl/TreeTemplateTools.h 2010-04-01 16:37:04.000000000 +0300
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+++ new/Phyl/TreeTemplateTools.h 2017-02-03 14:33:11.000000000 +0200
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@@ -191,7 +191,7 @@ class TreeTemplateTools
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static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
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{
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N* leaf = tree.getNode(leafName);
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- if (!leaf->hasfather())
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+ if (!leaf->hasFather())
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throw Exception("TreeTemplateTools::dropLeaf(). Leaf is the only node in the tree, can't remove it.");
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N* parent = leaf->getFather();
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if (parent->getNumberOfSons() > 2)
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@@ -203,7 +203,7 @@ class TreeTemplateTools
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else if (parent->getNumberOfSons() == 2)
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{
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//We have to delete the parent node as well:
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- N* brother = parent->getson(0);
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+ N* brother = parent->getSon(0);
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if (brother == leaf) brother = parent->getSon(1);
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if (!parent->hasFather())
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{
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@@ -212,7 +212,7 @@ class TreeTemplateTools
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{
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brother->setDistanceToFather(brother->getDistanceToFather() + leaf->getDistanceToFather());
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}
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- tree->setRootNode(brother);
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+ tree.setRootNode(brother);
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delete parent;
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delete leaf;
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}
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@@ -223,7 +223,7 @@ class TreeTemplateTools
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{
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brother->setDistanceToFather(brother->getDistanceToFather() + parent->getDistanceToFather());
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}
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- unsigned int pos = gParent->getsonPosition(parent);
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+ unsigned int pos = gParent->getSonPosition(parent);
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gParent->setSon(pos, brother);
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delete parent;
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delete leaf;
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19
academic/bpp1.9-phyl/slack-desc
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19
academic/bpp1.9-phyl/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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bpp1.9-phyl: bpp1.9-phyl (Bio++ 1.9 Phyl Library)
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bpp1.9-phyl:
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bpp1.9-phyl: Contains the Bio++ 1.9 Phyl Library.
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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bpp1.9-phyl:
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